Report on Research and Other Activities of
National Institute of Genetics(During 2014~2018)ᅜ❧㑇ఏᏛ◊✲ᡤ⮬ᕫホ౯ሗ࿌᭩National Institute of Genetics
October 2019ᅜ❧㑇ఏᏛ◊✲ᡤ2019 ᖺ 10 ᭶

CONTENTS
1.

Preface

2.

Overview of National Institute of Genetics

2

3.

4.

z Our Mission

2

z History3z Organization5

z Outline of Departments and Centers for Research Infrastructures

6

Research Achievements and Self Evaluation

7

z Department of Informatics

7

z Department of Genomics and Evolutionary Biology

10z Department of Gene Function and Phenomics

13

z Department of Chromosome Science18

z Center for Frontier Research

21Intellectual Infrastructure Center

22

z Bioinformation and DDBJ Center22

z Advanced Genomics Center29

z Genetic Resource Center

32

5.

Joint Research and Research Meeting (NIG-JOINT), and International Symposium

41

6.

Education and Outreach42

z Graduate Education42z Education: Outreach47

7.

Activities to Promote International Interaction and Cooperation

51

8.

Office for Research Development

53

9.

NIG INNOVATION

55

10.

Office for Gender Equality

56

11.

Publication Lists

57

Preface
Director-General: Fumio Hanaoka
The National Institute of Genetics (NIG) recently celebrated its 70th anniversary since its founding andcontinues to strive for excellence in research, service and education. To pursue our commitment to future
development, we have initiated an evaluation by an external review committee and have compiled this reportwhich summarizes the activity of NIG during the 5 years from January 2014 to December 2018.
NIG was established in 1949 by the Japanese Ministry of Education for comprehensive studies of genetics. In
1984, it was reorganized into an Inter-University Research Institute, and the new designation established an
additional official role of NIG: collaboration with researchers at universities. For this purpose, NIG now
provides three services: DNA Databank of Japan (DDBJ), Advanced Genomics Services, and Bioresource
Services, in addition to collaborative research. In 1988, NIG joined in the establishment of SOKENDAI (theGraduate School of Advanced Studies). NIG is in charge of the Department of Genetics of SOKENDAI andmaintains a Ph.D course for fostering the next generations of researchers.
In 2004, sixteen Inter-University Research Institutes were incorporated and grouped into 4 Research
Organizations. NIG chose to belong to Research Organization of Information and Systems, which consists of
the National Institutes of Polar Research (NIPR), Statistical Mathematics (ISM), Informatics (NII), andGenetics (NIG). This choice reflects our institute’s desire to play a central role in the integration of
informatics and systems approaches in the biological systems and for strengthening research infrastructure,including open-use databases, to make use of massive genomic information.
Presently, NIG has four missions: (1) cutting-edge research in genetics and related fields, (2) collaboration
with, and services to, researchers at universities, (3) graduate education and human resource development, and(4) contributions to society. It is my hope that this report will be valueable for the external evaluation of NIG.

‑1‑

Overview of National Institute of Genetics
Our Mission
Research
NIG conducts top-level research in life sciences leveraging on approaches and resources in Genetics. NIG also
develops new research fields within the broader concept of Genetics.
Education and Career Development
NIG takes part in graduate level education. It also offers various systems to enhance research ability of young
researchers.
Intellectual Infrastructure and Collaboration Research
NIG provides various research infrastructures (genetic resources and information/services) to the scientificcommunity. It also functions as a hub for international and domestic collaborations.
Social Contribution
NIG actively disseminates the achievements from genetic research to the society. It also promotes alliance
between industry and academia.

‑2‑History
1949

Jun. 1
Aug. 10

1953

1954
1955
1960
1962
1964
1969
1974
1975

Jan. 1
Aug. 1
Jul. 1
Sep. 15
Oct. 1
Apr. 30
Apr. 1
Apr. 1
Apr. 1

1976
1983
1984

Apr. 1Mar. 1
Oct. 1
Oct. 1
Oct. 1
Apr. 121985

Apr. 1

1987
1988

Jan. 12Apr. 8Oct. 1

1989
1993

Oct. 1
Apr. 1

1994
1995
1996

Jun. 24
Apr. 1
May. 111997

Apr. 1

Established under the jurisdiction of the Ministry of Education, Science, Sports andCulture. Started with an administrative department and three research departments.
Prof. Kan Oguma was elected the 1st Director.
Three research departments were reorganized as the Departments of Morphological
Genetics, Cytological Genetics and Physiological Genetics.
Department of Biochemical Genetics was added.
Department of Applied Genetics was added.
Department of Induced Mutation was added
Prof. Hitoshi Kihara was elected the 2nd Director.
Department of Human Genetics was added
Department of Microbial Genetics was added.
Department of Population Genetics was added.
Prof. Daigoro Moriwaki was elected the 3rd Director. Department of Molecular Biology
was added.
Plant Genetic Stock Laboratory was established.
Dr. Yataro Tajima was elected the 4th Director.
Animal Section was added in the Genetic Stock Center.
Microbial Section was added in the Genetic Stock Center.
Dr. Ei Matsunaga was elected the 5th Director
Reorganized as an inter-university research institute for joint use by universities. The DNA
Research Center (DNA Structure and Recombinant DNA Laboratories) and theExperimental Farm were established. The Genetic Stock Research Center was expanded
into five laboratories: the Genetic Resources Laboratory was added and the Animal
Section was divided into the Mammalian and Invertebrate Laboratories.
The DNA Synthesis and DNA Data Analysis Laboratories were added in the DNA
Research Center
The DNA Data Bank of Japan began its operations.
The Radio-isotope Center was established. The Gene Library Laboratory was added in the
DNA Research Center.
The Graduate University for Advanced Studies was established. The Department of
Genetics, School of Life Science of the University began accepting students.
Dr. Jun-ichi Tomizawa was elected the 6th Director.
The Mammalian Development Laboratory was added in the Genetic Stock ResearchCenter.
The Gene Function Research Laboratory was added in the DNA Research Center.
The Center for Information Biology was established.
The DNA Research Center was reorganized as the Structural Biology Center consisting of
5 laboratories (Biological Macromolecules, Molecular Biomechanism, Multicellular
Organization, Biomolecular Structure and Gene Network).
The Genetic Stock Research Center was reorganized as the Genetic Strains ResearchCenter consisting of 5 laboratories (Mammalian Genetics, Mammalian Development,
Plant Genetics, Microbial Genetics and Invertebrate Genetics), and as the Center for
Genetic Resource Information consisting of 2 laboratories (Genetic Informatics and

‑3‑

1998

Oct. 1
Apr. 92001

Apr. 1

2002

Apr. 1

2003

Apr. 1

2004

Apr. 1

2005

Dec. 1
Apr. 1

2006

Apr. 12011
2012

Oct. 1
Apr. 1

2014
2015

Dec. 1
Apr. 1
Apr. 1

2018
2019

Dec. 1
Jan. 1

Genetic Resources).
Dr. Yoshiki Hotta was elected the 7th Director
The Division of Early Embryogenesis was added in the Department of Developmental
Genetics. The Division of Brain Function was added in the Department of Integrated
Genetics.
The Center for Information Biology was reorganized as the Center for Information
Biology and DNA Data Bank of Japan. The new center consists of 5 laboratories. The
Laboratory of Molecular Classification of theformer center was renamed as the Laboratory for Research and Development of Biological
Databases in the new center. The Laboratory for Gene-Expression Analysis was added in
the new center.
Two laboratories, Mouse Genomics Resource Laboratory and Model Fish Genomics
Resource Laboratory, were added to the Genetic Strains Research Center.
The Molecular Mechanisms was added to the molecular Genetics. The Laboratry for
Frontier Research was added to the Genetic Strains Research Center. Two laboratories,
Comparative Genomics Laboratory andPublicity and Intellectual Propery Unit, were added to the Center for Genetic Resource
Information.
Reorganized as Research Organization of Information and Systems, Inter-University
Research Institute Corporation, together with three other national institutes.
Dr. Yuji Kohara was elected the 8th Director.
Intellectual Property Unit was added.
Renamed as NIG INNOVATION (as of 2018 Apr.1)
The Center for Frontier Research was established. The Laboratory for Cell Lineage,
Neural Morphogenesis and Cell Architecture was added in the new center.
Advanced Genomics Center was established
Research centers were reorganized. Intellectual Infrastructure Centers (Genetic Resource
Center and DDBJ Center) and Support Centers (IT Unit, Mouse Research Supporting
Unit) were established.
Dr. Isao Katsura was elected the 9th Director.
Office for Research Development was added.
Unit for Experimental Animal Care was established. Office for Female Researcher
Development was added. Renamed as Office for Gender Equality (as of 2017 Apr. 1)
Dr. Fumio Hanaoka was elected the 10th Director.
The existing 5 departments, 3 research centers (Genetic Strains Research Center,
Structural Biology Center and Center for Information Biology), Experimental Farm andRadio-isotope Center were abolished. Four research departments (Dept. of Informatics,
Dept. of Genomics and Evolutionary Biology, Dept. of Gene Function and Phenomics andDept. of Chromosome Science) were established. The DDBJ Center, as one of theIntellectual Infrastructure Centers, was renamed as the Bioinformation and DDBJ Center.
The Support Center was reorganized. (The Radioisotope Unit was added.)‑4‑

2UJDQL]DWLRQ

$GYLVRU\&RPPLWWHH

9LFH'LUHFWRU&RXQFLOIRU6WUDWHJ\3ODQQLQJ࣭
&RXQFLOIRULQWUD52,6OLDLVRQDQG&RRUGLQDWLRQ

࣭+LURQRUL1,.,
࣭7RVKLKLNR6+,52,6+,
࣭+LUR\XNL$5$.,
࣭<XPLNR6$*$

5HVHDUFK'HSDUWPHQW'HSDUWPHQWRI,QIRUPDWLFV%LRORJLFDO1HWZRUNV± 0DVDQRUL$5,7$*HQHWLF,QIRUPDWLFV± 6KRNR.$:$0272*HQRPH(YROXWLRQ± .HQ.852.$:$*HQRPH,QIRUPDWLFV± <DVXND]X1$.$085$*HQH([SUHVVLRQ$QDO\VLV ± .RXVDNX 2.8%2/DERUDWRU\IRU5HVHDUFKDQG'HYHORSPHQWRI%LRORJLFDO'DWDEDVHV± 7RVKLKLVD 7$.$*,,QWHUQDWLRQDO6WUDWHJLF$GYLVRU
9LVLWLQJ)DFXOW\
࣭7DNDR. +(16&+ ࣭-RKQ);',))/(<࣭)UHGHULF%(5*(5 ࣭'LGLHU67$,1,(5࣭6WHYHQ+(1,.2)) ࣭<XQ;LQ )8
࣭.L\RVKL0,=88&+, ࣭=LKHQJ <$1*
࣭/\QQ-25'(
࣭)HQJ=+$1*'HSDUWPHQWRI*HQRPLFVDQG(YROXWLRQDU\%LRORJ\(YROXWLRQDU\*HQHWLFV'1$'DWD$QDO\VLV+XPDQ*HQHWLFV(FRORJLFDO*HQHWLFV3RSXODWLRQ*HQHWLFV3ODQW*HQHWLFV&RPSDUDWLYH*HQRPLFV$GYLVRU\%RDUG'LUHFWRU*HQHUDO)XPLR+$1$2.$

,QWHOOHFWXDO,QIUDVWUXFWXUH&HQWHU± +LURVKL$.$6+,± .D]XKR ,.(2± ,WXUR ,128(± -XQ.,7$12± 1DUX\D 6$,728± <XWDND6$72± $WVXVKL72<2'$%LRLQIRUPDWLRQDQG''%-&HQWHU

࣭+LJK3HUIRUPDQFH&RPSXWLQJ'LYLVLRQ
࣭'DWDEDVH'LYLVLRQ$GYDQFHG*HQRPLFV&HQWHU

࣭6HTXHQFLQJ'LYLVLRQ
࣭'DWD$QDO\VLV'LYLVLRQ'HSDUWPHQWRI*HQH)XQFWLRQDQG3KHQRPLFV%UDLQ)XQFWLRQ± 7DWVXPL+,5$7$/DERUDWRU\RI0DPPDOLDQ1HXUDO&LUFXLWV± 7DNXML ,:$6$72/DERUDWRU\RI0ROHFXODUDQG'HYHORSPHQWDO%LRORJ\± .RLFKL.$:$.$0,
0RXVH*HQRPLFV5HVRXUFH ± 7VX\RVKL.2,'(
6\PELRVLVDQG&HOO(YROXWLRQ ± 6KLQ\D 0,<$*,6++,0$
0LFURELDO3K\VLRORJ\± +LURQRUL1,.,
3ODQW&\WRJHQHWLFV± .HQLFKL 1212085$
0DPPDOLDQ'HYHORSPHQW± <XPLNR6$*$
0RGHO)LVK*HQHWLFV± 1RUL\RVKL 6$.$,0XOWLFHOOXODU2UJDQL]DWLRQ± +LWRVKL6$:$
0DPPDOLDQ*HQHWLFV± 7RVKLKLNR6+,52,6+,*HQH1HWZRUN± (PLNR68=8.,*HQHWLF5HVRXUFH&HQWHU

࣭%LRUHVRXUFH0DQDJHPHQW'LYLVLRQ
࣭3ODQW5HVRXUFH'HYHORSPHQW'LYLVLRQ࣭'LYLVLRQIRUGHYHORSPHQWRI
JHQHWLFHQJLQHHUHGPRXVHUHVRXUFH

࣭%LRUHVRXUFH'DWDEDVH'LYLVLRQ

6XSSRUW&HQWHU

࣭,78QLW࣭5DGLRLVRWRSH8QLW
࣭8QLWIRU([SHULPHQWDO$QLPDO&DUH'HSDUWPHQWRI&KURPRVRPH6FLHQFH
0LFURELDO*HQHWLFV(SLJHQRPLFV0ROHFXODU&HOO(QJLQHHULQJ&HOO$UFKLWHFWXUH*HQRPH'\QDPLFV,QYHUWHEUDWH*HQHWLFV

1,*,1129$7,21

± +LUR\XNL$5$.,± 7HWVXML .$.87$1,± 0DVDWR.$1(0$.,± $NDWVXNL.,085$± .D]XKLUR0$(6+,0$± .XQLDNL 6$,72

2IILFHIRU5HVHDUFK'HYHORSPHQW
2IILFHIRU*HQGHU(TXDOLW\'HSDUWPHQWRI$GPLQLVWUDWLRQ&HQWHUIRU)URQWLHU5HVHDUFK࣭*HQHUDO$IIDLUVDQG3URMHFW6HFWLRQ࣭)LQDQFLDO$IIDLUV6HFWLRQ

6\VWHPV1HXURVFLHQFH± )XPL .8%2
&KURPRVRPH%LRFKHPLVWU\ ± <DVXWR 085$<$0$&HOO'\QDPLFVDQG2UJDQL]DWLRQ± <RVKLKLVD2'$
4XDQWLWDWLYH0HFKDQRELRORJ\ ± <XWD6+,0$0272

7HFKQLFDOVHFWLRQ‑5‑

Outline of Departments and Centers for Research
Infrastructures
Department of Informatics
Develop technologies and resources that enable users to extract actionable information from data and knowledge
in life sciences.

Department of Genomics and Evolutionary Biology
Research many aspects of organisms with special reference to genome sequence analyses and their evolutionary
histories.

Department of Gene Function and Phenomics
Research on genetic traits at the cellular and organismal levels and on characteristics of biological and genetic
resources.

Department of Chromosome Science
Research on genetic mechanisms, such as inheritance, modifications and expression of genetic information.

Center for Frontier Research
The Center for Frontier Research provides promising young scientists with independent positions and an
opportunity of developing new frontiers in genetics and related research fields. The Center thereby brings up
scientists who will play crucial roles in academic fields in the future.

Bioinformation and DDBJ Center
Bioinformation and DDBJ Center collaborates with NCBI (USA) and ENA/EBI (Europe) to maintain theInternational Nucleotide Sequence Database Collaboration (INSDC). It also provides a public supercomputing
system.

Advanced Genomics Center
This center is designed to conduct most advanced genomic researches and to provide resources based on newgeneration sequencing pipeline to the community.

Genetic Resource Center
The center develops and preserves forefront bioresources of various organisms, and distributes them to domestic
and overseas universities and institutes. The related information is open to the public through the databases. The
center participates actively in “National BioResource Project (NBRP)” of AMED.

‑6‑

Research Achievements and Self Evaluation
Department of Informatics
Biological Networks Laboratory
Masanori Arita Group
Starting from November 2013 at NIG, our laboratory has been creating bioinformatics tools and standards toaccelerate life sciences. In cheminformatics, we maintain internationally acknowledged databases called
MassBank and LipidBank for over 10 years. In the last 5 years, we developed a software tool for non-targeted
metabolomics that realizes comprehensive acquisition of MS/MS information [808]. Then through the
integration with metabolome repositories, we could identify five hitherto unknown metabolites [811, 371]. The
quest for better identification continues and we actively participate in international efforts for data
standardization toward FAIR data principles [628, 839, 44].
In genomics, we have advanced computational classification and characterization of Lactobacillus andBifidobacterium based on their genomic features. Using our efficient genome-annotation tool [781], wecharacterized functional features of the above two genera [663], and also discovered new Lactobacillus species
such as L. paragasseri from a genome sequence archive [734, 785]. Most genomics works have been performed
with Sokendai graduate students.

Genetic Informatics Laboratory
Shoko Kawamoto GroupWe are working on research and development of databases and information systems for the National BioResource Project (NBRP) since 2002. Former PI, Yukiko Yamazaki had been developing more than 20 resource
organism's databases, which distribute experimental organisms for academic researcher, until her retirement in2016 [680]. Based on each organism's database, we had been developing a search engine that allows users to
conduct the cross-species search for experimental resources, by applying biological ontologies such as gene
ontology, plant ontology, and disease ontology. Further, we made several organism's genome sequences
available to the public via genome browser in order to increase the biological resource availability [736]. From
2017, we are in charge of the system development for Japanese Rare Disease Models & Mechanisms Network(J-RDMM) under Japan's initiative on rare and undiagnosed diseases (IRUD) project funded by the Japan
Agency for Medical Research and Development (AMED).

Genome Evolution Laboratory
Ken Kurokawa GroupThe Genome Evolution Laboratory was launched in April 2016 as a new laboratory in NIG. In our laboratory,
we are interested in understanding about microbial genome evolution and microbial community dynamics, andwe are currently reaching out in the following two major research directions; I. Facilitate the development of‑7‑

an integrated database for microbes “MicrobeDB.jp” [469, 150], II. Study microbial community dynamics [498,409, 572, 834, 571, 136, 835, 529]. Our research interests blend a background in microbial genomics andmetagenomics with bioinformatics and integrated database developments that are just now allowing theprospect of illuminating microbial community dynamics. We are trying to gain a better understanding of how
microbial diversity maintain as well as how it emerged [149, 398]. We are also trying to propose a new
evolutionary scenario by recovering DNA information from paleontological remains [873, 664].

Genome Informatics Laboratory
Yasukazu Nakamura Group
Ultra high-throughput sequencing technologies allow biologists to obtain larger amounts of nucleotide sequence
data. To facilitate for reuse such huge nucleotide data, it is necessary to create a high-quality sequence databaseas reference data. It is also important to equip automated annotation system that make it possible fast andaccurate results for reliable sequencing analysis. Our laboratory is in charge of DNA Data Bank of Japan(DDBJ) [328] and attempts to develop advanced database management systems and to improve the quality ofannotations in genome databases. We have been constructing an automatic annotation system for prokaryotes:
DDBJ Fast Annotation and Submission Tool (DFAST) [780]. We are also providing several high-quality
annotated genome information for important plant species such as a liverwort Marchantia polymorpha [43] anda japanese orange Citrus unshu [687].

Gene-Expression Analysis Laboratory
Kousaku Okubo GroupOur body of biomedical knowledge is developed in two steps: StepA: accumulating and exchanging situations
captured in descriptions and data; and StepB: conceptualizing situations into a coherent set of dogmatic ormathematical statements that can be employ in decision-making. The overwhelming output of A, mainly due tothe technological assistance by diagnostic, laboratory and communication machines, is making a stressful
situation of “information over-load” or “data deluge”. Our laboratory focuses on developing new technologies
to facilitate step B to enhance the return from our investment in biomedicine[586, 77].

‑8‑

Laboratory for Research and Development of Biological Databases
Toshihisa Takagi GroupWe have developed data sharing and data analysis infrastructures to cope with the recent explosion of genome
data. We have addressed a series of crucial issues for the genome data sharing, including the performance issues
in database construction and genome data analysis, reproducibility of the data analysis, sustainability of
database management, and security and policy issues for the personal genome data management [402, 401, 328].
We have contributed to the operation of unrestricted-access nucleotide sequence databases of International
Nucleotide Sequence Database Collaboration (INSDC) [57, 402, 401, 328, 272]. In addition, we havecontributed to the establishment of the controlled-access database of personal genome in Japan, Japanese
Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in
the Japan Science and Technology Agency (JST) [329, 402, 401, 328]. Our group has also constructed thecontrolled-access database for specific researchers, "AMED Genome group sharing Database (AGD)". Finally,
we have been developing a data analysis environment for personal genomes on the NIG supercomputer alongwith the databases.

‑9‑Department of Genomics and Evolutionary Biology
Evolutionary Genetics Laboratory
Hiroshi Akashi Group
Our research aims to identify the causes of genome evolution. We are especially interested in applying
population genetics theory to large scale within- and between-species DNA data to test whether new mutationsin the genome often have subtle functional and fitness effects related to fundamental biological processes suchas transcription and translation. The power and robustness of our statistical approaches is critical for suchanalyses and method development has been a major recent focus [410, 413, 411]. We have developed methods
that allow inference of ancestral and derived nucleotide states that account for biased characters and changes inbiases over time, and that are accurate for within-species variation. These methods enhance the resolving powerof evolutionary sequence analysis and will allow us to address key biological questions including recent
fluctuations in genome-wide codon usage adaptation, relationships between chromatin structure and genome
evolution, and the biophysical basis of prevalent weak selection in protein evolution [396].

DNA Data Analysis Laboratory
Kazuho Ikeo GroupWe have been conducting research on molecular classification, evolution of symbiosis [891], and diseases
mechanisms [652] using comparative genomics, molecular evolution, and bioinformatics. At the same time, we
engaged in a Hydra strain conservation project. In the project based on external grants, we promoted NGS data
analysis support to promote the use of NGS data for drug discovery in BINDS program (AMED). In Programfor Basic and Clinical Research on Hepatitis (AMED), we tried analyzing transcriptome and SNPs concessions
to elucidate the molecular mechanism of liver cancer onset. In CREST(JST), we worked on technology
development for single cell transcriptome, especially development of data analysis method. In the
SHINGAKUJYUTSU (JSPS), we are working for clarifying state transition of disease on the single cell level.
The result obtained through these activities were published (51 papers) and released as databases and analysis
tools. Four postdoctoral fellows and one SOKENDAI student and two additional students from other university
participated in the research.

Human Genetics Laboratory
Ituro Inoue Group
Our research goal is to elucidate causalities of common diseases such as intracranial aneurysms andendometriosis and their pathogenesis. We employ next generation sequencing technologies to identify
causalities of monogenic diseases as well as common diseases. Using the vast amount of genomic information
at hand, we combine gene expression profiles of the response tissues together with clinical information tounderstand the global picture of diseases. [157, 226, 503, 707]‑10‑

Ecological Genetics Laboratory
Jun Kitano Group
Our research goal is to identify molecular changes underlying naturally occurring phenotypic variation andspeciation and understand how such variations arise and spread within natural populations. Because of recent
advances in genomic technologies, an increasing number of candidate genomic loci or genes responsible foradaptation and speciation have been identified. Molecular changes or causative mutations, however, have beenrarely elucidated. Without knowing causative mutations, we cannot understand how many mutations areimportant, whether each mutation is additive or epistatic, or what kind of selective pressures have acted on eachmutation. To this end, we take an integrative approach across diverse disciplines using stickleback fishes (genus
Gasterosteus and Pungitius) and medake fishes (genus Oryzias) as models [619, 602, 878]. Thus far, we haveidentified several causative genes and mutations (unpublished data). Further investigation of these mutations
will lead to a better understanding of the mechanisms underlying naturally occurring phenotypic variations.

Population Genetics Laboratory
Naruya Saitou GroupWe study evolution of organisms at the genomic levels through computer analyses and genome sequencing.
We published a total of 20 papers during these five years. Among them, we reported human evolution withspecial reference to the origin and formation of people on Japanese Archipelago using modern and ancientgenomes in eight papers [e.g., 251 and 271] and evolution of conserved noncoding sequences in various
eukaryotic organism genomes in five papers [e.g., 36 and 143]. Saitou published “Introduction to Evolutionary
Genomics Second Edition” (2018, Springer) and edited “Evolution of the Human Genome Volume I” (2017,
Springer). The Google Scholar citations of the neighbor-joining method paper (Saitou and Nei, 1987) exceeded
53,000 at the end of 2018. In addition, Saitou devised and described two new methods (swift neighbor-joining
method and external edge elimination) in his 2018 book.

Plant Genetics Laboratory
Yutaka Sato GroupOur group is trying to address a basic question on how do plants shape themselves and reproduce their offspring.
In order to answer the question, we first aim to elucidate the mechanism of plant embryogenesis using rice as amodel system [121, 233, 347]. We are focusing on processes of the patterning of apical-basal or dorsal-ventral
axis formation, the organogenesis during early stages of rice embryogenesis and post embryonic development[173]. We are taking a molecular genetic approach using a series of rice embryogenesis defective mutants aswell as comparative embryology and genomics approaches mainly among grass species. Secondly, we are trying
to describe the mechanism generating the diversity of plant reproduction systems [727]. Our work takes anadvantages of the wild accessions of Oryza collections at NIG; the vast diversiy in seed traits among Oryza
species is powerful and convenient. We are also responsible for management, preservation, propagation, anddistribution of rice genetic resources of wild rice species collected at NIG under the National BioResource
Project (NBRP).

‑11‑

Comparative Genomics Laboratory
Atsushi Toyoda GroupThe Comparative Genomics Laboratory was established in April 2008 with the task to understand basic rulesof biological systems using cutting-edge DNA sequencing and analysis technologies. To date, we have
employed comparative genomics approaches to identify genomic features and provide new insights into thegenetic diversity of wild Oryza species and the terrestrialization process in the Chara genome [622, 562, 530].
Furthermore, through de novo sequencing of different types of algae, two silkworm species, and the organisms
living in the extreme environmental conditions, we have shed light on critical mechanisms for the evolution ofmulticellularity, the history of domestication, and the process of cryptobiosis, respectively [118, 113, 129]. In
addition, we characterized the allotetraploid origin of Xenopus laevis by genome comparison to the diploid X.
tropicalis as international collaborative research [671]. Since FY 2018, we have been supporting and developing
metagenomic and bioinformatic analyses to promote human microbiome research.

‑12‑

Department of Gene Function and Phenomics
Brain Function Laboratory
Tatsumi Hirata GroupThe brain is made up of an enormous number of neurons, whose wiring patterns determine the characteristics
of an animals’ behavior and mental activities. The Brain Function Lab focuses on genetic mechanisms that
determine the axon wiring patterns which develop through sequential steps such as neuronal migration and axon
guidance. Using gene knockout mice for various axon guidance-related molecules, we revealed molecularmechanisms that control specific aspects of axon guidance and neuronal migration [437, 265, 61]. For example,
in one paper [860], we provided the evidence that the famous guidance molecule netrin-1 guides hindbrain
commissural axons by short-range actions but not by the long-range chemoattraction as had been believed fora long time. We also advanced the study of brain development from the evolutionary point of view [726, 534,
533]. By sharing our special techniques and materials, we performed intra-institutional [437, 655] and interuniversity [561, 227, 265, 228, 61, 399, 533, 860] collaborations. Since 2015, a new assistant professor, Yan
ZHU has joined the lab and started a new model involving mouse hindbrain [799, 900].

Laboratory of Mammalian Neural Circuits
Takuji Iwasato Laboratory
We aim to understand development of neuronal circuits in the mammalian central nervous system. During thelast 5 years, we have published 18 papers, including 10 papers in which we are the main contributors. Our mainachievements in this period are as follows: (პ) We have developed the “Supernova”, which is a versatile vector
system for single-cell labeling and gene function studies in vivo [457, 382]. (ჟ) We have developed in vivo
imaging systems for neonatal mouse cortex and used them to reveal dynamic mechanisms of dendritic
refinement of layer 4 (L4) neurons [457, 510], and unique spatial patterns and features of spontaneous activity[456, 510] in the neonatal barrel cortex. (რ) By generating conditional knockout mice of the adenylyl cyclase
1 and NMDA receptor NR1 subunit, we revealed pre- and post-synaptic mechanisms of thalamocortical circuit
refinement in the developing somatosensory system [722]. (ს) By generating series of knockout mice of Įchimaerin and its isoforms, we revealed that this molecule plays important roles in cognitive function [243],
spine development [242] and midline barrier establishment in corticospinal axon guidance [287].

Laboratory of Molecular and Developmental Biology
Koichi Kawakami GroupWe have developed Tol2-transposon mediated genetic methods, including transgenesis, gene trapping, enhancer
trapping and the Gal4-UAS system in zebrafish [296]. By using these methods, we have performed a largescale genetic screen and generated more than 1,500 transgenic lines expressing Gal4 in specific cells, tissues,and organs. Further, we constructed a database named zTrap which facilitates collaboration with researchers
world-wide who can find transgenic fish of interests in our collection based on expression patterns. Thus, ourtransgenic fish serve as powerful resources to study developmental biology, organogenesis, neuroscience andhuman diseases [830, 295, 68, 33]. We aimed to apply these methods to analyze functional neural circuits
controlling fish behaviors. First, we expressed GCaMP in various brain regions via the Gal4-UAS system, and‑13‑

successfully imaged the neuronal activity during hunting behaviors in real-time [485]. Second, we expressed
the neurotoxin gene to inhibit the activity of Gal4-expressing neurons and successfully identified neurons
essential for fear conditioning in zebrafish [705, 372].

Mouse Genomics Resource Laboratory
Tsuyoshi Koide GroupThe aim of this laboratory is to clarify the genetic and neural basis of behavior in mice. We mainly study
aggression, home-cage activity, anxiety, social behavior and tameness. Tameness is a major behavioral factor
for domestication. We conducted selective breeding for tameness using genetically heterogeneous wild-derived
mouse stock and successfully established mice exhibiting high tameness. By using these mice, we mapped
genetic loci associated with the tameness [418]. To understand how social stress affect behaviors, we analyzed
social hierarchy in groups of male mice in home cage and investigated emotional behavior as well as
hippocampal gene expression in the dominant and subordinate mice. We found significantly different emotional
behavior and expression of genes associated with the serotonergic system between dominant and subordinate
mice [180]. In order to understand genetic and neural mechanism associated with aggression, we conductedgenetic mapping [747] and neurobehavioral analysis and found a neural system associate with escalated
aggression [743].

Symbiosis and Cell Evolution Laboratory
Shin-ya Miyagishima Group
Several lineages of eukaryotes acquired the capability of photosynthesis through endosymbiotic events in whicha cyanobacterial or photosynthetic eukaryotic cell was integrated into previously nonphotosynthetic eukaryotic
cells. However, it is still unclear how the permanent endosymbiotic relationship was established by coordinatedproliferation of a host and an endosymbiotic cell. By using several unicellular algae and newly developed
molecular genetic tools in the red alga Cyanidioschyzon merolae [85, 86], we have shown the following.
Chloroplast division is restricted to the S phase by the host cell cycle [591]. Alternatively, host cell cycle
progression (prophase to metaphase) requires initiation of chloroplast division [718]. The G1/S transition isrestricted to (subjective) evening and night when oxygenic photosynthesis in chloroplasts and respiration in
mitochondria are compromised by host nuclear regulation [444]. Thus, our studies have begun to reveal how
activities of eukaryotic cells and endosymbiotic organelles are coordinated by the interactive signaling between
them to coordinate their proliferation.

Microbial Physiology Laboratory
Hironori Niki Group
Bacteria and yeast are important model organisms to elucidate the fundamental mechanisms of cell proliferation.
Our laboratory studies the mechanisms behind the cell division cycle and adaptations to external stresses underenvironments. We focused on compaction of chromosomal DNA as a nucleoid inside a tiny bacterial cell during
cell division. Bacterial condensin is an essential factor for packaging of a nucleoid to properly segregate intodaughter cells. We found that bacterial condensin topologically loads on DNA, and preferentially binds tosingle-stranded, rather than double-stranded, DNA [519]. In a bacterial cell, bacterial condensin loads on‑14‑

rDNAs that are located near replication origins [867]. In addition, we study hyphal development and growth byusing a new model organism, Schizosaccharomyces japonicus that is closely related to the fission yeast S.
pombe [517]. However, S. japonicus is dimorphic yeast and non-pathogenic. We established new investigative
methodologies to investigated S. japonicus [20, 22, 96] and have revealed that several biological processes
conserved in S. pombe as well as some that are not conserved[21, 536].

Plant Cytogenetics Laboratory
Ken-ichi Nonomura Group
This laboratory aims to unveil genetic mechanisms driving plant reproduction; including meiotic cell-fatedecision, meiosis, reproductive organ development and meristem maintenance. In the last five years, wereported that the Argonaute protein MEL1 associates with 21- and 24-nt non-codingRNAs (phasiRNAs) in rice
reproductive organs [335, 334] and is required for meiotic chromatin modifications [379]. The 24-nt phasiRNAs
were produced in tapetal cells surrounding male meiocytes [587, 588]. These results imply the nature ofphasiRNAs in non-cell autonomous regulation of meiotic events. We also revealed a DNA consensus boundwith MEL2, the rice protein required for meiosis entry [453]. In meristem research, we analyzed KNOX proteinsand cofactors in rice and maize [807, 805, 383].
Furthermore, this laboratory is responsible for the maintenance of rice genetic resources with Plant Resource
Development division. For this purpose, molecular markers were developed [516] and genetic diversity ofnatural populations was explored [592].

Mammalian Development Laboratory
Yumiko Saga GroupWe use mouse genetics to elucidate molecular mechanisms involved in several developmental processes suchas germ cell development and somitogenesis. Recent achievements are as follows: (I) Germ cells are first
specified as primordial germ cells (PGCs) in the early embryonic stage. However, it is largely unknown what
factor is responsible for sexual fate determination in germ cells. We demonstrated that two factors (STRA8 andSMAD4) work as sex determinants since female germ cells lacking both Smad4 and Stra8 develop as malegonocyte-like cells in ovaries [843]. (II) In the male germ cells, an RNA binding protein NANOS2 is essential
to promote male pathway. We have identified DND1, another RNA binding protein, as a partner of NANOS2
to recruit target RNAs [844, 724, 285]. (III) NANOS2 is also required for sustainable spermatogenesis in adulttestes. We showed mechanisms of NANOS2 action in spermatogonial stem cells (SSCs) and demonstrated how
NANOS2 expression is regulated in SSCs [899, 898]. (IV) Previously we identified a transcription factor Mesp2
and the target gene Ripply2 as factors required for somite segmentation. We found that Ripply2 directly binds
Tbx6 (an enhancer of Mesp2) to degrade it to define the segmental border [896].

Model Fish Genetics Laboratory
Noriyoshi Sakai Group
Our lab focuses on germ cell development in zebrafish. To analyze molecular mechanisms to regulate germ
cells efficiently, we developed techniques to recapitulate the entire process of spermatogenesis entirely in cell
culture, from spermatogonial stem cell propagation to differentiation of functional sperm, [306]. This culture‑15‑

technique was applied for spermatogonia of the endangered endemic cyprinid Gnathopogon caerulescens [146].
We also established subcutaneous grafting methods of a fragment of the hyperplastic testis and a whole bodyof the embryo for in vivo assay, which enable continuous growth of the hyperplastic testis and development ofembryonic lethal mutants beyond the lethal stage to the spermatogenic stage [305]. Furthermore, weinvestigated the meiotic process and found formation of a clear telomere bouquet structure and initiation ofsynapsis from the telomere region in zebrafish spermatocytes, unlike the mouse [639]. In addition, weestablished a new inbred zebrafish line from the AB line by complete sib-pair mating for more than 20th
generations. The inbred line, ABM, is healthier and more readily maintained compared to the previously
established IM line.

Multicellular Organization Laboratory
Hitoshi Sawa GroupThe relationship between cell size and cell cycle was reported only in Xenopus. We showed in C. elegans
embryos that cell cycle duration and cell size exhibited a power law distribution as in Xenopus. However, theabsolute powers in C. elegans were different from that in Xenopus and depends on cell types [30]. PIGN is
known to be an enzyme for glycosylphosphatidylinositol (GPI)-anchor biosynthesis in the endoplasmic
reticulum (ER). We showed that independent of this enzymatic activity, PIGN functions to prevents protein
aggregation in ER in C. elegans and in mammalian cells [197]. The adenomatous polyposis coli (APC) protein
is a tumor suppressor that inhibits canonical Wnt signaling and stabilizes microtubules by binding to their plus
ends. We have shown in C. elegans embryo that APC on the cell cortex attenuates spindle-pulling forces toprevent excess movements of centrosome during asymmetric division [712].

Mammalian Genome Laboratory
Toshihiko Shiroishi Group
1. Mechanism and evolution of enhancers regulating tissue-specific Shh expression
We identified remote enhancers that regulate Shh expression specifically in various different endodermal tissues
by genetic analyses of spontaneous mouse mutants and gene-modification methodologies including genome
editing. Furthermore, we conducted comparative analyses of the enhancer sequences across a wide-range ofvertebrates and experimental analyses with mice and medaka fishes, and we found that evolution of the Shhenhancers has been involved in morphological change of respiratory laryngeal structure in vertebrates [637].
2. Mechanism of mouse speciation
Reproductive isolation promotes speciation. A good example is hybrid male sterility observed in mouse, which
may be caused by genetic incompatibility between diverged genetic factors in two mouse subspecies. Genetic
factors responsible for the sterility are disproportionately located on the X chromosome. Our studies showedthat evolutionary divergence of transcriptional regulation causes genetic incompatibilities in the hybrid males,
and results in reproductive isolation [567].

‑16‑

Gene Network Laboratory
Emiko Suzuki Group
Our laboratory is studying molecular and cellular mechanisms of tissue development and function, using
Drosophila melanogaster as a model system. We have been focused on two lines of projects. The first topic isepithelial cell competition for the homeostasis of normal tissue development. We found new mechanisms forcell competition and also found special epithelial areas, tumor hot spots, in which abnormal outcome of cellcompetition leads to tumors [767]. The second line of research focuses on formation and function of neuronal
circuits. By studying the taste system, we identified the neurons crucial for the connection between sensory
inputs and the feeding motor system, and the neurons which connect sensory inputs and higher order neurons
involved in the reward system associated with olfaction. We also carried out many collaborative projects
including 28 NIG Collaborative Research Programs (NIG-JOINT) on neuronal functions, offering our expertiseof electron microscopy for the analyses of subcellular structures [669, 710].

‑17‑Department of Chromosome Science
Microbial Genetics Laboratory
Hiroyuki Araki GroupWe have studied eukaryotic chromosome DNA replication using budding yeast as a model organism and havemade some important discoveries. First, we solved the crystal structures of the Sld3 and Sld7 proteins, which
form a complex working at the initiation step of DNA replication, and revealed that two Sld3 molecules areconnected by two Sld7 molecules in an anti-parallel manner. This structure suggests simultaneous loading of
Sld3 onto a pair of helicase cores, Mcm2-7, preloaded on replication origins [235, 236]. Second, we analyzed
assembly of replication proteins at origins and revealed new mechanisms, which include automatic splitting ofa pair of Mcm2-7 after the assembly and formation of a replicative helicase, Cdc45-Mcm2-7-GINS (CMG)
complex [169, 454]. Thirdly, we showed that DNA polymerase modulates the activity of CMG helicase to pause
the replication fork at the barrier [168]. This finding suggests a novel regulation of the CMG helicase activity
by DNA polymerase when the replication forks face barriers on chromosome.

Epigenomics Laboratory
Tetsuji Kakutani GroupIn Arabidopsis mutants defective in DNA methylation, diverse transposable elements (TEs) were mobilized,
indicating that DNA methylation is important for immobilizing them (Miura et al 2001 Nature; Tsukahara et al2009 Nature). VANDAL21, one of the TEs immobilized by DNA methylation, encodes a protein with antisilencing effect; that protein, called VANC, induces loss of DNA methylation, expression of encoded genes andmobilization of VANDAL21 (Fu et al 2013 EMBO J). We have shown that this anti-silencing system issequence-specific and that the proteins and targets coevolve to differentiate the sequence specificity [184]. An
important remaining question is how this anti-silencing is accomplished, after sequence-specific binding of thisprotein.
Silent epigenetic marks, such as DNA methylation and methylation of lysine 9 of histone H3 (H3K9me), arefound not only in promoters but also in internal regions (body) of transcription units. Despite its prevalence, thebiological significance of gene body silent modifications remains enigmatic. We showed that H3K9meassociated removal of H3K4 monomethylation (H3K4me1) in gene bodies mediates transcriptional silencing.
Mutations in an Arabidopsis H3K9 demethylase gene IBM1 induce ectopic H3K9me2 accumulation in gene
bodies, with accompanying severe developmental defects (Saze et al 2008 Science). Through suppressor
screening of the ibm1-induced developmental defects, we showed that gene-body H3K9me2/H3K4me1
mediates heterochromatin silencing and epigenome differentiation [207].

‑18‑

Molecular Cell Engineering Laboratory
Masato Kanemaki GroupOur group pioneered auxin-inducible degron (AID) technology to rapidly degrade a degron-fused protein ofinterest in nonplant cells. To apply this technology to control endogenous proteins in human cells, we developed
a new method to tag endogenous genes using the CRISPR–Cas9 genome editing and generated conditional cellsof RAD21 cohesin and DHC1 dynein [513]. The plasmids for making AID mutants were deposited at Addgene
and NBRP, which have distributed more than 2000 plasmids to researchers all over the world. We published areview paper to promote the use of degron technologies [512]. We also used the AID technology to reveal a
backup mechanism to deal with a failure in DNA replication and showed a pathway to form mitotic
chromosomes [514, 101].

Cell Architecture Laboratory
Akatsuki Kimura Group
This laboratory aims to understand how the spatial organization of cells is accomplished in terms of genetics,
mechanics, and self-organization. For this purpose, we combine genetics with quantitative microscopy andmechanical modeling of cells, using Caenorhabditis elegans as a primary model organism. A major question is
how nanometer-sized macromolecules can measure micrometer-sized cellular spaces. We have revealed how
the cell nucleus finds the center of the cell [779] and discovered scaling relationships between the nuclear sizeand chromosome compaction [122] and between nuclear size and chromosome mobility [24]. We also
succeeded in constructing a mechanical model that accounts for the relationship between eggshell shape andthe cell arrangement within the eggshell [856]. Another question is how the macromolecules in a cell behavescollectively. As a collective behavior, we focus on cytoplasmic streaming, and have succeeded in constructing
mechanical models of actin-based [531] and microtubule-based [313] streaming.

Genome Dynamics Laboratory
Kazuhiro Maeshima GroupHow is the long strand of genomic DNA organized in the cell? For the past 5 years, using various imaging
technologies, we have been contributing to change people’s view on chromatin structure from a static regular
one to a more irregular and dynamic one [387, 393]. By combining super-resolution imaging and single
nucleosome tracking, we revealed that chromatin forms numerous dynamic compact domains that act asfunctional units of the genome [538]. This compact organization seems to generate a spring-like force that
resists various mechanical stresses [684]. Furthermore, to better understand the chromatin environments inliving cells and given the ease with which chromatin structure and dynamics can be modulated in the cellularenvironment by free cations and macromolecular crowding, we developed new imaging methods and visualized
free Mg2+ behavior [391] and density of total materials [202] in living cells, shedding new light on the natureof chromatin and how it is regulated.

‑19‑

Invertebrate Genetics Laboratory
Kuniaki Saito GroupThe genome-sequencing project stimulated many studies that revealed conservation and difference of thegenetic systems in many model organisms. The fruit fly Drosophila that has 14,066 genes in its genome wasstudied extensively in genetics and reverse genetics. However, biological function of a half of its genes is still
obscure. To develop a genetic resource for comprehensive analyses of fly genes, we are establishing RNAi andknock out mutants. By mid2018, we comprehensively generated fly lines that can knock down 10,000 genes
using RNAi and knock out 2,500 genes by the CRISPR/Cas9 system. These strains are open to all researchers
globally and are widely utilized for studying gene functios [225, 339]. As a result of collaborations, more than
20 research papers were published. These achievements demonstrate our substantial contribution to the fly
research community and the development of a promising approach to clarify complex systems of genetic
networks underlying fly genome function.

‑20‑

Center for Frontier Research
The Center for Frontier Research is an “incubation” system to foster human resources and new research fields.
Promising young scientists conduct research as principal investigators (tenure-track associate professors) to
explore new frontiers in genetics and related areas, taking advantage of NIG’s research infrastructure andsupport systems. Those who obtain tenure establish new research divisions in NIG to lead the new fields thatthey contributed to creating.
During the tenure-track period of 5 years each faculty is provided ample laboratory facilities, generous funding(a total of 36 million JPY of research funds as well as a postdoctoral fellow and a technician position) andlimited service and teaching duties. Before finishing the term, the tenure evaluation is conducted based on thecandidate’s potential to lead a new research field. The criteria could be fulfilled by a discovery of a newphenomenon, concept, technique, or molecule that foreshadows a new research field, followed by ademonstration of the path to the establishment of such a field.
In the past five years, four CFR members succeeded to obtain tenure and were appointed as professors of newLabs in NIG. In addition, four new members (including one female scientist) were selected through a highly
competitive selection process (international recruitments).

Systems Neuroscience Laboratory
Fumi Kubo Group
Animals generate a range of behaviors depending on visual information that they receive from the outside world.
Using zebrafish as a model, our lab studies the neural circuit mechanisms by which visual inputs produce goaldirected behavioral outputs. In particular, we aim to understand the roles of genetically defined neuron types
and their circuit connectivity underlying the visually guided behaviors. Our approaches include behavioral,
genetic and optical techniques, as well as quantitative data analyses. In our lab, started in Dec 2017, we haveestablished an infrastructure for imaging neural activity of larval zebrafish in vivo using two-photon microscopy,
combined with simultaneous visual stimulation. We have developed optogenetic tools to analyze the function
and morphology of single neurons in vivo [72]. Furthermore, we have applied these optogenetic methods to avisual processing circuit to reveal the function and connectivity of the underlying neural circuit (Kramer et al.,in preparation).

Chromosome Biochemistry Laboratory
Yasuto Murayama Group
Our laboratory studies the molecular mechanism that enables proper organization and faithful segregation ofchromosomes. The ring-shaped structural maintenance of chromosomes (SMC) complexes are major architectsof chromosomes, which topologically entrap DNA. SMC complexes play vital roles in chromosome
condensation, sister chromatid cohesion, DNA repair and transcriptional regulation. They are thought toorganize chromosomes by tethering more than one DNA strand by topological embrace. Using purified proteins,
we have successfully reconstituted topological DNA binding by cohesin, the SMC1-SMC3 complex whichmediates sister chromatid cohesion as well as higher-order chromosomal structures in interphase. Our studies‑21‑

provide important molecular insights into DNA entry into and exit out of the cohesin ring. In addition, we havealso demonstrated DNA-DNA tethering by cohesin [480]. The biochemical approaches provide an
unprecedented opportunity to understand fundamental mechanisms of how SMC proteins organize chromosome
architecture [481].

Cell Dynamics and Organization Laboratory
Yoshihisa Oda Group
Cell polarization and patterning are fundamental processes essential for a range of cellular activities. We havebeen focused on the plant metaxylem vessel cell differentiation, in which pitted cell wall patterns are establishedat the cell surface through formation of plasma membrane domains occupied with ROP GTPases as a model of
intracellular patterning. We have revealed that the plasma membrane domains are generated in a cellautonomous manner via a reaction-diffusion mechanism [489]. The size and shape of the plasma membrane
domains are regulated by two novel proteins that have opposite effects on the interaction between the plasma
membrane and microtubules [656, 713]. We also found that a novel tethering protein complex mediates
microtubule-dependent targeting of exocytotic vesicles to promote cell wall development at the outside of theplasma membrane domains [547, 828]. In addition to these studies, we revealed the mechanisms underlying cellfate determination of vascular cells [553] and pith parenchyma cells [81].

Quantitative Mechanobiology Laboratory
Yuta Shimamoto Group
Our laboratory studies how cells generate, sense, and respond to mechanical force to properly function. It has
been widely recognized that mechanical force plays essential roles in regulating cellular processes. However,examining forces in cells has been challenging, as existing methods are limited in their physical access to theintracellular space without perturbing cell’s physiology. In the past five years, we have been developing
quantitative micromanipulation tools (e.g., force-calibrated microneedles, optical tweezers), integrating
microscopy imaging and reconstitution assays to examine the mechanical integrity of the mitotic apparatus, theprotein machinery essential for proper segregation of chromosomes during cell division [49, 737, 738]. We also
applied our methods to analyze the mechanical properties of other subcellular organelles, such as the cell
nucleus [684] and the endoplasmic reticulum [313], revealing unprecedented roles in governing subcellular
processes. Our approach further enabled us to build quantitative physical models, which elucidate how thesestructures generate and respond to force while maintaining overall integrity.

‑22‑Intellectual Infrastructure Center
Bioinformation and DDBJ Center
Head: Masanori Arita
I.

Overview

The DNA Data Bank of Japan (DDBJ) Center is engaged in four major activities. (1) Since 1987 it has been amember of the International Nucleotide Sequence Database Collaboration (INSDC), a public resource for life
sciences that includes the National Center for Biotechnology Information (NCBI) of the USA and the European
Bioinformatics Institute (EBI). (2) The DDBJ provides supercomputing services to Japanese researchers in thelife sciences, especially for biological sequence analyses. Each year, more than 600 registered users from 130
institutions use our computing service. (3) The DDBJ develops software tools to accelerate research efforts.
To keep our computing environment useful and up-to-date, its interface and application tools are constantly
updated and refactored. Computation nodes can be also reserved for the smooth performance of scheduled
analyses (paid service). (4) Our outreach and educational activities include lectures and workshops. Below wesummarize our activities of the past five years.
II. Activities (2014 – 2018)
A. Management of INSD databases and other repositories
As of December 2018, the DDBJ Center hosts multiple public databases (Table 1). Six are INSDC databases
and two, the Genomic Expression Archive (GEA) and the Japanese Genotype-Phenotype Archive (JGA) areoutside the INSDC. The INSDC policy guarantees free and unrestricted access to DNA data; it does not fully
apply to personal genomes and expressions. However, with the exception of personal information, the threehost institutions (DDBJ, NCBI, and EBI) seek to exchange as much (meta) data in each database as possible tosupport scientific endeavors through global coordination. The database content is searchable on our web
interface at https://www.ddbj.nig.ac.jp/.
Table 1. Database categories of INSDC and the two coordinated repositories
Annotated/
Assembled
sequences

Capillary
reads

NGS
reads

Study

EBI

Trace
SRA BioProject
Archive
European Nucleotide Archive (ENA)

DDBJ

DDBJ

NCBI

GenBank

Trace
Archive

SRA

BioProject‑23‑

SampleAssembly

Functional
genomics

Genotypeandphenotype

BioSample

Assembly

GEO

dbGaP

ArrayExpress
GEA(2018 - )EGA
JGA(2013 - )BioSample

Assembly

The submission trend for annotated sequences is shown in Table 2. There is a mild but steady shift fromtraditional web-based- to large-scale submissions (denoted as mass data). Most data submissions to DDBJ comefrom Japan. Others are from Asian and middle-eastern countries. Altogether, these sources account for a little
less than 10% of all INSDC submissions. Statistics of internet access to DDBJ, obtained via domain names in
2018, show that about 50% access come from companies (‘.com’ and ‘.net’), 20% from ‘.jp’ (Japan), 7% from‘.gov’ (US government), and 23% from anonymous origins or unknown addresses.
Table 2. The number of DDBJ submissions for annotated sequences
Web Submission
Submitters

Mass Data Submission

Submissions

Submitters

Submissions

2018.Jan 㹼 Dec

2268

3979

350

2716

2017.Jan 㹼 Dec

2124

3555

346

1410

2016.Jan 㹼 Dec

2387

4105

346

986

2015.Jan 㹼 Dec

2417

4110

327

970

2014.Jan 㹼 Dec

2499

4034

352

920

Besides submissions from researchers, patent-related DNA- and amino-acid sequences are handled by INSDC
in collaboration with patent offices in Japan, the USA, and Europe. DDBJ also cooperates with the Korean
Bioinformation Center to publish data from Korean patent offices. Integrated submissions to the three hostinstitutions and patent information are published quarterly in the DDBJ release.
In the last decade, the availability of next-generation sequencers (NGS) has drastically changed the landscapeof the life sciences. INSDC has provided the Sequence Read Archive (SRA) for NGS data since 2009; its size
now exceeds 4 petabytes (PB). To streamline associated metadata, INSDC started the BioProject database forproject information and the BioSample database for biological source- and material information. The size trendof the public DRA (the SRA at DDBJ) is shown in Table 3. Its size decreased in 2018 because storage shortage
forced us to stop mirroring NCBI/EBI SRA data in April 2017. We have prepared an additional 30 PB ofstorage and the mirroring will restarted in 2019.
Table 3. DDBJ SRA file size
DRA file size
2018. Jan

3.88 PB (1.07 fastq + 2.81 SRA)

2017. Jan

3.68 PB (1.06 fastq + 2.62 SRA)

2016. Jan

2.44 PB (0.655 fastq + 1.78 SRA)

2015. Jan

1.35 PB (0.27 fastq + 1.08 SRA)

2014. Jan

0.92 PB (0.25 fastq + 0.67 SRA)

‑24‑

The other important trend is the rapid accumulation of personal genomes. As personal information must not be
copied across countries without permission, each institution controls access to submitted data by restricting user
access. In October 2013, DDBJ started the Japanese Genotype-Phenotype Archive (JGA) in collaboration with
the National Bioscience Database Center (NBDC), which organizes access guidelines and data-sharing policies
for Japan (http://humandbs.biosciencedbc.jp/en/guidelines). Under these policies, JGA offers restricted accesssimilar to the Database of Genotypes and Phenotypes (dbGaP) at the NCBI and the European Genome-phenome
Archive (EGA) at EBI. The size increase in personal genomes in JGA is slower than expected (Table 4),
probably due to the data-sharing policies of funders of research in Japan.
Table 4. Cumulative growth of JGA data
Archived numbers(parentheses show the number of available data)
study

samplefile size (T bytes)

2018. Jan

123 (72)

204130106.192017. Jan82 (30)

8785

46.3

2016. Jan46 (20)

6199

14.32

2015. Jan

10 (5)

6199

14.32

2014. JanNot available

B. Management of the NIG supercomputer
The DDBJ Center hosts a sequence analysis platform on its supercomputing system. The UNIX-based system
is comprised of 554 general-purpose calculation nodes (64-GB memory each), 10 de novo assembly nodes (2TB memory each), and one 10-TB memory node. Over 200 software tools, mainly designed for sequence
analysis, are pre-installed on the system. Its use by small-scale users is free (up to 30 TB of disk space). Users
exceeding this threshold must pay a prorated volume fee. Users are required to renew their application every
budget year, indicate the specific purpose of usage, and submit their publication records. All user names,
affiliations, purposes, and publications are available on our website [https://sc.ddbj.nig.ac.jp/ja/report (inJapanese only)]. Because the Japanese law, the Foreign Exchange and Foreign Trade Act, prohibits the exportof supercomputers, the system is available to Japanese researchers and their colleagues only. The number ofregistered users is listed in Table 5; the number increases toward the end of our budget year. The number ofusers becomes lowest at the time of our supercomputer application in April because accounts are closed if theirowners do not apply for their continuation. We estimate the average number of active users to be 600. The
total number of user institutions is 130.
The supercomputer traffic is highly congested; the CPU occupancy by assembly nodes surpasses 70%
throughout the year (up-to-date information is available online at https://sc.ddbj.nig.ac.jp/ja/statistics). Since
2017, the DDBJ Center offered several paid services such as scheduled priority data processing and the secure
analysis platform for private genomes. The price list for these services is available on our homepage[https://sc.ddbj.nig.ac.jp/ja/application (in Japanese)].

‑25‑

Table 5. Trend of registered users and number of published research papers
Login user
(standard)

Login user
(large scale)

DDBJ usage

Maintenance

Total

Research papers
reported by users

2018 Dec

616

199

88

18

921

35 (partial data)

2017 Dec

557

182

92

15

846

95

2016 Dec

549

165

88

14

816

83

2015 Dec

519

139

83

15

756

43

2014 Dec

380

105

82

13

580

53

In addition to ssh login services, the supercomputer resources can be accessed via two web services. The DDBJ
Pipeline and the MiGAP annotation system provide web interfaces to analyze genome sequences from web
browsers. In 2018 the cumulative number of user accounts of these web systems exceeded 3000 (Table 6).
Both web services ceased at the end of budget year 2018 to increase the transparency of user control and to copewith staff changes. Upon their termination, the DDBJ Center provides alternative web services, i.e. the DFAST
annotation system for small bacterial genomes and the Maser one-stop platform for NGS data, on a stand-alone
server.
Table 6. Cumulative number of web service users

MiGAP users

DDBJ Pipeline users

Total

2018 Dec

1000

1824

2824

2017 Dec

908

1622

2530

2016 Dec

767

1363

2130

2015 Dec

667

952

1619

2014 Dec

537

694

1231

C. Development of software tools to accelerate research
The computing environment of DDBJ has been constantly updated. In 2017, DDBJ started the Group Cloud
service (DGC) to provide a secure database system for a private use (a paid service). The first instance of thisservice was the AMED Genome group sharing Database (AGD), on which private genome data are shared
among restricted users; traditional person-by-person access restrictions apply. To analyze private genomes in
JGA or AGD, in September 2018 DDBJ started to offer a secure computing environment specifically designed
for private information (a paid service). DDBJ also installed a 15-PB hard disk and a 15-PB tape archive toaccommodate the increase in data.
By the end of budget year 2018, our computation facility will be updated. The new system specifications include
204 general-purpose computing nodes (136 AMD EPYC with 512 GB-, 52 Intel Xeon with 384 GB-, and 16
NVIDIA GPU with 384 GB memory), 10 de novo assembly nodes (3-TB memory each), one 12-TB memory
node, and 10 PB of Lustre file storage.
D. Education and outreach
Each year, the DDBJ Center organizes at least three lecture series. The full list is available athttps://www.ddbj.nig.ac.jp/training.html. Since 2015, DDBJ has collaborated with the Database Center for Life‑26‑

Science (DBCLS), the Protein Data Bank Japan (PDBj), and the NBDC in organizing an annual all-in-one
training course for beginners. In 2017, DDBJ started to organizes a new lecture course, the “DDBJSupercomputer Training & Educational Program” (D-STEP). It trains intermediate- to upper level data
scientists to handle omics data in life sciences.
In commemoration of its 30th anniversary in 2017, DDBJ organized the NIG International Symposium “Life,
Environment, and Evolution Revealed by Genomes” (https://www.ddbj.nig.ac.jp/ddbj3). Support came fromdifferent sources including Mishima City and six companies. Invited and oral presentations and poster sessions
from eight neighboring high schools attracted 293 participants in the course of three days. Video lectures areavailable online from TogoTV at DBCLS.
Between March and July of 2017, the Shizuoka Shinbun newspaper published 16 articles on the 30-year historyof DDBJ. All lecture materials and database statistics are available on our website(https://www.ddbj.nig.ac.jp/activities.html).
III. Staff and organization
The DDBJ staff includes 4 full-, 2 associate-, and 4 assistant professors and 13 annotators/curators. In 2017,
the job title “annotator” was changed to “curator” and 3 curators were chosen as “coordinators” to organize
DDBJ activities. Since 2017, attendance management is processed online. Faculty members communicate withall curators through regular interviews and self-evaluation sheets. Budget information is provided in our annual
report available on our website.
Faculty
Professors

Associate Professors
Assistant Professors

Masanori Arita
Yasukazu Nakamura
Toshihisa Takagi
Kosaku Okubo
Osamu Ogasawara
Nozomu Sakurai
Yasuhiro Tanizawa
Kazuo Hara
Takeshi Kawashima
Eri Kaminuma(2013 -; Head, 2018 - )(2009 - )(2009 - 2018; Head, 2012 - 2017)(2003 - ; Head 2009 - 2011)(2003 - )(2018 - )(2018 -)
(2016 - 2017)(2017 - )(2009 - 2017)

Curator (* … coordinator)
Yoshihiro Okuda Ph. D
Toshiaki Tokimatsu Ph. D
Shiho Mukaida Ph. D
Hideo Aono
Asami Fukuda
Yuichi Kodama Ph. D *Takehide Kosuge Ph. D *KyungBum Lee Ph. D
Jun Mashima Ph. D *Toshihisa Okido Ph. D
Katsunaga Sakai Ph. D
Haru Tsutsui
Noriko Furuya Ph. D(2016 - )(2016 - )(2016 - 2017)(2001 - )(2005 - )(2008 - )(2002 - )(2006 - )(1999 - )(2001 - )(2002 - )(1995 - )(2013 - 2014)‑27‑

IV. Timeline of major DDBJ activities
Event

2014

2015

2016

2017

ICM host

DDBJ

NCBI

EBI

Collaboration

DBCLS
branchstarted in
Mishima

All-in-one
lecturecourse with
NBDC,
PDBj, and
DBCLS

Semantic web
database with
DBCLS

JGA

Onlinesubmission
startedSecurity
update (filetransfer)

GEA(preparation)

Paid service(preparation)

Group Cloud(AGD)

Outreach(regularlecturecourses(3 per year)

30th
anniversary
symposium

DDBJ

2018
NCBI
Personal
genomewith
TohokuMedicalMegabank
Off-premiseserver at
TohokuMedicalMegabank

Mirroring ofArrayExpress‑28‑

Onlinesubmission
startedAdvancedreservation

Platform
for
personal
genomes
DS
WorkshopAdvanced Genomics Center
Head: Ken Kurokawa
I. Overview
With the rapid development of Next-generation sequencing technologies (NGS) and of technologies to analyze
these DNA sequences, human genome project was succeeded in completing the whole genome sequence ofhuman. This project triggered an independent field of science “Genomics” which is likely to lead to newopportunities for all life science fields. Due to further development of current sequencing technologies, genomesof diverse organisms, from bacteria to humans, are decoded and new biological discoveries are successively
brought about on the basis of their genome information. Also, not only the genome of a single organisms but
also the genomes from the environmental samples such as soil, water, and human feces are being deciphered(i.e. metagenomics, eDNA). In addition, integrated analysis of heterogeneous data such as biologicalinformation and environmental information is also developing, and genome information become effectively
utilized not only for life science but also variety fields of research. In these situations, the NIG Advanced
Genomics Center (AGC), which was established in 2011, is expected to accelerate the genome science by
providing cutting-edge technologies to research communities through its service cores that specialize in genome
analysis, bioinformatics, and multi-omics analysis. To answer the heavy demand of genome analyses from theuniversities and research communities, the AGC promotes activities focusing on the following five missions, 1.
Continual development of advanced genomics technologies, 2. Development of bioinformatic technologies, 3.
Promotion of collaborative research, 4. Promotion of open science and open data, 5. Education on advanced
genomics. Projects for the AGC support are selected from the applications which are based on NIG-Joint
program. The major criteria for successful applications are as follows, 1. Applications that are expected to
produce outcome exceeding the initial plan of the applicant's project by receiving the AGC support, 2.
Applications that contain challenging tasks that require advanced technologies, 3. Applications that contain
request for advanced technologies that are not available in commercial service.
II. Major research tasks on the AGC
In addition to the NIG-joint program, the AGC is promoting the following four research projects throughprovision of public funds.
A. National BioResource Project (AMED)(from FY2011)
The major purpose of this project is to collect, preserve, and provide bioresources (such as experimental animals
and plants) that are essential experimental materials for life sciences research. The role of the AGC is to analyze
genome sequences of bioresources.
B. Platform for Advanced Genome Science (MEXT)(from FY2016)
The mission of this project is to advance technologies in genomics and bioinformatics and to provide them fora wide range of research projects that are supported by the KAKENHI. The AGC is the analysis center for thisproject.
C. Human Microbiome Project (AMED)(from FY2017)
This program is aim to achieve a better understanding of the molecular mechanisms of host-microbiome
interactions and symbiosis. The AGC is the analysis center for this project.

‑29‑

D. Promotion of Microbiome Research (ROIS)(from FY2018)
This project is aimed at strengthening the function of the AGC to support rapidly developing microbiome
research. Establish a research platform for metagenomics by circulating “3A cycles” (Analysis - Accumulation- Application), and contribute to the enhancement of the international competitiveness of universities andindustries in microbiome research.
III. Sequencing facilities
As mentioned above, NGS technologies are essential in genome science. However, NGS technologies advanceat remarkable rates, and the equipment often becomes obsolete in about 3 years. Therefore, in order to provide
advanced genomics techniques, it is necessary to keep equipment up-to-date. Unfortunately, this is a major
hurdle for universities and laboratories. The AGC has always upgraded or introduced NGS to the latest version(e.g., HiSeq2000 (2011), HiSeq2500 (2012), PacBio RSII (2014), PacBio Sequel (2015), GridION (2017),
NovaSeq6000 (2018))(Table 1), and has been achieving technologies advances in order to full use of NGS
Table 1. Sequencing facilities in the AGC
Performance
MachineNum

Type

Sequence
lengthData volume

Running time

ABI 3730xl

2

Capillary~800bp~77kb

2h

NovaSeq 6000

1

DNA synthesis~150bp~6Tb

48h

HiSeq 2500

3

DNA synthesis

250bp~300Gb

60h

MiSeq

1

DNA synthesis

300bp

~15Gb

6.5h

PacBio RSII

1Single molecule

~15kb

~1Gb

6h

PacBio Sequel

1Single molecule

~15kb

~8Gb

6h

GirdION

1

Single molecule

~1Mb

~8Gb

48h

IV. Data productivity of the AGC
By utilizing the next-generation sequencers, we have produced a vast amount of sequence data of genomes frombacteria to human (Figure 1). These data are analyzed using NIG supercomputer, and these are released to theworld through DDBJ.

‑30‑

1.E+07

350

4000

300

3500

Number of Organisms

Base pairs (Mbp)

1.E+06
1.E+05
1.E+04
1.E+03

3000

250

2500
200
2000
150
1500

Number of samples

1.E+08100

1.E+021000
50

1.E+01
1.E+00

500

0

2014

2015
HiSeq

PacBio2016
Sanger

2017

2018

0
2014

NanoPore

2015

2016
Organisms

2017

2018

SamplesFigure 1. Total amount of sequenced base (left), number of organisms and samples (right).

V. Publications through the AGC activities
2018:

Genome analysis of California poppy (Papaveraceae)(Plant Cell Physiol.). 18 publications in total.

2017:

Elucidation of the evolutionary mechanism of gene expression on Stickleback (Evolution). 18 publications in total.

2016:
Genome analysis of Xenopus laevis (Nature), Genome analysis of morning glory (Nat. Commun.), Genome analysis of
Bearbear (Nat. Commun.). 15 publications in total.
2015:
Genome analysis of Acytostelium subglobosum (Slime mold)(BMC Genomics), High resolution analysis of Marmoset
genome (Science. Rep.). 14 publications in total.
2014:
Sex chromosome analysis of Stickleback (PLoS Genet.), Development of genome assemble software (Genome Res.), Genetic
analysis of Killifish sex determination (Nat. Commun.). 15 publications in total.

‑31‑

Genetic Resource Center
Head: Hironori Niki
I.

Overview

The Genetic Resource Center is composed of two divisions of "Bioresource Division" and "Database Division."
The Bioresource Division takes responsibility for the development, preservation, and distribution of forefront
bioresources of various organisms including E.coli/B.subtilis. Rice, Mouse, Drosophila, Zebrafish, C. elegans,and Hydra, and of collected wild species of those organisms. The Database Division makes the above
information available to the public through websites shown below. The BRC/NIG participates activity in the"National Bioresource Project (NBRP)" under the organization of Japan Agency for Medical Research andDevelopment (AMED) and takes a role for management, E.coli/B.subtilis. Rice, Mouse, Drosophila, Zebrafish
as the central or sub-central organization for each organism in the project. Furthermore, the Database Divisionalso contributes to NBRP as the national center of bioresource information, by taking responsibility for thedevelopment and management of the relevant database.
Bioresource Management Division
E. coli & B. subtilis Resource (Prof. Hironori Niki)
Drosophila Resource (Prof. Kuniaki Saito)
Hydra Resource (Associate Prof. Kazuho Ikeo)
Mouse Resource (Prof. Toshihiko Shiroishi)
Rice Resource (Prof. Yutaka Sato)
Zebrafish Resource (Prof. Kouichi Kawakami)
Gene Library (Project Prof. Yuji Kohara)
Plant Resource Development Division(Associate Prof. Kenichi Nonomura)Division for Development of Genetic-Engineered Mouse Resource(Prof. Yumiko Saga)
Bioresource Database Division(Associate Prof. Shoko Kawamoto)II. Bioresource Management Division
A. E. coli & B. subtilis Resource (Prof. Hironori Niki)
An international resource center for representative model Gram-positive and-negative bacteria, Escherichia coli,
and Bacillus subtilis have been established in NIG. Now the center for prokaryotes has collected and stored themost extensive genetic resources of E. coli and B. subtilis in the world. We provide for all life science andapplied sciences researchers globally. We further promote the collection and preservation of more helpful E.
coli and B. subtilis resources for researchers. For the resource collection, it is crucial for careful selection andchecks on genetic resources of both the model organisms from researchers. We mostly chose resources that‑32‑

were described in published scientific papers. To improve the collected resources qualitatively, we carried out
a whole-genome sequencing for bacterial strains. The whole genome data are opened as the genetic informationof the strain.
The resources distributed by the center are all non-pathogenetic strains, E. coli strains are derived from strain
K12, and B. subtilis strains are derived from the strain 168. We provide gene mutants, DNA clones of bacterial
genes, phages, and cloning vectors. Also, A whole set of genome-wide mutant libraries are supplied forresearches: the Keio collection is a set of single-gene deletion mutants of E. coli K12 (3,909 strains), BKS is aset of single-gene deletion mutants of B. subtilis 168 (3,974 strains).

The number of the stocked resources
2014
E.coli/B.subtilis etc.

2015

56,733

2016

60,817

2017

60,8882018*

64,99765,067*Sep. 2018
The number of requests for resources
2014

2015

2016

2017

2018*

Total

orders

231

218

523

263

144

1,379

strains

41,19550,336

72,157

39,14028,466231,294

orders

218

166

144

141

52

721

strains

169,532

118,259

111,675

116,178

39,709555,353

orders

449

384

667

404

197

2,100

strains

210,727

168,595

183,832

155,318

68,175

786,647

Domestic

International

Total*Sep. 2018

B. Drosophila Resource (Prof. Kuniaki Saito)
The international resource center for "Drosophila" in NIG comprehensively maintains, manages, and globally
distributes to research communities the genetic resources, such as mutant strains including genome-editing(FlyCas9) and RNAi strains of Drosophila melanogaster, which are useful as a basis or platform for life sciencestudies. We have collected new resources that meet the current and the future needs of users, which weregathered from the expanding and diversifying community through the mailing list, the web sites, the Drosophila
Board meeting, and domestic international scientific conferences. We also manage the consortium of National
Bioresource Project for Drosophila, which consists of the five institutions, NIG, Kyoto Institute of Technology,
Ehime University, Kyorin University, and Miyazaki University, and control collaborative roles as theinternationally acclaimed stock centers in Japan. To encourage and support the use of collected resources, weanalyzed and opened the whole-genome sequencing data for Drosophila wild-type strains.
We provided RNAi and genome-editing strains (>35,000 strains in the latest 5 years) and plasmid vectors related
to CRISPR/Cas9 system (>130 plasmids in the latest 5 years) to contribute to the acceleration of leading-edge
research activities in user communities.

‑33‑

The number of the stocked resources
2014
Drosophilamelanogaster, etc.
*Sep. 20182015

25,987

2016

27,121

2017

27,7742018*

29,43829,790The number of requests for resources
2014

2015

2016

2017

2018*

Total

orders

85

106

113

151

69

524

strains

698

2,324

2,186

3,709

2,411

11,328orders

255

278

253

252

107

1,145

strains

4,475

7,136

4,231

3,967

4,193

24,002orders

340

384

366

403

176

1,669

strains

5,173

9,460

6,417

7,676

6,604

35,330

Domestic

International

Total*Sep. 2018

C. Hydra Resource (Associate Prof. Kazuho Ikeo)
Hydra is a popular model organism because of its strong regenerative capacity and its primitive nervous systemtermed nerve net. Hydra has been used not only for research but also for educational purposes at high schools
and universities. The stock strains maintained at NIG originates from the collection of domestic strains by Dr.
T. Sugiyama with later inclusion of foreign strains and transgenic strains from other research groups. The
distribution of strains to institutions, schools and individuals has been performed at constant levels for years,
however, in recent years, use of strains constructed by genome editing has become more popular than the useof mutant strains. Since there are requests to maintain transgenic strains, we have added such strains to the stock
to make it more updated. At the same time, it is expected to increase the use of symbiotic lines for environmental
problems and evolutionary research. However, more efforts are needed to keep the project.
The number of the stocked resources


2014

Hydra
*Sep. 2018

2015
214

180

The number of requests for resources
2014
Domestic
International
Total

2016

2017
195

2015

2016

2018*
195

2017

195

Total

2018*

orders

15

16

28

11

4

74

strains

35

48

96

17

6

202

orders

4

2

2

3

2

13

strains

14

25

24

5

2

70

orders

19

18

30

14

6

87

strains

49

73

120

22

8

272

*Sep. 2018‑34‑

D. Mouse Resource (Prof. Toshihiko Shiroishi)
The NIG mouse bioresource project aims to improve the value of mouse genetic resources collected andpreserved by NIG for many years and to disseminate the genetic resources for research community. Ourcollections include inbred strains derived from wild mice belonging to different mouse sub-species, andconsomic strains, in which every chromosome of a classical inbred strain C57BL/6J is replaced by thecounterpart of Japanese wild mouse-derived MSM/Ms strain. We distribute all these resources for researchcommunity every year. In addition, we have sequenced whole genome of ten inbred strains established fromwild mice, which are collectively referred to as “Michima Battery” and preserved in the NIG mouse bioresource
project. Furthermore, we have developed a database named “NIG_MoG” (Mouse Genome) that provides
information of genome polymorphisms between the reference sequence of C57BL/6J and those of “Mishima
Battery”. Now, NIG_MoG is accessed by many world-wide users.
The number of resources provided
Strain2014
Molossiuns

2015

2016

2017

2018

103(0)

75(84)

105(0)

73(412)64(80)

Inbred

7(0)

0(0)

0(0)

0(0)

0(0)

Congenic

0(0)

4(0)

0(0)

0(0)

0(0)

Wild

0(0)

2(0)

0(0)

3(0)

1(0)

Mutant

0(0)

0(0)

6(0)

0(80)

0(0)

Consomic

23(0)110(0)52(0)103(0)

19(0)Others0(171)

0(0)

15(0)

16(0)

45(0)

Total

133(171)

191(84)178(0)

195(492)

129(80)Class of user

2014

2015

2017

2018

2016

National Univ.

91(83)

72(0)

75(0)

14(0)

10(0)

National Inst.

10(0)

5(84)

0(0)

6(84)

0(0)

Public Inst.

7(0)102(0)53(0)148(0)

64(80)

Private Univ.

25(0)

0(0)

0(0)

4(80)

0(0)

Industry

0(0)

0(0)

24(0)

0(328)

10(0)High School

0(0)

0(0)

9(0)

7(0)

0(0)

Oversea

0(88)

12(0)

5(0)

16(0)

45(0)

191(84)178(0)

195(492)

129(80)Total
133(171)*Parenthesis is the number of frozen embryos.

E. Rice Resource (Prof. Yutaka Sato)
An international resource center for the valuable collections of rice genetic resources have been established in
NIG. Our center collects, preserves and provides wide varieties of genetic resources, such as wild and cultivatedaccessions of rice in addition to experimental strains. We also provide information on these resources from ourdatabase to rice research community. Following effort have been made to meet various research needs in
different research areas in rice science.
(1) Preservation and provision of worldwide collection of wild rice species (23 species, 1,700 accessions).
Characterization and reclassification of the wild accessions. Development of DNA markers that classify the‑35‑wild rice species.
(2) Collection of experimental rice strains derived from wild species such as chromosome segment substitutionlines (CSSLs).
(3) Characterization of genomes of the collection of wild rice species using NGS.
(4) Operation and management of Oryzabase database for releasing rice resources and genome information.
By the support of National Bioresource Project, we are in charge of increasing the use of our genetic resources.
In order to accomplish this aim, we are conducting the advertisement through Oryzabase, issues of Newslettersand open-field tour at NIG.

The number of the stocked resources
2014
NIG rice resources

2015

7,280

2016

7,556

2017

8,442

2018*

10,599

11,799*Sep. 2018
The number of requests for resources
2014

2015

2016

2017

2018*

Total

orders

24

10

19

53

10

116

strains

518

99

350

1,318

78

2,363

orders

4

5

3

10

1

23

strains

73

90

384

372

2

921

orders

28

15

22

63

11

139

strains

591

189

734

1,690

80

3,284

Domestic

International

Total*Sep. 2018

F. Zebrafish Resource (Prof. Kouichi Kawakami)
Zebrafish is an important model animal for basic biology in vertebrates and also for disease modeling and drug
discovery. The zebrafish resouce center offers unique zebrafish resources that have been generated in NIG. One
is a collection of transgenic zebrafish generated by Kawakami lab by using the transposon-mediatedtransgenesis and gene/enhancer trap methods. These transgenic fish can be used to visualize and manipulate
specific cells, tissues and organs genetically. The other is a zebrafish inbred line generated by Sakai lab. Thisline should be useful for standardized experiments.
For the past 15 years, Kawakami lab has been performing a large-scale gene trap screen and collected more than
1,000 lines that express Gal4 in spatially and temporally restricted fashions. From the zebrafish resource center,to date more than 2,000 lines have been shipped to researchers world wide.
Further, the transposon system developed by Kawakami lab can be applied not only to zebrafish but also toother vertebrate systems including mouse, chick, frog, and mammalian culture cells such as ES and iPS cells,
and have been distributed to more than 2,000 labs world wide.
These activities have led to more than 100 collaborative publications [578, 830, 79, 756, 832, 761, 815, 551,
829, 845, 660, 324, 35, 627, 345, 116, 870, 344, 41, 568, 170, 38, 605, 455, 261, 677, 705, 894, 203, 141, 620,
555, 893, 90, 125, 827, 872, 153, 296, 406, 374, 381, 239, 68, 866].

‑36‑

Lines generated and collected for the last 5 years:
2014
60
Total: 920
2015

60

Total: 980

2016

60

Total: 1040

2017

65

Total: 1105

2018

65

Total: 1170

Lines (transgenic fish) shipped out for the last 5 years:
2014

255

(Japan:69, Abroad:255)

2015

264

(Japan:103, Abroad:161)

2016

248

(Japan:75, Abroad:173)

2017

112

(Japan:28, Abroad:84)

2018

161

(Japan:27, Abroad:134)

Lines (inbred line) shipped out for the last 5 years:
2014

2(Japan:0, Abroad:2)

2015

2

(Japan:0, Abroad:2)

2016

2

(Japan:0, Abroad:2)

2017

0

(Japan:0, Abroad:0)

2018

0

(Japan:0, Abroad:0)

Transposon system distributed for the last 5 years:
2014
153(Japan:49, Abroad:104), Total:1792
2015

116

(Japan:21, Abroad:95) , Total:1908

2016

92

(Japan:14, Abroad:78) , Total:2000

2017

66

(Japan:20, Abroad:46) , Total:2066

2018

113

(Japan:28, Abroad:85) , Total:2179

The databases:
zTrap㸦zebrafish gene trap and enhancer trap database㸧
http://kawakami.lab.nig.ac.jp/ztrap/
zeBrain㸦zebrafish brain atlas㸧
http://zebrain.nig.ac.jp/zebrain/
ZIGS㸦Zebrafish inbred line database㸧
http://zigs.nig.ac.jp‑37‑

G. Gene Library (Project Prof. Yuji Kohara)
We are storing and distributing the following genomic/cDNA clones: 1) the ordered genomic clones of E. coli,
3,400 clones and the mini-set 476 clones (Cell, 50, 495 (1987)), 2) the nematode C. elegans cDNA clones,
140,000 clones, most of which are full-length and are added the information on their expression patterns(available at NEXTDB https://nematode.lab.nig.ac.jp/), 3) full-length cDNA and BAC/fosmid clones of variousorganisms of animals, plants and microorganisms that have been analyzed at the former DNA sequencing centerof this institute. Thus far, more than 100,000 E. coli genomic clone have been distributed to 28 countries since1987. The requests for the E. coli clones and the various organisms clones are almost vanishing, thus the
distribution will be terminated. Stating in 1994, more than 40,000 C.elegans cDNA clones have been distributed
to 26 countries, and, although the requests are reducing, the clones are still actively used world wide for various
research.

1) E. coli ordered genomic clones
Year

2014

2015

2016

2017

2018

Total*

Number of requests

1

0

0

0

 0

847

 From Japan

1

0

0

0

 0

241

 From other countries

0

0

0

0

 0

606

Number of shipped clones

476

0

0

0

 0

101,588

 To Japan

476

0

0

0

 0

18,158

 To other countries

0

0

0

0

 0

83,429Number of shipped countries

1

0

0

0

 0

28

* total number from the start of distribution2) C. elegans cDNA clones
Year

2014

2015

2016

2017

2018

Number of requests

65

52

39

38

19

8,564

 From Japan

17

12

7

10

2

1,278

 From other countries

48

40

32

28

17

7,286

Number of shipped clones

290

260

185

168

80

40,255

 To Japan

62

37

11

45

3

8,264

 To other countries

228

223

174

123

77

31,991

9

9

10

11

7

26

Number of shipped countries

Total** total number from the start of distribution

III. Plant Resource Development Division(Associate Prof. Ken-ichi Nonomura)This division aims to support for domestic and overseas researchers to grow and/or develop non-transgenic andtransgenic plant resources at NIG, using the open fields, greenhouses, controlled growth chambers andequipment. It is also in charge of the mission to conserve rice genetic resources, including about 4,000‑38‑

accessions of world's landraces and a thousand or more of wild rice relatives in cooperation with the Plant
Genetics laboratory and the Plant Cytogenetics laboratory, in the support of the National Bioresource Project(NBRP). For the last five years, the division has supported 22 researches in total as NIG-Joint programs, andconsequently, 16 scientific papers with the results obtained by means of our supports have been published.
IV. Division for Development of Genetic-Engineered Mouse Resource(Prof. Yumiko Saga)
This division was newly established to support mouse researches inside and outside of NIG. The major tasks ofthis division are (1) making a new mouse line, (2) preserving mouse lines already established, (3) cleaning ofmice for introducing new lines to our mouse facility (SPF grade). Especially, we have good technologies tocreate new mouse lines using genetic manipulation such as microinjection, ES-mediated gene-knockout.
Current development of Cas9-technology made possible to generate new mouse models quickly, thus further
demands are rising.
We just started to accept requests from outside of NIG from 2017. We charge a researcher for some costs.
Mouse cleaning includes re-establishing lines via frozen embryos, frozen sperm and from live animals. The
number of chimera production is very high since it includes F0 chimera analyses without delivery.

Number of requests from inside and outside of NIG
Contents of orders

2016(NIG)

2017(NIG)

2017(outside)

Mouse cleaning

10

13

N/A

Embryo freeze

17

10

N/A

Sperm freeze

31

22

N/A

Transgenic mouse production

4

2

3

Transgenic mouse production via Cas9

8

8

4

Gene modification into ES cells

34

16

2

32
(3 clones/each)39(3 clones/each)

2

4

15

0

Chimera mouse production via ES cells
Other works

V. Bioresource Database Division(Associate Prof. Shoko Kawamoto)
This division is responsible for the developing and maintaining the information systems for the genetic resource
center, including overall information of the National BioResource Project (NBRP) other than in NIG. To support
the distribution of resources provided by the resource center, we have developed web applications for the
information retrieval and online ordering system of the resources. There are 21 resource organisms databasesthat we have developed: mice, fly, C.elegans, Silkworms, Medaka, Zebrafish, C.intestinalis, Tropical clawedfrog, Rice, Wheat, Barley, Chrysanthemum, Morning glory, Lotus/Glycine, Tomato, Paramecium, cellularslime molds, Algae, E.coli, B.subtilis, Yeast. Among these organisms, we also provided 12 species genome
sequences via the genome browser for the researcher. From our portal site(http://nbrp.jp), the resource user canbe accessed to 6.5 million bioresources and 30,000 reference papers related to NBRP resources through the
integrated cross-referenced search. The average number of users per month in our website reached 80,000‑39‑unique IP addresses (FY2017), and users are gradually increasing. In order to make it convenient for the foreign
academic researchers, we developed an electronic material transfer agreement system for the E.coli and fly, sothat resource user can order resources through our web site and don’t need to exchange paper contract.
The number of the records in the databases
FY

2014

2015

2016

2017

2018*

Total

6,372,927

6,517,277

6,530,479

6,535,055

6,543,821

2016

2017

2018*

*Sep. 2018
The number of monthly average users of the websites
FY
Total

2014
66,8942015
62,077*from Apr. to Sep. 2018‑40‑

64,51480,64583,657

Joint Research and Research Meeting (NIG-JOINT),
and International Symposium
In order to give researchers opportunities to use NIG facilities and equipment and to encourage collaborative
research that leverages our infrastructure, “Joint Research” and “Joint Research Meeting” have been conducted
between researchers from inside and outside of NIG.
Originally, joint research was categorized into two groups: Collaborative Research (A), which supports only
travel expenses to visit NIG, and Collaborative Research (B), which supports both travel and research expenses.
To further promote collaborative researches from foreign institution and universities, Collaborative Research(A2) which is applicable only to foreign researchers was newly founded in 2015 and renamed to “International
Joint Research” in 2017. In addition, the English name of Collaborative Research has been changed to uniquename “NIG-JOINT” in 2017, so that publications of Collaborative Research can be easily searchable andrecognized.
Joint Research Meeting and International Symposium support travel expenses (other expenses for International
Symposium) for participants in scientific meetings that are held among researchers from inside and outside of
NIG. These scientific gatherings have been contributing to scientific community by facilitating discussions andcollaborations.
As shown in the following chart (plus one International Symposium every year), NIG has been continuously
supporting a number of scientists for joint research and research meetings to help advertising the importance of
NIG as an Inter-University Research Institute.

2014
2015
2016
2017
2018

Collaborative
Research(A)/NIG-JOINT(A)
87
63
68
92
91

Collaborative
Research(B)/
NIG-JOINT(B)
8
7
5
6
4

Collaborative
Research (A2)/
NIG-JOINT(I)
5
6
5
5

‑41‑

Collaborative/
Joint Research
Meeting
18
13
13
18
19

Total

113
88
92
121
119

Education and Outreach
Graduate education
Achievements of graduate education
Graduate Education at NIG
The NIG functions as the “Department of Genetics of SOKENDAI (The Graduate University for Advanced
Studies)” and offers the graduate programs for 5 years and 3 years, both of which award a PhD degree uponsuccessful completion. The objective of education is to foster graduate students to become independentscientists who can conduct their original research in various fields of life sciences related to genetics. For thisobjective, students receive research-based education by NIG faculty members with the aid of rich facilities andresources. NIG also accepts graduate students affiliated to other universities as “Special Collaborative ResearchStudents”, who can take part in the educational programs of the Department of Genetics.
Education Philosophy
The Department of Genetics embraces the idea that every single student gets the attention of the entire facultyfrom various disciplines. This is enabled by the extremely high ratio of faculty to students (~1.4 faculty/student)
at NIG. The selection of students involves all the NIG faculty members. After admission, each student is
supported by a special “Progress Committee” organized by 1~4 faculty members outside the student’s host lab.
With the support of the Progress Committee, students complete assignments and activities set each semester
throughout the program, and by doing so, develop their ability and skills that are necessary to become an
independent researcher.
General Admission
Applicants to the general admission have decreased for the past 10 years (Table 1). This decrease is apparently
due to the overall decline of young Japanese population because other Japanese universities face exactly thesame problem. A bright side of the situation is the high enrolment ratio (enrolled/admitted), which has continued
throughout the history of our graduate program. This means that our graduation programs have a strong
competitive advantage and that the applicants have a specific motivation to study at NIG under expert guidanceof the faculty. As explained above, our programs aim to educate a small number of students, catering to theneeds of individual students, so that the official number of enrollment is only 9 students per year (5-year and 3year courses combined). Thus, we did not compromise the student quality to preserve the numbers, but rather
have maintained the selection standard accepting fewer students.

‑42‑

Table 1 The number of students accepted in different types of admission

Admission of International Students
We made an effort to expand the potential pool of students by reaching out globally. Since 2007, we haveoffered an international graduate program (IGP) that accepts international graduate students with full financial
support (Table 1). Because this IGP program was designed to recruit students competitively with Western
universities, the selection schedule was not appropriate for recruiting students supported by Japanese
Government (MEXT) scholarship. In fact, in the exams of 2013 and 2014, we failed to fill the two scholarshipslots for international students promised by MEXT in the newly adopted International Priority Graduate
Program (2014-2018) with collaboration of SOKENDAI Life Science Departments. To counteract the situation,
we created a new admission path for international students in an optimized schedule for awarding MEXT
Scholarship (EA-MEXT). This EA-MEXT targets international students who prioritize the Department of
Genetics for their graduate studies. The candidates are selected together with those in the general admission, sothat it is clear and easy to set the selection level of EA-MEXT equal to or higher than that of the generaladmission. The EA-MEXT selection started in 2015, and afterward has effectively recruited international
students who fulfill requirements for the MEXT scholarship (Table 1). In 2017, we unified the two different
recruiting paths for international students, IGP and EA-MEXT, and then renamed it to NIG Global Scholar(NIG-GS).
Admission of Special Collaborative Research Students
Special Collaborative Research Students technically belong to other universities but perform their PhD study
at NIG under the guidance of NIG faculty. The accepted numbers show a slight increasing trend in recent years(Table 2). Based on the equal treatment policy for students who conduct PhD study at NIG regardless ofaffiliation, NIG started financial support for qualified Special Collaborative Research Students by Research
Assistant (RA) employment equivalent to SOKENDAI students in 2017. The Students are also eligible to livein the student dormitory since 2016.

‑43‑

Table 2 The number of special collaborative research students accepted each year

Globalization of the Graduate Program
The proportion of international students at the
Department of Genetics has greatly increased for the
past years (Fig.1). Currently, more than 40% of thestudents are international students, whose national
origins are diverse: India, Malaysia, America,
Pakistan, China, Taiwan, Kazakhstan, Philippine,
Ghana, etc. Many students got to know about NIG
by NIG intern program. As will be explain later, thisintern program is hugely popular amonginternational undergraduate students and quite
effective to increase the publicity of our graduate
program.

Fig.1 Proportion of international students

The Department of Genetics has prepared a goodenvironment for both Japanese and international
students to actively study together. All the lectures are now given in English with fully-equipped Syllabi in
English and Japanese dual-languages. Students present and discuss their research in English on every occasionsuch as open presentation for a Master’s degree, progress poster presentation or PhD defense. To train theirscientific presentation skills, NIG faculty members developed “NIG method” education program for scientificpresentations based on the longtime observation and analyses of student presentations, which will be touched
upon later. This program is taught by the NIG English Instructor, Todd Gorman, as a year-round course.
Our graduate programs enable international students to complete without any knowledge of Japanese language.
All the required information is provided in English. The support members of the Education Office are proficientin English. The daily life of an international student is supported by a Japanese tutor who is appointed fromSOKENDAI students. Upon request, one-to-one Japanese language classes are provided by a qualified teacher
for free. Mental health counseling sessions on a regular basis are provided at NIG by a specialist who cancommunicate in Japanese and English.
PhD Degree Conferment
The numbers of PhD awarded in recent years are shown in Table 3. The PhD thesis is evaluated by five members
including internal three or four faculties and one or two external experts. Internal members are usually selectedfrom the student’s Progress Committee, and therefore well aware of the student’s performances and capabilities
through the program period. The PhD evaluation processes exclude the student’s supervisor, allowing fair,
objective evaluation and criticism. To guarantee the quality of PhD thesis, pre-examination started in 2017. In
the pre-examination, the Progress Committee reads a manuscript of the PhD thesis and makes a decision onwhether it can go ahead to the PhD evaluation or should be waited for revision.

‑44‑

Table 3 The number of PhDs awarded each

Lectures and Courses
Lecture courses were reorganized in 2015-2017. The main purpose of this change is to make it clear for students
what they should learn in the graduate program in relation with the degree criteria. After the reorganization,
attendance of each course is much increased.
SOKENDAI promotes inter-department multi-disciplinary education programs. The Department of Genetics
installed remote lecture systems in two lecture rooms, so that the students can freely attend lectures provided
by NIPS (Department of Physiological Sciences), NIBB (Department of Basic Biology) or ESB (Department
of Evolutionary Studies of Biosystems) in geographically distant locations. Using the systems, the Departmentof Genetics also broadcasts our lectures to other departments. The mutual collaboration in education among
departments is effective to promote broad perspectives in students.
Student Dormitory
A student dormitory was built on campus in 2011 and the second one in 2016. Currently, 20 Sokendai Students
and 3 Special Collaborative Research Students live in the dormitory. Such in-kind support is cost effective andhighly appreciated by students. Unfortunately, the rooms will be almost occupied at the end of 2018, and somestudents may have to be evacuated depending on their financial situations.
Financial Support
The Department of Genetics employs graduate students (excluding JSPS fellowship, IGP and MEXT
scholarship holders) as Research Assistants (RA). The salary is about 600,000 yen/year.
Travel Support for International Meetings and Courses
In 2016, the Department of Genetics launched travel support for students who give a presentation atinternational meetings. So far 14 students have been supported and presented their studies abroad. The
Department also offers support for students to take a high-profile education course provided by researchorganizations; if a student is accepted to participate in a course provided by Marine Biological Laboratory, Cold
Spring Harbor Laboratory, EMBO or Welcome Genome Campus, the tuition and travel costs will be supported.
One student was supported to participate in a course in 2017.
AwardsFunded with a generous donation by Professor Emeritus Hiroko Morishima, the following two awards were
established; 1) The Morishima Award, started in 2012, is given to students who receive a PhD degree withoutstanding performance. Seven students have been awarded so far. 2) Hiroko Morishima Progress Award,
started in 2017, is given to students at each Student Poster Presentation to appreciate their eager effort inresearch. Twelve students have been awarded so far.
Student Requests and Responses
In 2015, one-to-one interviews were conducted for all the students. To collect requests and problems fromstudents on regular basis, we made a student survey page, in which students can enter any problems, concerns‑45‑

or requests anytime anonymously or onymously. The issues brought up are individually addressed by the
Education Research Committee. Because most problems stemmed from information shortage from faculty tostudents, student information page was also constructed. With this page, all the students can now share the samedetailed information promptly provided by the Education Research Committee or Education Office.

‑46‑

Education: Outreach
Close Network of Research Groups
NIG is famous for active interactions and discussions among the in-house researchers. Because each researchgroup is small, many groups have joint lab meetings with other labs, and collaborations between groups arevery common. Younger scientists and students also actively and freely visit other research groups to acquire
new techniques and knowledge, which is another advantage of small groups. NIG also hosts various types ofresearchers, such as postdoctoral fellows, collaborative researchers and visiting scientists from abroad.
Interacting and networking with researchers with diverse levels and backgrounds is an ideal way for younger
people to develop broad and balanced views as mature scientists.

The NIG Postdoctoral Fellow program
We employs young promising researchers as NIG postdoctoral research fellows and involve them in research
activities at the institute for a limited amount of time, aiming at further development of research at NIG andfostering researchers with excellent research ability.
NIG Postdoctoral Research Fellow (NIG Postdoc) Result of Recruitment
Number of Candidates
Number of Successful
Number ofInterviewed
Candidates
Fiscal YearAcceptance Rate
Applicants(Those who passed the(Those who passed thePreliminary Screening)
Secondary Screening)
2018
16
8
4
25.0%
2017
9
6
4
44.4%
2016
17
9
5
29.4%
2015
14
9
5
35.7%
2014
13
8
5
38.5%
Average Age of Successful Candidates in 2018: 29.3 years old (as of date arrival at post)

NIG Colloquia
Seminars are held every Friday by researchers at the institute to discuss their progress during the past year.
Presentations are made not only by faculty, but also by fifth year graduate students as a part of their D5 Progress
Report.

Biological Symposia
Biological Symposia are held throughout the year, featuring distinguished speakers in many areas of biologicalsciences, from universities and institutions worldwide.

‑47‑

The NIG INTERN program
We accept four to seven undergraduate and postgraduate students from overseas every summer. The internstudents work in an assigned laboratory for 6 to 8 weeks and give an oral presentation at the end of the program.
We got more than 400 applications last year and have hosted 29 students in total from India, Serbia, Philippines,
UAE, UK, USA, Kazakhstan, Russia, Spain, Vietnam, Sweden, Mongols, Belarus, and Taiwan in the last 5
years. Among these intern students, three of them became SOKENDAI students and are currently studying at
NIG.

Short Internship for Domestic Students
NIG (the Department of Genetics) offers a week-long internship program for domestic undergraduate students.
There are the spring course that is held in the fixed time during the spring vacation (February-March) and theflexible course scheduled on an as-requested basis. Undergraduate students from various universities acrossJapan apply and are accepted in this program (see the table below). During the program, students conduct
experiments individual host labs and join various activities undertaken at NIG such as seminars, journal clubs
or student gatherings. This program assists in the development of young researchers and helps to increaseawareness of NIG among undergraduate students (the vast majority of students who go on to graduate studeis
in Japan remain at their undergraduate institutes).
The number of applicants and students accepted in the program

International Strategic Advisor/Visiting Faculty
NIG selects and invites outstanding researchers from abroad as an international strategy advisor or visiting
professor. The aim is to gain advice on the operation of the institute and to gain strong research cooperation.
International Strategic Advisor
HENSCH, Takao K
BERGER, Frederic
MIZUUCHI, Kiyoshi
HENIKOFF, Steven
STAINIER, Didier
EXCOFFIER, Laurent
YANG, Ziheng
Visiting Faculty
HENIKOFF, Steven
MIZUUCHI, Kiyoshi
FU, Yun-Xin
YANG, Ziheng
ZHANG, Feng

International Strategic Advisor (Professor, Center for Brain Science, Harvard University)
International Strategic Advisor (Senior group leader, Gregor Mendel InstituteInternational Strategic Advisor (NIH Distinguished Investigator, National Institutes of Health)International Strategic Advisor (Member, Fred Hutchinson Cancer Research Center)
Visiting Professor (Director, MAX Planck Institute)
Visiting Professor (Professor, University of Bern)
Visiting Professor (Professor, University College London)

Visiting Professor (Member, Fred Hutchinson Cancer Research Center)
Visiting Professor (Distinguished Investigator, NIDDKD, NIH)
Visiting Professor (Professor, School of Public Health, University of Texas Health Science Center at Houston)
Visiting Professor (Professor, University College London)
Visiting Associate Professor (Assistant Professor, McGovern Institute for Brain Research at MIT)

‑48‑

2018
2018
2017
2017
2016
2016
2016

2018
2018
2018
2018
2016-2018

DIFFLEY, John F.X.
STAINIER, Didier
JORDE, Lynn
YANG, Ziheng
ZENG, Hongkui
EXCOFFIER, Laurent
ZILBERMAN, Daniel
BELMONT, Andrew S.
DEKKER, Job
SHERRATT, DavidROTHSTEIN, Rodney
ENGERT, Florian
LONG, Manyuan
SASAKI, Hiroyuki
FURLONG, Eileen E. M.
von HAESELER, Arndt
MARTIENSSEN, Robert A.

Visiting Professor (Associate Research Director, The Francis Crick Institute)
Visiting Professor (Director, MAX Planck Institute)
Visiting Professor (Professor, University of Utah School of Medicine)
Visiting Professor (Professor, University College London)
Visiting Professor (Senior Director, Allen Institute for Brain Science)
Visiting Professor (Professor, University of Bern)
Visiting Associate Professor (Associate Professor, University of California, Berkeley)
Visiting Professor (Professor, University of Illinois at Urbana-Champaign)
Visiting Professor (Professor, University of Massachusetts Medical School)
Visiting Professor (Professor, Oxford University)
Visiting Professor (Professor, Columbia University Medical Center)
Visiting Professor (Professor, Harvard University)
Visiting Professor (Professor, University of Chicago)
Visiting Professor (Professor, Kyushu University)
Visiting Professor (Joint Head of Unit and Senior Scientist, EMBL)
Visiting Professor (Scientific Director of the Center for Integrative Bioinformatics Vienna)
Visiting Professor (Howard Hughes Medical Institute, Cold Spring Harbor Laboratory)

2016-20182016-20182016-20182016-20172015-20172015-20172015-20172014-20162014-20162014-20152014-20152014-20152014-20152014-2015
2014
2014
2014

Lecture courses organized by DDBJ
Each year, the DDBJ Center organizes three lecture courses. The full list is available athttps://www.ddbj.nig.ac.jp/training.html. There are three types of programs. The “DDBJing” program provides
practical information to submit / access INSD databases and to use the NIG supercomputer. Most lectures were
provided as hands-on style of max 20 beginners. The All-in-One program is a joint lecture with the Database
Center for Life Science, the Protein Data Bank Japan, and the National Bioscience Database Center. This is themost introductory program covering the activities of the four research institutions. For intermediate- to upper
level scientists, DDBJ provides the “DDBJ-Supercomputer Training & Educational Program” (D-STEP) since2017. This program focuses on the analysis of omics data and attracts much attention.
Location of the lecture courses. Parentheses are number of participants. Okinawa events are organized by
invitation.)

DDBJingAll-in-One

2014

2015

2016

2017

2018

Mishima (?),
Tokyo (?)

Tokyo (20),
Okinawa* (?),
Tokyo (20)Osaka

Mishima (14)Okinawa* (60)

Hiroshima (37)Osaka

MishimaTokyo

Mishima (25)Mishima (20),
Yokohama (100)

D-STEPInternational Training Course for Bio-Resource
NIG organized international training courses for bio-resources. In 2015, a training course for “zebrafish imazing
and transgenesis” was held with participants from all over the world under the direction of Prof. Kawakami. In
2015 and 2016, international researchers visited Kawakami lab and performed genetic screens to find zebrafish
that will be useful for their research (“self-screen” course). In 2017, a training course for “Drosophila subspeciesclassification” was held under the direction of Prof. Saito. Thus, NIG is aiming to promote international‑49‑

collaborations and establish a basis of international activities.

‑50‑

Activities to Promote International Interaction
and Cooperation
An important mission of NIG is to strengthen interactions among researchers worldwide. The research
infrastructure provided by the three “Intellectual Infrastructure Centers” as well as international collaborations
and international symposia are the major mechanisms for this mission. Such activities resulted in theestablishment of Memoranda of Understanding (MOU) between NIG and partner institutions (Table 1). As
these activities will be detailed in other parts of this report (section 4,5), this section will focus on theinternational atmosphere of NIG and globalization of the Japanese scientific community.
[Atmosphere] As an international hub for research in genetics, NIG hosts many researchers and students fromthe world (Table 2). All faculty searches are fully open to international researchers, and as of January 2019 NIG
faculty include two international (non-Japanese) members. NIG graduate program is internationally renowned,
and more than 40% of the current students are international students (section 6). As such NIG adopts an “English
as common language” policy. All educational programs, and almost all seminars conducted in English. All
notices sent from the Department of Administration are Japanese-English bilingual, and English translations ofsome administration documents have been prepared and are posted on the homepage.
The Internationalization Promotion Committee, established in 2010, strives to maintain and enrich thisinternational environment ( https://www.nig.ac.jp/jimu/soken/info-int/HelpDesk.html ). For example, theEnglish Help Desk provides various supports to new international members, e.g. visa issues, setting up life in
Mishima, and finding medical and child-care. The committee also supports various social activities to enhanceinternationalization, and arranges free Japanese lessons to those who are interested in acquiring Japanese
proficiency. These activities help create a true international environment at NIG to nurture researchers who canflourish in the global scientific community.
[Globalization] NIG also assists globalization of the scientific community through disseminating the
educational program for scientific communication developed by NIG faculty, dubbed as “NIG Method”. This
program, which is used in the scientific presentation course at NIG, has won critical acclaim from the attendants
including international students, postdocs and faculty members, for its effect on simultaneously developing
English presentation ability and scientific thinking (section 6). To share this resource with the researchcommunity, in 2014 NIG initiated activities to disseminate this program through seminars, workshops andinvited lectures (Table 3). Through facilitating communication between researchers, we hope to strengtheninternational and interdisciplinary collaborations and thereby expand the output of the scientific community as
a whole.

‑51‑

Table 1 Memorandum of Understanding established during 2014-2018
datePartner institution (country)
2015.7.24

The University of Melbourne (Australia)

2015.10.16

University of the Philippines, Diliman (Philippines)

2018.5.11

College of Life Science, National Taiwan University (Taiwan)

2018.6.1

The Brain Research Institute, Monash Sunway (Malaysia)

2018.6.1

Universiti Kebangsaan Malaysia (Malaysia)

2018.6.1

National Science and Technology Development Agency by National Center for Genetic
Engineering and Biotechnology (Kingdom of Thailand)

2018.6.18

College of Pharmacy, Kyungpook National University (Republic of Korea)

Table 2 Biological Symposia
year

Total number

Speakers from abroad

2014

80

59

2015

60

35

2016

72

42

2017

50

25

2018

64

43

Table 3 Introductory seminars, workshops and lectures on the scientific presentation educational program “NIG
Method” (2014-2018)
category
Number of institutions (total number of events)4
SOKENDAI Departments

141 (172)

Universities in Japan (other than SOKENDAI)

18 (25)

Academic Societies/Groups

4

Private Companies

1

Institutions outside Japan5 (6)Open workshops3

(4)

Notes
1.

The number of SOKENDAI Departments to which NIG provided seminars, workshops or lectures. This number
does not include the Department of Genetics (NIG) itself.

2.

Four of these correspond to lectures in SOKENDAI Freshman course, an event attended by all new incoming
students. Five are full courses on scientific presentation offered at other departments of SOKENDAI, taught by
the NIG English instructor, Todd Gorman.

3.

These workshops were organized by NIG and were open to researchers in other institutions.

4.

Of a total of 51 events held in Japan, 10 were offered in English to accommodate international audience.

‑52‑

Office for Research Development
Director: Yasushi Hiromi
The Office for Research Development (ORD) was established in 2014 as part of the ROIS recruitment of
University Research Administrators (URAs) under MEXT’s “Program for Promoting the Enhancement ofResearch Universities”. While the objective of this program in a university would be to enhance the research
capacity of the university organization itself, NIG has set ORD’s objective to “contribute to enhancing research
capacity of NIG as well as the entire scientific community”, because ROIS’s mission is to assist Universities
and their researchers. ORD aims to elevate scientific output through enhancing the research capacity of
individual researchers, in and out of NIG. Staff members of ORD are all former or current faculty members of
NIG, and can act as a soundboard for researchers with new results and ideas. ORD also designs and organizes
seminars, and workshops aimed at enlightening and stimulating the way that research is conducted.
ORD also takes part in the institutional research (IR) for NIG and ROIS, and public relations of NIG,
collaborating with NIG’s Department of Administration, NIG Innovation, as well as URAs stationed in the ROIS
headquarters and other institutions of ROIS. Major activities in the past 5 years are summarized in Table 1.
Table 1 Major activities of ORD (2014-2018)
Category
Activities (number of cases/events)
Enhancing Research Activities
Advising/commenting from a scientific viewpoint
࣭Manuscripts1 (43)࣭Grant applications1 (95)࣭Presentations2 (24)Workshops/seminars (16)Seminars and Workshops to disseminate the Educational Program on
Scientific Presentation developed at NIG3 (53)Institutional Research (IR)Acknowledgement study of NIG collaboration grant system [2015]
Study on female applicant ratio in NIG faculty searches [2016]
Follow-up study of RPD researchers -- toward career support offemale researchers [2016]
Report on the contributions of ROIS to the Japanese scientificcommunity4 [2017].
Historical Survey “Research infrastructure function of NIG -Establishment and development of DDBJ”5 [2017]
Annual compilation of reports of institutional output (publications,research infrastructure services, graduate education)

Public Relations

NIG homepage renewal/update6
Press Release of research outputs7 (71)Annual NIG Brochure production8
Annual events such as NIG Open House, Public Lecture, Introductory
session of the NIG graduate program: co-organize and publicize‑53‑Notes1.

These activities are done as a group discussion of the applicant and the three ORD staff members, thereby
providing diverse viewpoints.

2.

This activity, called Presentation DOJO, is carried out by a group of volunteer members of NIG (mostly
assistant professors), organized by ORD. https://sites.google.com/site/nigrest/3.

Details of this program can be found in section 6,7.

4.

This report includes contributions of various research infrastructure provided by each institution (ResourceSharing), as well as funded collaborations with ROIS researchers (Joint-Research). The compilation work wasdone in collaboration with other URAs of ROIS. The report was sent to 758 Universities in Japan to improve
ROIS functions based on the feedback.

5.

Shizuoka Shimbun (SBS) 2017.3.31-7.10.

6.

ORD organized homepage renewal in 2014, and since has been responsible for its updating and maintenance.
https://www.nig.ac.jp/nig/

7.

Prior to 2015 NIG faculty had been sending out press release only sporadically. ORD established a facultyORD collaboration system for preparing press release, and dramatically increased the dissemination of NIG’s
research output through media coverage.

8.

https://www.nig.ac.jp/nig/about-nig/annual-report‑54‑

NIG INNOVATION
Director: Mutsuaki Suzuki
NIG INNOVATION (a section for technology transfer management) has had a successful achievement fromFY 2013 to FY 2018 (as of 5th March 2019). Our total income through technology transfer has increased year
by year and reached more than ? 113 million in these five years. It is noteworthy that the income for FY2018(as of 5th March 2019) has already come to a record level of ?35 million, more than three times of the income
for FY2013.
This great leap has been achieved because we have concluded an unprecedented number of collaborative
research agreements with industries in FY2018. We also have changed the name of our department to “NIG
INNOVATION” to centralize the technology transfer activities more in FY2018.
Other highlights are the close collaboration with local community. We have provided average 30 laboratory
tours, courses, lectures and visiting lectures to the local government and schools in the past five years and built
a trustful and long-term partnership.

‑55‑

Office for Gender Equality
Director: Tatsumi Hirata
The Office for Female Support was established at NIG in 2014 and then renamed as the Office for Gender
Equality in 2017. Initiatives and achievements made by the Office are as follows:1.

A multi-purpose nursery room was made in the main building in July 2015. Anyone who works or studies
at NIG can use the room upon request.

2.

In-house temporary childcare is provided in the multi-purpose nursery room to NIG employees whenpublic childcare service are closed. Since Aug, 2016, 29 employees have used this service in total 16 days.

3.

To raise the money for the in-house temporary childcare, a donation fund was created in Apr 2017. This
fund has received donations from 9 people so far.

4.

A career-building seminar was held in Izu-nagaoka on March11-12, 2017. Both male and female
researchers engaged in active discussion and exchanged valuable information.

5.

Requests about childcare and working rules received from NIG employees were submitted to ROIS andMishima City Office in July 2018.

6.

The homepage of the Gender Equality Office was renewed in Aug 2018.

7.

Childcare support for participants of NIG meetings was launched in Dec 2018.

8.

A childcare assistance program by NIG, started in 2009, allocates a lab assistant to a female faculty
member who is rearing a child to the 6th grade. Another program by ROIS, started in 2014, allocates a
lab assistant to a researcher including post-doc who has difficulty in family care. The number of NIG
researchers supported by the two programs is shown in the table.

‑56‑

Publication Lists
1.

Aghakhanian, F., Yunus, Y., Naidu, R., Jinam, T., Manica, A., Hoh, B.P., and Phipps, M.E. (2015) Unravelling the genetic history of Negritos and indigenous
populations of Southeast Asia. Genome Biol Evol 7,1206-1215.

2.

Ahmadloo, S., Nakaoka, H., Hayano, T., Hosomichi, K., You, H., Utsuno, E., Sangai, T., Nishimura, M., Matsushita, K., Hata, A., Nomura, F., and Inoue,
I. (2017). Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2. J Hum Genet 62, 561-567.

3.

Ajima, R., Bisson, J.A., Helt, J.C., Nakaya, M.A., Habas, R., Tessarollo, L., He, X., Morrisey, E.E., Yamaguchi, T.P., and Cohen, E.D. (2015) DAAM1 andDAAM2 are co-required for myocardial maturation and sarcomere assembly. Dev Biol 408,126-139.

4.

Ajima, R., Suzuki, E., and Saga, Y. (2017). Pofut1 point-mutations that disrupt O-fucosyltransferase activity destabilize the protein and abolish Notch1
signaling during mouse somitogenesis. PLoS One 12, e0187248.

5.

Akamatsu, Y., and Kobayashi, T. (2015) The Human RNA Polymerase I Transcription Terminator Complex Acts as a Replication Fork Barrier That
Coordinates the Progress of Replication with rRNA Transcription Activity. Mol Cell Biol 35,1871-1881.

6.

Akanuma, G., Kazo, Y., Tagami, K., Hiraoka, H., Yano, K., Suzuki, S., Hanai, R., Nanamiya, H., Kato-Yamada, Y., and Kawamura, F. (2016) Ribosome
dimerization is essential for the efficient regrowth of Bacillus subtilis. Microbiology 162, 448-458.

7.

Akatsuka, H., Kuga, S., Masuhara, K., Davaadorj, O., Okada, C., Iida, Y., Okada, Y., Fukunishi, N., Suzuki, T., Hosomichi, K., Ohtsuka, M., Tanaka, M.,
Inoue, I., Kimura, M., and Sato, T. (2017). AMBRA1 is involved in T cell receptor-mediated metabolic reprogramming through an ATG7-independent
pathway. Biochem Biophys Res Commun 491, 1098-1104.

8.

Akbari, O.S., Bellen, H.J., Bier, E., Bullock, S.L., Burt, A., Church, G.M., Cook, K.R., Duchek, P., Edwards, O.R., Esvelt, K.M., Gantz, V.M., Golic, K.G.,
Gratz, S.J., Harrison, M.M., Hayes, K.R., James, A.A., Kaufman, T.C., Knoblich, J., Malik, H.S., Matthews, K.A., O'Connor-Giles, K.M., and Parks, A.L.,
Perrimon, N., Port, F., Russell, S., Ueda, R. and Wildonger, J. (2015) BIOSAFETY. Safeguarding gene drive experiments in the laboratory. Science 349,927929.

9.

Akiba, T., Hibara, K., Kimura, F., Tsuda, K., Shibata, K., Ishibashi, M., Moriya, C., Nakagawa, K., Kurata, N., Itoh, J., and Ito, Y. (2014). Organ fusion anddefective shoot development in oni3 mutants of rice. Plant Cell Physiol. 55, 42-51.

10.

Akihito, Akishinonomiya, F., Ikeda, Y., Aizawa, M., Nakagawa, S., Umehara, Y., Yonezawa, T., Mano, S., Hasegawa, M., Nakabo, T., and Gojobori, T.
(2016) Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA
analyses. Gene 576, 593-602.

11.

Akter, A., Ooka, T., Gotoh, Y., Yamamoto, S., Fujita, H., Terasoma, F., Kida, K., Taira, M., Nakadouzono, F., Gokuden, M., Hirano, M., Miyashiro, M.,
Inari, K., Shimazu, Y., Tabara, K., Toyoda, A., Yoshimura, D., Itoh, T., Kitano, T., Sato, M.P., Katsura, K., Mondal, S.I., Ogura, Y., Ando, S., and Hayashi,
T. (2017). Extremely Low Genomic Diversity of Rickettsia Japonica Distributed in Japan. Genome Biol Evol 9, 124-133.

12.

Amakawa, Y., Sakata, Y., Hoki, Y., Arata, S., Shioda, S., Fukagawa, T., Sasaki, H., and Sado, T. (2015) A new Xist allele driven by a constitutively active
promoter is dominated by Xist locus environment and exhibits the parent-of-origin effects. Development 142,4299-4308.

13.

Amano, T., Sagai, T., Seki, R., and Shiroishi, T. (2017). Two Types of Etiological Mutation in the Limb-Specific Enhancer of Shh. G3 (Bethesda) 7, 29912998.

14.

Ameku, T., Yoshinari, Y., Texada, M.J., Kondo, S., Amezawa, K., Yoshizaki, G., Shimada-Niwa, Y., and Niwa, R. (2018). Midgut-derived neuropeptide F
controls germline stem cell proliferation in a mating-dependent manner. PLoS Biol. 16, e2005004.

15.

An, Y., Kawaguchi, A., Zhao, C., Toyoda, A., Sharifi-Zarchi, A., Mousavi, S.A., Bagherzadeh, R., Inoue, T., Ogino, H., Fujiyama, A., et al. (2018). Draft
genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians. Zool. Lett. 4, 24.

16.

An, Y., Toyoda, A., Zhao, C., Fujiyama, A., and Agata, K. (2015) A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it forscreening DNA libraries. PLoS One 10,e0116997.

17.

Andachi, Y., and Kohara, Y. (2016) A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans. RNA 22, 1099-1106.

18.

Ando, T., Matsuda, T., Goto, K., Hara, K., Ito, A., Hirata, J., Yatomi, J., Kajitani, R., Okuno, M., Yamaguchi, K., et al. (2018). Repeated inversions withina pannier intron drive diversification of intraspecific colour patterns of ladybird beetles. Nat. Commun. 9, 3843.

19.

Aoki-Kinoshita, K.F., Kinjo, A.R., Morita, M., Igarashi, Y., Chen, Y.A., Shigemoto, Y., Fujisawa, T., Akune, Y., Katoda, T., Kokubu, A., Mori, T., Nakao,
M., Kawashima, S., Okamoto, S., Katayama, T., and Ogishima, S. (2015) Implementation of linked data in the life sciences at BioHackathon 2011. J Biomed
Semantics 6,3.

20.

Aoki, K., and Niki, H. (2017). Transformation of Schizosaccharomyces japonicus. CSH Protocols 2017, pdb.prot091850.

21.

Aoki, K., and Niki, H. (2017). Release of condensin from mitotic chromosomes requires the Ran-GTP gradient in the reorganized nucleus. Biol Open 6,
1614-1628.

22.

Aoki, K., Furuya, K., and Niki, H. (2017). Schizosaccharomyces japonicus: A Distinct Dimorphic Yeast Among the Fission Yeasts. CSH Protocols. 2017,
pdb.top082651.

23.

Ara, T., Enomoto, M., Arita, M., Ikeda, C., Kera, K., Yamada, M., Nishioka, T., Ikeda, T., Nihei, Y., Shibata, D., Kanaya, S., and Sakurai, N. (2015)
Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. Front Bioeng Biotechnol 3,38.

24.

Arai, R., Sugawara, T., Sato, Y., Minakuchi, Y., Toyoda, A., Nabeshima, K., Kimura, H., and Kimura, A. (2017). Reduction in chromosome mobility
accompanies nuclear organization during early embryogenesis in Caenorhabditis elegans. Sci Rep 7, 3631.

‑57‑

25.

Arakaki, Y., Fujiwara, T., Kawai-Toyooka, H., Kawafune, K., Featherston, J., Durand, P.M., Miyagishima, S.Y., and Nozaki, H. (2017). Evolution ofcytokinesis-related protein localization during the emergence of multicellularity in volvocine green algae. BMC Evol Biol 17, 243.

26.

Arakawa, H., Suzuki, A., Zhao, S., Tsytsarev, V., Lo, F.S., Hayashi, Y., Itohara, S., Iwasato, T., and Erzurumlu, R.S. (2014). Thalamic NMDA receptor
function is necessary for patterning of the thalamocortical somatosensory map and for sensorimotor behaviors. J. Neurosci. 34, 12001-12014.

27.

Arakawa, T., Tanave, A., Ikeuchi, S., Takahashi, A., Kakihara, S., Kimura, S., Sugimoto, H., Asada, N., Shiroishi, T., Tomihara, K., Tsuchiya, T., andKoide, T. (2014). A male-specific QTL for social interaction behavior in mice mapped with automated pattern detection by a hidden Markov model
incorporated into newly developed freeware. J. Neurosci. Methods 234, 127-134.

28.

Araki, H. (2016) Elucidating the DDK-dependent step in replication initiation. EMBO J 35, 907-908.

29.

Arata, Y., Hiroshima, M., Pack, C.G., Ramanujam, R., Motegi, F., Nakazato, K., Shindo, Y., Wiseman, P.W., Sawa, H., Kobayashi, T.J., Brandao, H.B.,
Shibata, T., and Sako, Y. (2016) Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic
Boundary. Cell Rep 16, 2156-2168.

30.

Arata, Y., Takagi, H., Sako, Y., and Sawa, H. (2015) Power law relationship between cell cycle duration and cell volume in the early embryonic developmentof Caenorhabditis elegans. Front Physiol 5,529.

31.

Arimura, Y., Shirayama, K., Horikoshi, N., Fujita, R., Taguchi, H., Kagawa, W., Fukagawa, T., Almouzni, G., and Kurumizaka, H. (2014). Crystal structureand stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3. Sci. Rep. 4, 7115.

32.

Arnott, Z.L.P., Nozaki, S., Monteiro, D.C.F., Morgan, H.E., Pearson, A.R., Niki, H., and Webb, M.E. (2017). The Mechanism of Regulation of Pantothenate
Biosynthesis by the PanD-PanZ.AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan).
Biochemistry 56, 4931-4939.

33.

Asakawa, K., and Kawakami, K. (2018). Protocadherin-Mediated Cell Repulsion Controls the Central Topography and Efferent Projections of the Abducens
Nucleus. Cell Rep. 24, 1562-1572.

34.

Asamizu, E., Ichihara, H., Nakaya, A., Nakamura, Y., Hirakawa, H., Ishii, T., Tamura, T., Fukami-Kobayashi, K., Nakajima, Y., and Tabata, S. (2014).
Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. Plant Cell Physiol. 55, e8.

35.

Auer, T.O., Xiao, T., Bercier, V., Gebhardt, C., Duroure, K., Concordet, J.P., Wyart, C., Suster, M., Kawakami, K., Wittbrodt, J., Baier, H. Del, and BeneF. (2015) Deletion of a kinesin I motor unmasks a mechanism of homeostatic branching control by neurotrophin-3. Elife 4,e05061.

36.

Babarinde, I.A., and Saitou, N. (2016) Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian
Expression Dynamics. Mol Biol Evol 33, 1807-1817.

37.

Bachtrog, D., Mank, J.E., Peichel, C.L., Kirkpatrick, M., Otto, S.P., Ashman, T.L., Hahn, M.W., Kitano, J., Mayrose, I., Ming, R., Perrin, N., Ross, L.,
Valenzuela, N., and Vamosi, J.C. (2014). Sex determination: why so many ways of doing it? PLoS Biol. 12, e1001899.

38.

Bohm, U.L., Prendergast, A., Djenoune, L., Nunes, Figueiredo S., Gomez, J., Stokes, C., Kaiser, S., Suster, M., Kawakami, K., Charpentier, M., Concordet,
J.P., Rio, J.P., Del, Bene F., and Wyart, C. (2016) CSF-contacting neurons regulate locomotion by relaying mechanical stimuli to spinal circuits. Nat
Commun 7, 10866.

39.

Bolleman, J.T., Mungall, C.J., Strozzi, F., Baran, J., Dumontier, M., Bonnal, R.J., Buels, R., Hoehndorf, R., Fujisawa, T., Katayama, T., and Cock, P.J.
(2016) FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J Biomed Semantics 7, 39.

40.

Borgius, L., Nishimaru, H., Caldeira, V., Kunugise, Y., Low, P., Reig, R., Itohara, S., Iwasato, T., and Kiehn, O. (2014). Spinal glutamatergic neurons
defined by EphA4 signaling are essential components of normal locomotor circuits. J. Neurosci. 34, 3841-3853.

41.

Bourgeois, A., Esteves, de Lima J., Charvet, B., Kawakami, K., Stricker, S., and Duprez, D. (2015) Stable and bicistronic expression of two genes in somiteand lateral plate-derived tissues to study chick limb development. BMC Dev Biol 15,39.

42.

Bowman, J.L., Araki, T., Arteaga-Vazquez, M.A., Berger, F., Dolan, L., Haseloff, J., Ishizaki, K., Kyozuka, J., Lin, S.S., Nagasaki, H., Nakagami, H.,
Nakajima, K., Nakamura, Y., Ohashi-Ito, K., Sawa, S., Shimamura, M., Solano, R., Tsukaya, H., Ueda, T., Watanabe, Y., Yamato, K.T., Zachgo, S., andKohchi, T. (2016) The Naming of Names: Guidelines for Gene Nomenclature in Marchantia. Plant Cell Physiol 57, 257-261.

43.

Bowman, J.L., Kohchi, T., Yamato, K.T., Jenkins, J., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., et al. (2017). Insights into Land Plant Evolution
Garnered from the Marchantia polymorpha Genome. Cell 171, 287-304.e15.

44.

Burla, B., Arita, M., Arita, M., Bendt, A.K., Cazenave-Gassiot, A., Dennis, E.A., Ekroos, K., Han, X., Ikeda, K., Liebisch, G., et al. (2018). MS-based
lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J. Lipid Res. 59, 2001-2017.

45.

Carroll, A.J., Salek, R.M., Arita, M., Kopka, J., and Walther, D. (2016) Metabolome Informatics and Statistics: Current State and Emerging Trends. Front
Bioeng Biotechnol 4, 63.

46.

Carroni, M., De, March M., Medagli, B., Krastanova, I., Taylor, I.A., Amenitsch, H., Araki, H., Pisani, F.M., Patwardhan, A., and Onesti, S. (2017). New
insights into the GINS complex explain the controversy between existing structural models. Sci Rep 7, 40188.

47.

Cha, J., Bartos, A., Park, C., Sun, X., Li, Y., Cha, S.W., Ajima, R., Ho, H.Y., Yamaguchi, T.P., and Dey, S.K. (2014). Appropriate crypt formation in theuterus for embryo homing and implantation requires Wnt5a-ROR signaling. Cell Rep. 8, 382-392.

48.

Chalamalasetty, R.B., Ajima, R., Garriock, R.J., Kennedy, M.W., Tessarollo, L., and Yamaguchi, T.P. (2016) A new gain-of-function mouse line to study
the role of Wnt3a in development and disease. Genesis 54, 497-502.

49.

Chang, C.C., Huang, T.L., Shimamoto, Y., Tsai, S.Y., and Hsia, K.C. (2017). Regulation of mitotic spindle assembly factor NuMA by Importin-beta. J Cell
Biol 216, 3453-3462.

50.

Chen, C., Lim, H.H., Shi, J., Tamura, S., Maeshima, K., Surana, U., and Gan, L. (2016) Budding yeast chromatin is dispersed in a crowded nucleoplasm in‑58‑

vivo. Mol Biol Cell 27, 3357-3368.
51.

Chen, C.C., Fu, S.F., Norikazu, M., Yang, Y.W., Liu, Y.J., Ikeo, K., Gojobori, T., and Huang, H.J. (2015) Comparative miRNAs analysis of Two contrastingbroccoli inbred lines with divergent head-forming capacity under temperature stress. BMC Genomics 16,1026.

52.

Chen, J., Reiher, W., Hermann-Luibl, C., Sellami, A., Cognigni, P., Kondo, S., Helfrich-Forster, C., Veenstra, J.A., and Wegener, C. (2016) Allatostatin A
Signalling in Drosophila Regulates Feeding and Sleep and Is Modulated by PDF. PLoS Genet 12, e1006346.

53.

Cheng, C., Tarutani, Y., Miyao, A., Ito, T., Yamazaki, M., Sakai, H., Fukai, E., and Hirochika, H. (2015) Loss of function mutations in the rice
chromomethylase OsCMT3a cause a burst of transposition. Plant J 83,1069-1081.

54.

Chisada, S., Kurokawa, T., Murashita, K., Ronnestad, I., Taniguchi, Y., Toyoda, A., Sakaki, Y., Takeda, S., and Yoshiura, Y. (2014). Leptin receptordeficient (knockout) medaka, Oryzias latipes, show chronical up-regulated levels of orexigenic neuropeptides, elevated food intake and stage specific effects
on growth and fat allocation. Gen. Comp. Endocrinol. 195, 9-20.

55.

Chng, W.A., Koch, R., Li, X., Kondo, S., Nagoshi, E., and Lemaitre, B. (2017). Transforming Growth Factor beta/Activin signaling in neurons increases
susceptibility to starvation. PLoS One 12, e0187054.

56.

Chung, B.Y., Ro, J., Hutter, S.A., Miller, K.M., Guduguntla, L.S., Kondo, S., and Pletcher, S.D. (2017). Drosophila Neuropeptide F Signaling Independently
Regulates Feeding and Sleep-Wake Behavior. Cell Rep 19, 2441-2450.

57.

Cochrane, G., Karsch-Mizrachi, I., and Takagi, T. (2016) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res 44, D48-50.

58.

Copetti, D., Zhang, J., El, Baidouri M., Gao, D., Wang, J., Barghini, E., Cossu, R.M., Angelova, A., Maldonado, L. C.E., Roffler, S., Ohyanagi, H., Wicker,
T., Fan, C., Zuccolo, A., Chen, M., Costa, de Oliveira A., Han, B., Henry, R., Hsing, Y.I., Kurata, N., Wang, W., Jackson, S.A., Panaud, O., and Wing, R.A.
(2015) RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 16,538.

59.

Danielsen, E.T., Moeller, M.E., Yamanaka, N., Ou, Q., Laursen, J.M., Soenderholm, C., Zhuo, R., Phelps, B., Tang, K., Zeng, J., Kondo, S., Nielsen, C.H.,
Harvald, E.B., Faergeman, N.J., Haley, M.J., O'Connor, K.A., King-Jones, K., O'Connor, M.B., and Rewitz, K.F. (2016) A Drosophila Genome-Wide Screen
Identifies Regulators of Steroid Hormone Production and Developmental Timing. Dev Cell 37, 558-570.

60.

Davis, O.M., Ogita, N., Inagaki, S., Takahashi, N., and Umeda, M. (2016) DNA damage inhibits lateral root formation by up-regulating cytokinin
biosynthesis genes in Arabidopsis thaliana. Genes Cells 21, 1195-1208.

61.

de, Frutos C.A., Bouvier, G., Arai, Y., Thion, M.S., Lokmane, L., Keita, M., Garcia-Dominguez, M., Charnay, P., Hirata, T., Riethmacher, D., Grove, E.A.,
Tissir, F., Casado, M., Pierani, A., and Garel, S. (2016) Reallocation of Olfactory Cajal-Retzius Cells Shapes Neocortex Architecture. Neuron 92, 435-448.

62.

Deivasigamani, S., Verma, H.K., Ueda, R., Ratnaparkhi, A., and Ratnaparkhi, G.S. (2014). A genetic screen identifies Tor as an interactor of VAPB in a
Drosophila model of amyotrophic lateral sclerosis. Biol. Open 3, 1127-1138.

63.

Dou, X., Kuriki, S., Maeno, A., Takada, T., and Shiroishi, T. (2014). Influence analysis in quantitative trait loci detection. Biom. J. 56, 697-719.

64.

Dudzic, J.P., Kondo, S., Ueda, R., Bergman, C.M., Lemaitre, B. (2015) Drosophila innate immunity: regional and functional specialization ofprophenoloxidases. BMC Biol 13,81.

65.

Eaton, J.D., Davidson, L., Bauer, D.L. V, Natsume, T., Kanemaki, M.T., and West, S. (2018). Xrn2 accelerates termination by RNA polymerase II, whichis underpinned by CPSF73 activity. Genes Dev. 32, 127-139.

66.

Endo, A., Maeno, S., Tanizawa, Y., Kneifel, W., Arita, M., Dicks, L., and Salminen, S. (2018). Fructophilic Lactic Acid Bacteria, a Unique Group ofFructose-Fermenting Microbes. Appl. Environ. Microbiol. 84, e01290-18.

67.

Endo, A., Tanizawa, Y., Tanaka, N., Maeno, S., Kumar, H., Shiwa, Y., Okada, S., Yoshikawa, H., Dicks, L., Nakagawa, J., and Arita, M. (2015) Comparative
genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp. BMC Genomics 16,1117.

68.

Enya, S., Kawakami, K., Suzuki, Y., and Kawaoka, S. (2018). A novel zebrafish intestinal tumor model reveals a role for cyp7a1-dependent tumor-livercrosstalk in causing adverse effects on the host. Dis. Model. Mech. 11, dmm032383.

69.

Fan, Z., Zhao, G., Li, P., Osada, N., Xing, J., Yi, Y., Du, L., Silva, P., Wang, H., Sakate, R., Zhang, X., Xu, H., Yue, B., and Li, J. (2014). Whole-genome
sequencing of tibetan macaque (Macaca Thibetana) provides new insight into the macaque evolutionary history. Mol. Biol. Evol. 31, 1475-1489.

70.

Fawcett, J.A., Iida, T., Takuno, S., Sugino, R.P., Kado, T., Kugou, K., Mura, S., Kobayashi, T., Ohta, K., Nakayama, J., and Innan, H. (2014). Population
genomics of the fission yeast Schizosaccharomyces pombe. PLoS One 9, e104241.

71.

Federhen, S., Clark, K., Barrett, T., Parkinson, H., Ostell, J., Kodama, Y., Mashima, J., Nakamura, Y., Cochrane, G., and Karsch-Mizrachi, I. (2014). Towardricher metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. Stand. Genomic
Sci. 9, 1275-1277.

72.

Förster, D., Kramer, A., Baier, H., and Kubo, F. (2018). Optogenetic precision toolkit to reveal form, function and connectivity of single neurons. Methods
150, 42-48.

73.

Forth, S., Hsia, K.C., Shimamoto, Y., and Kapoor, T.M. (2014). Asymmetric friction of nonmotor MAPs can lead to their directional motion in active
microtubule networks. Cell 157, 420-432.

74.

Fountain, T., Ravinet, M., Naylor, R., Reinhardt, K., and Butlin, R.K. (2016) A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug
Cimex lectularius G3-GENES GENOMES GENETICS 6, 4059-4066.

75.

Fox, D. 3rd, Yan, Z., Ling, C., Zhao, Y., Lee, D.Y., Fukagawa, T., Yang, W., and Wang, W. (2014). The histone-fold complex MHF is remodeled by
FANCM to recognize branched DNA and protect genome stability. Cell Res. 24, 560-575.

76.

Fu, C.L., Wang, X.F., Cheng, Q., Wang, D., Hirose, S., and Liu, Q.X. (2016) The T-box transcription factor Midline regulates wing development by‑59‑

repressing wingless and hedgehog in Drosophila. Sci Rep 6, 27981.
77.

Fujieda, K and Okubo, K. (2016). A reusable anatomically segmented digital mannequin for public health communication. J. Vis. Commun. Med. 39, 1826.

78.

Fujii, G., Imamura, S., Era, A., Miyagishima, S.Y., Hanaoka, M., and Tanaka, K. (2015). The nuclear-encoded sigma factor SIG4 directly activatestranscription of chloroplast psbA and ycf17 genes in the unicellular red alga Cyanidioschyzon merolae. FEMS Microbiol Lett 362.

79.

Fujii, J., Kodama, M., Oike, A., Matsuo, Y., Min, M.S., Hasebe, T., Ishizuya-Oka, A., Kawakami, K., and Nakamura, M. (2014). Involvement of androgen
receptor in sex determination in an amphibian species. PLoS One 9, e93655.

80.

Fujii, M., Sakaguchi, A., Kamata, R., Nagao, M., Kikuchi, Y., Evans, S.M., Yoshizumi, M., Shimono, A., Saga, Y., and Kokubo, H. (2017). Sfrp5 identifies
murine cardiac progenitors for all myocardial structures except for the right ventricle. Nat Commun 8, 14664.

81.

Fujimoto, M., Sazuka, T., Oda, Y., Kawahigashi, H., Wu, J., Takanashi, H., Ohnishi, T., Yoneda, J.-I., Ishimori, M., Kajiya-Kanegae, H., et al. (2018).
Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems. Proc. Natl. Acad. Sci. U. S. A. 115, E8783-E8792.

82.

Fujimoto, S., Kawajiri, M., Kitano, J., and Yamahira, K. (2014). Female mate preference for longer fins in medaka. Zoolog. Sci. 31, 703-708.

83.

Fujisawa, T., Narikawa, R., Maeda, S.I., Watanabe, S., Kanesaki, Y., Kobayashi, K., Nomata, J., Hanaoka, M., Watanabe, M., Ehira, S., Suzuki, E., Awai,K., and Nakamura, Y. (2017). CyanoBase: a large-scale update on its 20th anniversary. Nucleic Acids Res 45, D551-D554.

84.

Fujita, Y., Tominaga, T., Abe, H., Kangawa, Y., Fukushima, N., Ueda, O., Jishage, K.-I., Kishi, S., Murakami, T., Saga, Y., et al. (2018). An adjustment in
BMP4 function represents a treatment for diabetic nephropathy and podocyte injury. Sci. Rep. 8, 13011.

85.

Fujiwara, T., Kanesaki, Y., Hirooka, S., Era, A., Sumiya, N., Yoshikawa, H., Tanaka, K., and Miyagishima, S.Y. (2015) A nitrogen source-dependent
inducible and repressible gene expression system in the red alga Cyanidioschyzon merolae. Front Plant Sci 6,657.

86.

Fujiwara, T., Ohnuma, M., Kuroiwa, T., Ohbayashi, R., Hirooka, S., and Miyagishima, S.Y. (2017). Development of a Double Nuclear Gene-Targeting
Method by Two-Step Transformation Based on a Newly Established Chloramphenicol-Selection System in the Red Alga Cyanidioschyzon merolae. Front
Plant Sci 8, 343.

87.

Fukagawa, T., and Earnshaw, W.C. (2014). Neocentromeres. Curr. Biol. 24, R946-7.

88.

Fukagawa, T., and Earnshaw, W.C. (2014). The centromere: chromatin foundation for the kinetochore machinery. Dev. Cell 30, 496-508.

89.

Fukuda, K., Masuda, A., Naka, T., Suzuki, A., Kato, Y., and Saga, Y. (2018). Requirement of the 3’-UTR-dependent suppression of DAZL in oocytes forpre-implantation mouse development. PLoS Genet. 14, e1007436.

90.

Fukuda, R., Gunawan, F., Beisaw, A., Jimenez-Amilburu, V., Maischein, H.M., Kostin, S., Kawakami, K., and Stainier, D.Y. (2017). Proteolysis regulates
cardiomyocyte maturation and tissue integration. Nat Commun 8, 14495.

91.

Funabiki, M., Kato, H., Miyachi, Y., Toki, H., Motegi, H., Inoue, M., Minowa, O., Yoshida, A., Deguchi, K., Sato, H., Ito, S., Shiroishi, T., Takeyasu, K.,
Noda, T., and Fujita, T. (2014). Autoimmune disorders associated with gain of function of the intracellular sensor MDA5. Immunity 40, 199-212.

92.

Funato, N., Kokubo, H., and Saga, Y. (2016) Transcriptomic analyses of Hand2 transgenic embryos. Genom Data 9, 60-62.

93.

Funato, N., Kokubo, H., Nakamura, M., Yanagisawa, H., and Saga, Y. (2016) Specification of jaw identity by the Hand2 transcription factor. Sci Rep 6,28405.

94.

Furuhashi, T., Ogawa, T., Naka, R., Nakazawa, M., Okazawa, K., Padermschoke, A., Nishio, K., Yokota, Hirai M., Arita, M., and Ohta, D. (2015) Wax
ester and lipophilic compound profiling of Euglena gracilis by gas chromatography-mass spectrometry: toward understanding of wax ester fermentation
under hypoxia. Metabolomics 11,175-183.

95.

Furuta, M., Hori, T., and Fukagawa, T. (2016) Chromatin binding of RCC1 during mitosis is important for its nuclear localization in interphase. Mol Biol
Cell 27, 371-381.

96.

Furuya, K. and Niki, H. (2017). Mating, Spore Dissection, and Selection of Diploid Cells in Schizosaccharomyces japonicus. Cold Spring Harbor Protocols
2017, pdb.prot091843.

97.

Ganley, A.R., and Kobayashi, T. (2014). Ribosomal DNA and cellular senescence: new evidence supporting the connection between rDNA and aging.
FEMS Yeast Res. 14, 49-59.

98.

Gaouda, H., Hamaji, T., Yamamoto, K., Kawai-Toyooka, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Nozaki, H., et al. (2018).
Exploring the Limits and Causes of Plastid Genome Expansion in Volvocine Green Algae. Genome Biol. Evol. 10, 2248-2254.

99.

Garbacz, M., Araki, H., Flis, K., Bebenek, A., Zawada, A.E., Jonczyk, P., Makiela-Dzbenska, K., and Fijalkowska, I.J. (2015) Fidelity consequences of theimpaired interaction between DNA polymerase epsilon and the GINS complex. DNA Repair (Amst) 29,23-35.

100.

Gavelis, G.S., Hayakawa, S., White, R.A. 3rd, Gojobori, T., Suttle, C.A., Keeling, P.J., and Leander, B.S. (2015) Eye-like ocelloids are built from different
endosymbiotically acquired components. Nature 523,204-207.

101.

Gibcus, J.H., Samejima, K., Goloborodko, A., Samejima, I., Naumova, N., Nuebler, J., Kanemaki, M.T., Xie, L., Paulson, J.R., Earnshaw, W.C., et al.
(2018). A pathway for mitotic chromosome formation. Science 359, eaao6135.

102.

Gojobori, T., Ikeo, K., Katayama, Y., Kawabata, T., Kinjo, A.R., Kinoshita, K., Kwon, Y., Migita, O., Mizutani, H., Muraoka, M., Nagata, K., Omori, S.,
Sugawara, H., Yamada, D., and Yura, K. (2016) VaProS: a database-integration approach for protein/genome information retrieval. J Struct Funct Genomics
17, 69-81.

103.

Goto, G.H., Ogi, H., Biswas, H., Ghosh, A., Tanaka, S., and Sugimoto, K. (2017). Two separate pathways regulate protein stability of ATM/ATR-related
protein kinases Mec1 and Tel1 in budding yeast. PLoS Genet 13, e1006873.

‑60‑

104.

Gotoh, H., Miyakawa, H., Ishikawa, A., Ishikawa, Y., Sugime, Y., Emlen, D.J., Lavine, L.C., and Miura, T. (2014). Developmental link between sex andnutrition; doublesex regulates sex-specific mandible growth via juvenile hormone signaling in stag beetles. PLoS Genet. 10, e1004098.

105.

Gotoh, H., Zinna, R.A., Ishikawa, Y., Miyakawa, H., Ishikawa, A., Sugime, Y., Emlen, D.J., Lavine, L.C., and Miura, T. (2017). The function of appendage
patterning genes in mandible development of the sexually dimorphic stag beetle. Dev Biol 422, 24-32.

106.

Grants, J.M., Ying, L.T., Yoda, A., You, C.C., Okano, H., Sawa, H., and Taubert, S. (2016) The Mediator Kinase Module Restrains Epidermal Growth
Factor Receptor Signaling and Represses Vulval Cell Fate Specification in Caenorhabditis elegans. Genetics 202, 583-599.

107.

Grothman, G.T., Johansson, C., Chilton, G., Kagoshima, H., Tsujimoto, M., and Suzuki, A.C. (2017). Gilbert Rahm and the Status of Mesotardigrada Rahm,
1937. Zoolog Sci 34, 5-10.

108.

Guo, C., Nakazawa, Y., Woodbine, L., Bjorkman, A., Shimada, M., Fawcett, H., Jia, N., Ohyama, K., Li, T.S., Nagayama, Y., Mitsutake, N., PanHammarstrom, Q., Gennery, A.R., Lehmann, A.R., Jeggo, P.A., and Ogi, T. (2015) XRCC4 deficiency in human subjects causes a marked neurologicalphenotype but no overt immunodeficiency. J Allergy Clin Immunol 136,1007-1017.

109.

Gupta, A., and Kitagawa, D. (2018). Ultrastructural diversity between centrioles of eukaryotes. J. Biochem. 164, 1-8.

110.

Gupta, A., Tsuchiya, Y., Ohta, M., Shiratsuchi, G., and Kitagawa, D. (2017). NEK7 is required for G1 progression and procentriole formation. Mol Biol
Cell 28, 2123-2134.

111.

Hahn, M.W., Schmidt, J., Koll, U., Rohde, M., Verbarg, S., Pitt, A., Nakai, R., Naganuma, T., and Lang, E. (2017). Silvanigrella aquatica gen. nov., sp.
nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales
in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., andreclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. Int J Syst Evol Microbiol 67, 2555-2568.

112.

Hamaji, T., Kawai-Toyooka, H., Toyoda, A., Minakuchi, Y., Suzuki, M., Fujiyama, A., Nozaki, H., and Smith, D.R. (2017). Multiple Independent Changes
in Mitochondrial Genome Conformation in Chlamydomonadalean Algae. Genome Biology and Evolution 9, 993-999.

113.

Hamaji, T., Kawai-Toyooka, H., Uchimura, H., Suzuki, M., Noguchi, H., Minakuchi, Y., Toyoda, A., Fujiyama, A., Miyagishima, S.-Y., Umen, J.G., et al.
(2018). Anisogamy evolved with a reduced sex-determining region in volvocine green algae. Commun. Biol. 1, 17.

114.

Hamaji, T., Mogi, Y., Ferris, P.J., Mori, T., Miyagishima, S., Kabeya, Y., Nishimura, Y., Toyoda, A., Noguchi, H., Fujiyama, A., Olson, B.J., Marriage,
T.N., Nishii, I., Umen, J.G., and Nozaki, H. (2016) Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes
in Volvocine Algal Mating Haplotypes. G3 (Bethesda) 6, 1179-1189.

115.

Hamashima, K., Mori, M., Andachi, Y., Tomita, M., Kohara, Y., and Kanai, A. (2015) Analysis of genetic code ambiguity arising from nematode-specificmisacylated tRNAs. PLoS One 10,e0116981.

116.

Hamed, M., Odul, J., Miller, A.S., Kawakami, K., and Kitamoto, A. (2015) NAS: Neuron Analyzer Suite for Automatic Analysis of Neuronal Activities
from Calcium Imaging Data. International Journal of Pharma Medicine and Biological Sciences 4,167-170.

117.

Hanada, K., Tezuka, A., Nozawa, M., Suzuki, Y., Sugano, S., Nagano, A.J., Ito, M., and Morinaga, S.-I. (2018). Functional divergence of duplicate genes
several million years after gene duplication in Arabidopsis. DNA Res. 25, 327-339.

118.

Hanschen, E.R., Marriage, T.N., Ferris, P.J., Hamaji, T., Toyoda, A., Fujiyama, A., Neme, R., Noguchi, H., Minakuchi, Y., Suzuki, M., Kawai-Toyooka,
H., Smith, D.R., Sparks, H., Anderson, J., Bakaric, R., Luria, V., Karger, A., Kirschner, M.W., Durand, P.M., Michod, R.E., Nozaki, H., and Olson, B.J.
(2016) The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nat Commun 7, 11370.

119.

Hansen, J.C., Connolly, M., McDonald, C.J., Pan, A., Pryamkova, A., Ray, K., Seidel, E., Tamura, S., Rogge, R., and Maeshima, K. (2018). The 10-nm
chromatin fiber and its relationship to interphase chromosome organization. Biochem. Soc. Trans. 46, 67-76.

120.

Hara, K., Suzuki, I., Kobayashi, K., Fukumizu, K., and Radovanoviü, M. (2016) Flattening the Density Gradient for Eliminating Spatial Centrality to Reduce
Hubness In Proc. the 30th AAAI Conference on Artificial Intelligence (AAAI)1659-1665.

121.

Hara, T., Katoh, H., Ogawa, D., Kagaya, Y., Sato, Y., Kitano, H., Nagato, Y., Ishikawa, R., Ono, A., Kinoshita, T., Takeda, S., and Hattori, T. (2015). RiceSNF2 family helicase ENL1 is essential for syncytial endosperm development. Plant J., 81, 1-12.

122.

Hara, Y., Adachi, K., Kagohashi, S., Yamagata, K., Tanabe, H., Kikuchi, S., Okumura, S.I., and Kimura, A. (2016). Scaling relationship between intranuclear DNA density and chromosomal condensation in metazoan and plant. Chromosome Science, 19, 43-49.

123.

Harvanek, Z.M., Lyu, Y., Gendron, C.M., Johnson, J.C., Kondo, S., Promislow, D.E.L., and Pletcher, S.D. (2017). Perceptive costs of reproduction drive
ageing and physiology in male Drosophila. Nat Ecol Evol 1, 152.

124.

Hasegawa, K., and Saga, Y. (2014). FGF8-FGFR1 signaling acts as a niche factor for maintaining undifferentiated spermatogonia in the mouse. Biol. Reprod.
91, 145.

125.

Hasegawa, T., Hall, C.J., Crosier, P.S., Abe, G., Kawakami, K., Kudo, A., and Kawakami, A. (2017). Transient inflammatory response mediated byinterleukin-1beta is required for proper regeneration in zebrafish fin fold. Elife 6, e22716.

126.

Hasegawa, Y., and Arita, M. (2014). Circadian clocks optimally adapt to sunlight for reliable synchronization. J. R. Soc. Interface 11, 20131018.

127.

Hasegawa, Y., Arita, M. (2014). Optimal implementations for reliable circadian clocks. Phys. Rev. Lett. 113, 108101.

128.

Hashimoto, S., Tabuchi, Y., Yurino, H., Hirohashi, Y., Deshimaru, S., Asano, T., Mariya, T., Oshima, K., Takamura, Y., Ukita, Y., Ametani, A., Kondo,N., Monma, N., Takeda, T., Misu, S., Okayama, T., Ikeo, K., Saito, T., Kaneko, S., Suzuki, Y., Hattori, M., Matsushima, K., and Torigoe, T. (2017).
Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues. Sci Rep 7, 14225.

129.

Hashimoto, T., Horikawa, D.D., Saito, Y., Kuwahara, H., Kozuka-Hata, H., Shin-I, T., Minakuchi, Y., Ohishi, K., Motoyama, A., Aizu, T., Enomoto, A.,
Kondo, K., Tanaka, S., Hara, Y., Koshikawa, S., Sagara, H., Miura, T., Yokobori, S., Miyagawa, K., Suzuki, Y., Kubo, T., Oyama, M., Kohara, Y., Fujiyama,‑61‑

A., Arakawa, K., Katayama, T., Toyoda, A., and Kunieda, T. (2016) Extremotolerant tardigrade genome and improved radiotolerance of human cultured
cells by tardigrade-unique protein. Nat Commun 7, 12808.
130.

Hatanaka, Y., Namikawa, T., Yamauchi, K., and Kawaguchi, Y. (2016) Cortical Divergent Projections in Mice Originate from Two Sequentially Generated,
Distinct Populations of Excitatory Cortical Neurons with Different Initial Axonal Outgrowth Characteristics. Cereb Cortex 26, 2257-2270.

131.

Hatanaka, Y., Zhu, Y., Torigoe, M., Kita, Y., and Murakami, F. (2016) From migration to settlement: the pathways, migration modes and dynamics ofneurons in the developing brain. Proc Jpn Acad Ser B Phys Biol Sci 92, 1-19.

132.

Hayakawa, S., Takaku, Y., Hwang, J.S., Horiguchi, T., Suga, H., Gehring, W., Ikeo, K., and Gojobori, T. (2015) Function and evolutionary origin of
unicellular camera-type eye structure. PLoS One 10,e0118415.

133.

Hayano, T., Matsui, H., Nakaoka, H., Ohtake, N., Hosomichi, K., Suzuki, K., and Inoue, I. (2016) Germline Variants of Prostate Cancer in Japanese Families.
PLoS One 11, e0164233.

134.

Hayano, T., Yamada, S., Hosomichi, K., Nakaoka, H., Yoshihara, K., Adachi, S., Kashima, K., Tanaka, K., Enomoto, T., and Inoue, I. (2015) Identificationof novel exonic mobile element insertions in epithelial ovarian cancers. Human Genome Variation 2,15030.

135.

Hayano, T., Yokota, Y., Hosomichi, K., Nakaoka, H., Yoshihara, K., Adachi, S., Kashima, K., Tsuda, H., Moriya, T., Tanaka, K., Enomoto, T., and Inoue,
I. (2014). Molecular characterization of an intact p53 pathway subtype in high-grade serous ovarian cancer. PLoS One 9, e114491.

136.

Hayase, E., Hashimoto, D., Nakamura, K., Noizat, C., Ogasawara, R., Takahashi, S., Ohigashi, H., Yokoi, Y., Sugimoto, R., Matsuoka, S., Ara, T.,
Yokoyama, E., Yamakawa, T., Ebata, K., Kondo, T., Hiramine, R., Aizawa, T., Ogura, Y., Hayashi, T., Mori, H., Kurokawa, K., Tomizuka, K., Ayabe, T.,
and Teshima, T. (2017). R-Spondin1 expands Paneth cells and prevents dysbiosis induced by graft-versus-host disease. J Exp Med 214, 3507-3518.

137.

Hayashi, K., Kawai, Y.L., Yura, K., Yoshida, M.A., Ogura, A., Hata, K., Nakabayashi, K., and Okamura, K. (2016) Complete genome sequence of themitochondrial DNA of the sparkling enope squid, Watasenia scintillans. Mitochondrial DNA A DNA Mapp Seq Anal 27, 1842-1843.

138.

Hayashi, S., Kobayashi, T., Yano, T., Kamiyama, N., Egawa, S., Seki, R., Takizawa, K., Okabe, M., Yokoyama, H., and Tamura, K. (2015) Evidence foran amphibian sixth digit. Zoological Lett 1,17.

139.

Hayashi, Y., Nishimune, H., Hozumi, K., Saga, Y., Harada, A., Yuzaki, M., Iwatsubo, T., Kopan, R., and Tomita, T. (2016) A novel non-canonical Notch
signaling regulates expression of synaptic vesicle proteins in excitatory neurons. Sci Rep 6, 23969.

140.

Hayatsu, M., Tago, K., Uchiyama, I., Toyoda, A., Wang, Y., Shimomura, Y., Okubo, T., Kurisu, F., Hirono, Y., Nonaka, K., Akiyama, H., Itoh, T., andTakami, H. (2017). An acid-tolerant ammonia-oxidizing gamma-proteobacterium from soil. ISME J 11, 1130-1141.

141.

Heanue, T.A., Boesmans, W., Bell, D.M., Kawakami, K., Vanden, Berghe P., and Pachnis, V. (2016) A Novel Zebrafish ret Heterozygous Model ofHirschsprung Disease Identifies a Functional Role for mapk10 as a Modifier of Enteric Nervous System Phenotype Severity. PLoS Genet 12, e1006439.

142.

Hentze, J.L., Carlsson, M.A., Kondo, S., Nassel, D.R., and Rewitz, K.F. (2015) The Neuropeptide Allatostatin A Regulates Metabolism and Feeding
Decisions in Drosophila. Sci Rep 5,11680.

143.

Hettiarachchi, N., and Saitou, N. (2016) GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence ofVertebrates. Genome Biol Evol 8, 3377-3392.

144.

Hettiarachchi, N., Kryukov, K., Sumiyama, K., and Saitou, N. (2014). Lineage-specific conserved noncoding sequences of plant genomes: their possible
role in nucleosome positioning. Genome Biol. Evol. 6, 2527-2542.

145.

Higaki, S., Kuwata, N., Tanaka, K., Tooyama, I., Fujioka, Y., Sakai, N., and Takada, T. (2017). Successful vitrification of whole juvenile testis in thecritically endangered cyprinid honmoroko (Gnathopogon caerulescens). Zygote 25, 652-661.

146.

Higaki, S., Shimada, M., Kawamoto, K., Todo, T., Kawasaki, T., Tooyama, I., Fujioka, Y., Sakai, N., and Takada, T. (2017). In vitro differentiation of fertile
sperm from cryopreserved spermatogonia of the endangered endemic cyprinid honmoroko (Gnathopogon caerulescens). Sci Rep 7, 42852.

147.

Higaki, S., Shimada, M., Koyama, Y., Fujioka, Y., Sakai, N., and Takada, T. (2015) Development and characterization of an embryonic cell line fromendangered endemic cyprinid Honmoroko Gnathopogon caerulescens (Sauvage, 1883). In Vitro Cell Dev Biol Anim 51,763-768.

148.

Higaki, S., Todo, T., Teshima, R., Tooyama, I., Fujioka, Y., Sakai, N., and Takada, T. (2018). Cryopreservation of male and female gonial cells by
vitrification in the critically endangered cyprinid honmoroko Gnathopogon caerulescens. Fish Physiol. Biochem. 44, 503-513.

149.

Higashi, K., Kawai, Y., Baba, T., Kurokawa, K., and Oshima, T. (2018). Essential cellular modules for the proliferation of the primitive cell. Geosci. Front.
9, 1155-1161.

150.

Higashi, K., Suzuki, S., Kurosawa, S., Mori, H., and Kurokawa, K. (2018). Latent environment allocation of microbial community data. PLoS Comput. Biol.
14, e1006143.

151.

Higashino, T., Takada, T., Nakaoka, H., Toyoda, Y., Stiburkova, B., Miyata, H., Ikebuchi, Y., Nakashima, H., Shimizu, S., Kawaguchi, M., Sakiyama, M.,
Nakayama, A., Akashi, A., Tanahashi, Y., Kawamura, Y., Nakamura, T., Wakai, K., Okada, R., Yamamoto, K., Hosomichi, K., Hosoya, T., Ichida, K.,
Ooyama, H., Suzuki, H., Inoue, I., Merriman, T.R., Shinomiya, N., and Matsuo, H. (2017). Multiple common and rare variants of ABCG2 cause gout. RMD
Open 3, e000464.

152.

Higuchi, T., Agostini, S., Casareto, B.E., Suzuki, Y., and Yuyama, I. (2015) The northern limit of corals of the genus Acropora in temperate zones isdetermined by their resilience to cold bleaching. Sci Rep 5,18467.

153.

Hino, K., Horigome, K., Nishio, M., Komura, S., Nagata, S., Zhao, C., Jin, Y., Kawakami, K., Yamada, Y., Ohta, A., Toguchida, J., and Ikeya, M. (2017).
Activin-A enhances mTOR signaling to promote aberrant chondrogenesis in fibrodysplasia ossificans progressiva. J Clin Invest 127, 3339-3352.

154.

Hiraide, Y., Oshima, K., Fujisawa, T., Uesaka, K., Hirose, Y., Tsujimoto, R., Yamamoto, H., Okamoto, S., Nakamura, Y., Terauchi, K., Omata, T., Ihara,
K., Hattori, M., and Fujita, Y. (2015) Loss of cytochrome cM stimulates cyanobacterial heterotrophic growth in the dark. Plant Cell Physiol 56,334-345.

‑62‑

155.

Hiraki, H., Kagoshima, H., Kraus, C., Schiffer, P.H., Ueta, Y., Kroiher, M., Schierenberg, E., and Kohara, Y. (2017). Genome analysis of Diploscapter
coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction. BMC Genomics 18, 478.

156.

Hiramatsu, N., Todo, T., Sullivan, C.V., Schilling, J., Reading, B.J., Matsubara, T., Ryu, Y.W., Mizuta, H., Luo, W., Nishimiya, O., Wu, M., Mushirobira,Y., Yilmaz, O., and Hara, A. (2015) Ovarian yolk formation in fishes: Molecular mechanisms underlying formation of lipid droplets and vitellogenin-derived
yolk proteins. Gen Comp Endocrinol 221,9-15.

157.

Hirata J, Hosomichi K, Sakaue S, Kanai M, Nakaoka H, Ishigaki K, Suzuki K, Akiyama M, Kishikawa T, Ogawa K, Masuda T, Yamamoto K, Hirata M,
Matsuda K, Momozawa Y, Inoue I, Kubo M, Kamatani Y, and Okada Y.  Genetic and phenotypic landscape of the MHC region in the Japanese
population. Nat Genetics 51, 470-480.

158.

Hirata, A., Nokihara, K., Kawamoto, Y., Bando, T., Sasaki, A., Ide, S., Maeshima, K., Kasama, T., and Sugiyama, H. (2014). Structural evaluation of tandem
hairpin pyrrole-imidazole polyamides recognizing human telomeres. J. Am. Chem. Soc. 136, 11546-11554.

159.

Hirata, H., Takahashi, A., Shimoda, Y., and Koide, T. (2016) Caspr3-Deficient Mice Exhibit Low Motor Learning during the Early Phase of the Accelerated
Rotarod Task. PLoS One 11, e0147887.

160.

Hirata, H., Umemori, J., Yoshioka, H., Koide, T., Watanabe, K., and Shimoda, Y. (2016) Cell adhesion molecule contactin-associated protein 3 is expressedin the mouse basal ganglia during early postnatal stages. J Neurosci Res 94, 74-89.

161.

Hirooka, S., and Miyagishima, S.Y. (2016) Cultivation of Acidophilic Algae Galdieria sulphuraria and Pseudochlorella sp. YKT1 in Media Derived from
Acidic Hot Springs. Front Microbiol 7, 2022.

162.

Hirooka, S., Higuchi, S., Uzuka, A., Nozaki, H., and Miyagishima, S.Y. (2014). Acidophilic green alga Pseudochlorella sp. YKT1 accumulates high amountof lipid droplets under a nitrogen-depleted condition at a low-pH. PLoS One 9, e107702.

163.

Hirooka, S., Hirose, Y., Kanesaki, Y., Higuchi, S., Fujiwara, T., Onuma, R., Era, A., Ohbayashi, R., Uzuka, A., Nozaki, H., Yoshikawa, H., and Miyagishima,
S.Y. (2017). Acidophilic green algal genome provides insights into adaptation to an acidic environment. Proc Natl Acad Sci U S A 114, E8304-E8313.

164.

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., andKanesaki, Y. (2016) Complete genome sequence of cyanobacterium Fischerella sp. NIES-3754, providing thermoresistant optogenetic tools. J Biotechnol
220, 45-46.

165.

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., andKanesaki, Y. (2016) Complete Genome Sequence of Cyanobacterium Leptolyngbya sp. NIES-3755. Genome Announc 4, e00090-00016.

166.

Hirose, Y., Fujisawa, T., Ohtsubo, Y., Katayama, M., Misawa, N., Wakazuki, S., Shimura, Y., Nakamura, Y., Kawachi, M., Yoshikawa, H., Eki, T., andKanesaki, Y. (2016) Complete genome sequence of cyanobacterium Nostoc sp. NIES-3756, a potentially useful strain for phytochrome-based
bioengineering. J Biotechnol 218, 51-52.

167.

Hirose, Y., Suda, K., Liu, Y.G., Sato, S., Nakamura, Y., Yokoyama, K., Yamamoto, N., Hanano, S., Takita, E., Sakurai, N., Suzuki, H., Nakamura, Y.,
Kaneko, T., Yano, K., Tabata, S., and Shibata, D. (2015) The Arabidopsis TAC Position Viewer: a high-resolution map of transformation-competent artificial
chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia-0 genome. Plant J 83,1114-1122.

168.

Hizume, K., Endo, S., Muramatsu, S., Kobayashi, T., and Araki, H. (2018). DNA polymerase İ-dependent modulation of the pausing property of the CMG
helicase at the barrier. Genes Dev. 32, 1315-1320.

169.

Hizume, K., Kominami, H., Kobayashi, K., Yamada, H., and Araki, H. (2017). Flexible DNA Path in the MCM Double Hexamer Loaded on DNA.
Biochemistry 56, 2435-2445.

170.

Ho, J.C., Hsiao, C.D., Kawakami, K., and Tse, W.K. (2016) Triclosan (TCS) exposure impairs lipid metabolism in zebrafish embryos. Aquat Toxicol 173,
29-35.

171.

Hoa, N.N., Akagawa, R., Yamasaki, T., Hirota, K., Sasa, K., Natsume, T., Kobayashi, J., Sakuma, T., Yamamoto, T., Komatsu, K., Kanemaki, M.T.,
Pommier, Y., Takeda, S., and Sasanuma, H. (2015). Relative contribution of four nucleases CtIP Dna2 Exo1 and Mre11 to the initial step of DNA doublestrand break repair by homologous recombination in both the chicken DT40 and human TK6 cell lines. Genes Cells 20, 1059-1076.

172.

Homma, M., Nagashima, S., Fukuda, T., Yanagi, S., Miyakawa, H., Suzuki, E., and Morimoto, T. (2014). Downregulation of Centaurin gamma1A increases
synaptic transmission at Drosophila larval neuromuscular junctions. Eur. J. Neurosci 40, 3158-3170.

173.

Honda, E., Yew, C.-L., Yoshikawa, T., Sato, Y., Hibara, K.-I., and Itoh, J.-I. (2018). LEAF LATERAL SYMMETRY1, a Member of the WUSCHELRELATED HOMEOBOX3 Gene Family, Regulates Lateral Organ Development Differentially from Other Paralogs, NARROW LEAF2 and NARROW
LEAF3 in Rice. Plant Cell Physiol. 59, 376-391.

174.

Hori-Tanaka, Y., Yura, K., Takai-Igarashi, T., and Tanaka, H. (2015) Structural classification of steroid-binding sites on proteins by coarse-grained atomic
environment and its correlation with their biological function. Steroids 96,81-88.

175.

Hori, K., Maruyama, F., Fujisawa, T., Togashi, T., Yamamoto, N., Seo, M., Sato, S., Yamada, T., Mori, H., Tajima, N., Moriyama, T., Ikeuchi, M., Watanabe,M., Wada, H., Kobayashi, K., Saito, M., Masuda, T., Sasaki-Sekimoto, Y., Mashiguchi, K., Awai, K., Shimojima, M., Masuda, S., Iwai, M., Nobusawa, T.,
Narise, T., Kondo, S., Saito, H., Sato, R., Murakawa, M., Ihara, Y., Oshima-Yamada, Y., Ohtaka, K., Satoh, M., Sonobe, K., Ishii, M., Ohtani, R., KanamoriSato, M., Honoki, R., Miyazaki, D., Mochizuki, H., Umetsu, J., Higashi, K., Shibata, D., Kamiya, Y., Sato, N., Nakamura, Y., Tabata, S., Ida, S., Kurokawa,K., and Ohta, H. (2014). Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun. 5, 3978.

176.

Hori, K., Yamada, Y., Purwanto, R., Minakuchi, Y., Toyoda, A., Hirakawa, H., and Sato, F. (2018). Mining of the Uncharacterized Cytochrome P450 Genes
Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence. Plant Cell Physiol. 59, 222-233.

177.

Hori, T., Kagawa, N., Toyoda, A., Fujiyama, A., Misu, S., Monma, N., Makino, F., Ikeo, K., and Fukagawa, T. (2017). Constitutive centromere-associatednetwork controls centromere drift in vertebrate cells. J Cell Biol 216, 101-113.

‑63‑

178.

Hori, T., Shang, W.H., Toyoda, A., Misu, S., Monma, N., Ikeo, K., Molina, O., Vargiu, G., Fujiyama, A., Kimura, H., Earnshaw, W.C., and Fukagawa, T.
(2014). Histone H4 Lys 20 monomethylation of the CENP-A nucleosome is essential for kinetochore assembly. Dev. Cell 29, 740-749.

179.

Horii, Y., and Kawaguchi, M. (2015) Higher detection sensitivity of anxiolytic effects of diazepam by ledge-free open arm with opaque walled closed arm
elevated plus maze in male rats. Behav Brain Res 294,131-140.

180.

Horii, Y., Nagasawa, T., Sakakibara, H., Takahashi, A., Tanave, A., Matsumoto, Y., Nagayama, H., Yoshimi, K., Yasuda, M.T., Shimoi, K., and Koide, T.
(2017). Hierarchy in the home cage affects behaviour and gene expression in group-housed C57BL/6 male mice. Sci Rep 7, 6991.

181.

Horikawa, Y., Hosomichi, K., Enya, M., Ishiura, H., Suzuki, Y., Tsuji, S., Sugano, S., Inoue, I., and Takeda, J. (2018). No novel, high penetrant gene mightremain to be found in Japanese patients with unknown MODY. J. Hum. Genet. 63, 821-829.

182.

Horiuchi, Y., Harushima, Y., Fujisawa, H., Mochizuki, T., Fujita, M., Ohyanagi, H., and Kurata, N. (2015). Global expression differences and tissue specificexpression differences in rice evolution result in two contrasting types of differentially expressed genes. BMC Genomics 23, 1099.

183.

Hosaka, A., and Kakutani, T. (2018). Transposable elements, genome evolution and transgenerational epigenetic variation. Curr. Opin. Genet. Dev. 49, 4348.

184.

Hosaka, A., Saito, R., Takashima, K., Sasaki, T., Fu, Y., Kawabe, A., Ito, T., Toyoda, A., Fujiyama, A., Tarutani, Y., and Kakutani, T. (2017). Evolution ofsequence-specific anti-silencing systems in Arabidopsis. Nat Commun 8, 2161.

185.

Hoshino, A., Jayakumar, V., Nitasaka, E., Toyoda, A., Noguchi, H., Itoh, T., Shin-I, T., Minakuchi, Y., Koda, Y., Nagano, A.J., Yasugi, M., Honjo, M.N.,
Kudoh, H., Seki, M., Kamiya, A., Shiraki, T., Carninci, P., Asamizu, E., Nishide, H., Tanaka, S., Park, K.I., Morita, Y., Yokoyama, K., Uchiyama, I.,
Tanaka, Y., Tabata, S., Shinozaki, K., Hayashizaki, Y., Kohara, Y., Suzuki, Y., Sugano, S., Fujiyama, A., Iida, S., and Sakakibara, Y. (2016) Genome
sequence and analysis of the Japanese morning glory Ipomoea nil. Nat Commun 7, 13295.

186.

Hosomichi, K., Mitsunaga, S., Nagasaki, H., and Inoue, I. (2014). A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multisamples sequencing exemplified by HLA-B. BMC Genomics 15, 645.

187.

Hosomichi, K., Shiina, T., Tajima, A., and Inoue, I. (2015) The impact of next-generation sequencing technologies on HLA research. J Hum Genet 60,665673.

188.

Hsia, K.C., Wilson-Kubalek, E.M., Dottore, A., Hao, Q., Tsai, K.L., Forth, S., Shimamoto, Y., Milligan, R.A., and Kapoor, T.M. (2014). Reconstitution of
the augmin complex provides insights into its architecture and function. Nat. Cell Biol. 16, 852-863.

189.

Huang, C.L., Ho, C.W., Chiang, Y.C., Shigemoto, Y., Hsu, T.W., Hwang, C.C., Ge, X.J., Chen, C., Wu, T.H., Chou, C.H., Huang, H.J., Gojobori, T., Osada,N., and Chiang, T.Y. (2014). Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae). Plant J. 80,
834-847.

190.

Huang, C.L., Pu, P.H., Huang, H.J., Sung, H.M., Liaw, H.J., Chen, Y.M., Chen, C.M., Huang, M.B., Osada, N., Gojobori, T., Pai, T.W., Chen, Y.T., Hwang,
C.C., and Chiang, T.Y. (2015) Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts..
BMC Genomics 16,188.

191.

Hyakutake, K., Kawasaki, T., Zhang, J., Kubota, H., Abe, S.I., and Takamune, K. (2015) Asymmetrical allocation of JAK1 mRNA during spermatogonial
stem cell division in Xenopus laevis. Dev Growth Differ 57,389-399.

192.

Iatsenko, I., Kondo, S., Mengin-Lecreulx, D., and Lemaitre, B. (2016) PGRP-SD, an Extracellular Pattern-Recognition Receptor, Enhances PeptidoglycanMediated Activation of the Drosophila Imd Pathway. Immunity 45, 1013-1023.

193.

Ichino, F., Bono, H., Nakazato, T., Toyoda, A., Fujiyama, A., Iwabuchi, K., Sato, R., and Tabunoki, H. (2018). Construction of a simple evaluation system
for the intestinal absorption of an orally administered medicine using Bombyx mori larvae. Drug Discov. Ther. 12, 7-15.

194.

Ide, S., and Dejardin, J. (2015) End-targeting proteomics of isolated chromatin segments of a mammalian ribosomal RNA gene promoter. Nat Commun
6,6674.

195.

Igarashi, Y., Zhang, H., Tan, E., Sekino, M., Yoshitake, K., Kinoshita, S., Mitsuyama, S., Yoshinaga, T., Chow, S., Kurogi, H., et al. (2018). Whole-Genome
Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation. Genes (Basel). 9, E474.

196.

Igawa, T., Nozawa, M., Nagaoka, M., Komaki, S., Oumi, S., Fujii, T., and Sumida, M. (2015) Microsatellite marker development by multiplex ion torrent
PGM sequencing: a case study of the endangered Odorrana narina complex of frogs. J Hered 106,131-137.

197.

Ihara, S., Nakayama, S., Murakami, Y., Suzuki, E., Asakawa, M., Kinoshita, T., and Sawa, H. (2017). PIGN prevents protein aggregation in the endoplasmic
reticulum independently of its function in the GPI synthesis. J Cell Sci 130, 602-613.

198.

Iida, N., Okuda, Y., Ogasawara, O., Yamashita, S., Takeshima, H., and Ushijima, T. (2018). MACON: a web tool for computing DNA methylation dataobtained by the Illumina Infinium Human DNA methylation BeadArray. Epigenomics 10, 249-258.

199.

Iida, N., Yamao, F., Nakamura, Y., and Iida, T. (2014). Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence.
Genes Cells 19, 517-527.

200.

Ikebe, R., Kuwabara, Y., Chikada, T., Niki, H., and Shiomi, D. (2018). The periplasmic disordered domain of RodZ promotes its self-interaction in
Escherichia coli. Genes Cells 23, 307-317.

201.

Imai, R., Komeda, S., Shimura, M., Tamura, S., Matsuyama, S., Nishimura, K., Rogge, R., Matsunaga, A., Hiratani, I., Takata, H., Uemura, M., Iida, Y.,
Yoshikawa, Y., Hansen, J.C., Yamauchi, K., Kanemaki, M.T., and Maeshima, K. (2016) Chromatin folding and DNA replication inhibition mediated by ahighly antitumor-active tetrazolato-bridged dinuclear platinum(II) complex. Sci Rep 6, 24712.

202.

Imai, R., Nozaki, T., Tani, T., Kaizu, K., Hibino, K., Ide, S., Tamura, S., Takahashi, K., Shribak, M., and Maeshima, K. (2017). Density imaging ofheterochromatin in live cells using orientation-independent-DIC microscopy. Mol Biol Cell 28, 3349-3359.

‑64‑

203.

Imamura, K., Sahara, N., Kanaan, N.M., Tsukita, K., Kondo, T., Kutoku, Y., Ohsawa, Y., Sunada, Y., Kawakami, K., Hotta, A., Yawata, S., Watanabe, D.,
Hasegawa, M., Trojanowski, J.Q., Lee, V.M., Suhara, T., Higuchi, M., and Inoue, H. (2016) Calcium dysregulation contributes to neurodegeneration in
FTLD patient iPSC-derived neurons. Sci Rep 6, 34904.

204.

Imamura, S., Kawase, Y., Kobayashi, I., Sone, T., Era, A., Miyagishima, S.Y., Shimojima, M., Ohta, H., and Tanaka, K. (2015) Target of rapamycin (TOR)
plays a critical role in triacylglycerol accumulation in microalgae. Plant Mol Biol 89,309-318.

205.

Inaba, Y., Shinohara, K., Botilde, Y., Nabeshima, R., Takaoka, K., Ajima, R., Lamri, L., Takeda, H., Saga, Y., Nakamura, T., and Hamada, H. (2016)
Transport of the outer dynein arm complex to cilia requires a cytoplasmic protein Lrrc6. Genes Cells 21, 728-739.

206.

Inagaki, S., Henry, I.M., Lieberman, M.C., and Comai, L. (2015) High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.
PLoS One 10,e0139672.

207.

Inagaki, S., Takahashi, M., Hosaka, A., Ito, T., Toyoda, A., Fujiyama, A., Tarutani, Y., and Kakutani, T. (2017). Gene-body chromatin modification
dynamics mediate epigenome differentiation in Arabidopsis. EMBO J 36, 970-980.

208.

Inahashi, H., Shelley, I.J., Yamauchi, T., Nishiuchi, S., Takahashi-Nosaka, M., Matsunami, M., Ogawa, A., Noda, Y., and Inukai, Y. (2018). OsPIN2, which
encodes a member of the auxin efflux carrier proteins, is involved in root elongation growth and lateral root formation patterns via the regulation of auxin
distribution in rice. Physiol. Plant. 164, 216-225.

209.

Inoue, J., Sato, Y., Sinclair, R., Tsukamoto, K., and Nishida, M. (2015) Rapid genome reshaping by multiple-gene loss after whole-genome duplication inteleost fish suggested by mathematical modeling. Proc Natl Acad Sci U S A 112,14918-14923.

210.

Inoue, K., Urushibara, K., Kanai, M., Yura, K., Fujii, S., Ishigami-Yuasa, M., Hashimoto, Y., Mori, S., Kawachi, E., Matsumura, M., Hirano, T., Kagechika,
H., and Tanatani, A. (2015) Design and synthesis of 4-benzyl-1-(2H)-phthalazinone derivatives as novel androgen receptor antagonists. Eur J Med Chem
102,310-319.

211.

International, Glossina Genome Initiative (2014). Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science 344,
380-386.

212.

Ishiguro, K., Kim, J., Shibuya, H., Hernandez-Hernandez, A., Suzuki, A., Fukagawa, T., Shioi, G., Kiyonari, H., Li, X.C., Schimenti, J., Hoog, C., and
Watanabe, Y. (2014). Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes. Genes Dev. 28, 594-607.

213.

Ishihama, A., Kori, A., Koshio, E., Yamada, K., Maeda, H., Shimada, T., Makinoshima, H., Iwata, A., and Fujita, N. (2014). Intracellular concentrations of
65 species of transcription factors with known regulatory functions in Escherichia coli. J. Bacteriol. 196, 2718-2727.

214.

Ishihama, A., Shimada, T., and Yamazaki, Y. (2016) Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription
factors. Nucleic Acids Res 44, 2058-2074.

215.

Ishikawa, A., Kusakabe, M., Kume, M., and Kitano, J. (2016) Comparison of freshwater tolerance during spawning migration between two sympatricJapanese marine threespine stickleback species EVOLUTIONARY ECOLOGY RESEARCH 17, 525-534.

216.

Ishikawa, A., Kusakabe, M., Yoshida, K., Ravinet, M., Makino, T., Toyoda, A., Fujiyama, A., and Kitano, J. (2017). Different contributions of local- anddistant-regulatory changes to transcriptome divergence between stickleback ecotypes. Evolution 71, 565-581.

217.

Ishikawa, M., Shimizu, H., Nozawa, M., Ikeo, K., and Gojobori, T. (2016) Two-step evolution of endosymbiosis between hydra and algae. Mol Phylogenet
Evol 103, 19-25.

218.

Ishikawa, M., Yuyama, I., Shimizu, H., Nozawa, M., Ikeo, K., and Gojobori, T. (2016) Different Endosymbiotic Interactions in Two Hydra Species Reflect
the Evolutionary History of Endosymbiosis. Genome Biol Evol 8, 2155-2163.

219.

Ishimine, M., Lee, H.-C., Nakaoka, H., Orita, H., Kobayashi, T., Mizuguchi, K., Endo, M., Inoue, I., Sato, K., and Yokomizo, T. (2018). The Relationshipbetween TP53 Gene Status and Carboxylesterase 2 Expression in Human Colorectal Cancer. Dis. Markers 2018, 5280736.

220.

Ishiura, H., Doi, K., Mitsui, J., Yoshimura, J., Matsukawa, M.K., Fujiyama, A., Toyoshima, Y., Kakita, A., Takahashi, H., Suzuki, Y., et al. (2018).
Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy. Nat. Genet. 50, 581-590.

221.

Ishiwata, S., Miyazaki, M., Sato, K., Nakagome, K., Shintani, S.A., Kobirumaki-Shimozawa, F., Fukuda, N., Suzuki, K., Takagi, J., Shimamoto, Y., andItabashi, T. (2017). Dynamic properties of bio-motile systems with a liquid-crystalline structure. Molecular Crystals and Liquid Crystals 647, 127-150.

222.

Ito, H., and Kakutani, T. (2014). Control of transposable elements in Arabidopsis thaliana. Chromosome Res. 22, 217-223.

223.

Ito, H., Hasegawa, K., Hasegawa, Y., Nishimaki, T., Hosomichi, K., Kimura, S., Ohba, M., Yao, H., Onimaru, M., Inoue, I., and Inoue, H. (2015) Silver
Nanoscale Hexagonal Column Chips for Detecting Cell-free DNA and Circulating Nucleosomes in Cancer Patients. Sci Rep 5,10455.

224.

Ito, H., Kim, J.M., Matsunaga, W., Saze, H., Matsui, A., Endo, T.A., Harukawa, Y., Takagi, H., Yaegashi, H., Masuta, Y., Masuda, S., Ishida, J., Tanaka,M., Takahashi, S., Morosawa, T., Toyoda, T., Kakutani, T., Kato, A., and Seki, M. (2016) A Stress-Activated Transposon in Arabidopsis Induces
Transgenerational Abscisic Acid Insensitivity. Sci Rep 6, 23181.

225.

Ito, H., Sato, K., Kondo, S., Ueda, R., and Yamamoto, D. (2016) Fruitless Represses robo1 Transcription to Shape Male-Specific Neural Morphology and
Behavior in Drosophila. Curr Biol 26, 1532-1542.

226.

Ito, J., Sugimoto, R., Nakaoka, H., Yamada, S., Kimura, T., Hayano, T., and Inoue, I. (2017). Systematic identification and characterization of regulatory
elements derived from human endogenous retroviruses. PLoS Genet 13, e1006883.

227.

Ito, T., Bai, T., Tanaka, T., Yoshida, K., Ueyama, T., Miyajima, M., Negishi, T., Kawasaki, T., Takamatsu, H., Kikutani, H., Kumanogoh, A., and Yukawa,
K. (2014). Estrogen-dependent proteolytic cleavage of semaphorin 4D and plexin-B1 enhances semaphorin 4D-induced apoptosis during postnatal vaginal
remodeling in pubescent mice. PLoS One 9, e97909.

228.

Ito, T., Bai, T., Tanaka, T., Yoshida, K., Ueyama, T., Miyajima, M., Negishi, T., Kawasaki, T., Takamatsu, H., Kikutani, H., Kumanogoh, A., and Yukawa,‑65‑

K. (2015) Semaphorin 4D induces vaginal epithelial cell apoptosis to control mouse postnatal vaginal tissue remodeling. Mol Med Rep 11,829-836.
229.

Ito, T., Tarutani, Y., To, T.K., Kassam, M., Duvernois-Berthet, E., Cortijo, S., Takashima, K., Saze, H., Toyoda, A., Fujiyama, A., Colot, V., and Kakutani,
T. (2015) Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis. PLoS Genet 11,e1005154.

230.

Itoh, H., Matsui, M., Kumagai, T., Arita, M., Machida, M., and Shibata, T. (2017). Genome Sequence of the Fungal Strain 14919 Producing 3-Hydroxy-3Methylglutaryl-Coenzyme A Reductase Inhibitor FR901512. Genome Announc 5, e00129-17.

231.

Itoh, H., Matsui, M., Miyamura, Y., Takeda, I., Ishii, J., Kumagai, T., Machida, M., Shibata, T., and Arita, M. (2018). Biosynthesis of Novel Statins by
Combining Heterologous Genes from Xylaria and Aspergillus. ACS Synth. Biol. 2018 7, 2783-2789.

232.

Itoh, H., Miura, A., Matsui, M., Arazoe, T., Nishida, K., Kumagai, T., Arita, M., Tamano, K., Machida, M., and Shibata, T. (2018). Knockout of the SREBP
system increases production of the polyketide FR901512 in filamentous fungal sp. No. 14919 and lovastatin in Aspergillus terreus ATCC20542. Appl.
Microbiol. Biotechnol. 102, 1393-1405.

233.

Itoh, J., Sato, Y., Sato, Y., Hibara, K., Shimizu-Sato, S., Kobayashi, H., Takehisa, H., Sanguinet, K.A., Namiki, N., and Nagamura, Y. (2016). Genomewide analysis of spatiotemporal gene expression patterns during early embryogenesis in rice. Development, 143, 1217-1227.

234.

Itoh, K., Akimoto, Y., Kondo, S., Ichimiya, T., Aoki, K., Tiemeyer, M., and Nishihara, S. (2018). Glucuronylated core 1 glycans are required for precise
localization of neuromuscular junctions and normal formation of basement membranes on Drosophila muscles. Dev. Biol. 436, 108-124.

235.

Itou, H., Muramatsu, S., Shirakihara, Y., and Araki, H. (2014). Crystal structure of the homology domain of the eukaryotic DNA replication proteins
Sld3/Treslin. Structure 22, 1341-1347.

236.

Itou, H., Shirakihara, Y., and Araki, H. (2015) The quaternary structure of the eukaryotic DNA replication proteins Sld7 and Sld3. Acta Crystallogr D Biol
Crystallogr 71,1649-1656.

237.

Itou, H., Yagura, M., Shirakihara, Y., and Itoh, T. (2015) Structural basis for replication origin unwinding by an initiator primase of plasmid ColE2-P9:
duplex DNA unwinding by a single protein. J Biol Chem 290,3601-3611.

238.

Iwano, M., Igarashi, M., Tarutani, Y., Kaothien-Nakayama, P., Nakayama, H., Moriyama, H., Yakabe, R., Entani, T., Shimosato-Asano, H., Ueki, M.,
Tamiya, G., and Takayama, S. (2014). A pollen coat-inducible autoinhibited Ca2+-ATPase expressed in stigmatic papilla cells is required for compatible
pollination in the Brassicaceae. Plant Cell 26, 636-649.

239.

Iwasaki, M., Kuroda, J., Kawakami, K., and Wada, H. (2018). Epidermal regulation of bone morphogenesis through the development and regeneration of
osteoblasts in the zebrafish scale. Dev. Biol. 437, 105-119.

240.

Iwasato, T., and Erzurumlu, R.S. (2018). Development of tactile sensory circuits in the CNS. Curr. Opin. Neurobiol. 53, 66-75.

241.

Iwata, R., and Iwasato, T. (2016) In vitro Assay for Dendritic Spine Retraction of Hippocampal Neurons with Sparse Labeling Bio-Protocol 6, e1937.

242.

Iwata, R., Matsukawa, H., Yasuda, K., Mizuno, H., Itohara, S., and Iwasato, T. (2015) Developmental RacGAP alpha2-Chimaerin Signaling Is a Determinantof the Morphological Features of Dendritic Spines in Adulthood. J Neurosci 35,13728-13744.

243.

Iwata, R., Ohi, K., Kobayashi, Y., Masuda, A., Iwama, M., Yasuda, Y., Yamamori, H., Tanaka, M., Hashimoto, R., Itohara, S., and Iwasato, T. (2014).
RacGAP alpha2-chimaerin function in development adjusts cognitive ability in adulthood. Cell Rep. 8, 1257-1264.

244.

Izutsu, M., Toyoda, A., Fujiyama, A., Agata, K., and Fuse, N. (2015) Dynamics of Dark-Fly Genome Under Environmental Selections. G3 (Bethesda) 6,
365-376.

245.

Jia, D., Tamori, Y., Pyrowolakis, G., and Deng, W.M. (2014). Regulation of broad by the Notch pathway affects timing of follicle cell development. Dev.
Biol. 392, 52-61.

246.

Jia, N., Nakazawa, Y., Guo, C., Shimada, M., Sethi, M., Takahashi, Y., Ueda, H., and Nagayama, Y., Ogi, T. (2015) A rapid, comprehensive system forassaying DNA repair activity and cytotoxic effects of DNA-damaging reagents. Nat Protoc 10,12-24.

247.

Jia, S., Muto, A., Orisme, W., Henson, H.E., Parupalli, C., Ju, B., Baier, H., and Taylor, M.R. (2014). Zebrafish Cacna1fa is required for cone photoreceptor
function and synaptic ribbon formation. Hum. Mol. Genet. 23, 2981-2994.

248.

Jin, M., Pomp, O., Shinoda, T., Toba, S., Torisawa, T., Furuta, K., Oiwa, K., Yasunaga, T., Kitagawa, D., Matsumura, S., Miyata, T., Tan, T.T., Reversade,B., and Hirotsune, S. (2017). Katanin p80, NuMA and cytoplasmic dynein cooperate to control microtubule dynamics. Sci Rep 7, 39902.

249.

Jinam, T.A., Kanzawa-Kiriyama, H., and Saitou, N. (2015) Human genetic diversity in the Japanese Archipelago: dual structure and beyond. Genes Genet
Syst 90,147-152.

250.

Jinam, T.A., Kanzawa-Kiriyama, H., Inoue, I., Tokunaga, K., Omoto, K., and Saitou, N. (2015) Unique characteristics of the Ainu population in Northern
Japan. J Hum Genet 60,565-571.

251.

Jinam, T.A., Phipps, M.E., Aghakhanian, F., Majumder, P.P., Datar, F., Stoneking, M., Sawai, H., Nishida, N., Tokunaga, K., Kawamura, S., Omoto, K.,
and Saitou, N. (2017). Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. Genome Biol Evol 9,
2013-2022.

252.

Jong, L.W., Fujiwara, T., Nozaki, H., and Miyagishima, S.Y. (2017). Cell size for commitment to cell division and number of successive cell divisions in
multicellular volvocine green algae Tetrabaena socialis and Gonium pectorale. Proc Jpn Acad Ser B Phys Biol Sci 93, 832-840.

253.

Joseph, B., Kondo, S., and Lai, E.C. (2018). Short cryptic exons mediate recursive splicing in Drosophila. Nat. Struct. Mol. Biol. 25, 365-371.

254.

Kabayama, Y., Toh, H., Katanaya, A., Sakurai, T., Chuma, S., Kuramochi-Miyagawa, S., Saga, Y., Nakano, T., and Sasaki, H. (2017). Roles of MIWI, MILI
and PLD6 in small RNA regulation in mouse growing oocytes. Nucleic Acids Res 45, 5387-5398.

255.

Kadowaki, M., Fujimaru, Y., Taguchi, S., Ferdouse, J., Sawada, K., Kimura, Y., Terasawa, Y., Agrimi, G., Anai, T., Noguchi, H., Toyoda, A., Fujiyama,‑66‑

A., Akao, T., and Kitagaki, H. (2017). Chromosomal Aneuploidy Improves the Brewing Characteristics of Sake Yeast. Appl Environ Microbiol 83, e0162017.
256.

Kagawa, N., Hori, T., Hoki, Y., Hosoya, O., Tsutsui, K., Saga, Y., Sado, T., and Fukagawa, T. (2014). The CENP-O complex requirement varies among
different cell types. Chromosome Res. 22, 293-303.

257.

Kagoshima, H., and Kohara, Y. (2015) Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy18 in C. elegans. Dev Biol 399,325-336.

258.

Kajitani, R., Toshimoto, K., Noguchi, H., Toyoda, A., Ogura, Y., Okuno, M., Yabana, M., Harada, M., Nagayasu, E., Maruyama, H., Kohara, Y., Fujiyama,A., Hayashi, T., and Itoh, T. (2014). Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res.
24, 1384-1395.

259.

Kakioka, R., Muto, N., Takeshima, H., Gaje, A.C., Cruz, R.S., Alama, U.B., Guzman, A.M.T., Traifalgar, R.F.M., Babaran, R.P., Muda, O., et al. (2018).
Cryptic genetic divergence in Scolopsis taenioptera (Perciformes: Nemipteridae) in the western Pacific Ocean. Ichthyol. Res. 65, 92-100.

260.

Kamada, M., Hase, S., Sato, K., Toyoda, A., Fujiyama, A., and Sakakibara, Y. (2014). Whole genome complete resequencing of Bacillus subtilis natto bycombining long reads with high-quality short reads. PLoS One 9, e109999.

261.

Kamezaki, A., Sato, F., Aoki, K., Asakawa, K., Kawakami, K., Matsuzaki, F., and Sehara-Fujisawa, A. (2016) Visualization of Neuregulin 1 ectodomain
shedding reveals its local processing in vitro and in vivo. Sci Rep 6, 28873.

262.

Kamijyo, A., Yura, K., and Ogura, A. (2015) Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure.
Gene 555,73-79.

263.

Kamimura, Y., Tanaka, H., Kobayashi, Y., Shikanai, T., and Nishimura, Y. (2018). Chloroplast nucleoids as a transformable network revealed by live
imaging with a microfluidic device. Commun. Biol. 1, 47.

264.

Kan, L., Grozhik, A.V., Vedanayagam, J., Patil, D.P., Pang, N., Lim, K.S., Huang, Y.C., Joseph, B., Lin, C.J., Despic, V., Guo, J., Yan, D., Kondo, S., Deng,
W.M., Dedon, P.C., Jaffrey, S.R., and Lai, E.C. (2017). The m(6)A pathway facilitates sex determination in Drosophila. Nat Commun 8, 15737.

265.

Kanatani, S., Honda, T., Aramaki, M., Hayashi, K., Kubo, K., Ishida, M., Tanaka, D.H., Kawauchi, T., Sekine, K., Kusuzawa, S., Kawasaki, T., Hirata, T.,
Tabata, H., Uhlen, P., and Nakajima, K. (2015) The COUP-TFII/Neuropilin-2 is a molecular switch steering diencephalon-derived GABAergic neurons in
the developing mouse brain. Proc Natl Acad Sci U S A 112,E4985-94.

266.

Kanazawa, T., Era, A., Minamino, N., Shikano, Y., Fujimoto, M., Uemura, T., Nishihama, R., Yamato, K.T., Ishizaki, K., Nishiyama, T., Kohchi, T.,
Nakano, A., and Ueda, T. (2016) SNARE Molecules in Marchantia polymorpha: Unique and Conserved Features of the Membrane Fusion Machinery. Plant
Cell Physiol 57, 307-324.

267.

Kanda, N., Ichikawa, M., Ono, A., Toyoda, A., Fujiyama, A., Abe, J., Tsuchikane, Y., Nishiyama, T., and Sekimoto, H. (2017). CRISPR/Cas9-based
knockouts reveal that CpRLP1 is a negative regulator of the sex pheromone PR-IP in the Closterium peracerosum-strigosum-littorale complex. Sci Rep 7,17873.

268.

Kanesaki, Y., Hirose, M., Hirose, Y., Fujisawa, T., Nakamura, Y., Watanabe, S., Matsunaga, S., Uchida, H., and Murakami, A. (2018). Draft Genome
Sequence of the Nitrogen-Fixing and Hormogonia-Inducing Cyanobacterium Nostoc cycadae Strain WK-1, Isolated from the Coralloid Roots of Cycas
revoluta. Genome Announc. 6, e00021-18.

269.

Kanesaki, Y., Masutani, H., Sakanaka, M., Shiwa, Y., Fujisawa, T., Nakamura, Y., Yokota, A., Fukiya, S., Suzuki, T., and Yoshikawa, H. (2014). Complete
Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency. Genome Announcements 2, e01311-14.

270.

Kanno, K., Kokubo, H., Takahashi, A., Koide, T., and Ishiura, S. (2014). Enhanced prepulse inhibition and low sensitivity to a dopamine agonist in HESR1
knockout mice. J. Neurosci. Res. 92, 287-297.

271.

Kanzawa-Kiriyama, H., Kryukov, K., Jinam, T.A., Hosomichi, K., Saso, A., Suwa, G., Ueda, S., Yoneda, M., Tajima, A., Shinoda, K.I., Inoue, I., and Saitou,
N. (2017). A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet 62, 213-221.

272.

Karsch-Mizrachi, I., Takagi, T., Cochrane, G., International Nucleotide Sequence Database, and Collaboration (2018). The international nucleotide sequence
database collaboration. Nucleic Acids Res. 46, D48-D51.

273.

Katagiri, S., Akahori, M., Hayashi, T., Yoshitake, K., Gekka, T., Ikeo, K., Tsuneoka, H., and Iwata, T. (2014). Autosomal recessive cone-rod dystrophy
associated with compound heterozygous mutations in the EYS gene. Doc. Ophthalmol. 128, 211-217.

274.

Katagiri, S., Akahori, M., Sergeev, Y., Yoshitake, K., Ikeo, K., Furuno, M., Hayashi, T., Kondo, M., Ueno, S., Tsunoda, K., Shinoda, K., Kuniyoshi, K.,
Tsurusaki, Y., Matsumoto, N., Tsuneoka, H., and Iwata, T. (2014). Whole exome analysis identifies frequent CNGA1 mutations in Japanese population with
autosomal recessive retinitis pigmentosa. PLoS One 9, e108721.

275.

Katagiri, S., Hayashi, T., Akahori, M., Itabashi, T., Nishino, J., Yoshitake, K., Furuno, M., Ikeo, K., Okada, T., Tsuneoka, H., and Iwata, T. (2014). RHO
mutations (p.W126L and p.A346P) in two Japanese families with autosomal dominant retinitis pigmentosa. J. Ophthalmol. 2014, 210947.

276.

Katagiri, S., Hayashi, T., Kondo, M., Tsukitome, H., Yoshitake, K., Akahori, M., Ikeo, K., Tsuneoka, H., and Iwata, T. (2016) RPE65 Mutations in Two
Japanese Families with Leber Congenital Amaurosis. Ophthalmic Genet 37, 161-169.

277.

Katagiri, S., Hayashi, T., Yoshitake, K., Akahori, M., Ikeo, K., Gekka, T., Tsuneoka, H., and Iwata, T. (2016). Novel C8orf37 Mutations in Patients with
Early-onset Retinal Dystrophy, Macular Atrophy, Cataracts, and High Myopia. Ophthalmic Genet 37, 68-75.

278.

Katagiri, S., Hayashi, T., Yoshitake, K., Sergeev, Y., Akahori, M., Furuno, M., Nishino, J., Ikeo, K., Tsunoda, K., Tsuneoka, H., and Iwata, T. (2015)
Congenital Achromatopsia and Macular Atrophy Caused by a Novel Recessive PDE6C Mutation (p.E591K). Ophthalmic Genet 36,137-144.

279.

Kataoka, T., Tamura, M., Maeno, A., Wakana, S., and Shiroishi, T. (2017). Genetic Dissection of Trabecular Bone Structure with Mouse Intersubspecific‑67‑Consomic Strains. G3 (Bethesda) 7, 3449-3457.
280.

Katayama, Y., Sakamoto, T., Takanami, K., and Takei, Y. (2018). The Amphibious Mudskipper: A Unique Model Bridging the Gap of Central Actions ofOsmoregulatory Hormones Between Terrestrial and Aquatic Vertebrates. Front. Physiol. 9, 1112.

281.

Kato, H., Mori, H., Maruyama, F., Toyoda, A., Oshima, K., Endo, R., Fuchu, G., Miyakoshi, M., Dozono, A., Ohtsubo, Y., Nagata, Y., Hattori, M., Fujiyama,A., Kurokawa, K., and Tsuda, M. (2015) Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res
22,413-424.

282.

Kato, H., Ogawa, N., Ohtsubo, Y., Oshima, K., Toyoda, A., Mori, H., Nagata, Y., Kurokawa, K., Hattori, M., Fujiyama, A., and Tsuda, M. (2015) Complete
Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), Isolated from a Phenanthrene-Degrading Consortium.
Genome Announc 3,e00782.

283.

Kato, S., Ishii, A., Nishi, A., Kuriki, S., and Koide, T. (2014). Segregation of a QTL cluster for home-cage activity using a new mapping method based on
regression analysis of congenic mouse strains. Heredity (Edinb) 113, 416-423.

284.

Kato, S., Matsumoto, A., Yoshimura, K., Katsuki, T., Iwamoto, K., Kawahara, T., Mukai, Y., Tsuda, Y., Ishio, S., Nakamura, K., Moriwaki, K., Shiroishi,T., Gojobori, T., and Yoshimaru, H. (2014). Origins of Japanese flowering cherry (Prunus subgenus Cerasus) cultivars revealed using nuclear SSR markers.
Tree Genetics & Genomes 10, 477-487.

285.

Kato, Y., Katsuki, T., Kokubo, H., Masuda, A., and Saga, Y. (2016) Dazl is a target RNA suppressed by mammalian NANOS2 in sexually differentiating
male germ cells. Nat Commun 7, 11272.

286.

Kato, Y.S., Yagi, T., Harris, S.A., Ohki, S.Y., Yura, K., Shimizu, Y., Honda, S., Kamiya, R., Burgess, S.A., and Tanokura, M. (2014). Structure of the
microtubule-binding domain of flagellar dynein. Structure 22, 1628-1638.

287.

Katori, S., Noguchi-Katori, Y., Itohara, S., and Iwasato, T. (2017). Spinal RacGAP alpha-Chimaerin Is Required to Establish the Midline Barrier for Proper
Corticospinal Axon Guidance. J Neurosci 37, 7682-7699.

288.

Katori, S., Noguchi-Katori, Y., Okayama, A., Kawamura, Y., Luo, W., Sakimura, K., Hirabayashi, T., Iwasato, T., and Yagi, T. (2017). ProtocadherinalphaC2 is required for diffuse projections of serotonergic axons. Sci Rep 7, 15908.

289.

Kawafune, K., Hongoh, Y., Hamaji, T., Sakamoto, T., Kurata, T., Hirooka, S., Miyagishima, S.Y., and Nozaki, H. (2015) Two different rickettsial bacteria
invading Volvox carteri. PLoS One 10,e0116192.

290.

Kawai-Toyooka, H., Mori, T., Hamaji, T., Suzuki, M., Olson, B.J., Uemura, T., Ueda, T., Nakano, A., Toyoda, A., Fujiyama, A., and Nozaki, H. (2014).
Sex-specific posttranslational regulation of the gamete fusogen GCS1 in the isogamous volvocine alga Gonium pectorale. Eukaryot. Cell 13, 648-656.

291.

Kawai, M., Futagami, T., Toyoda, A., Takaki, Y., Nishi, S., Hori, S., Arai, W., Tsubouchi, T., Morono, Y., Uchiyama, I., Ito, T., Fujiyama, A., Inagaki, F.,
and Takami, H. (2014). High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary
metagenomes. Front. Microbiol. 5, 80.

292.

Kawajiri, M., Fujimoto, S., Yoshida, K., Yamahira, K., and Kitano, J. (2015) Genetic Architecture of the Variation in Male-Specific Ossified Processes on
the Anal Fins of Japanese Medaka. G3 (Bethesda) 5,2875-2884.

293.

Kawajiri, M., Yoshida, K., Fujimoto, S., Mokodongan, D.F., Ravinet, M., Kirkpatrick, M., Yamahira, K., and Kitano, J. (2014). Ontogenetic stage-specificquantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations. Mol. Ecol. 23, 52585275.

294.

Kawakami, K., and Murakami, Y. (2017). Preface to Vertebrate Brains: evolution, structures and functions. Dev Growth Differ 59, 160-162.

295.

Kawakami, K., Asakawa, K., Hibi, M., Itoh, M., Muto, A., and Wada, H. (2016) Gal4 Driver Transgenic Zebrafish: Powerful Tools to Study Developmental
Biology, Organogenesis, and Neuroscience. Adv Genet 95, 65-87.

296.

Kawakami, K., Largaespada, D.A., and Ivics, Z. (2017). Transposons As Tools for Functional Genomics in Vertebrate Models. Trends Genet 33, 784-801.

297.

Kawamoto, Y., Sasaki, A., Chandran, A., Hashiya, K., Ide, S., Bando, T., Maeshima, K., and Sugiyama, H. (2016) Targeting 24 bp within Telomere Repeat
Sequences with Tandem Tetramer Pyrrole-Imidazole Polyamide Probes. J Am Chem Soc, 14100-14107.

298.

Kawamoto, Y., Sasaki, A., Hashiya, K., Ide, S., Bando, T., Maeshima, K., and Sugiyama, H. (2015) Tandem trimer pyrrole-imidazole polyamide probes
targeting 18 base pairs in human telomere sequences. Chem. Sci., 6, 2307-2312.

299.

Kawanabe, T., Ishikura, S., Miyaji, N., Sasaki, T., Wu, L.M., Itabashi, E., Takada, S., Shimizu, M., Takasaki-Yasuda, T., Osabe, K., Peacock, W.J., Dennis,
E.S., and Fujimoto, R. (2016) Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci U S A 113, E6704-E6711.

300.

Kawano, S., Fujisawa, H., Takada, T., and Shiroishi, T. (2015) Sparse principal component regression with adaptive loading. Computational Statistics &Data Analysis 89,192-203.

301.

Kawano, S., Fujisawa, H., Takada, T., and Shiroishi, T. (2018). Sparse principal component regression for generalized linear models. Comput. Stat. Data
Anal. 124, 180-196.

302.

Kawano, T., Hosomichi, K., Inoue, I., Shimono, R., Onishi, S., Nakame, K., Kaji, T., Matsufuji, H., and Ieiri, S. (2017). Identification of a novel variant of
the RET proto-oncogene in a novel family with Hirschsprung's disease. Pediatr Surg Int 33, 1041-1046.

303.

Kawasaki, J., Kawamura, M., Ohsato, Y., Ito, J., and Nishigaki, K. (2017). Presence of a Shared 5'-Leader Sequence in Ancestral Human and MammalianRetroviruses and Its Transduction into Feline Leukemia Virus. J Virol 91, e00829-17.

304.

Kawasaki, T., and Sakai, N. (2016) Allogeneic transplantation of testicular hyperplasia in rag1 mutant zebrafish Bio-protocol 6, e1992.

305.

Kawasaki, T., Maeno, A., Shiroishi, T., and Sakai, N. (2017). Development and growth of organs in living whole embryo and larval grafts in zebrafish. Sci‑68‑Rep 7, 16508.
306.

Kawasaki, T., Siegfried, K.R., and Sakai, N. (2016) Differentiation of zebrafish spermatogonial stem cells to functional sperm in culture. Development 143,566-574.

307.

Kawashima, K., Matsumoto, T., and Akashi, H. (2016). Disease Outbreaks: Critical Biological Factors and Control Strategies. In Urban Resilience, (Cham:
Springer International Publishing), pp. 173-204.

308.

Kawashima, S., Katayama, T., Hatanaka, H., Kushida, T., and Takagi, T. (2018). NBDC RDF portal: a comprehensive repository for semantic data in life
sciences. Database (Oxford). 2018, bay123.

309.

Kawazura, T., Matsumoto, K., Kojima, K., Kato, F., Kanai, T., Niki, H., and Shiomi, D. (2017). Exclusion of assembled MreB by anionic phospholipids atcell poles confers cell polarity for bidirectional growth. Mol Microbiol 104, 472-486.

310.

Kikuchi, A., Nakazato, T., Ito, K., Nojima, Y., Yokoyama, T., Iwabuchi, K., Bono, H., Toyoda, A., Fujiyama, A., Sato, R., and Tabunoki, H. (2017).
Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes. BMC
Genomics 18, 83.

311.

Kim, J.M., To, T.K., Tanaka, M., Endo, T.A., Matsui, A., Ishida, J., Robertson, F.C., Toyoda, T., and Seki, M. (2014). Highly reproducible ChIP-on-chip
analysis to identify genome-wide protein binding and chromatin status in Arabidopsis thaliana. Methods Mol. Biol. 1062, 405-426.

312.

Kimura, A., Celani, A., Nagao, H., Stasevich, T., and Nakamura, K. (2015) Estimating cellular parameters through optimization procedures: elementary
principles and applications. Front Physiol 6,60.

313.

Kimura, K., Mamane, A., Sasaki, T., Sato, K., Takagi, J., Niwayama, R., Hufnagel, L., Shimamoto, Y., Joanny, J.F., Uchida, S., and Kimura, A. (2017).
Endoplasmic-reticulum-mediated microtubule alignment governs cytoplasmic streaming. Nat Cell Biol 19, 399-406.

314.

Kimura, T., Takehana, Y., and Naruse, K. (2017). pnp4a Is the Causal Gene of the Medaka Iridophore Mutant guanineless. G3 (Bethesda) 7, 1357-1363.

315.

Kinjo, S., Kiyomoto, M., Yamamoto, T., Ikeo, K., and Yaguchi, S. (2018). HpBase: A genome database of a sea urchin, Hemicentrotus pulcherrimus. Dev.
Growth Differ. 60, 174-182.

316.

Kinjo, S., Monma, N., Misu, S., Kitamura, N., Imoto, J., Yoshitake, K., Gojobori, T., and Ikeo, K. (2018). Maser: one-stop platform for NGS big data fromanalysis to visualization. Database (Oxford). 2018, bay027.

317.

Kishimoto, K., Washio, Y., Yoshiura, Y., Toyoda, A., Ueno, T., Fukuyama, H., Kato, K., and Kinoshita, M. (2018). Production of a breed of red sea bream
Pagrus major with an increase of skeletal muscle mass and reduced body length by genome editing with CRISPR/Cas9. Aquaculture 495, 415-427.

318.

Kitano, J., and Mori, S. (2016) Toward conservation of genetic and phenotypic diversity in Japanese sticklebacks. Genes Genet Syst 91, 77-84.

319.

Kitano, J., Ishikawa, A., and Lema, S.C. (2014). Integrated genomics approaches in evolutionary and ecological endocrinology. Adv. Exp. Med. Biol. 781,
299-319.

320.

Kitano, T., and Kim, C.G., Blancher, A., and Saitou, N. (2016) No Distinction of Orthology/Paralogy between Human and Chimpanzee Rh Blood Group
Genes. Genome Biol Evol 8, 519-527.

321.

Kitazumi, A., Pabuayon, I.C.M., Ohyanagi, H., Fujita, M., Osti, B., Shenton, M.R., Kakei, Y., Nakamura, Y., Brar, D.S., Kurata, N., et al. (2018). Potentialof Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation. Sci. Rep. 8, 16346.

322.

Knierim, E., Hirata, H., Wolf, N.I., Morales-Gonzalez, S., Schottmann, G., Tanaka, Y., Rudnik-Schoneborn, S., Orgeur, M., Zerres, K., Vogt, S., van, Riesen
A., Gill, E., Seifert, F., Zwirner, A., Kirschner, J., Goebel, H.H., Hubner, C., Stricker, S., Meierhofer, D., Stenzel, W., and Schuelke, M. (2016) Mutationsin Subunits of the Activating Signal Cointegrator 1 Complex Are Associated with Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures. Am J
Hum Genet 98, 473-489.

323.

Kobayashi, M., Nagasaki, H., Garcia, V., Just, D., Bres, C., Mauxion, J.P., Le, Paslier M.C., Brunel, D., Suda, K., Minakuchi, Y., Toyoda, A., Fujiyama,A., Toyoshima, H., Suzuki, T., Igarashi, K., Rothan, C., Kaminuma, E., Nakamura, Y., Yano, K., and Aoki, K. (2014). Genome-wide analysis of intraspecific
DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum). Plant Cell Physiol. 55, 445-454.

324.

Kobayashi, T., Iwamoto, Y., Takashima, K., Isomura, A., Kosodo, Y., Kawakami, K., Nishioka, T., Kaibuchi, K., and Kageyama, R. (2015) Deubiquitinating
enzymes regulate Hes1 stability and neuronal differentiation. FEBS J 282,2411-2423.

325.

Kobiyama, A., Ikeo, K., Reza, M.S., Rashid, J., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., Sato, S., Ogata, T., et al. (2018). Metagenome-based
diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay. Gene 665, 149-154.

326.

Koblmüller, S., Albertson, R.C., Genner, M.J., Sefc, K.M., and Takahashi, T. (2015) Preface: Advances in cichlid research: behavior, ecology, andevolutionary biology. Hydrobiologia 748,1-5.

327.

Kochi, T., Shimizu, M., Shirakami, Y., Yoshimi, K., Kuramoto, T., Tanaka, T., Moriwaki, H. (2015) Utility of Apc-mutant rats with a colitis-associatedcolon carcinogenesis model for chemoprevention studies. Eur J Cancer Prev 24,180-187.

328.

Kodama, Y., Mashima, J., Kosuge, T., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., and Takagi, T. (2018). DNA Data Bank of Japan: 30th
anniversary. Nucleic Acids Res. 46, D30-D35.

329.

Kodama, Y., Mashima, J., Kosuge, T., Katayama, T., Fujisawa, T., Kaminuma, E., Ogasawara, O., Okubo, K., Takagi, T., and Nakamura, Y. (2015) The
DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. Nucleic Acids Res 43,D18-22.

330.

Koga, H., Fujitani, H., Morino, Y., Miyamoto, N., Tsuchimoto, J., Shibata, T.F., Nozawa, M., Shigenobu, S., Ogura, A., Tachibana, K., Kiyomoto, M.,
Amemiya, S., and Wada, H. (2016) Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton. PLoS One 11,
e0149067.

‑69‑

331.

Kohn, A.B., Sanford, R.S., Yoshida, M.A., and Moroz, L.L. (2015) Parallel Evolution and Lineage-Specific Expansion of RNA Editing in Ctenophores.
Integr Comp Biol 55,1111-1120.

332.

Komaki, S., Igawa, T., Nozawa, M., Lin, S.M., Oumi, S., and Sumida, M. (2014). Development and characterization of 14 microsatellite markers for
Buergeria japonica (Amphibia, Anura, Rhacophoridae). Genes Genet. Syst. 89, 35-39.

333.

Komaki, S., Lin, S.M., Nozawa, M., Oumi, S., Sumida, M., and Igawa, T. (2017). Fine-scale demographic processes resulting from multiple overseas
colonization events of the Japanese stream tree frog, Buergeria japonica. Journal of Biogeography 44, 1586-1597.

334.

Komiya, R., Nonomura, K. (2014). Isolation and bioinformatic analyses of small RNAs interacting with germ cell-specific argonaute in rice. Methods Mol.
Biol. 1093, 235-245.

335.

Komiya, R., Ohyanagi, H., Niihama, M., Watanabe, T., Nakano, M., Kurata, N., and Nonomura, K. (2014). Rice germline-specific Argonaute MEL1 protein
binds to phasiRNAs generated from more than 700 lincRNAs. Plant J. 78, 385-397.

336.

Komiyama, T., Iwama, H., Osada, N., Nakamura, Y., Kobayashi, H., Tateno, Y., and Gojobori, T. (2014). Dopamine receptor genes and evolutionary
differentiation in the domestication of fighting cocks and long-crowing chickens. PLoS One 9, e101778.

337.

Kondo, M., Sekine, T., Miyakoshi, T., Kitajima, K., Egawa, S., Seki, R., Abe, G., and Tamura, K. (2018). Flight feather development: its early specialization
during embryogenesis. Zool. Lett. 4, 2.

338.

Kondo, S. (2014). New horizons in genome engineering of Drosophila melanogaster. Genes Genet. Syst. 89, 3-8.

339.

Kondo, S., Vedanayagam, J., Mohammed, J., Eizadshenass, S., Kan, L., Pang, N., Aradhya, R., Siepel, A., Steinhauer, J., and Lai, E.C. (2017). New genes
often acquire male-specific functions but rarely become essential in Drosophila. Genes Dev 31, 1841-1846.

340.

Konno, Y., Nagaoka, S., Kimura, I., Takahashi Ueda, M., Kumata, R., Ito, J., Nakagawa, S., Kobayashi, T., Koyanagi, Y., and Sato, K. (2018). A naturally
occurring feline APOBEC3 variant that loses anti-lentiviral activity by lacking two amino acid residues. J. Gen. Virol. 99, 704-709.

341.

Kono, H., Tamura, M., Osada, N., Suzuki, H., Abe, K., Moriwaki, K., Ohta, K., and Shiroishi, T. (2014). Prdm9 polymorphism unveils mouse evolutionary
tracks. DNA Res. 21, 315-326.

342.

Kosaka, T., Toh, H., Fujiyama, A., Sakaki, Y., Watanabe, K., Meng, X.Y., Hanada, S., and Toyoda, A. (2014). Physiological and genetic basis for selfaggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2. Environ. Microbiol. Rep. 6, 268-277.

343.

Kosuge, T., Mashima, J., Kodama, Y., Fujisawa, T., Kaminuma, E., Ogasawara, O., Okubo, K., Takagi, T., and Nakamura, Y. (2014). DDBJ progress report:
a new submission system for leading to a correct annotation. Nucleic Acids Res. 42, D44-9.

344.

Kotani, Y., Morito, D., Yamazaki, S., Ogino, K., Kawakami, K., Takashima, S., Hirata, H., and Nagata, K. (2015) Neuromuscular regulation in zebrafish
by a large AAA+ ATPase/ubiquitin ligase, mysterin/RNF213. Sci Rep 5,16161.

345.

Koyanagi, M., Wada, S., Kawano-Yamashita, E., Hara, Y., Kuraku, S., Kosaka, S., Kawakami, K., Tamotsu, S., Tsukamoto, H., Shichida, Y., and Terakita,
A. (2015) Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions. BMC Biol 13,73.

346.

Kraus, C., Schiffer, P.H., Kagoshima, H., Hiraki, H., Vogt, T., Kroiher, M., Kohara, Y., and Schierenberg, E. (2017). Differences in the genetic control ofearly egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. Evodevo 8, 16.

347.

Kubo, F.C., Yasui, Y., Kumamaru, T., Sato, Y., Hirano, H.Y. (2016). Genetic analysis of rice mutants responsible for narrow leaf phenotype and reduced
vein number. Genes Genet. Syst., 91, 235-240.

348.

Kubo, T., Takashi, T., Ashikari, M., Yoshimura, A., and Kurata, N. (2016) Two Tightly Linked Genes at the hsa1 Locus Cause Both F1 and F2 Hybrid
Sterility in Rice. Mol Plant 9, 221-232.

349.

Kubo, T., Yoshimura, A., and Kurata, N. (2016) Pollen Killer Gene S35 Function Requires Interaction with an Activator That Maps Close to S24, Another
Pollen Killer Gene in Rice. G3 (Bethesda) 6, 1459-1468.

350.

Kubota, S., Iwasaki, T., Hanada, K., Nagano, A.J., Fujiyama, A., Toyoda, A., Sugano, S., Suzuki, Y., Hikosaka, K., Ito, M., and Morinaga, S. (2015) A
Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species. PLoS Genet 11,e1005361.

351.

Kubota, Y., Tsuyama, K., Takabayashi, Y., Haruta, N., Maruyama, R., Iida, N., and Sugimoto, A. (2014). The PAF1 complex is involved in embryonic
epidermal morphogenesis in Caenorhabditis elegans. Dev. Biol. 391, 43-53.

352.

Kudo, T., Kobiyama, A., Rashid, J., Reza, M.S., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., Ikeo, K., Sato, S., et al. (2018). Seasonal changes in theabundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis. Gene 665,
174-184.

353.

Kudo, Y., Nikaido, M., Kondo, A., Suzuki, H., Yoshida, K., Kikuchi, K., and Okada, N. (2015) A microsatellite-based genetic linkage map and putative
sex-determining genomic regions in Lake Victoria cichlids. Gene 560,156-164.

354.

Kudoh, T., Takahashi, M., Osabe, T., Toyoda, A., Hirakawa, H., Suzuki, Y., Ohmido, N., and Onodera, Y. (2018). Molecular insights into the nonrecombining nature of the spinach male-determining region. Mol. Genet. Genomics 293, 557-568.

355.

Kuga, T., Nie, H., Kazami, T., Satoh, M., Matsushita, K., Nomura, F., Maeshima, K., Nakayama, Y., and Tomonaga, T. (2014). Lamin B2 prevents
chromosome instability by ensuring proper mitotic chromosome segregation. Oncogenesis 3, e94.

356.

Kume, M., and Kitano, J. (2017). Genetic and stable isotope analyses of threespine stickleback from the Bering and Chukchi seas. Ichthyological Research64, 478-480.

357.

Kume, M., Mori, S., Kitano, J., Sumi, T., and Nishida, S. (2018). Impact of the huge 2011 Tohoku-oki tsunami on the phenotypes and genotypes of Japanese
coastal threespine stickleback populations. Sci. Rep. 8, 1684.

‑70‑

358.

Kuniyoshi, K., Ikeo, K., Sakuramoto, H., Furuno, M., Yoshitake, K., Hatsukawa, Y., Nakao, A., Tsunoda, K., Kusaka, S., Shimomura, Y., and Iwata, T.
(2015) Novel nonsense and splice site mutations in CRB1 gene in two Japanese patients with early-onset retinal dystrophy. Doc Ophthalmol 130,49-55.

359.

Kuniyoshi, K., Sakuramoto, H., Yoshitake, K., Abe, K., Ikeo, K., Furuno, M., Tsunoda, K., Kusaka, S., Shimomura, Y., and Iwata, T. (2014). Longitudinalclinical course of three Japanese patients with Leber congenital amaurosis/early-onset retinal dystrophy with RDH12 mutation. Doc. Ophthalmol. 128, 219228.

360.

Kuniyoshi, K., Sakuramoto, H., Yoshitake, K., Ikeo, K., Furuno, M., Tsunoda, K., Kusaka, S., Shimomura, Y., and Iwata, T. (2015) Reduced rod
electroretinograms in carrier parents of two Japanese siblings with autosomal recessive retinitis pigmentosa associated with PDE6B gene mutations. Doc
Ophthalmol 131,71-79.

361.

Kuppuraj, G., Kruise, D., and Yura, K. (2014). Conformational behavior of flavin adenine dinucleotide: conserved stereochemistry in bound and free states.
J. Phys. Chem. B 118, 13486-13497.

362.

Kuramoto, T., Yokoe, M., Tanaka, D., Yuri, A., Nishitani, A., Higuchi, Y., Yoshimi, K., Tanaka, M., Kuwamura, M., Hiai, H., Kabashima, K., and Serikawa,T. (2015) Atopic dermatitis-like skin lesions with IgE hyperproduction and pruritus in KFRS4/Kyo rats. J Dermatol Sci 80,116-123.

363.

Kurata, N. (2015) Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentiallyexpressed genes. BMC Genomics 16,1099.

364.

Kurata, T., Nakanishi, S., Hashimoto, M., Taoka, M., Yamazaki, Y., Isobe, T., and Kato, J. (2015) Novel essential gene Involved in 16S rRNA processingin Escherichia coli. J Mol Biol 427,955-965.

365.

Kuriki, S., Harushima, Y., Fujisawa, H., and Kurata, N. (2014). Approximate tail probabilities of the maximum of a chi-square field on multi-dimensionallattice points and their applications to detection of loci interactions Ann. Inst. Stat. Math. 66, 725-757.

366.

Kurosaki, T., Miyoshi, K., Myers, J.R., and Maquat, L.E. (2018). NMD-degradome sequencing reveals ribosome-bound intermediates with 3’-end nontemplated nucleotides. Nat. Struct. Mol. Biol. 25, 940-950.

367.

Kurusu, T., Koyano, T., Hanamata, S., Kubo, T., Noguchi, Y., Yagi, C., Nagata, N., Yamamoto, T., Ohnishi, T., Okazaki, Y., Kitahata, N., Ando, D.,
Ishikawa, M., Wada, S., Miyao, A., Hirochika, H., Shimada, H., Makino, A., Saito, K., Ishida, H., Kinoshita, T., Kurata, N., and Kuchitsu, K. (2014).
OsATG7 is required for autophagy-dependent lipid metabolism in rice postmeiotic anther development. Autophagy 10, 878-888.

368.

Kusakabe, M., Ishikawa, A., and Kitano, J. (2014). Relaxin-related gene expression differs between anadromous and stream-resident stickleback(Gasterosteus aculeatus) following seawater transfer. Gen. Comp. Endocrinol. 205, 197-206.

369.

Kusakabe, M., Ishikawa, A., Ravinet, M., Yoshida, K., Makino, T., Toyoda, A., Fujiyama, A., and Kitano, J. (2017). Genetic basis for variation in salinity
tolerance between stickleback ecotypes. Mol Ecol 26, 304-319.

370.

Lacroix, B., Bourdages, K.G., Dorn, J.F., Ihara, S., Sherwood, D.R., Maddox, P.S., and Maddox, A.S. (2014). In situ imaging in C. elegans reveals
developmental regulation of microtubule dynamics. Dev. Cell. 29, 203-216.

371.

Lai, Z., Tsugawa, H., Wohlgemuth, G., Mehta, S., Mueller, M., Zheng, Y., Ogiwara, A., Meissen, J., Showalter, M., Takeuchi, K., et al. (2018). Identifying
metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nat. Methods 15, 53-56.

372.

Lal, P., Tanabe, H., Suster, M.L., Ailani, D., Kotani, Y., Muto, A., Itoh, M., Iwasaki, M., Wada, H., Yaksi, E., et al. (2018). Identification of a neuronal
population in the telencephalon essential for fear conditioning in zebrafish. BMC Biol. 16, 45.

373.

Laurie, L.E., Kokubo, H., Nakamura, M., Saga, Y., and Funato, N. (2016) The Transcription Factor Hand1 Is Involved In Runx2-Ihh-Regulated
Endochondral Ossification. PLoS One 11, e0150263.

374.

Leacock, S., Syed, P., James, V.M., Bode, A., Kawakami, K., Keramidas, A., Suster, M., Lynch, J.W., and Harvey, R.J. (2018). Structure/Function Studiesof the Į4 Subunit Reveal Evolutionary Loss of a GlyR Subtype Involved in Startle and Escape Responses. Front. Mol. Neurosci. 11, 23.

375.

Li, D., Ono, N., Sato, T., Sugiura, T., Altaf-Ul-Amin, M., Ohta, D., Suzuki, H., Arita, M., Tanaka, K., Ma, Z., and Kanaya, S. (2015) Targeted Integrationof RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species. Plant Cell Physiol 56,843-851.

376.

Li, D., Sinha, T., Ajima, R., Seo, H.S., Yamaguchi, T.P., and Wang, J. (2016) Spatial regulation of cell cohesion by Wnt5a during second heart fieldprogenitor deployment. Dev Biol 412, 18-31.

377.

Liang, Z., Zickler, D., Prentiss, M., Chang, F.S., Witz, G., Maeshima, K., and Kleckner, N. (2015) Chromosomes Progress to Metaphase in Multiple Discrete
Steps via Global Compaction/Expansion Cycles. Cell 161,1124-1137.

378.

Lin, C.J., Wen, J., Bejarano, F., Hu, F., Bortolamiol-Becet, D., Kan, L., Sanfilippo, P., Kondo, S., and Lai, E.C. (2017). Characterization of a TUTase/RNase
complex required for Drosophila gametogenesis. RNA 23, 284-296.

379.

Liu, H., and Nonomura, K.I. (2016) A wide reprogramming of histone H3 modifications during male meiosis I in rice is dependent on the Argonaute protein
MEL1. J Cell Sci 129, 3553-3561.

380.

Liu, Q.X., Wang, X.F., Ikeo, K., Hirose, S., Gehring, W.J., and Gojobori, T. (2014). Evolutionarily conserved transcription factor Apontic controls the G1/S
progression by inducing cyclin E during eye development. Proc. Natl. Acad. Sci. USA 111, 9497-9502.

381.

Lopez-Baez, J.C., Simpson, D.J., LLeras Forero, L., Zeng, Z., Brunsdon, H., Salzano, A., Brombin, A., Wyatt, C., Rybski, W., Huitema, L.F.A., et al. (2018).
Wilms Tumor 1b defines a wound-specific sheath cell subpopulation associated with notochord repair. Elife 7, e30657.

382.

Luo, W., Mizuno, H., Iwata, R., Nakazawa, S., Yasuda, K., Itohara, S., and Iwasato, T. (2016) Supernova: A Versatile Vector System for Single-Cell
Labeling and Gene Function Studies in vivo. Sci Rep 6, 35747.

383.

Maeno, A., and Tsuda, K. (2018). Micro-computed Tomography to Visualize Vascular Networks in Maize Stems. BIO-PROTOCOL 8, e2682.

‑71‑

384.

Maeno, S., Tanizawa, Y., Kanesaki, Y., Kubota, E., Kumar, H., Dicks, L., Salminen, S., Nakagawa, J., Arita, M., and Endo, A. (2016) Genomic
characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation. Syst Appl Microbiol 39, 516-526.

385.

Maeshima, K., Funakoshi, T., and Imamoto, N. (2014). Cell-fusion method to visualize interphase nuclear pore formation. Methods Cell Biol. 122, 239-254.

386.

Maeshima, K., Hibino, K., and Hudson, D.F. (2018). Condensins under the microscope. J. Cell Biol. 217, 2229-2231.

387.

Maeshima, K., Ide, S., Hibino, K., and Sasai, M. (2016) Liquid-like behavior of chromatin. Curr Opin Genet Dev 37, 36-45.

388.

Maeshima, K., Imai, R., Hikima, T., and Joti, Y. (2014). Chromatin structure revealed by X-ray scattering analysis and computational modeling. Methods
70,154-161.

389.

Maeshima, K., Imai, R., Tamura, S., and Nozaki, T. (2014). Chromatin as dynamic 10-nm fibers. Chromosoma 123, 225-237.

390.

Maeshima, K., Kaizu, K., Tamura, S., Nozaki, T., Kokubo, T., and Takahashi, K. (2015) The physical size of transcription factors is key to transcriptional
regulation in chromatin domains. J Phys Condens Matter 27,064116.

391.

Maeshima, K., Matsuda, T., Shindo, Y., Imamura, H., Tamura, S., Imai, R., Kawakami, S., Nagashima, R., Soga, T., Noji, H., et al. (2018). A Transient Risein Free Mg2+ Ions Released from ATP-Mg Hydrolysis Contributes to Mitotic Chromosome Condensation. Curr. Biol. 28, 444-451.

392.

Maeshima, K., Nishino, Y., and Joti, Y. (2014). Irregular organization in the human chromosomes revealed by X-ray scattering. SPring-8 Research Frontiers
2013, 32-33.

393.

Maeshima, K., Rogge, R., Tamura, S., Joti, Y., Hikima, T., Szerlong, H., Krause, C., Herman, J., Seidel, E., DeLuca, J., Ishikawa, T., and Hansen, J.C.
(2016) Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J 35, 1115-1132.

394.

Maeshima, K., Tamura, S., and Shimamoto, Y. (2018). Chromatin as a nuclear spring. Biophys. Physicobiology 15, 189-195.

395.

Mahmoudi, Saber M., and Saitou, N. (2017). Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development.
Genome Biol Evol 9, 2037-2048.

396.

Mallik, S., Akashi, H., and Kundu, S. (2015) Assembly constraints drive co-evolution among ribosomal constituents. Nucleic Acids Res 43,5352-5363.

397.

Manning, S.A., Dent, L.G., Kondo, S., Zhao, Z.W., Plachta, N., and Harvey, K.F. (2018). Dynamic Fluctuations in Subcellular Localization of the Hippo
Pathway Effector Yorkie In Vivo. Curr. Biol. 28, 1651-1660.

398.

Maruyama S, Kurokawa K, Ebisuzaki T, Sawaki Y, Suda K, and Santosh M. (2018). Nine requirements for the origin of Earth's life: Not at the hydrothermalvent, but in a nuclear geyser system. Geoscience Front., doi: 10.1016/j.gsf.2018.09.011.

399.

Maruyama, K., Kawasaki, T., Hamaguchi, M., Hashimoto, M., Furu, M., Ito, H., Fujii, T., Takemura, N., Karuppuchamy, T., Kondo, T., Kawasaki, T.,
Fukasaka, M., Misawa, T., Saitoh, T., Suzuki, Y., Martino, M.M., Kumagai, Y., and Akira, S. (2016) Bone-protective Functions of Netrin 1 Protein. J Biol
Chem 291, 23854-23868.

400.

Maruyama, S., Kurokawa, K., and Isozaki, Y. (2018). Overview of the Special Issue “The Hadean World (Part I): The Birth of a Habitable Trinity Planet.”
J. Geogr. (Chigaku Zasshi) 127, 573-576.

401.

Mashima, J., Kodama, Y., Fujisawa, T., Katayama, T., Okuda, Y., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., and Takagi, T. (2017). DNA
Data Bank of Japan. Nucleic Acids Res 45, D25-D31.

402.

Mashima, J., Kodama, Y., Kosuge, T., Fujisawa, T., Katayama, T., Nagasaki, H., Okuda, Y., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., andTakagi, T. (2016) DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res 44, D51-57.

403.

Masui, R., Takahata, Y., Inoue, M., Iio, Y., Okanishi, H., Kim, K., Nakagawa, N., Yura, K., and Kuramitsu, S. (2014). Structural insights of post-translational
modification sites in the proteome of Thermus thermophilus. J. Struct. Funct. Genomics 15, 137-151.

404.

Masumoto, H., and Matsuyama, S. (2018). The combination of NAD+-dependent deacetylase gene deletion and the interruption of gluconeogenesis causes
increased glucose metabolism in budding yeast. PLoS One 13, e0194942.

405.

Matsubara, Y., Kato, T., Kashimada, K., Tanaka, H., Zhi, Z., Ichinose, S., Mizutani, S., Morio, T., Chiba, T., Ito, Y., Saga, Y., Takada, S., and Asahara, H.
(2015) TALEN-Mediated Gene Disruption on Y Chromosome Reveals Critical Role of EIF2S3Y in Mouse Spermatogenesis. Stem Cells Dev 24,1164-1170.

406.

Matsuda, K., Yoshida, M., Kawakami, K., Hibi, M., and Shimizu, T. (2017). Granule cells control recovery from classical conditioned fear responses in thezebrafish cerebellum. Sci Rep 7, 11865.

407.

Matsui, A., Mizunashi, K., Tanaka, M., Kaminuma, E., Nguyen, A.H., Nakajima, M., Kim, J.M., Nguyen, D.V., Toyoda, T., and Seki, M. (2014). tasiRNAARF pathway moderates floral architecture in arabidopsis plants subjected to drought stress. Biomed Res. Int. 2014, 303451.

408.

Matsui, M., Yokoyama, T., Nemoto, K., Kumagai, T., Terai, G., Arita, M., Machida, M., and Shibata, T. (2015) Genome Sequence of Fungal Species
No.11243, Which Produces the Antifungal Antibiotic FR901469. Genome Announc 3,e00118.

409.

Matsuki, T., Yahagi, K., Mori, H., Matsumoto, H., Hara, T., Tajima, S., Ogawa, E., Kodama, H., Yamamoto, K., Yamada, T., Matsumoto, S., and Kurokawa,
K. (2016) A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nat Commun 7, 11939.

410.

Matsumoto, T., Akashi, H., and Yang, Z. (2015) Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide
Substitution. Genetics 200,873-890.

411.

Matsumoto, T., and Akashi, H. (2018). Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation
Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations. G3 (Bethesda). 8, 1755-1769.

412.

Matsumoto, T., and Kitano, J. (2016) The intricate relationship between sexually antagonistic selection and the evolution of sex chromosome fusions. J
Theor Biol 404, 97-108.

‑72‑

413.

Matsumoto, T., John, A., Baeza-Centurion, P., Li, B., and Akashi, H. (2016) Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino
Acid Fixations. Mol Biol Evol 33, 1580-1589.

414.

Matsumoto, T., Mineta, K., Osada, N., and Araki, H. (2015) An Individual-Based Diploid Model Predicts Limited Conditions Under Which Stochastic Gene
Expression Becomes Advantageous. Front Genet 6,336.

415.

Matsumoto, T., Terai, Y., Okada, N., and Tachida, H. (2014). Sensory drive speciation and patterns of variation at selectively neutral genes. Evolutionary
Ecology 28, 591- 609.

416.

Matsumoto, T., Yasumoto, A.A., Nitta, K., Hirota, S.K., Yahara, T., and Tachida, H. (2015) Difference in flowering time can initiate speciation of nocturnally
flowering species. J Theor Biol 370,61-71.

417.

Matsumoto, T., Yoshida, K., and Kitano, J. (2017). Contribution of gene flow to the evolution of recombination suppression in sex chromosomes. J Theor
Biol 431, 25-31.

418.

Matsumoto, Y., Goto, T., Nishino, J., Nakaoka, H., Tanave, A., Takano-Shimizu, T., Mott, R.F., and Koide, T. (2017). Selective breeding and selection
mapping using a novel wild-derived heterogeneous stock of mice revealed two closely-linked loci for tameness. Sci Rep 7, 4607.

419.

Matsumura, S., Kojidani, T., Kamioka, Y., Uchida, S., Haraguchi, T., Kimura, A., and Toyoshima, F. (2016) Interphase adhesion geometry is transmitted to
an internal regulator for spindle orientation via caveolin-1 Nat Commun. 7, 11858.

420.

Matsunami, K., Nishida, N., Kaneko, N., Ikeo, K., Toyo-Oka, L., Takeuchi, H., Matsuura, K., Tamori, A., Nomura, H., Yoshiji, H., Imamura, M., Masaki,N., Hayakawa, T., Ide, T., Shimada, N., Ikeda, F., Hino, K., Nishiguchi, S., Okuse, C., Nojiri, S., Sawamoto, K., Tokunaga, K., Joh, T., and Tanaka, Y.
(2016) Genome-Wide Association Study Identifies ZNF354C Variants Associated with Depression from Interferon-Based Therapy for Chronic Hepatitis C.
PLoS One 11, e0164418.

421.

Matsunami, M., Kitano, J., Kishida, O., Michimae, H., Miura, T., and Nishimura, K. (2015) Transcriptome analysis of predator- and prey-induced phenotypic
plasticity in the Hokkaido salamander (Hynobius retardatus). Mol Ecol 24,3064-3076.

422.

Matsuno, M., Horiuchi, J., Yuasa, Y., Ofusa, K., Miyashita, T., Masuda, T., and Saitoe, M. (2015) Long-term memory formation in Drosophila requires
training-dependent glial transcription. J Neurosci 35,5557-5565.

423.

Matsuo, H., Nakayama, A., Sakiyama, M., Chiba, T., Shimizu, S., Kawamura, Y., Nakashima, H., Nakamura, T., Takada, Y., Oikawa, Y., Takada, T.,
Nakaoka, H., Abe, J., Inoue, H., Wakai, K., Kawai, S., Guang, Y., Nakagawa, H., Ito, T., Niwa, K., Yamamoto, K., Sakurai, Y., Suzuki, H., Hosoya, T.,
Ichida, K., Shimizu, T., and Shinomiya, N. (2014). ABCG2 dysfunction causes hyperuricemia due to both renal urate underexcretion and renal urate overload.
Sci. Rep. 4, 3755.

424.

Matsuo, H., Yamamoto, K., Nakaoka, H., Nakayama, A., Sakiyama, M., Chiba, T., Takahashi, A., Nakamura, T., Nakashima, H., Takada, Y., Danjoh, I.,
Shimizu, S., Abe, J., Kawamura, Y., Terashige, S., Ogata, H., Tatsukawa, S., Yin, G., Okada, R., Morita, E., Naito, M., Tokumasu, A., Onoue, H., Iwaya,
K., Ito, T., Takada, T., Inoue, K., Kato, Y., Nakamura, Y., Sakurai, Y., Suzuki, H., Kanai, Y., Hosoya, T., Hamajima, N., Inoue, I., Kubo, M., Ichida, K.,
Ooyama, H., Shimizu, T., and Shinomiya, N. (2016) Genome-wide association study of clinically defined gout identifies multiple risk loci and its association
with clinical subtypes. Ann Rheum Dis 75, 652-659.

425.

Matsuoka, S., Gupta, S., Suzuki, E., Hiromi, Y., and Asaoka, M. (2014). gone early, a novel germline factor, ensures the proper size of the stem cell precursor
pool in the Drosophila ovary. PLoS One 9, e113423.

426.

Matsuura, K., Sawai, H., Ikeo, K., Ogawa, S., Iio, E., Isogawa, M., Shimada, N., Komori, A., Toyoda, H., Kumada, T., Namisaki, T., Yoshiji, H., Sakamoto,N., Nakagawa, M., Asahina, Y., Kurosaki, M., Izumi, N., Enomoto, N., Kusakabe, A., Kajiwara, E., Itoh, Y., Ide, T., Tamori, A., Matsubara, M., Kawada,N., Shirabe, K., Tomita, E., Honda, M., Kaneko, S., Nishina, S., Suetsugu, A., Hiasa, Y., Watanabe, H., Genda, T., Sakaida, I., Nishiguchi, S., Takaguchi,K., Tanaka, E., Sugihara, J., Shimada, M., Kondo, Y., Kawai, Y., Kojima, K., Nagasaki, M., Tokunaga, K., and Tanaka, Y. (2017). Genome-Wide
Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection.
Gastroenterology 152, 1383-1394.

427.

Matsuura, R., Ashikawa, T., Nozaki, Y., and Kitagawa, D. (2016) LIN-41 inactivation leads to delayed centrosome elimination and abnormal chromosome
behavior during female meiosis in Caenorhabditis elegans. Mol Biol Cell 27, 799-811.

428.

Mauthner, S.E., Hwang, R.Y., Lewis, A.H., Xiao, Q., Tsubouchi, A., Wang, Y., Honjo, K., Skene, J.H., Grandl, J., and Tracey, W.D. Jr (2014). Balboa binds
to pickpocket in vivo and is required for mechanical nociception in Drosophila larvae. Curr. Biol. 24, 2920-2925.

429.

McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J.V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente
Castro, C., et al. (2018). The prehistoric peopling of Southeast Asia. Science 361, 88-92.

430.

MetaSUB, International Consortium. (2016) The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium
inaugural meeting report. Microbiome 4, 24.

431.

Minami, A., Yano, K., Gamuyao, R., Nagai, K., Kuroha, T., Ayano, M., Nakamori, M., Koike, M., Kondo, Y., Niimi, Y., et al. (2018). Time-Course
Transcriptomics Analysis Reveals Key Responses of Submerged Deepwater Rice to Flooding. Plant Physiol. 176, 3081-3102.

432.

Minamikawa, M.F., Nonaka, K., Kaminuma, E., Kajiya-Kanegae, H., Onogi, A., Goto, S., Yoshioka, T., Imai, A., Hamada, H., Hayashi, T., Matsumoto, S.,
Katayose, Y., Toyoda, A., Fujiyama, A., Nakamura, Y., Shimizu, T., and Iwata, H. (2017). Genome-wide association study and genomic prediction in citrus:
Potential of genomics-assisted breeding for fruit quality traits. Sci Rep 7, 4721.

433.

Minamino, M., Tei, S., Negishi, L., Kanemaki, M.T., Yoshimura, A., Sutani, T., Bando, M., and Shirahige, K. (2018). Temporal Regulation of ESCO2
Degradation by the MCM Complex, the CUL4-DDB1-VPRBP Complex, and the Anaphase-Promoting Complex. Curr. Biol. 28, 2665-2672.

434.

Minegishi, K., Hashimoto, M., Ajima, R., Takaoka, K., Shinohara, K., Ikawa, Y., Nishimura, H., McMahon, A.P., Willert, K., Okada, Y., Sasaki, H., Shi,
D., Fujimori, T., Ohtsuka, T., Igarashi, Y., Yamaguchi, T.P., Shimono, A., Shiratori, H., and Hamada, H. (2017). A Wnt5 Activity Asymmetry andIntercellular Signaling via PCP Proteins Polarize Node Cells for Left-Right Symmetry Breaking. Dev Cell 40, 439-452.e4.

‑73‑

435.

Minegishi, Y., Sheng, X., Yoshitake, K., Sergeev, Y., Iejima, D., Shibagaki, Y., Monma, N., Ikeo, K., Furuno, M., Zhuang, W., Liu, Y., Rong, W., Hattori,
S., and Iwata, T. (2016) CCT2 Mutations Evoke Leber Congenital Amaurosis due to Chaperone Complex Instability. Sci Rep 6, 33742.

436.

Mineta, K., Matsumoto, T., Osada, N., and Araki, H. (2015) Population genetics of non-genetic traits: evolutionary roles of stochasticity in gene expression.
Gene 562,16-21.

437.

Mita, S., de, Monasterio-Schrader P., Funfschilling, U., Kawasaki, T., Mizuno, H., Iwasato, T., Nave, K.A., Werner, H.B., and Hirata, T. (2015) Transcallosal
Projections Require Glycoprotein M6-Dependent Neurite Growth and Guidance. Cereb Cortex 25,4111-4125.

438.

Mito, T., Ishizaki, H., Suzuki, M., Morishima, H., Ota, A., Ishikawa, K., Nakada, K., Maeno, A., Shiroishi, T., and Hayashi, J. (2015) Transmitochondrial
mito-miceDelta and mtDNA mutator mice, but not aged mice, share the same spectrum of musculoskeletal disorders. Biochem Biophys Res Commun
456,933-937.

439.

Mitsunaga, S., Hosomichi, K., Okudaira, Y., Nakaoka, H., Suzuki, Y., Kuwana, M., Sato, S., Kaneko, Y., Homma, Y., Oka, A., Shiina, T., Inoko, H., andInoue, I. (2015) Aggregation of rare/low-frequency variants of the mitochondria respiratory chain-related proteins in rheumatoid arthritis patients. J Hum
Genet 60,449-454.

440.

Miura, H., Inoko, H., Tanaka, M., Nakaoka, H., Kimura, M., Gurumurthy, C.B., Sato, M., and Ohtsuka, M. (2015) Assessment of Artificial MiRNA
Architectures for Higher Knockdown Efficiencies without the Undesired Effects in Mice. PLoS One 10,e0135919.

441.

Miwa, S., Kihira, E., Yoshioka, A., Nakasone, K., Okamoto, S., Hatano, M., Igarashi, M., Eguchi, Y., Kato, A., Ichikawa, N., Sekine, M., Fujita, N.,
Kanesaki, Y., Yoshikawa, H., and Utsumi, R. (2016) Identification of the Three Genes Involved in Controlling Production of a Phytotoxin Tropolone in
Burkholderia plantarii. J Bacteriol 198, 1604-1609.

442.

Miyagi, R., Akiyama, N., Osada, N., and Takahashi, A. (2015) Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation
variation in Drosophila melanogaster. Mol Ecol 24,5829-5841.

443.

Miyagishima, S.Y. (2017). Chloroplast division: A handshake across membranes. Nat Plants 3, 17025.

444.

Miyagishima, S.Y., Fujiwara, T., Sumiya, N., Hirooka, S., Nakano, A., Kabeya, Y., and Nakamura, M. (2014). Translation-independent circadian control of
the cell cycle in a unicellular photosynthetic eukaryote. Nat. Commun. 5, 3807.

445.

Miyagishima, S.Y., Kabeya, Y., Sugita, C., Sugita, M., and Fujiwara, T. (2014). DipM is required for peptidoglycan hydrolysis during chloroplast division.
BMC Plant Biol. 14, 57.

446.

Miyagishima, S.Y., Nakamura, M., and Uzuka, A., Era, A. (2014). FtsZ-less prokaryotic cell division as well as FtsZ- and dynamin-less chloroplast andnon-photosynthetic plastid division. Front. Plant Sci. 5, 459.

447.

Miyamoto, K., Fujita, M., Shenton, M.R., Akashi, S., Sugawara, C., Sakai, A., Horie, K., Hasegawa, M., Kawaide, H., Mitsuhashi, W., Nojiri, H., Yamane,
H., Kurata, N., Okada, K., and Toyomasu, T. (2016) Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice. Plant J 87, 293-304.

448.

Miyamoto, M., Motooka, D., Gotoh, K., Imai, T., Yoshitake, K., Goto, N., Iida, T., Yasunaga, T., Horii, T., Arakawa, K., Kasahara, M., and Nakamura, S.
(2014). Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. BMC Genomics 15, 699.

449.

Miyamoto, N., Yoshida, M.A., Koga, H., and Fujiwara, Y. (2017). Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm
Osedax japonicus inferred from transcriptome and gene expression analyses. BMC Evol Biol 17, 17.

450.

Miyasaka, Y., Shitara, H., Suzuki, S., Yoshimoto, S., Seki, Y., Ohshiba, Y., Okumura, K., Taya, C., Tokano, H., Kitamura, K., Takada, T., Hibino, H.,
Shiroishi, T., Kominami, R., Yonekawa, H., and Kikkawa, Y. (2016) Heterozygous mutation of Ush1g/Sans in mice causes early-onset progressive hearing
loss, which is recovered by reconstituting the strain-specific mutation in Cdh23. Hum Mol Genet 25, 2045-2059.

451.

Miyasaka, Y., Uno, Y., Yoshimi, K., Kunihiro, Y., Yoshimura, T., Tanaka, T., Ishikubo, H., Hiraoka, Y., Takemoto, N., Tanaka, T., et al. (2018). CLICK:
one-step generation of conditional knockout mice. BMC Genomics 19, 318.

452.

Miyazaki, K.W., Miyazaki, K., Tanaka, K.F., Yamanaka, A., Takahashi, A., Tabuchi, S., and Doya, K. (2014). Optogenetic activation of dorsal raphe
serotonin neurons enhances patience for future rewards. Curr. Biol. 24, 2033-2040.

453.

Miyazaki, S., Sato, Y., Asano, T., Nagamura, Y., and Nonomura, K. (2015) Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosisexpressed genes containing U-rich RNA consensus sequences in the 3'-UTR. Plant Mol Biol 89,293-307.

454.

Miyazawa-Onami, M., Araki, H., and Tanaka, S. (2017). Pre-initiation complex assembly functions as a molecular switch that splits the Mcm2-7 double
hexamer. EMBO Rep 18, 1752-1761.

455.

Mizoguchi, T., Kawakami, K., and Itoh, M. (2016) Zebrafish lines expressing UAS-driven red probes for monitoring cytoskeletal dynamics. Genesis 54,
483-489.

456.

Mizuno, H., Ikezoe, K., Nakazawa, S., Sato, T., Kitamura, K., and Iwasato, T. (2018). Patchwork-Type Spontaneous Activity in Neonatal Barrel Cortex
Layer 4 Transmitted via Thalamocortical Projections. Cell Rep. 22, 123-135.

457.

Mizuno, H., Luo, W., Tarusawa, E., Saito, Y.M., Sato, T., Yoshimura, Y., Itohara, S., and Iwasato, T. (2014). NMDAR-regulated dynamics of layer 4
neuronal dendrites during thalamocortical reorganization in neonates. Neuron 82, 365-379.

458.

Mizuno, H., Nakazawa, S., and Iwasato, T. (2018). In Vivo Two-photon Imaging of Cortical Neurons in Neonatal Mice. J. Vis. Exp 140, e58340.

459.

Mizuno, R., Kamioka, Y., Kabashima, K., Imajo, M., Sumiyama, K., Nakasho, E., Ito, T., Hamazaki, Y., Okuchi, Y., Sakai, Y., and Kiyokawa, E., Matsuda,
M. (2014). In vivo imaging reveals PKA regulation of ERK activity during neutrophil recruitment to inflamed intestines. J. Exp. Med. 211, 1123-1136.

460.

Mizuta, Y., and Tsuda, K. (2018). Three-Dimensional Multiphoton Imaging of Transcription Factor by ClearSee. Methods Mol. Biol. 1830, 257-268.

461.

Mizutani, H., Sugawara, H., Buckle, A.M., Sangawa, T., Miyazono, K.I., Ohtsuka, J., Nagata, K., Shojima, T., Nosaki, S., Xu, Y., Wang, D., Hu, X.,‑74‑

Tanokura, M., and Yura, K. (2017). REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding. BMC Struct Biol 17, 4.
462.

Mochizuki, T., Tanizawa, Y., Fujisawa, T., Ohta, T., Nikoh, N., Shimizu, T., Toyoda, A., Fujiyama, A., Kurata, N., Nagasaki, H., Kaminuma, E., andNakamura, Y. (2017). DNApod: DNA polymorphism annotation database from next-generation sequence read archives. PLoS One 12, e0172269.

463.

Mokodongan, D.F., Montenegro, J., Mochida, K., Fujimoto, S., Ishikawa, A., Kakioka, R., Yong, L., Mulis, Hadiaty, R.K., Mandagi, I.F., et al. (2018).
Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae). Mol. Phylogenet. Evol.
118, 194-203.

464.

Monden, Y., Fujii, N., Yamaguchi, K., Ikeo, K., Nakazawa, Y., Waki, T., Hirashima, K., Uchimura, Y., and Tahara, M. (2014). Efficient screening of longterminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site. Genome 57, 245-252.

465.

Monma, N., Gojobori, T., and Ikeo, K. (2014). Human genome network platform: a resource for TFRN analysis. Methods Mol. Biol. 1164, 147-162.

466.

Monteiro, D.C., Patel, V., Bartlett, C.P., Nozaki, S., Grant, T.D., Gowdy, J.A., Thompson, G.S., Kalverda, A.P., Snell, E.H., Niki, H., Pearson, A.R., andWebb, M.E. (2015) The structure of the PanD/PanZ protein complex reveals negative feedback regulation of pantothenate biosynthesis by coenzyme A.
Chem Biol 22,492-503.

467.

Moreno-Juan, V., Filipchuk, A., Anton-Bolanos, N., Mezzera, C., Gezelius, H., Andres, B., Rodriguez-Malmierca, L., Susin, R., Schaad, O., Iwasato, T.,
Schule, R., Rutlin, M., Nelson, S., Ducret, S., Valdeolmillos, M., Rijli, F.M., and Lopez-Bendito, G. (2017). Prenatal thalamic waves regulate cortical area
size prior to sensory processing. Nat Commun 8, 14172.

468.

Mori, H., Maruyama, F., Kato, H., Toyoda, A., Dozono, A., Ohtsubo, Y., Nagata, Y., Fujiyama, A., Tsuda, M., and Kurokawa, K. (2014). Design andexperimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify
eukaryotic rRNA genes. DNA Res. 21, 217-227.

469.

Mori, H., Maruyama, T., Yano, M., Yamada, T., and Kurokawa, K. (2018). VITCOMIC2: visualization tool for the phylogenetic composition of microbialcommunities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. BMC Syst. Biol. 12, 30.

470.

Mori, T., Hosomichi, K., Chiga, M., Mandai, S., Nakaoka, H., Sohara, E., Okado, T., Rai, T., Sasaki, S., Inoue, I., and Uchida, S. (2017). Comprehensive
genetic testing approach for major inherited kidney diseases, using next-generation sequencing with a custom panel. Clin Exp Nephrol 21, 63-75.

471.

Mori, T., Igawa, T., Tamiya, G., Miyagishima, S.Y., and Berger, F. (2014). Gamete attachment requires GEX2 for successful fertilization in Arabidopsis.
Curr. Biol. 24, 170-175.

472.

Morimoto, K., and Tamori, Y. (2017). Induction and Diagnosis of Tumors in Drosophila Imaginal Disc Epithelia. J Vis Exp.

473.

Morita, Y., Andersen, P., Hotta, A., Tsukahara, Y., Sasagawa, N., Hayashida, N., Koga, C., Nishikawa, M., Saga, Y., Evans, S.M., Koshiba-Takeuchi, K.,
Nishinakamura, R., Yoshida, Y., Kwon, C., and Takeuchi, J.K. (2016) Sall1 transiently marks undifferentiated heart precursors and regulates their fate. J
Mol Cell Cardiol 92, 158-162.

474.

Moriya, H., Inoue, I., Ikeuchi, M., Ishii, N., and Motojima, M. (2014). Survey of attitudes of Jjapanese women toward genetic/genomic research. Tissue andData Banking 9, 29-38.

475.

Moriyama, Y., Ito, F., Takeda, H., Yano, T., Okabe, M., Kuraku, S., Keeley, F.W., and Koshiba-Takeuchi, K. (2016) Evolution of the fish heart by
sub/neofunctionalization of an elastin gene. Nat Commun 7, 10397.

476.

Morrissey, M.A., Jayadev, R., Miley, G.R., Blebea, C.A., Chi, Q., Ihara, S., and Sherwood, D.R. (2016) SPARC Promotes Cell Invasion In Vivo byDecreasing Type IV Collagen Levels in the Basement Membrane. PLoS Genet 12, e1005905.

477.

Mouri, K., Sagai, T., Maeno, A., Amano, T., Toyoda, A., and Shiroishi, T. (2018). Enhancer adoption caused by genomic insertion elicits interdigital Shh
expression and syndactyly in mouse. Proc. Natl. Acad. Sci. U. S. A. 115, 1021-1026.

478.

Mukaida, S., Ogawa, T., Ohishi, K., Tanizawa, Y., Ohta, D., and Arita, M. (2016) The effect of rapamycin on biodiesel-producing protist Euglena gracilis.
Biosci Biotechnol Biochem 80, 1223-1229.

479.

Murakami, T., Segawa, T., Takeuchi, N., Barcaza Sepúlveda, G., Labarca, P., Kohshima, S., and Hongoh, Y. (2018). Metagenomic analyses highlight thesymbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community. Environ. Microbiol. 20, 4170-4183.

480.

Murayama Y, Samora CP., Kurokawa Y., Iwasaki H., and Uhlmann F. (2018). Establishment of DNA-DNA Interactions by the Cohesin Ring. Cell. 173,
465-77.

481.

Murayama, Y. (2018). DNA entry, exit and second DNA capture by cohesin: insights from biochemical experiments. Nucleus 9, 492-502.

482.

Muto N, Takeshima H., Traifalgar, R.F.M., and Motomura H, Muto F. (2017). Rapid and cost-effective molecular identification of the three mackerel speciesof the genus Rastrelliger (Perciformes: Scombridae) using PCR-RFLP analysis. Marine Biodiversity 47, 609-611.

483.

Muto-Fujita, A., Takemoto, K., Kanaya, S., Nakazato, T., Tokimatsu, T., Matsumoto, N., Kono, M., Chubachi, Y., Ozaki, K., and Kotera, M. (2017). Data
integration aids understanding of butterfly-host plant networks. Sci Rep 7, 43368.

484.

Muto, A., and Kawakami, K. (2018). Ablation of a Neuronal Population Using a Two-photon Laser and Its Assessment Using Calcium Imaging and
Behavioral Recording in Zebrafish Larvae. J. Vis. Exp. 136, e57485.

485.

Muto, A., Lal, P., Ailani, D., Abe, G., Itoh, M., and Kawakami, K. (2017). Activation of the hypothalamic feeding centre upon visual prey detection. Nat
Commun 8, 15029.

486.

Muto, N., Alama, U.B., Kakioka, R., Babaran, R.P., and Motomura, H. (2017). First record of Lutjanus madras (Perciformes: Lutjanidae) from the Pacific
Ocean, with comments on its intraspecific morphological variation. Cybium 41, 295-298.

487.

Nabeshima, Y., Washida, M., Tamura, M., Maeno, A., Ohnishi, M., Shiroishi, T., Imura, A., Razzaque, M.S., and Nabeshima, Y. (2014). Calpain 1 inhibitor‑75‑

BDA-410 ameliorates alpha-klotho-deficiency phenotypes resembling human aging-related syndromes. Sci. Rep. 4, 5847.
488.

Nagai, S., Hida, K., Urushizaki, S., Onitsuka, G., Yasuike, M., Nakamura, Y., Fujiwara, A., Tajimi, S., Kimoto, K., Kobayashi, T., Gojobori, T., and Ototake,M. (2016) Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based
technique. Gene 576, 667-675.

489.

Nagashima, Y., Tsugawa, S., Mochizuki, A., Sasaki, T., Fukuda, H., and Oda, Y. (2018). A Rho-based reaction-diffusion system governs cell wall patterning
in metaxylem vessels. Sci. Rep. 8, 11542.

490.

Nagayama, H., Matsumoto, Y., Tanave, A., Nihei, M., Goto, T., and Koide, T. (2018). Measuring Active and Passive Tameness Separately in Mice. J. Vis.
Exp. 138, e58048.

491.

Nagpal, H., and Fukagawa, T. (2016) Kinetochore assembly and function through the cell cycle. Chromosoma 125, 645-659.

492.

Nagpal, H., Hori, T., Furukawa, A., Sugase, K., Osakabe, A., Kurumizaka, H., and Fukagawa, T. (2015) Dynamic changes in CCAN organization through
CENP-C during cell-cycle progression. Mol Biol Cell 26,3768-3776.

493.

Nakabachi, A., Ishida, K., Hongoh, Y., Ohkuma, M., and Miyagishima, S.Y. (2014). Aphid gene of bacterial origin encodes a protein transported to an
obligate endosymbiont. Curr. Biol. 24, R640-1.

494.

Nakai, R., Baba, T., Niki, H., Nishijima, M., and Naganuma, T. (2015) Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of thefamily Microbacteriaceae, isolated from river water. Int J Syst Evol Microbiol 65, 4072-4079.

495.

Nakai, R., Fujisawa, T., Nakamura, Y., Baba, T., Nishijima, M., Karray, F., Sayadi, S., Isoda, H., Naganuma, T., and Niki, H. (2016) Genome sequence andoverview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. Stand Genomic Sci 11, 90.

496.

Nakai, R., Fujisawa, T., Nakamura, Y., Nishide, H., Uchiyama, I., Baba, T., Toyoda, A., Fujiyama, A., Naganuma, T., and Niki, H. (2016) Complete Genome
Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water. Genome Announc 4, e0061600616.

497.

Nakai, Y., and Naganuma, T. (2015) Oligoflexia, the newest class of the phylum Proteobacteria, consisting of only one cultured species and uncultured
bacterial phylotypes from diverse habitats. Phyrogenetics and Evolutionary Biology 3,100141-.

498.

Nakamura, Y., Yamamoto, N., Kino, Y., Yamamoto, N., Kamei, S., Mori, H., Kurokawa, K., and Nakashima, N. (2016) Establishment of a multi-species
biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl Microbiol Biotechnol 100, 7263-7279.

499.

Nakamura, Y., Yasuike, M., Nishiki, I., Iwasaki, Y., Fujiwara, A., Kawato, Y., Nakai, T., Nagai, S., Kobayashi, T., Gojobori, T., and Ototake, M. (2016) VGAP: Viral genome assembly pipeline. Gene 576, 676-680.

500.

Nakanaga, K., Ogura, Y., Toyoda, A., Yoshida, M., Fukano, H., Fujiwara, N., Miyamoto, Y., Nakata, N., Kazumi, Y., Maeda, S., et al. (2018). Naturally
occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic. Sci. Rep. 8, 8218.

501.

Nakano, H., Miyazawa, H., Maeno, A., Shiroishi, T., Kakui, K., Koyanagi, R., Kanda, M., Satoh, N., Omori, A., and Kohtsuka, H. (2017). A new speciesof Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella. BMC Evol Biol 17, 245.

502.

Nakaoka, H., and Inoue, I. (2015) Distribution of HLA haplotypes across Japanese Archipelago: similarity, difference and admixture. J Hum Genet 60,683690.

503.

Nakaoka, H., Gurumurthy, A., Hayano, T., Ahmadloo, S., Omer, W.H., Yoshihara, K., Yamamoto, A., Kurose, K., Enomoto, T., Akira, S., Hosomichi, K.,
and Inoue, I. (2016) Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PLoS Genet 12, e1005893.

504.

Nakaoka, H., Tajima, A., Yoneyama, T., Hosomichi, K., Kasuya, H., Mizutani, T., and Inoue, I. (2014). Gene expression profiling reveals distinct molecularsignatures associated with the rupture of intracranial aneurysm. Stroke 45, 2239-2245.

505.

Nakaoka, Y., Kimura, A., Tani, T., and Goshima, G. (2015) Cytoplasmic nucleation and atypical branching nucleation generate endoplasmic microtubulesin Physcomitrella patens. Plant Cell 27,228-242.

506.

Nakayama, A., Matsuo, H., Nakaoka, H., Nakamura, T., Nakashima, H., Takada, Y., Oikawa, Y., Takada, T., Sakiyama, M., Shimizu, S., Kawamura, Y.,
Chiba, T., Abe, J., Wakai, K., Kawai, S., Okada, R., Tamura, T., Shichijo, Y., Akashi, A., Suzuki, H., Hosoya, T., Sakurai, Y., Ichida, K., and Shinomiya,N. (2014). Common dysfunctional variants of ABCG2 have stronger impact on hyperuricemia progression than typical environmental risk factors. Sci. Rep.
4, 5227.

507.

Nakayama, A., Nakaoka, H., Yamamoto, K., Sakiyama, M., Shaukat, A., Toyoda, Y., Okada, Y., Kamatani, Y., Nakamura, T., Takada, T., Inoue, K.,
Yasujima, T., Yuasa, H., Shirahama, Y., Nakashima, H., Shimizu, S., Higashino, T., Kawamura, Y., Ogata, H., Kawaguchi, M., Ohkawa, Y., Danjoh, I.,
Tokumasu, A., Ooyama, K., Ito, T., Kondo, T., Wakai, K., Stiburkova, B., Pavelka, K., Stamp, L.K., Dalbeth, N., Sakurai, Y., Suzuki, H., Hosoyamada, M.,
Fujimori, S., Yokoo, T., Hosoya, T., Inoue, I., Takahashi, A., Kubo, M., Ooyama, H., Shimizu, T., Ichida, K., Shinomiya, N., Merriman, T.R., and Matsuo,
H. (2017). GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes. Ann Rheum Dis 76,
869-877.

508.

Nakayama, M., Suzuki, E., Tsunoda, S., and Hama, C. (2016) The Matrix Proteins Hasp and Hig Exhibit Segregated Distribution within Synaptic Clefts andPlay Distinct Roles in Synaptogenesis. J Neurosci 36, 590-606.

509.

Nakayama, S., Arima, K., Kawai, K., Mohri, K., Inui, C., Sugano, W., Koba, H., Tamada, K., Nakata, Y.J., Kishimoto, K., Arai-Shindo, M., Kojima, C.,
Matsumoto, T., Fujimori, T., Agata, K., and Funayama, N. (2015) Dynamic Transport and Cementation of Skeletal Elements Build Up the Pole-and-Beam
Structured Skeleton of Sponges. Curr Biol 25,2549-2554.

510.

Nakazawa, S., Mizuno, H., and Iwasato, T. (2018). Differential dynamics of cortical neuron dendritic trees revealed by long-term in vivo imaging in neonates.
Nat. Commun. 9, 3106.

‑76‑

511.

Naruse, M., Takahashi, H., Kurata, N., and Ito, Y. (2018). Cytokinin-induced expression of OSH1 in a shoot-regenerating rice callus. Plant Biotechnol. 35,
267-272.

512.

Natsume, T., and Kanemaki, M.T. (2017). Conditional Degrons for Controlling Protein Expression at the Protein Level. Annu Rev Genet 51, 83-102.

513.

Natsume, T., Kiyomitsu, T., Saga, Y., and Kanemaki, M.T. (2016) Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short
Homology Donors. Cell Rep 15, 210-218.

514.

Natsume, T., Nishimura, K., Minocherhomji, S., Bhowmick, R., Hickson, I.D., and Kanemaki, M.T. (2017). Acute inactivation of the replicative helicase in
human cells triggers MCM8-9-dependent DNA synthesis. Genes Dev 31, 816-829.

515.

Ngai, M.Y., and Saitou, N. (2016) The effect of perfection status on mutation rates of microsatellites in primates ANTHROPOLOGICAL SCIENCE 124,
85-92.

516.

Niihama, M., Mochizuki, M., Kurata, N., and Nonomura, K. (2015) PCR-based INDEL markers co-dominant between Oryza sativa, japonica cultivars andclosely-related wild Oryza species. Breed Sci 65,357-361.

517.

Niki, H. (2014). Schizosaccharomyces japonicus: the fission yeast is a fusion of yeast and hyphae. Yeast 31, 83-90.

518.

Niki, H. (2017). Open and Closed Questions about Open and Closed SMC. Structure 25, 569-570.

519.

Niki, H., and Yano, K. (2016) In vitro topological loading of bacterial condensin MukB on DNA, preferentially single-stranded DNA rather than doublestranded DNA. Sci Rep 6, 29469.

520.

Ninomiya, Y., Zhao, W., and Saga, Y. (2016) GBIQ: a non-arbitrary, non-biased method for quantification of fluorescent images. Sci Rep 6, 26454.

521.

Nishibuchi, I., Suzuki, H., Kinomura, A., Sun, J., Liu, N.A., Horikoshi, Y., Shima, H., Kusakabe, M., Harata, M., Fukagawa, T., Ikura, T., Ishida, T., Nagata,Y., and Tashiro, S. (2014). Reorganization of damaged chromatin by the exchange of histone variant H2A.Z-2. Int. J. Radiat. Oncol. Biol. Phys. 89, 736744.

522.

Nishihara, H., Kobayashi, N., Kimura-Yoshida, C., Yan, K., Bormuth, O., Ding, Q., Nakanishi, A., Sasaki, T., Hirakawa, M., Sumiyama, K., Furuta, Y.,
Tarabykin, V., Matsuo, I., and Okada, N. (2016) Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in
the Mammalian Secondary Palate. PLoS Genet 12, e1006380.

523.

Nishikawa, H., Iijima, T., Kajitani, R., Yamaguchi, J., Ando, T., Suzuki, Y., Sugano, S., Fujiyama, A., Kosugi, S., Hirakawa, H., Tabata, S., Ozaki, K.,
Morimoto, H., Ihara, K., Obara, M., Hori, H., Itoh, T., and Fujiwara, H. (2015) A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly.
Nat Genet 47,405-409.

524.

Nishimura, K., and Kanemaki, M.T. (2014). Rapid Depletion of Budding Yeast Proteins via the Fusion of an Auxin-Inducible Degron (AID). Curr. Protoc.
Cell Biol. 64, 20.9.1-20.9.16.

525.

Nishimura, T., Herpin, A., Kimura, T., Hara, I., Kawasaki, T., Nakamura, S., Yamamoto, Y., Saito, T.L., Yoshimura, J., Morishita, S., Tsukahara, T.,
Kobayashi, S., Naruse, K., Shigenobu, S., Sakai, N., Schartl, M., and Tanaka, M. (2014). Analysis of a novel gene, Sdgc, reveals sex chromosome-dependent
differences of medaka germ cells prior to gonad formation. Development 141, 3363-3369.

526.

Nishimura, T., Yamada, K., Fujimori, C., Kikuchi, M., Kawasaki, T., Siegfried, K.R., Sakai, N., and Tanaka, M. (2018). Germ cells in the teleost fish medaka
have an inherent feminizing effect. PLoS Genet. 14, e1007259.

527.

Nishino, J., Sugiyama, M., Nishida, N., Tokunaga, K., Mizokami, M., and Mano, S. (2014). The interaction of a single-nucleotide polymorphism with age
on response to interferon-alpha and ribavirin therapy in female patients with hepatitis C infection. J. Med. Virol. 86, 1130-1133.

528.

Nishioka, K., Wang, X.-F., Miyazaki, H., Soejima, H., and Hirose, S. (2018). Mbf1 ensures Polycomb silencing by protecting E(z) mRNA from degradation
by Pacman. Development 145, dev162461.

529.

Nishiyama, E., Higashi, K., Mori, H., Suda, K., Nakamura, H., Omori, S., Maruyama, S., Hongoh, Y., and Kurokawa, K. (2018). The Relationship Between
Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.
Front. Bioeng. Biotechnol. 6, 202.

530.

Nishiyama, T., Sakayama, H., de Vries, J., Buschmann, H., Saint-Marcoux, D., Ullrich, K.K., Haas, F.B., Vanderstraeten, L., Becker, D., Lang, D., et al.
(2018). The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization. Cell 174, 448-464.e24.

531.

Niwayama, R., Nagao, H., Kitajima, T.S., Hufnagel, L., Shinohara, K., Higuchi, T., Ishikawa, T., and Kimura, A. (2016) Bayesian Inference of Forces
Causing Cytoplasmic Streaming in Caenorhabditis elegans Embryos and Mouse Oocytes. PLoS One 11, e0159917.

532.

Nobusawa, T., Hori, K., Mori, H., Kurokawa, K., and Ohta, H. (2017). Differently localized lysophosphatidic acid acyltransferases crucial for triacylglycerol
biosynthesis in the oleaginous alga Nannochloropsis. Plant J 90, 547-559.

533.

Noguchi, K., Ishikawa, R., Kawaguchi, M., Miyoshi, K., Kawasaki, T., Hirata, T., Fukui, M., Kuratani, S., Tanaka, M., and Murakami, Y. (2017). Expression
patterns of Sema3A in developing amniote limbs: With reference to the diversification of peripheral nerve innervation. Dev Growth Differ 59, 270-285.

534.

Nomura, T., and Hirata, T. (2016). The neocortical homologues in nonmammalian amniotes: bridging the hierarchical concepts of homology throughcomparative neurogenesis. In: Kaas, I (ed.), Evolution of Nervous Systems, 2 edition, vol. 2, pp.195-204.

535.

Nonomura, K.I. (2018). Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction. Plant Reprod. 31, 21-29.

536.

Nozaki, S., Furuya, K., and Niki, H. (2018). The Ras1-Cdc42 pathway is involved in hyphal development of Schizosaccharomyces japonicus. FEMS Yeast
Res. 18, foy031.

537.

Nozaki, T., Imai, R., Tamura, S., and Maeshima, K. (2014). Single nucleosome imaging in living human cells. Cytologia 79, 1-2.

538.

Nozaki, T., Imai, R., Tanbo, M., Nagashima, R., Tamura, S., Tani, T., Joti, Y., Tomita, M., Hibino, K., Kanemaki, M.T., Wendt, K.S., Okada, Y., Nagai, T.,‑77‑and Maeshima, K. (2017). Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging. Mol Cell 67, 282-293.e7.
539.

Nozawa, M., Fujimi, M., Iwamoto, C., Onizuka, K., Fukuda, N., Ikeo, K., and Gojobori, T. (2016) Evolutionary Transitions of MicroRNA-Target Pairs.
Genome Biol Evol 8, 1621-1633.

540.

Nozawa, M., Fukuda, N., Ikeo, K., and Gojobori, T. (2014). Tissue- and stage-dependent dosage compensation on the neo-X chromosome in Drosophila
pseudoobscura. Mol. Biol. Evol. 31, 614-624.

541.

Nozawa, M., Ikeo, K., and Gojobori, T. (2018). Gene-by-Gene or Localized Dosage Compensation on the Neo-X Chromosome in Drosophila miranda.
Genome Biol. Evol. 10, 1875-1881.

542.

Nozawa, M., Onizuka, K., Fujimi, M., Ikeo, K., and Gojobori, T. (2016) Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda.
Nat Commun 7, 13659.

543.

Nozu, K., Minamikawa, S., Yamada, S., Oka, M., Yanagita, M., Morisada, N., Fujinaga, S., Nagano, C., Gotoh, Y., Takahashi, E., Morishita, T., Yamamura,T., Ninchoji, T., Kaito, H., Morioka, I., Nakanishi, K., Vorechovsky, I., and Iijima, K. (2017). Characterization of contiguous gene deletions in COL4A6
and COL4A5 in Alport syndrome-diffuse leiomyomatosis. J Hum Genet 62, 733-735.

544.

Oda, Y. (2015) Cortical microtubule rearrangements and cell wall patterning. Front Plant Sci 6, 236.

545.

Oda, Y. (2018). Emerging roles of cortical microtubule-membrane interactions. J. Plant Res. 131, 5-14.

546.

Oda, Y., Fukuda, H. (2014). Emerging roles of small GTPases in secondary cell wall development. Front. Plant Sci. 5, 428.

547.

Oda, Y., Iida, Y., Nagashima, Y., Sugiyama, Y., and Fukuda, H. (2015) Novel coiled-coil proteins regulate exocyst association with cortical microtubulesin xylem cells via the conserved oligomeric golgi-complex 2 protein. Plant Cell Physiol 56,277-286.

548.

Odaka, Y.S., Tohmonda, T., Toyoda, A., and Aruga, J. (2018). An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3. Sci. Rep. 8, 14954.

549.

Ode, K.L., Ukai, H., Susaki, E.A., Narumi, R., Matsumoto, K., Hara, J., Koide, N., Abe, T., Kanemaki, M.T., Kiyonari, H., and Ueda, H.R. (2017). KnockoutRescue Embryonic Stem Cell-Derived Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1. Mol Cell 65, 176-190.

550.

Ogawa, T., Furuhashi, T., Okazawa, A., Nakai, R., Nakazawa, M., Kind, T., Fiehn, O., Kanaya, S., Arita, M., and Ohta, D. (2014). Exploration of polar lipid
accumulation profiles in Euglena gracilis using LipidBlast, an MS/MS spectral library constructed in silico. Biosci. Biotechnol. Biochem. 78, 14-18.

551.

Ogino, K., Low, S.E., Yamada, K., Saint-Amant, L., Zhou, W., Muto, A., Asakawa, K., Nakai, J., Kawakami, K., Kuwada, J.Y., and Hirata, H. (2015) RING
finger protein 121 facilitates the degradation and membrane localization of voltage-gated sodium channels. Proc Natl Acad Sci U S A 112,2859-2864.

552.

Ogura, Y., Seto, K., Morimoto, Y., Nakamura, K., Sato, M.P., Gotoh, Y., Itoh, T., Toyoda, A., Ohnishi, M., and Hayashi, T. (2018). Genomic
Characterization of ȕ-Glucuronidase-Positive Escherichia coli O157:H7 Producing Stx2a. Emerg. Infect. Dis. 24, 2219-2227.

553.

Ohashi-Ito, K., Saegusa, M., Iwamoto, K., Oda, Y., Katayama, H., Kojima, M., Sakakibara, H., and Fukuda, H. (2014). A bHLH complex activates vascularcell division via cytokinin action in root apical meristem. Curr. Biol. 24, 2053-2058.

554.

Ohbayashi, R., Yamamoto, J.Y., Watanabe, S., Kanesaki, Y., Chibazakura, T., Miyagishima, S.Y., and Yoshikawa, H. (2017). Variety of DNA Replication
Activity Among Cyanobacteria Correlates with Distinct Respiration Activity in the Dark. Plant Cell Physiol 58, 279-286.

555.

Ohki, Y., Wenninger-Weinzierl, A., Hruscha, A., Asakawa, K., Kawakami, K., Haass, C., Edbauer, D., and Schmid, B. (2017). Glycine-alanine dipeptide
repeat protein contributes to toxicity in a zebrafish model of C9orf72 associated neurodegeneration. Mol Neurodegener 12, 6.

556.

Ohno, Y., Toyoshima, Y., Yurino, H., Monma, N., Xiang, H., Sumida, K., Kaneumi, S., Terada, S., Hashimoto, S., Ikeo, K., Homma, S., Kawamura, H.,
Takahashi, N., Taketomi, A., and Kitamura, H. (2017). Lack of interleukin-6 in the tumor microenvironment augments type-1 immunity and increases theefficacy of cancer immunotherapy. Cancer Sci 108, 1959-1966.

557.

Ohta, M., Ashikawa, T., Nozaki, Y., Kozuka-Hata, H., Goto, H., Inagaki, M., Oyama, M., and Kitagawa, D. (2014). Direct interaction of Plk4 with STIL
ensures formation of a single procentriole per parental centriole. Nat. Commun. 5, 5267.

558.

Ohta, M., Watanabe, K., Ashikawa, T., Nozaki, Y., Yoshiba, S., Kimura, A., and Kitagawa, D. (2018). Bimodal Binding of STIL to Plk4 Controls Proper
Centriole Copy Number. Cell Rep. 23, 3160-3169.e4.

559.

Ohta, S., Wood, L., Toramoto, I., Yagyu, K., Fukagawa, T., and Earnshaw, W.C. (2015) CENP-32 is required to maintain centrosomal dominance in bipolar
spindle assembly. Mol Biol Cell 26,1225-1237.

560.

Ohta, T., Kawashima, T., Shinozaki, N.O., Dobashi, A., Hiraoka, S., Hoshino, T., Kanno, K., Kataoka, T., Kawashima, S., Matsui, M., et al. (2018).
Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis “Somei-yoshino” across the Japanese archipelago.
J. Plant Res. 131, 709-717.

561.

Ohtani, Y., Miyata, M., Hashimoto, K., Tabata, T., Kishimoto, Y., Fukaya, M., Kase, D., Kassai, H., Nakao, K., Hirata, T., Watanabe, M., Kano, M., andAiba, A. (2014). The synaptic targeting of mGluR1 by its carboxyl-terminal domain is crucial for cerebellar function. J. Neurosci. 34, 2702-2712.

562.

Ohyanagi, H., Ebata, T., Huang, X., Gong, H., Fujita, M., Mochizuki, T., Toyoda, A., Fujiyama, A., Kaminuma, E., Nakamura, Y., Feng, Q., Wang, Z.X.,
Han, B., and Kurata, N. (2016) OryzaGenome: Genome Diversity Database of Wild Oryza Species. Plant Cell Physiol 57, e1.

563.

Ohyanagi, H., Nakamura, Y., and Yano, K. (2018). Plant and Cell Physiology’s 2018 Database Issue and Beyond. Plant Cell Physiol. 59, 1-2.

564.

Ohyanagi, H., Obayashi, T., and Yano, K. (2015) Editorial: Plant and Cell Physiology's 2015 database issue. Plant Cell Physiol 56,4-6.

565.

Ohyanagi, H., Takano, T., Terashima, S., Kobayashi, M., Kanno, M., Morimoto, K., Kanegae, H., Sasaki, Y., Saito, M., Asano, S., Ozaki, S., Kudo, T.,
Yokoyama, K., Aya, K., Suwabe, K., Suzuki, G., Aoki, K., Kubo, Y., Watanabe, M., Matsuoka, M., and Yano, K. (2015) Plant Omics Data Center: an
integrated web repository for interspecies gene expression networks with NLP-based curation. Plant Cell Physiol 56,e9.

‑78‑

566.

Oka, A., and Shiroishi, T. (2014). Regulatory divergence of X-linked genes and hybrid male sterility in mice. Genes Genet. Syst. 89, 99-108.

567.

Oka, A., Takada, T., Fujisawa, H., and Shiroishi, T. (2014). Evolutionarily diverged regulation of X-chromosomal genes as a primal event in mouse
reproductive isolation. PLoS Genet. 10, e1004301.

568.

Oka, M., Mura, S., Yamada, K., Sangel, P., Hirata, S., Maehara, K., Kawakami, K., Tachibana, T., Ohkawa, Y., Kimura, H., and Yoneda, Y. (2016)
Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes. Elife 5, e09540.

569.

Okabe, S., Tsuneoka, Y., Takahashi, A., Ooyama, R., Watarai, A., Maeda, S., Honda, Y., Nagasawa, M., Mogi, K., Nishimori, K., Kuroda, M., Koide, T.,
and Kikusui, T. (2017). Pup exposure facilitates retrieving behavior via the oxytocin neural system in female mice. Psychoneuroendocrinology 79, 20-30.

570.

Okahata, M., Ohta, A., Mizutani, H., Minakuchi, Y., Toyoda, A., and Kuhara, A. (2016) Natural variations of cold tolerance and temperature acclimation in
Caenorhabditis elegans. J Comp Physiol B 186, 985-998.

571.

Okai, S., Usui, F., Ohta, M., Mori, H., Kurokawa, K., Matsumoto, S., Kato, T., Miyauchi, E., Ohno, H., and Shinkura, R. (2017). Intestinal IgA as a modulatorof the gut microbiota. Gut Microbes 8, 486-492.

572.

Okai, S., Usui, F., Yokota, S., Hori-I, Y., Hasegawa, M., Nakamura, T., Kurosawa, M., Okada, S., Yamamoto, K., Nishiyama, E., Mori, H., Yamada, T.,
Kurokawa, K., Matsumoto, S., Nanno, M., Naito, T., Watanabe, Y., Kato, T., Miyauchi, E., Ohno, H., and Shinkura, R. (2016) High-affinity monoclonal
IgA regulates gut microbiota and prevents colitis in mice. Nat Microbiol 1, 16103.

573.

Okamoto, N., Tsuchiya, Y., Miya, F., Tsunoda, T., Yamashita, K., Boroevich, K.A., Kato, M., Saitoh, S., Yamasaki, M., Kanemura, Y., Kosaki, K., andKitagawa, D. (2017). A novel genetic syndrome with STARD9 mutation and abnormal spindle morphology. Am J Med Genet A 173, 2690-2696.

574.

Okamoto, Y., Iwasaki, W.M., Kugou, K., Takahashi, K.K., Oda, A., Sato, K., Kobayashi, W., Kawai, H., Sakasai, R., Takaori-Kondo, A., et al. (2018).
Replication stress induces accumulation of FANCD2 at central region of large fragile genes. Nucleic Acids Res. 46, 2932-2944.

575.

Okazaki, K., Kato, H., Iida, T., Shinmyozu, K., Nakayama, J.-I., Murakami, Y., and Urano, T. (2018). RNAi-dependent heterochromatin assembly in fission
yeast Schizosaccharomyces pombe requires heat-shock molecular chaperones Hsp90 and Mas5. Epigenetics Chromatin 11, 26.

576.

Okazaki, K., Miyagishima, S.Y., and Wada, H. (2015) Phosphatidylinositol 4-phosphate negatively regulates chloroplast division in Arabidopsis. Plant Cell
27,663-674.

577.

Oki, S., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., and Meno, C. (2018). ChIP-Atlas: a data-mining suite
powered by full integration of public ChIP-seq data. EMBO Rep. 19, e46255.

578.

Okigawa, S., Mizoguchi, T., Okano, M., Tanaka, H., Isoda, M., Jiang, Y.J., Suster, M., Higashijima, S., Kawakami, K., and Itoh, M. (2014). Different
combinations of Notch ligands and receptors regulate V2 interneuron progenitor proliferation and V2a/V2b cell fate determination. Dev. Biol. 391, 196-206.

579.

Okimoto, H., Tanaka, S., Araki, H., Ohashi, E., and Tsurimoto, T. (2016) Conserved interaction of Ctf18-RFC with DNA polymerase epsilon is critical for
maintenance of genome stability in Saccharomyces cerevisiae. Genes Cells 21, 482-491.

580.

Okudaira, Y., Hosomichi, K., Ozaki, Y., Shiina, T., and Mitsunaga, S. (2016) Correction of the HLA-DQB1*04:01:01 sequence at position 79 in exon 1.
HLA 87, 57-58.

581.

Okumura, K., Kagawa, N., Saito, M., Yoshizawa, Y., Munakata, H., Isogai, E., Fukagawa, T., and Wakabayashi, Y. (2017). CENP-R acts bilaterally as atumor suppressor and as an oncogene in the two-stage skin carcinogenesis model. Cancer Sci 108, 2142-2148.

582.

Okumura, M., Natsume, T., Kanemaki, M.T., and Kiyomitsu, T. (2018). Dynein-Dynactin-NuMA clusters generate cortical spindle-pulling forces as a multiarm ensemble. Elife 7, e36559.

583.

Okumura, T., Sasamura, T., Inatomi, M., Hozumi, S., Nakamura, M., Hatori, R., Taniguchi, K., Nakazawa, N., Suzuki, E., Maeda, R., Yamakawa, T., andMatsuno, K. (2015) Class I myosins have overlapping and specialized functions in left-right asymmetric development in Drosophila. Genetics 199,11831199.

584.

Oliveri, P., Fortunato, A.E., Petrone, L., Ishikawa-Fujiwara, T., Kobayashi, Y., Todo, T., Antonova, O., Arboleda, E., Zantke, J., Tessmar-Raible, K., andFalciatore, A. (2014). The Cryptochrome/Photolyase Family in aquatic organisms. Mar. Genomics 14, 23-37.

585.

Omer, W.H., Narita, A., Hosomichi, K., Mitsunaga, S., Hayashi, Y., Yamashita, A., Krasniqi, A., Iwasaki, Y., Kimura, M., and Inoue, I. (2014). Genomewide linkage and exome analyses identify variants of HMCN1 for splenic epidermoid cyst. BMC Med. Genet. 15, 115.

586.

Ono, H., Ogasawara, O., Okubo, K., and Bono, H. (2017). RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. Sci
Data 4, 170105.

587.

Ono, S., and Nonomura, K.-I. (2018). Microscopic Observation of Subcellular GFP-tagged Protein Localization in Rice Anthers. BIO-PROTOCOL Bio101,
e2956.

588.

Ono, S., Liu, H., Tsuda, K., Fukai, E., Tanaka, K., Sasaki, T., and Nonomura, K.-I. (2018). EAT1 transcription factor, a non-cell-autonomous regulator ofpollen production, activates meiotic small RNA biogenesis in rice anther tapetum. PLoS Genet. 14, e1007238.

589.

Ono, S., Sanetomo, R., and Hosaka, K. (2016) Genetic transmission of Solanum demissum (2n=6x=72) chromosomes from a pentaploid hybrid of S.
tuberosum (2n=4x=48) into the aneuploid BC1 progeny EUPHYTICA 207, 149-168.

590.

Onuma, R., and Horiguchi, T. (2016) Specificity of Chroomonas (Cryptophyceae) as a source of kleptochloroplast for Nusuttodinium aeruginosum(Dinophyceae) PHYCOLOGICAL RESEARCH 64, 35-43.

591.

Onuma, R., Mishra, N., and Miyagishima, S.Y. (2017). Regulation of chloroplast and nucleomorph replication by the cell cycle in the cryptophyte Guillardia
theta. Sci Rep 7, 2345.

592.

Orn, C., Shishido, R., Akimoto, M., Ishikawa, R., Htun, T.M., Nonomura, K., Koide, Y., Sarom, M., Vang, S., Sophany, S., Makara, O., and Ishii, T. (2015)‑79‑

Evaluation of genetic variation among wild rice populations in Cambodia. Breed Sci 65, 430-437.
593.

Osada, N. (2014). Extracting population genetics information from a diploid genome sequence Front. Ecol. Evol. 2, 7.

594.

Osada, N. (2015) Genetic diversity in humans and non-human primates and its evolutionary consequences. Genes Genet Syst 90,133-145.

595.

Osada, N. (2015) Genome-scale approaches for studying human and non-human primate evolution. Genes Genet Syst 90,121-122.

596.

Osada, N., Hettiarachchi, N., Adeyemi, Babarinde I., Saitou, N., and Blancher, A. (2015) Whole-genome sequencing of six Mauritian Cynomolgus macaques(Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck. Genome Biol Evol 7,821-830.

597.

Osada, N., Kohara, A., Yamaji, T., Hirayama, N., Kasai, F., Sekizuka, T., Kuroda, M., and Hanada, K. (2014). The genome landscape of the african greenmonkey kidney-derived vero cell line. DNA Res. 21, 673-683.

598.

Osada, N., Miyagi, R., and Takahashi, A. (2017). Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster.
Genetics 206, 2139-2148.

599.

Osakabe, A., Takahashi, Y., Murakami, H., Otawa, K., Tachiwana, H., Oma, Y., Nishijima, H., Shibahara, K.I., Kurumizaka, H., and Harata, M. (2014).
DNA binding properties of the actin-related protein Arp8 and its role in DNA repair. PLoS One 9, e108354.

600.

Padermshoke, A., Ogawa, T., Nishio, K., Nakazawa, M., Nakamoto, M., Okazawa, A., Kanaya, S., Arita, M., and Ohta, D. (2016) Critical Involvement ofEnvironmental Carbon Dioxide Fixation to Drive Wax Ester Fermentation in Euglena. PLoS One 11, e0162827.

601.

Park, J., Kondo, S., Tanimoto, H., Kohsaka, H., and Nose, A. (2018). Data-driven analysis of motor activity implicates 5-HT2A neurons in backward
locomotion of larval Drosophila. Sci. Rep. 8, 10307.

602.

Pennell, M.W., Kirkpatrick, M., Otto, S.P., Vamosi, J.C., Peichel, C.L., Valenzuela, N., and Kitano, J. (2015) Y fuse? Sex chromosome fusions in fishes
and reptiles. PLoS Genet 11,e1005237.

603.

Perkins, L.A., Holderbaum, L., Tao, R., Hu, Y., Sopko, R., McCall, K., Yang-Zhou, D., Flockhart, I., Binari, R., Shim, H.S., Miller, A., Housden, A., Foos,
M., Randkelv, S., Kelley, C., Namgyal, P., Villalta, C., Liu, L.P., Jiang, X., Huan-Huan, Q., Wang, X., Fujiyama, A., Toyoda, A., Ayers, K., Blum, A.,
Czech, B., Neumuller, R., Yan, D., Cavallaro, A., Hibbard, K., Hall, D., Cooley, L., Hannon, G.J., Lehmann, R., Parks, A., Mohr, S.E., Ueda, R., Kondo,
S., Ni, J.Q., and Perrimon, N. (2015) The Transgenic RNAi Project at Harvard Medical School: Resources and Validation. Genetics 201,843-852.

604.

Perpelescu, M., Hori, T., Toyoda, A., Misu, S., Monma, N., Ikeo, K., Obuse, C., Fujiyama, A., and Fukagawa, T. (2015) HJURP is involved in the expansionof centromeric chromatin. Mol Biol Cell 26,2742-2754.

605.

Pipalia, T.G., Koth, J., Roy, S.D., Hammond, C.L., Kawakami, K., and Hughes, S.M. (2016) Cellular dynamics of regeneration reveals role of two distinct
Pax7 stem cell populations in larval zebrafish muscle repair. Dis Model Mech 9, 671-684.

606.

Platani, M., Samejima, I., Samejima, K., Kanemaki, M.T., and Earnshaw, W.C. (2018). Seh1 targets GATOR2 and Nup153 to mitotic chromosomes. J. Cell
Sci. 131, jcs213140.

607.

Poon, C.L., Mitchell, K.A., Kondo, S., Cheng, L.Y., and Harvey, K.F. (2016) The Hippo Pathway Regulates Neuroblasts and Brain Size in Drosophilamelanogaster. Curr Biol 26, 1034-1042.

608.

Pramono, A.K., Kuwahara, H., Itoh, T., Toyoda, A., Yamada, A., and Hongoh, Y. (2017). Discovery and Complete Genome Sequence of a Bacteriophagefrom an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut. Microbes Environ 32, 112-117.

609.

Pui, H.P., and Saga, Y. (2017). Gonocytes-to-spermatogonia transition initiates prior to birth in murine testes and it requires FGF signaling. Mech Dev 144,
125-139.

610.

Pui, H.P., and Saga, Y. (2018). NANOS2 acts as an intrinsic regulator of gonocytes-to-spermatogonia transition in the murine testes. Mech. Dev. 149, 2740.

611.

Rabbani, B., Nakaoka, H., Akhondzadeh, S., Tekin, M., and Mahdieh, N. (2016) Next generation sequencing: implications in personalized medicine andpharmacogenomics. Mol Biosyst 12, 1818-1830.

612.

Rademacher, N., Kern, R., Fujiwara, T., Mettler-Altmann, T., Miyagishima, S.Y., Hagemann, M., Eisenhut, M., and Weber, A.P. (2016) Photorespiratory
glycolate oxidase is essential for the survival of the red alga Cyanidioschyzon merolae under ambient CO2 conditions. J Exp Bot 67, 3165-3175.

613.

Rashid, J., Kobiyama, A., Reza, M.S., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., Ikeo, K., Sato, S., Ogata, T., et al. (2018). Seasonal changes in thecommunities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing. Gene 665, 127-132.

614.

Rastogi, S., Borgo, B., Pazdernik, N., Fox, P., Mardis, E.R., Kohara, Y., Havranek, J., and Schedl, T. (2015) Caenorhabditis elegans glp-4 Encodes a Valyl
Aminoacyl tRNA Synthetase. G3 (Bethesda) 5,2719-2728.

615.

Ravinet, M., Faria, R., Butlin, R.K., Galindo, J., Bierne, N., Rafajlovic, M., Noor, M.A.F., Mehlig, B., and Westram, A.M. (2017). Interpreting the genomic
landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol 30, 1450-1477.

616.

Ravinet, M., Ishikawa, A., and Kitano, J. (2016) Trophic niche differentiation and phenotypic divergence among cryptic species of Japanese ninespine
sticklebacks EVOLUTIONARY ECOLOGY RESEARCH 17, 505-523.

617.

Ravinet, M., Takeuchi, N., Kume, M., Mori, S., and Kitano, J. (2014). Comparative analysis of Japanese three-spined stickleback clades reveals the Pacific
Ocean lineage has adapted to freshwater environments while the Japan Sea has not. PLoS One 9, e112404.

618.

Ravinet, M., Westram, A., Johannesson, K., Butlin, R., Andre, C., and Panova, M. (2016) Shared and nonshared genomic divergence in parallel ecotypes of
Littorina saxatilis at a local scale. Mol Ecol 25, 287-305.

619.

Ravinet, M., Yoshida, K., Shigenobu, S., Toyoda, A., Fujiyama, A., and Kitano, J. (2018). The genomic landscape at a late stage of stickleback speciation:
High genomic divergence interspersed by small localized regions of introgression. PLoS Genet. 14, e1007358.

‑80‑

620.

Reiten, I., Uslu, F.E., Fore, S., Pelgrims, R., Ringers, C., Diaz, Verdugo C., Hoffman, M., Lal, P., Kawakami, K., Pekkan, K., Yaksi, E., and Jurisch-Yaksi,
N. (2017). Motile-Cilia-Mediated Flow Improves Sensitivity and Temporal Resolution of Olfactory Computations. Curr Biol 27, 166-174.

621.

Ren, G.R., Hauser, F., Rewitz, K.F., Kondo, S., Engelbrecht, A.F., Didriksen, A.K., Schjott, S.R., Sembach, F.E., Li, S., Sogaard, K.C., Sondergaard, L.,
and Grimmelikhuijzen, C.J. (2015) CCHamide-2 Is an Orexigenic Brain-Gut Peptide in Drosophila. PLoS One 10,e0133017.

622.

Reuscher, S., Furuta, T., Bessho-Uehara, K., Cosi, M., Jena, K.K., Toyoda, A., Fujiyama, A., Kurata, N., and Ashikari, M. (2018). Assembling the genomeof the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Commun. Biol. 1, 162.

623.

Reza, M.S., Kobiyama, A., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., Ikeo, K., Sato, S., Ogata, T., Jimbo, M., et al. (2018). Basin-scale seasonalchanges in marine free-living bacterioplankton community in the Ofunato Bay. Gene 665, 185-191.

624.

Reza, M.S., Kobiyama, A., Yamada, Y., Ikeda, Y., Ikeda, D., Mizusawa, N., Ikeo, K., Sato, S., Ogata, T., Jimbo, M., et al. (2018). Taxonomic profiles inmetagenomic analyses of free-living microbial communities in the Ofunato Bay. Gene 665, 192-200.

625.

Reza, M.S., Mizusawa, N., Kumano, A., Oikawa, C., Ouchi, D., Kobiyama, A., Yamada, Y., Ikeda, Y., Ikeda, D., Ikeo, K., et al. (2018). Metagenomic
analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream, the Tama River, Tokyo. Fish. Sci. 84, 563-577.

626.

Rezansoff, A.M., Crispo, E., Blair, C., Cruz, E., Kitano, J., Vamosi, S.M., and Rogers, S.M. (2015) Toward the genetic origins of a potentially non-native
population of threespine stickleback (Gasterosteus aculeatus) in Alberta. Conserv Genet16,859-873.

627.

Rinkwitz, S., Geng, F.S., Manning, E., Suster, M., Kawakami, K., and Becker, T.S. (2015) BAC transgenic zebrafish reveal hypothalamic enhancer activity
around obesity associated SNP rs9939609 within the human FTO gene. Genesis 53,640-651.

628.

Rocca-Serra, P., Salek, R.M., Arita, M., Correa, E., Dayalan, S., Gonzalez-Beltran, A., Ebbels, T., Goodacre, R., Hastings, J., Haug, K., Koulman, A.,
Nikolski, M., Oresic, M., Sansone, S.A., Schober, D., Smith, J., Steinbeck, C., Viant, M.R., and Neumann, S. (2016) Data standards can boost metabolomics
research, and if there is a will, there is a way. Metabolomics 12, 14.

629.

Rodriguez-Bravo, V., Maciejowski, J., Corona, J., Buch, H.K., Collin, P., Kanemaki, M.T., Shah, J.V., and Jallepalli, P.V. (2014). Nuclear pores protect
genome integrity by assembling a premitotic and Mad1-dependent anaphase inhibitor. Cell 156, 1017-1031.

630.

Romero, V., Hosomichi, K., Nakaoka, H., Shibata, H., and Inoue, I. (2017). Structure and evolution of the filaggrin gene repeated region in primates. BMC
Evol Biol 17, 10.

631.

Romero, V., Nakaoka, H., Hosomichi, K., and Inoue, I. (2018). High Order Formation and Evolution of Hornerin in Primates. Genome Biol. Evol. 10, 31673175.

632.

Ron, M., Kajala, K., Pauluzzi, G., Wang, D., Reynoso, M.A., Zumstein, K., Garcha, J., Winte, S., Masson, H., Inagaki, S., Federici, F., Sinha, N., Deal,
R.B., Bailey-Serres, J., and Brady, S.M. (2014). Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene
expression and function using tomato as a model. Plant Physiol. 166, 455-469.

633.

Saba, R., Kato, Y., and Saga, Y. (2014). NANOS2 promotes male germ cell development independent of meiosis suppression. Dev Biol 385, 32-40.

634.

Saba, R., Wu, Q., and Saga, Y. (2014). CYP26B1 promotes male germ cell differentiation by suppressing STRA8-dependent meiotic and STRA8independent mitotic pathways. Dev. Biol. 389, 173-181.

635.

Saber, M.M., Adeyemi, Babarinde I., Hettiarachchi, N., and Saitou, N. (2016) Emergence and Evolution of Hominidae-Specific Coding and Noncoding
Genomic Sequences. Genome Biol Evol 8, 2076-2092.

636.

Sadahiro, T., Isomi, M., Muraoka, N., Kojima, H., Haginiwa, S., Kurotsu, S., Tamura, F., Tani, H., Tohyama, S., Fujita, J., et al. (2018). Tbx6 Induces
Nascent Mesoderm from Pluripotent Stem Cells and Temporally Controls Cardiac versus Somite Lineage Diversification. Cell Stem Cell 23, 382-395.e5.

637.

Sagai, T., Amano, T., Maeno, A., Kimura, T., Nakamoto, M., Takehana, Y., Naruse, K., Okada, N., Kiyonari, H., and Shiroishi, T. (2017). Evolution of Shhendoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder. Nat Commun 8, 14300.

638.

Sagai, T., Amano, T., Maeno, A., Kiyonari, H., Seo, H., Cho, S.W., and Shiroishi, T. (2017). SHH signaling directed by two oral epithelium-specificenhancers controls tooth and oral development. Sci Rep 7, 13004.

639.

Saito, K., Sakai, C., Kawasaki, T., and Sakai, N. (2014). Telomere distribution pattern and synapsis initiation during spermatogenesis in zebrafish. Dev.
Dyn. 243, 1448-1456.

640.

Saitou, N. (2014). Homo sapiens under Neutral Evolution. Genes Environ. 36, 99-102.

641.

Saitou, N. (2018). Chance, Finiteness, and History. Mol. Biol. Evol. 35, 1556-1557.

642.

Saitou, N., and Jinam, T.A. (2017). Language diversity of the Japanese archipelago and its relationship with human DNA diversity. Man in India 97, 205228.

643.

Saka, K., Takahashi, A., Sasaki, M., and Kobayashi, T. (2016) More than 10% of yeast genes are related to genome stability and influence cellular senescence
via rDNA maintenance. Nucleic Acids Res 44, 4211-4221.

644.

Sakata, K., Ohyanagi, H., Sato, S., Nobori, H., Hayashi, A., Ishii, H., Daub, C.O., Kawai, J., Suzuki, H., and Saito, T. (2015) System-wide analysis of thetranscriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiationtransitions. Sci Rep 5,8283.

645.

Sakiyama, M., Matsuo, H., Nakaoka, H., Kawamura, Y., Kawaguchi, M., Higashino, T., Nakayama, A., Akashi, A., Ueyama, J., Kondo, T., et al. (2018).
Common variant of BCAS3 is associated with gout risk in Japanese population: the first replication study after gout GWAS in Han Chinese. BMC Med.
Genet. 19, 96.

646.

Sakiyama, M., Matsuo, H., Nakaoka, H., Yamamoto, K., Nakayama, A., Nakamura, T., Kawai, S., Okada, R., Ooyama, H., Shimizu, T., and Shinomiya, N.

‑81‑

(2016) Identification of rs671, a common variant of ALDH2, as a gout susceptibility locus. Sci Rep 6, 25360.
647.

Sakurai, M., Ueda, H., Yano, T., Okada, S., Terajima, H., Mitsuyama, T., Toyoda, A., Fujiyama, A., Kawabata, H., and Suzuki, T. (2014). A biochemicallandscape of A-to-I RNA editing in the human brain transcriptome. Genome Res. 24, 522-534.

648.

Salek, R.M., Arita, M., Dayalan, S., Ebbels, T., Jones, A.R., Neumann, S., Rocca-Serra, P., Viant, M.R., and Vizca?no, J.A. (2015) Embedding standards inmetabolomics: the Metabolomics Society data standards task group. Metabolomics 11,782-783.

649.

Samejima, I., Spanos, C., Alves, Fde L., Hori, T., Perpelescu, M., Zou, J., Rappsilber, J., Fukagawa, T., and Earnshaw, W.C. (2015) Whole-proteome genetic
analysis of dependencies in assembly of a vertebrate kinetochore. J Cell Biol 211,1141-1156.

650.

Samejima, K., Booth, D.G., Ogawa, H., Paulson, J.R., Xie, L., Watson, C.A., Platani, M., Kanemaki, M.T., and Earnshaw, W.C. (2018). Functional analysis
after rapid degradation of condensins and 3D-EM reveals chromatin volume is uncoupled from chromosome architecture in mitosis. J. Cell Sci. 131,
jcs210187.

651.

Samejima, K., Ogawa, H., Ageichik, A.V., Peterson, K.L., Kaufmann, S.H., Kanemaki, M.T., and Earnshaw, W.C. (2014). Auxin-induced rapid degradationof inhibitor of caspase-activated DNase (ICAD) induces apoptotic DNA fragmentation, caspase activation, and cell death: a cell suicide module. J. Biol.
Chem. 289, 31617-31623.

652.

Sanosaka, T., Imamura, T., Hamazaki, N., Chai, M., Igarashi, K., Ideta-Otsuka, M., Miura, F., Ito, T., Fujii, N., Ikeo, K., and Nakashima, K. (2017). DNA
Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells. Cell Rep
20, 2992-3003.

653.

Sanuki, Y., Kubota, Y., Kanemaki, M.T., Takahashi, T.S., Mimura, S., and Takisawa, H. (2015) RecQ4 promotes the conversion of the pre-initiation complex
at a site-specific origin for DNA unwinding in Xenopus egg extracts. Cell Cycle 14,1010-1023.

654.

Sardell, J.M., Cheng, C., Dagilis, A.J., Ishikawa, A., Kitano, J., Peichel, C.L., and Kirkpatrick, M. (2018). Sex Differences in Recombination in Sticklebacks.
G3 (Bethesda). 8, 1971-1983.

655.

Sasaki, A., Ide, S., Kawamoto, Y., Bando, T., Murata, Y., Shimura, M., Yamada, K., Hirata, A., Nokihara, K., Hirata, T., Sugiyama, H., and Maeshima, K.
(2016) Telomere Visualization in Tissue Sections using Pyrrole-Imidazole Polyamide Probes. Sci Rep 6, 29261.

656.

Sasaki, T., Fukuda, H., and Oda, Y. (2017). CORTICAL MICROTUBULE DISORDERING1 Is Required for Secondary Cell Wall Patterning in Xylem
Vessels. Plant Cell 29, 3123-3139.

657.

Sasanuma, H. (2015) Relative contribution of four nucleases, CtIP, Dna2, Exo1 and Mre11, to the initial step of DNA double-strand break repair byhomologous recombination in both the chicken DT40 and human TK6 cell lines. Genes Cells 20,1059-1076.

658.

Sato, K., Kuroki, Y., Kumita, W., Fujiyama, A., Toyoda, A., Kawai, J., Iriki, A., Sasaki, E., Okano, H., and Sakakibara, Y. (2015) Resequencing of thecommon marmoset genome improves genome assemblies and gene-coding sequence analysis. Sci Rep 5,16894.

659.

Sato, N., Yoshida, M.A., and Kasugai, T. (2017). Impact of cryptic female choice on insemination success: Larger sized and longer copulating male squid
ejaculate more, but females influence insemination success by removing spermatangia. Evolution 71, 111-120.

660.

Sato, T., Sato, F., Kamezaki, A., Sakaguchi, K., Tanigome, R., Kawakami, K., and Sehara-Fujisawa, A. (2015) Neuregulin 1 Type II-ErbB Signaling
Promotes Cell Divisions Generating Neurons from Neural Progenitor Cells in the Developing Zebrafish Brain. PLoS One 10,e0127360.

661.

Sato, Y., Kujirai, T., Arai, R., Asakawa, H., Ohtsuki, C., Horikoshi, N., Yamagata, K., Ueda, J., Nagase, T., Haraguchi, T., Hiraoka, Y., Kimura, A.,
Kurumizaka, H., and Kimura, H. (2016) A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation. J Mol Biol 428, 3885-3902.

662.

Satrimafitrah, P., Barman, H.K., Ahmad, A., Nishitoh, H., Nakayama, T., Fukagawa, T., and Takami, Y. (2016) RbAp48 is essential for viability of vertebratecells and plays a role in chromosome stability. Chromosome Res 24, 161-173.

663.

Satti, M., Tanizawa, Y., Endo, A., and Arita, M. (2018). Comparative analysis of probiotic bacteria based on a new definition of core genome. J. Bioinform.
Comput. Biol. 16, 1840012.

664.

Segawa, T., Matsuzaki, R., Takeuchi, N., Akiyoshi, A., Navarro, F., Sugiyama, S., Yonezawa, T., and Mori, H. (2018). Bipolar dispersal of red-snow algae.
Nat. Commun. 9, 3094.

665.

Seike, T., and Niki, H. (2017). Mating response and construction of heterothallic strains of the fission yeast Schizosaccharomyces octosporus. FEMS Yeast
Res 17, fox045.

666.

Seike, T., Nakamura, T., and Shimoda, C. (2015) Molecular coevolution of a sex pheromone and its receptor triggers reproductive isolation in
Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 112,4405-4410.

667.

Seki, R., Kitajima, K., Matsubara, H., Suzuki, T., Saito, D., Yokoyama, H., and Tamura, K. (2015) AP-2beta is a transcriptional regulator for determinationof digit length in tetrapods. Dev Biol 407,75-89.

668.

Seki, R., Li, C., Fang, Q., Hayashi, S., Egawa, S., Hu, J., Xu, L., Pan, H., Kondo, M., Sato, T., Matsubara, H., Kamiyama, N., Kitajima, K., Saito, D., Liu,Y., Gilbert, M.T., Zhou, Q., Xu, X., Shiroishi, T., Irie, N., Tamura, K., and Zhang, G. (2017). Functional roles of Aves class-specific cis-regulatory elements
on macroevolution of bird-specific features. Nat Commun 8, 14229.

669.

Sekiya, M., Maruko-Otake, A., Hearn, S., Sakakibara, Y., Fujisaki, N., Suzuki, E., Ando, K., and Iijima, K.M. (2017). EDEM Function in ERAD Protects
against Chronic ER Proteinopathy and Age-Related Physiological Decline in Drosophila. Dev Cell 41, 652-664.e5.

670.

Seo, H., Amano, T., Seki, R., Sagai, T., Kim, J., Cho, S.W., and Shiroishi, T. (2018). Upstream Enhancer Elements of Shh Regulate Oral and Dental
Patterning. J. Dent. Res. 97, 1055-1063.

671.

Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., van, Heeringen S.J., Quigley,I., Heinz, S., Ogino, H., Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam, N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe, M.,‑82‑

Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe, S.S., van, Kruijsbergen I., Shu, S., Carlson, J., Kinoshita, T., Ohta, Y., Mawaribuchi, S., Jenkins, J.,
Grimwood, J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y., Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller, K., Haudenschild, C.,
Kitzman, J., Nakayama, T., Izutsu, Y., Robert, J., Fortriede, J., Burns, K., Lotay, V., Karimi, K., Yasuoka, Y., Dichmann, D.S., Flajnik, M.F., Houston,
D.W., Shendure, J., DuPasquier, L., Vize, P.D., Zorn, A.M., Ito, M., Marcotte, E.M., Wallingford, J.B., Ito, Y., Asashima, M., Ueno, N., Matsuda, Y.,
Veenstra, G.J., Fujiyama, A., Harland, R.M., Taira, M., and Rokhsar, D.S. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538,
336-343.
672.

Shang, W.H., Hori, T., Westhorpe, F.G., Godek, K.M., Toyoda, A., Misu, S., Monma, N., Ikeo, K., Carroll, C.W., Takami, Y., Fujiyama, A., Kimura, H.,
Straight, A.F., and Fukagawa, T. (2016) Acetylation of histone H4 lysine 5 and 12 is required for CENP-A deposition into centromeres. Nat Commun 7,
13465.

673.

Shen, Y., Wang, L., Hirose, S., Zhou, Z., and Liu, Q. (2018). The transcriptional factor Apt regulates neuroblast differentiation through activating CycE
expression. Biochem. Biophys. Res. Commun. 499, 889-894.

674.

Shenton, M., Iwamoto, C., Kurata, N., and Ikeo, K. (2016) Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition.
Rice (N Y) 9, 42.

675.

Shenton, M.R., Ohyanagi, H., Wang, Z.X., Toyoda, A., Fujiyama, A., Nagata, T., Feng, Q., Han, B., and Kurata, N. (2015) Rapid turnover of antimicrobialtype cysteine-rich protein genes in closely related Oryza genomes. Mol Genet Genomics 290,1753-1770.

676.

Shibata, E., Liu, Z., Kawasaki, T., Sakai, N., and Kawakami, A. (2018). Robust and local positional information within a fin ray directs fin length during
zebrafish regeneration. Dev. Growth Differ. 60, 354-364.

677.

Shibata, E., Yokota, Y., Horita, N., Kudo, A., Abe, G., Kawakami, K., and Kawakami, A. (2016) Fgf signalling controls diverse aspects of fin regeneration.
Development 143, 2920-2929.

678.

Shibata, Y., Sawa, H., and Nishiwaki, K. (2014). HTZ-1/H2A.z and MYS-1/MYST HAT act redundantly to maintain cell fates in somatic gonadal cells
through repression of ceh-22 in C. elegans. Development 141, 209-218.

679.

Shibuya, H., Watanabe, R., Maeno, A., Ichimura, K., Tamura, M., Wakana, S., Shiroishi, T., Ohba, K., Takeda, K., Tomita, H., et al. (2018). Melanocytes
contribute to the vasculature of the choroid. Genes Genet. Syst. 93, 51-58.

680.

Shikata, M., Hoshikawa, K., Ariizumi, T., Fukuda, N., Yamazaki, Y., and Ezura, H. (2016) TOMATOMA Update: Phenotypic and Metabolite Informationin the Micro-Tom Mutant Resource. Plant Cell Physiol 57, e11.

681.

Shimada, T., Yamazaki, Y., Tanaka, K., and Ishihama, A. (2014). The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzymeof Escherichia coli. PLoS One 9, e90447.

682.

Shimamoto, Y., Forth, S., and Kapoor, T.M. (2015) Measuring Pushing and Braking Forces Generated by Ensembles of Kinesin-5 Crosslinking Two
Microtubules. Dev Cell 34,669-681.

683.

Shimamoto, Y., Tamura, S., and Maeshima, K. (2018). DNA Works as a Spring in the Cell! Seibutsu Butsuri 58, 024-026.

684.

Shimamoto, Y., Tamura, S., Masumoto, H., and Maeshima, K. (2017). Nucleosome-nucleosome interactions via histone tails and linker DNA regulate
nuclear rigidity. Mol Biol Cell 28, 1580-1589.

685.

Shimizu, T., Kaminuma, E., Nonaka, K., Yoshioka, T., Goto, S., Matsumoto, T., Katayose, Y., Mochizuki, T., Tanizawa, Y., Toyoda, A., Fujiyama, A., andNakamura, Y. (2016) A genomic approach to selecting robust and versatile SNP sets from next-generation sequencing data for genome-wide association
study in citrus cultivars Acta Horticulturae, 1135.

686.

Shimizu, T., Kitajima, A., Nonaka, K., Yoshioka, T., Ohta, S., Goto, S., Toyoda, A., Fujiyama, A., Mochizuki, T., Nagasaki, H., Kaminuma, E., andNakamura, Y. (2016) Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes. PLoS One 11, e0166969.

687.

Shimizu, T., Tanizawa, Y., Mochizuki, T., Nagasaki, H., Yoshioka, T., Toyoda, A., Fujiyama, A., Kaminuma, E., and Nakamura, Y. (2017). Draft
Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach. Front Genet 8, 180.

688.

Shimono, K., Fujishima, K., Nomura, T., Ohashi, M., Usui, T., Kengaku, M., Toyoda, A., and Uemura, T. (2014). An evolutionarily conserved protein
CHORD regulates scaling of dendritic arbors with body size. Sci. Rep. 4, 4415.

689.

Shindo, Y., Iwamoto, K., Mouri, K., Hibino, K., Tomita, M., Kosako, H., Sako, Y., and Takahashi, K. (2016) Conversion of graded phosphorylation into
switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling. Nat Commun 7, 10485.

690.

Shinkai, S., Nozaki, T., Maeshima, K., and Togashi, Y. (2016) Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin
Domains in Living Human Cells. PLoS Comput Biol 12, e1005136.

691.

Shinkai, S., Nozaki, T., Maeshima, K., and Togashi, Y. (2017). Bridging the dynamics and organization of chromatin domains by mathematical modeling.
Nucleus 8, 353-359.

692.

Shinoda, Y., Ishii, C., Fukazawa, Y., Sadakata, T., Ishii, Y., Sano, Y., Iwasato, T., Itohara, S., and Furuichi, T. (2016) CAPS1 stabilizes the state of readily
releasable synaptic vesicles to fusion competence at CA3-CA1 synapses in adult hippocampus. Sci Rep 6, 31540.

693.

Shinya, M., Machiki, D., Henrich, T., Kubota, Y., Takisawa, H., and Mimura, S. (2014). Evolutionary diversification of MCM3 genes in Xenopus laevis
and Danio rerio. Cell Cycle 13, 3271-3281.

694.

Shiraki, T., and Kawakami, K. (2018). A tRNA-based multiplex sgRNA expression system in zebrafish and its application to generation of transgenic albino
fish. Sci. Rep. 8, 13366.

695.

Shirakihara, Y., Shiratori, A., Tanikawa, H., Nakasako, M., Yoshida, M., and Suzuki, T. (2015) Structure of a thermophilic F1-ATPase inhibited by anepsilon-subunit: deeper insight into the epsilon-inhibition mechanism. FEBS J 282,2895-2913.

‑83‑

696.

Shiratsuchi, G., Takaoka, K., Ashikawa, T., Hamada, H., and Kitagawa, D. (2015) RBM14 prevents assembly of centriolar protein complexes and maintains
mitotic spindle integrity. EMBO J 34,97-114.

697.

Shiroishi, T. (2014). "Legacy of Dr. Kazuo Moriwaki" (1930-2013). Mamm. Genome 25, 193-194.

698.

Simakov, O., and Kawashima, T. (2017). Independent evolution of genomic characters during major metazoan transitions. Dev Biol 427, 179-192.

699.

Simakov, O., Kawashima, T., Marletaz, F., Jenkins, J., Koyanagi, R., Mitros, T., Hisata, K., Bredeson, J., Shoguchi, E., Gyoja, F., Yue, J.X., Chen, Y.C.,
Freeman, R.M. Jr, Sasaki, A., Hikosaka-Katayama, T., Sato, A., Fujie, M., Baughman, K.W., Levine, J., Gonzalez, P., Cameron, C., Fritzenwanker, J.H.,
Pani, A.M., Goto, H., Kanda, M., Arakaki, N., Yamasaki, S., Qu, J., Cree, A., Ding, Y., Dinh, H.H., Dugan, S., Holder, M., Jhangiani, S.N., Kovar, C.L.,
Lee, S.L., Lewis, L.R., Morton, D., Nazareth, L.V., Okwuonu, G., Santibanez, J., Chen, R., Richards, S., Muzny, D.M., Gillis, A., Peshkin, L., Wu, M.,
Humphreys, T., Su, Y.H., Putnam, N.H., Schmutz, J., Fujiyama, A., Yu, J.K., Tagawa, K., Worley, K.C., Gibbs, R.A., Kirschner, M.W., Lowe, C.J., Satoh,N., Rokhsar, D.S., Gerhart, J. (2015) Hemichordate genomes and deuterostome origins.. Nature 527,459-465.

700.

Simecek, P., Forejt, J., Williams, R.W., Shiroishi, T., Takada, T., Lu, L., Johnson, T.E., Bennett, B., Deschepper, C.F., Scott-Boyer, M.P., Pardo-Manuel,de Villena F., and Churchill, G.A. (2017). High-Resolution Maps of Mouse Reference Populations. G3 (Bethesda) 7, 3427-3434.

701.

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M.H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake,A., Bonierbale, M., Brookes, A.J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J.W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova,
R., Cutts, R.J., Dassi, E., Di, Genova A., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R.C., Fujisawa, T., Gadaleta,
E., Garcia-Manteiga, J.M., Goodstein, D., Gray, K., Guerra-Assuncao, J.A., Haggarty, B., Han, D.J., Han, B.W., Harris, T., Harshbarger, J., Hastings, R.K.,
Hayes, R.D., Hoede, C., Hu, S., Hu, Z.L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson,
D., Lazarevic, D., Lee, J.H., Letellier, T., Li, C.Y., Lio, P., Liu, C.J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A.M., Moreews, F.,
Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S.,
Saddiq, A.A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, and W., Staines (2015) The BioMart community portal: an innovative
alternative to large, centralized data repositories. Nucleic Acids Res 43,W589-98.

702.

Spivakov, M., Auer, T.O., Peravali, R., Dunham, I., Dolle, D., Fujiyama, A., Toyoda, A., Aizu, T., Minakuchi, Y., Loosli, F., Naruse, K., Birney, E., andWittbrodt, J. (2014). Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic
resource in fish. G3 (Bethesda) 4, 433-445.

703.

Sriyudthsak, K., Mejia, R.F., Arita, M., and Hirai, M.Y. (2016) PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.
Nucleic Acids Res 44, W205-211.

704.

Stein, J.C., Yu, Y., Copetti, D., Zwickl, D.J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J.L., et al. (2018). Genomes of 13
domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat. Genet. 50, 285-296.

705.

Sternberg, J.R., Severi, K.E., Fidelin, K., Gomez, J., Ihara, H., Alcheikh, Y., Hubbard, J.M., Kawakami, K., Suster, M., and Wyart, C. (2016) Optimizationof a Neurotoxin to Investigate the Contribution of Excitatory Interneurons to Speed Modulation In Vivo. Curr Biol 26, 2319-2328.

706.

Stodberg, T., McTague, A., Ruiz, A.J., Hirata, H., Zhen, J., Long, P., Farabella, I., Meyer, E., Kawahara, A., Vassallo, G., Stivaros, S.M., Bjursell, M.K.,
Stranneheim, H., Tigerschiold, S., Persson, B., Bangash, I., Das, K., Hughes, D., Lesko, N., Lundeberg, J., Scott, R.C., Poduri, A., Scheffer, I.E., Smith, H.,
Gissen, P., Schorge, S., Reith, M.E., Topf, M., Kullmann, D.M., Harvey, R.J., Wedell, A., and Kurian, M.A. (2015) Mutations in SLC12A5 in epilepsy of
infancy with migrating focal seizures. Nat Commun 6,8038.

707.

Suda, K., Nakaoka, H., Yoshihara, K., Ishiguro, T., Tamura, R., Mori, Y., Yamawaki, K., Adachi, S., Takahashi, T., Kase, H., et al. (2018). Clonal Expansion
and Diversification of Cancer-Associated Mutations in Endometriosis and Normal Endometrium. Cell Rep. 24, 1777-1789.

708.

Suga, A., Mizota, A., Kato, M., Kuniyoshi, K., Yoshitake, K., Sultan, W., Yamazaki, M., Shimomura, Y., Ikeo, K., Tsunoda, K., and Iwata, T. (2016)
Identification of novel mutations in the LRR-Cap domain of C21orf2 in Japanese patients with retinitis pigmentosa and cone-rod dystrophy. Invest
Ophthalmol Vis Sci 57, 4255-4263.

709.

Sugawara, T., and Kimura, A. (2017). Physical properties of the chromosomes and implications for development. Dev Growth Differ 59, 405-414.

710.

Sugie, A., Hakeda-Suzuki, S., Suzuki, E., Silies, M., Shimozono, M., Mohl, C., Suzuki, T., and Tavosanis, G. (2015) Molecular Remodeling of the
Presynaptic Active Zone of Drosophila Photoreceptors via Activity-Dependent Feedback. Neuron 86,711-725.

711.

Sugihara, A., Nguyen, L.C., Shamim, H.M., Iida, T., Nakase, M., Takegawa, K., Senda, M., Jida, S., and Ueno, M. (2018). Mutation in fission yeast
phosphatidylinositol 4-kinase Pik1 is synthetically lethal with defect in telomere protection protein Pot1. Biochem. Biophys. Res. Commun. 496, 1284-1290.

712.

Sugioka, K., Fielmich, L.-E., Mizumoto, K., Bowerman, B., van den Heuvel, S., Kimura, A., and Sawa, H. (2018). Tumor suppressor APC is an attenuatorof spindle-pulling forces during C. elegans asymmetric cell division. Proc. Natl. Acad. Sci. U. S. A. 115, E954-E963.

713.

Sugiyama, Y., Wakazaki, M., Toyooka, K., Fukuda, H., and Oda, Y. (2017). A Novel Plasma Membrane-Anchored Protein Regulates Xylem Cell-Wall
Deposition through Microtubule-Dependent Lateral Inhibition of Rho GTPase Domains. Curr Biol 27, 2522-2528.e4.

714.

Sultana, N., Igawa, T., Nozawa, M., Islam, M.M., Hasan, M., Alam, M.S., Khan, M.M., and Sumida, M. (2014). Development and characterization of 27
new microsatellite markers for the Indian bullfrog Hoplobatrachus tigerinus and its congeneric species. Genes Genet. Syst. 89, 137-141.

715.

Sultana, Z., and Asakura, A. (2015) The complete larval development of Pagurus maculosus Komai & Imafuku, 1996 (Decapoda, Anomura, Paguridae)
reared in the laboratory, and a comparison with sympatric species. Zootaxa 3947,301-326.

716.

Sultana, Z., Asakura, A., Kinjo, S., Nozawa, M., Nakano, T., and Ikeo, K. (2018). Molecular phylogeny of ten intertidal hermit crabs of the genus Pagurusinferred from multiple mitochondrial genes, with special emphasis on the evolutionary relationship of Pagurus lanuginosus and Pagurus maculosus. Genetica.

717.

Sumiya, N., and Miyagishima, S.Y. (2017). Hierarchal order in the formation of chloroplast division machinery in the red alga Cyanidioschyzon merolae.
Commun Integr Biol 10, e1294298.

718.

Sumiya, N., Fujiwara, T., Era, A., and Miyagishima, S.Y. (2016) Chloroplast division checkpoint in eukaryotic algae. Proc Natl Acad Sci U S A 113, E7629-‑84‑

E7638.
719.

Sumiya, N., Fujiwara, T., Kobayashi, Y., Misumi, O., and Miyagishima, S.Y. (2014). Development of a heat-shock inducible gene expression system in the
red alga Cyanidioschyzon merolae. PLoS One 9, e111261.

720.

Sumiya, N., Kawase, Y., Hayakawa, J., Matsuda, M., Nakamura, M., Era, A., Tanaka, K., Kondo, A., Hasunuma, T., Imamura, S., and Miyagishima, S.Y.
(2015) Expression of Cyanobacterial Acyl-ACP Reductase Elevates the Triacylglycerol Level in the Red Alga Cyanidioschyzon merolae. Plant Cell Physiol
56,1962-1980.

721.

Suzuki, A., Ito, M., Hamaguchi, T., Mori, H., Takeda, Y., Baba, R., Watanabe, T., Kurokawa, K., Asakawa, S., Hirayama, M., et al. (2018). Quantificationof hydrogen production by intestinal bacteria that are specifically dysregulated in Parkinson’s disease. PLoS One 13, e0208313.

722.

Suzuki, A., Lee, L.J., Hayashi, Y., Muglia, L., Itohara, S., Erzurumlu, R.S., and Iwasato, T. (2015) Thalamic adenylyl cyclase 1 is required for barrel
formation in the somatosensory cortex. Neuroscience 290,518-529.

723.

Suzuki, A., Niimi, Y., and Saga, Y. (2014). Interaction of NANOS2 and NANOS3 with different components of the CNOT complex may contribute to thefunctional differences in mouse male germ cells. Biol. Open 3, 1207-1216.

724.

Suzuki, A., Niimi, Y., Shinmyozu, K., Zhou, Z., Kiso, M., and Saga, Y. (2016) Dead end1 is an essential partner of NANOS2 for selective binding of target
RNAs in male germ cell development. EMBO Rep 17, 37-46.

725.

Suzuki, A.C., Kagoshima, H., Chilton, G., Grothman, G.T., Johansson, C., and Tsujimoto, M. (2017). Meiofaunal Richness in Highly Acidic Hot Springs inUnzen-Amakusa National Park, Japan, Including the First Rediscovery Attempt for Mesotardigrada. Zoolog Sci 34, 11-17.

726.

Suzuki, I.K., and Hirata, T. (2014). A common developmental plan for neocortical gene-expressing neurons in the pallium of the domestic chicken Gallus
gallus domesticus and the Chinese softshell turtle Pelodiscus sinensis. Front. Neuroanat. 8, 20.

727.

Suzuki, M., Sato, Y., Wu, S., Kang, B.H., and McCarty, D.R. (2015). Conserved functions of the MATE transporter BIG EMBRYO 1 in regulation of lateralorgan size and initiation rate. Plant Cell, 27, 2288-2300.

728.

Suzuki, R., Yamazaki, T., Toyoda, A., and Kawano, S. (2014). A transformation system using rbcS N-terminal region fused with GFP demonstrates pyrenoid
targeting of the small subunit of rubisCO in Ulva compressa. Cytologia 79, 427-428.

729.

Suzuki, Ro, Ota S, and Yamazak T. (2016) Morphological changes of giant mitochondria in the unicellular to multicellular phase during parthenogenesis of
Ulva partita (Ulvophyceae) revealed by expression of mitochondrial targeting GFP and PEG transformation PHYCOLOGICAL RESEARCH 64, 176-184.

730.

Swann, J.B., Weyn, A., Nagakubo, D., Bleul, C.C., Toyoda, A., Happe, C., Netuschil, N., Hess, I., Haas-Assenbaum, A., Taniguchi, Y., Schorpp, M., andBoehm, T. (2014). Conversion of the thymus into a bipotent lymphoid organ by replacement of FOXN1 with its paralog, FOXN4. Cell Rep. 8, 1184-1197.

731.

Tabe, Y., Yamamoto, S., Saitoh, K., Sekihara, K., Monma, N., Ikeo, K., Mogushi, K., Shikami, M., Ruvolo, V., Ishizawa, J., Hail, N. Jr, Kazuno, S., Igarashi,M., Matsushita, H., Yamanaka, Y., Arai, H., Nagaoka, I., Miida, T., Hayashizaki, Y., Konopleva, M., and Andreeff, M. (2017). Bone Marrow Adipocytes
Facilitate Fatty Acid Oxidation Activating AMPK and a Transcriptional Network Supporting Survival of Acute Monocytic Leukemia Cells. Cancer Res 77,1453-1464.

732.

Tada, I., Saitoh, S., Aoyama, H., Shinzato, N., Yamamoto, N., Arita, M., and Ikematsu, S. (2017). Genome Sequence of Lactobacillus paracasei Strain LCIkematsu, Isolated from a Pineapple in Okinawa, Japan. Genome Announc 5, e01583-16.

733.

Tada, I., Tanizawa, Y., and Arita, M. (2017). Visualization of consensus genome structure without using a reference genome. BMC Genomics 18, 208.

734.

Tada, I., Tanizawa, Y., Endo, A., Tohno, M., and Arita, M. (2017). Revealing the genomic differences between two subgroups in Lactobacillus gasseri.
Biosci Microbiota Food Health 36, 155-159.

735.

Tagawa, K., Arimoto, A., Sasaki, A., Izumi, M., Fujita, S., Humphreys, T., Fujiyama, A., Kagoshima, H., Shin-I, T., Kohara, Y., Satoh, N., and Kawashima,
T. (2014). A cDNA resource for gene expression studies of a hemichordate, Ptychodera flava. Zoolog. Sci. 31, 414-420.

736.

Takada, T., Yoshiki, A., Obata, Y., Yamazaki, Y., and Shiroishi, T. (2015) NIG_MoG: a mouse genome navigator for exploring intersubspecific genetic
polymorphisms. Mamm Genome 26,331-337.

737.

Takagi, J., and Shimamoto, Y. (2017). High-quality frozen extracts of Xenopus laevis eggs reveal size-dependent control of metaphase spindle
micromechanics. Mol Biol Cell 28, 2170-2177.

738.

Takagi, J., and Shimamoto, Y. (2018). Mechanical heterogeneity and roles of parallel microtubule arrays in governing meiotic spindle length. BioRxiv
385633.

739.

Takagi, J., Itabashi, T., Suzuki, K., Shimamoto, Y., Kapoor, T.M., and Ishiwata, S. (2014). Micromechanics of the vertebrate meiotic spindle examined bystretching along the pole-to-pole axis. Biophys. J. 106, 735-740.

740.

Takagi, M., Natsume, T., Kanemaki, M.T., and Imamoto, N. (2016) Perichromosomal protein Ki67 supports mitotic chromosome architecture. Genes Cells
21, 1113-1124.

741.

Takagi, M., Ono, T., Natsume, T., Sakamoto, C., Nakao, M., Saitoh, N., Kanemaki, M.T., Hirano, T., and Imamoto, N. (2018). Ki-67 and condensins support
the integrity of mitotic chromosomes through distinct mechanisms. J. Cell Sci. 131, jcs212092.

742.

Takahashi, A., and Miczek, K.A. (2014). Neurogenetics of aggressive behavior: studies in rodents. Curr. Top. Behav. Neurosci. 17, 3-44.

743.

Takahashi, A., Lee, R.X., Iwasato, T., Itohara, S., Arima, H., Bettler, B., Miczek, K.A., and Koide, T. (2015) Glutamate input in the dorsal raphe nucleus asa determinant of escalated aggression in male mice. J Neurosci 35,6452-6463.

744.

Takahashi, A., Nagayasu, K., Nishitani, N., Kaneko, S., and Koide, T. (2014). Control of intermale aggression by medial prefrontal cortex activation in themouse. PLoS One 9, e94657.

‑85‑

745.

Takahashi, A., Okada, R., Nagao, K., Kawamata, Y., Hanyu, A., Yoshimoto, S., Takasugi, M., Watanabe, S., Kanemaki, M.T., Obuse, C., and Hara, E.
(2017). Exosomes maintain cellular homeostasis by excreting harmful DNA from cells. Nat Commun 8, 15287.

746.

Takahashi, A., Shiroishi, T., and Koide, T. (2014). Genetic mapping of escalated aggression in wild-derived mouse strain MSM/Ms: association withserotonin-related genes. Front. Neurosci. 8, 156.

747.

Takahashi, A., Sugimoto, H., Kato, S., Shiroishi, T., and Koide, T. (2015) Mapping of Genetic Factors That Elicit Intermale Aggressive Behavior on Mouse
Chromosome 15: Intruder Effects and the Complex Genetic Basis. PLoS One 10,e0137764.

748.

Takahashi, K., Hayano, T., Sugimoto, R., Kashiwagi, H., Shinoda, M., Nishijima, Y., Suzuki, T., Suzuki, S., Ohnuki, Y., Kondo, A., et al. (2018). Exomeand copy number variation analyses of Mayer-Rokitansky-Küster- Hauser syndrome. Hum. Genome Var. 5, 27.

749.

Takahashi, T., and Koblmüller, S. (2014). A new species of Petrochromis (Perciformes: Cichlidae) from Lake Tanganyika. Ichthyological Research 81, 252264.

750.

Takahashi, T., and Moreno, E. (2015) A RAD-based phylogenetics for Orestias fishes from Lake Titicaca. Mol Phylogenet Evol 93,307-317.

751.

Takahashi, T., and Sota, T. (2016) A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 100, 234-242.

752.

Takahashi, Y., Murakami, H., Akiyama, Y., Katoh, Y., Oma, Y., Nishijima, H., Shibahara, K.I., Igarashi, K., and Harata, M. (2017). Actin Family Proteinsin the Human INO80 Chromatin Remodeling Complex Exhibit Functional Roles in the Induction of Heme Oxygenase-1 with Hemin. Front Genet 8, 17.

753.

Takaku, Y., Hwang, J.S., Wolf, A., Bottger, A., Shimizu, H., David, C.N., and Gojobori, T. (2014). Innexin gap junctions in nerve cells coordinate
spontaneous contractile behavior in Hydra polyps. Sci. Rep. 4, 3573.

754.

Takami, H., Toyoda, A., Uchiyama, I., Itoh, T., Takaki, Y., Arai, W., Nishi, S., Kawai, M., Shin-Ya, K., and Ikeda, H. (2017). Complete genome sequenceand expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1. DNA Res 24, 169-177.

755.

Takao, D., and Kamimura, S. (2017). Simulation of intra-ciliary diffusion suggests a novel role of primary cilia as a cell-signaling enhancer. Dev GrowthDiffer 59, 415-422.

756.

Takehana, Y., Matsuda, M., Myosho, T., Suster, M.L., Kawakami, K., Shin-I, T., Kohara, Y., Kuroki, Y., Toyoda, A., Fujiyama, A., Hamaguchi, S.,
Sakaizumi, M., and Naruse, K. (2014). Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena. Nat. Commun.
5, 4157.

757.

Takehana, Y., Sakai, M., Narita, T., Sato, T., Naruse, K., and Sakaizumi, M. (2016) Origin of Boundary Populations in Medaka (Oryzias latipes Species
Complex). Zoolog Sci 33, 125-131.

758.

Takenaka, Y., Ikeo, K., and Shigeri, Y. (2016) Molecular Cloning of Secreted Luciferases from Marine Planktonic Copepods. Methods Mol Biol 1461, 3341.

759.

Takenouchi, T., Kuchikata, T., Yoshihashi, H., Fujiwara, M., Uehara, T., Miyama, S., Yamada, S., and Kosaki, K. (2017). Diagnostic use of computational
retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype. Am J Med Genet A 173, 1353-1357.

760.

Takeuchi, K., Nishino, T., Mayanagi, K., Horikoshi, N., Osakabe, A., Tachiwana, H., Hori, T., Kurumizaka, H., and Fukagawa, T. (2014). The centromeric
nucleosome-like CENP-T-W-S-X complex induces positive supercoils into DNA. Nucleic Acids Res. 42, 1644-1655.

761.

Takeuchi, M., Matsuda, K., Yamaguchi, S., Asakawa, K., Miyasaka, N., Lal, P., Yoshihara, Y., Koga, A., Kawakami, K., Shimizu, T., and Hibi, M. (2015)
Establishment of Gal4 transgenic zebrafish lines for analysis of development of cerebellar neural circuitry. Dev Biol 397,1-17.

762.

Takeuchi, T., Koyanagi, R., Gyoja, F., Kanda, M., Hisata, K., Fujie, M., Goto, H., Yamasaki, S., Nagai, K., Morino, Y., Miyamoto, H., Endo, K., Endo, H.,
Nagasawa, H., Kinoshita, S., Asakawa, S., Watabe, S., Satoh, N., and Kawashima, T. (2016) Bivalve-specific gene expansion in the pearl oyster genome:
implications of adaptation to a sessile lifestyle. Zoological Lett 2, 3.

763.

Takeuchi, Y., Ishikawa, A., Oda, Y., and Kitano, J. (2018). Lateralized expression of left-right axis formation genes is shared by adult brains of lefty andrighty scale-eating cichlids. Comp. Biochem. Physiol. Part D. Genomics Proteomics 28, 99-106.

764.

Talukder, A., and Ishihama, A. (2015) Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli. Sci China
Life Sci 58,902-911.

765.

Tamori, Y., and Deng, W.M. (2014). Compensatory cellular hypertrophy: the other strategy for tissue homeostasis. Trends Cell Biol. 24, 230-237.

766.

Tamori, Y., and Deng, W.M. (2017). Tissue-Intrinsic Tumor Hotspots: Terroir for Tumorigenesis. Trends Cancer 3, 259-268.

767.

Tamori, Y., Suzuki, E., and Deng, W.M. (2016) Epithelial Tumors Originate in Tumor Hotspots, a Tissue-Intrinsic Microenvironment. PLoS Biol 14,
e1002537.

768.

Tamura, M., Amano, T., and Shiroishi, T. (2014). The Hand2 gene dosage effect in developmental defects and human congenital disorders. Curr. Top. Dev.
Biol. 110, 129-152.

769.

Tamura, M., Shiroishi, T. (2015) GSDM family genes meet autophagy. Biochem J 469,e5-7.

770.

Tamura, R., Nakaoka, H., Yoshihara, K., Mori, Y., Yachida, N., Nishikawa, N., Motoyama, T., Okuda, S., Inoue, I., and Enomoto, T. (2018). Novel MXD4NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma. Genes. Chromosomes Cancer 57, 557-563.

771.

Tamura, R., Yoshihara, K., Saito, T., Ishimura, R., Martínez-Ledesma, J.E., Xin, H., Ishiguro, T., Mori, Y., Yamawaki, K., Suda, K., et al. (2018). Noveltherapeutic strategy for cervical cancer harboring FGFR3-TACC3 fusions. Oncogenesis 7, 4.

772.

Tamura, R., Yoshihara, K., Yamawaki, K., Suda, K., Ishiguro, T., Adachi, S., Okuda, S., Inoue, I., Verhaak, R.G., and Enomoto, T. (2015) Novel kinasefusion transcripts found in endometrial cancer. Sci Rep 5,18657.

‑86‑

773.

Tanaka, K., Arita, M., Li, D., Ono, N., Tezuka, Y., and Kanaya, S. (2015) Metabolomic characterization of a low phytic acid and high anti-oxidative cultivarof turmeric. Nat Prod Commun 10,329-334.

774.

Tanaka, K., Arita, M., Sakurai, H., Ono, N., and Tezuka, Y. (2015) Analysis of chemical properties of edible and medicinal ginger by metabolomics approach.
Biomed Res Int 2015,671058.

775.

Tanaka, K.M., Takahashi, A., Fuse, N., and Takano-Shimizu-Kouno, T. (2014). A novel cell death gene acts to repair patterning defects in Drosophilamelanogaster. Genetics 197, 739-742.

776.

Tanaka, S., Miyazawa-Onami, M., Iida, T., and Araki, H. (2015) iAID: an improved auxin-inducible degron system for the construction of a 'tight' conditional
mutant in the budding yeast Saccharomyces cerevisiae. Yeast 32,567-581.

777.

Tanaka, S., Tanaka, J., Miwa, Y., Horikawa, D.D., Katayama, T., Arakawa, K., Toyoda, A., Kubo, T., and Kunieda, T. (2015) Novel mitochondria-targeted
heat-soluble proteins identified in the anhydrobiotic Tardigrade improve osmotic tolerance of human cells. PLoS One 10,e0118272.

778.

Tanaka, W., and Arita, M. (2018). Physicochemical Prediction of Metabolite Fragmentation in Tandem Mass Spectrometry. Mass Spectrom. (Tokyo, Japan)
7, A0066.

779.

Tanimoto, H., Kimura, A., and Minc, N. (2016) Shape-motion relationships of centering microtubule asters. J Cell Biol 212, 777-787.

780.

Tanizawa, Y., Fujisawa, T., and Nakamura, Y. (2018). DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.
Bioinformatics 34, 1037-1039.

781.

Tanizawa, Y., Fujisawa, T., Kaminuma, E., Nakamura, Y., and Arita, M. (2016) DFAST and DAGA: web-based integrated genome annotation tools andresources. Biosci Microbiota Food Health 35, 173-184.

782.

Tanizawa, Y., Fujisawa, T., Mochizuki, T., Kaminuma, E., Nakamura, Y., and Tohno, M. (2014). Draft Genome Sequence of Lactobacillus oryzae Strain
SG293T. Genome Announcements 2, e00861-14.

783.

Tanizawa, Y., Fujisawa, T., Mochizuki, T., Kaminuma, E., Suzuki, Y., Nakamura, Y., and Tohno, M. (2014). Draft Genome Sequence of Weissella oryzae
SG25T, Isolated from Fermented Rice Grains. Genome Announcements 2, e00667-14.

784.

Tanizawa, Y., Kobayashi, H., Kaminuma, E., Sakamoto, M., Ohkuma, M., Nakamura, Y., Arita, M., and Tohno, M. (2017). Genomic characterization
reconfirms the taxonomic status of Lactobacillus parakefiri. Biosci Microbiota Food Health 36, 129-134.

785.

Tanizawa, Y., Tada, I., Kobayashi, H., Endo, A., Maeno, S., Toyoda, A., Arita, M., Nakamura, Y., Sakamoto, M., Ohkuma, M., et al. (2018). Lactobacillus
paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses. Int. J. Syst. Evol. Microbiol. 68, 3512-3517.

786.

Tanizawa, Y., Tohno, M., Kaminuma, E., Nakamura, Y., and Arita, M. (2015) Complete genome sequence and analysis of Lactobacillus hokkaidonensis
LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage.. BMC Genomics 16,240.

787.

Tatsumoto, S., Go, Y., Fukuta, K., Noguchi, H., Hayakawa, T., Tomonaga, M., Hirai, H., Matsuzawa, T., Agata, K., and Fujiyama, A. (2017). Direct
estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing. Sci Rep 7, 13561.

788.

Terui, R., Nagao, K., Kawasoe, Y., Taki, K., Higashi, T.L., Tanaka, S., Nakagawa, T., Obuse, C., Masukata, H., and Takahashi, T.S. (2018). Nucleosomesaround a mismatched base pair are excluded via an Msh2-dependent reaction with the aid of SNF2 family ATPase Smarcad1. Genes Dev. 32, 806-821.

789.

The Tree of Sex Consortium: Ashman T L., Bachtrog, D., Blackmon, H., Goldberg, E., Hahn, M., Kirkpatrick, M., Kitano, J., Mank, J., Mayrose, I., Ming,
R., Otto, S. P., Peichel, C. L., Pennell, M. W., Perrin, N., Ross, L., Valenzuela, N., and Vamosi, J. C. (2014). Tree of Sex: A database of sexual systems.
Scientific Data 1, 140015.

790.

Thorne, M.A., Kagoshima, H., Clark, M.S., Marshall, C.J., and Wharton, D.A. (2014). Molecular analysis of the cold tolerant Antarctic nematode,
Panagrolaimus davidi. PLoS One 9, e104526.

791.

To, T.K., and Kim, J.M. (2014). Epigenetic regulation of gene responsiveness in Arabidopsis. Front. Plant Sci. 4, 548.

792.

To, T.K., Saze, H., and Kakutani, T. (2015) DNA Methylation within Transcribed Regions. Plant Physiol 168,1219-1225.

793.

Tohno, M., Tanizawa, Y., Irisawa, T., Masuda, T., Sakamoto, M., Arita, M., Ohkuma, M., and Kobayashi, H. (2017). Lactobacillus silagincola sp. nov. and
Lactobacillus pentosiphilus sp. nov., isolated from silage. Int J Syst Evol Microbiol 67, 3639-3644.

794.

Toki, H., Inoue, M., Minowa, O., Motegi, H., Saiki, Y., Wakana, S., Masuya, H., Gondo, Y., Shiroishi, T., Yao, R., and Noda, T. (2014). Novelretinoblastoma mutation abrogating the interaction to E2F2/3, but not E2F1, led to selective suppression of thyroid tumors. Cancer Sci. 105, 1360-1368.

795.

Toki, H., Minowa, O., Inoue, M., Motegi, H., Karashima, Y., Ikeda, A., Kaneda, H., Sakuraba, Y., Saiki, Y., Wakana, S., Suzuki, H., Gondo, Y., Shiroishi,T., and Noda, T. (2016) Novel allelic mutations in murine Serca2 induce differential development of squamous cell tumors. Biochem Biophys Res Commun
476, 175-182.

796.

Tonosaki, K., Sekine, D., Ohnishi, T., Ono, A., Furuumi, H., Kurata, N., and Kinoshita, T. (2018). Overcoming the species hybridization barrier by ploidy
manipulation in the genus Oryza. Plant J. 93, 534-544.

797.

Tonoyama, Y., Shinya, M., Toyoda, A., Kitano, T., Oga, A., Nishimaki, T., Katsumura, T., Oota, H., Wan, M.T., Yip, B.W.P., et al. (2018). Abnormal
nuclear morphology is independent of longevity in a zmpste24-deficient fish model of Hutchinson-Gilford progeria syndrome (HGPS). Comp. Biochem.
Physiol. C. Toxicol. Pharmacol. 209, 54-62.

798.

Torigoe, M., Yamauchi, K., Kimura, T., Uemura, Y., and Murakami, F. (2016) Evidence That the Laminar Fate of LGE/CGE-Derived Neocortical
Interneurons Is Dependent on Their Progenitor Domains. J Neurosci 36, 2044-2056.

799.

Torigoe, M., Yamauchi, K., Zhu, Y., Kobayashi, H., and Murakami, F. (2015) Association of astrocytes with neurons and astrocytes derived from distinct
progenitor domains in the subpallium. Sci Rep 5, 12258.

‑87‑

800.

Toyomasu, T., Goda, C., Sakai, A., Miyamoto, K., Shenton, M.R., Tomiyama, S., Mitsuhashi, W., Yamane, H., Kurata, N., and Okada, K. (2018).
Characterization of diterpene synthase genes in the wild rice species Oryza brachyatha provides evolutionary insight into rice phytoalexin biosynthesis.
Biochem. Biophys. Res. Commun. 503, 1221-1227.

801.

Toyomasu, T., Miyamoto, K., Shenton, M.R., Sakai, A., Sugawara, C., Horie, K., Kawaide, H., Hasegawa, M., Chuba, M., Mitsuhashi, W., Yamane, H.,
Kurata, N., and Okada, K. (2016) Characterization and evolutionary analysis of ent-kaurene synthase like genes from the wild rice species Oryza rufipogon.
Biochem Biophys Res Commun 480, 402-408.

802.

Tsuboko, S., Kimura, T., Shinya, M., Suehiro, Y., Okuyama, T., Shimada, A., Takeda, H., Naruse, K., Kubo, T., and Takeuchi, H. (2014). Genetic control
of startle behavior in medaka fish. PLoS One 9, e112527.

803.

Tsuchida, S., Maruyama, F., Ogura, Y., Toyoda, A., Hayashi, T., Okuma, M., and Ushida, K. (2017). Genomic Characteristics of Bifidobacterium
thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates.
Front Microbiol 8, 1540.

804.

Tsuchiya, Y., Yoshiba, S., Gupta, A., Watanabe, K., and Kitagawa, D. (2016) Cep295 is a conserved scaffold protein required for generation of a bona fidemother centriole. Nat Commun 7, 12567.

805.

Tsuda, K., Abraham-Juarez, M.J., Maeno, A., Dong, Z., Aromdee, D., Meeley, R., Shiroishi, T., Nonomura, K.I., and Hake, S. (2017). KNOTTED1
Cofactors, BLH12 and BLH14, Regulate Internode Patterning and Vein Anastomosis in Maize. Plant Cell 29, 1105-1118.

806.

Tsuda, K., and Hake, S. (2015) Diverse functions of KNOX transcription factors in the diploid body plan of plants. Curr Opin Plant Biol 27,91-96.

807.

Tsuda, K., Kurata, N., Ohyanagi, H., and Hake, S. (2014). Genome-wide study of KNOX regulatory network reveals brassinosteroid catabolic genes
important for shoot meristem function in rice. Plant Cell 26, 3488-3500.

808.

Tsugawa, H., Cajka, T., Kind, T., Ma, Y., Higgins, B., Ikeda, K., Kanazawa, M., VanderGheynst, J., Fiehn, O., and Arita, M. (2015) MS-DIAL: dataindependent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods 12,523-526.

809.

Tsugawa, H., Ikeda, K., Tanaka, W., Senoo, Y., Arita, M., and Arita, M. (2017). Comprehensive identification of sphingolipid species by in silico retention-time and tandem mass spectral library. J Cheminform 9, 19.

810.

Tsugawa, H., Kanazawa, M., Ogiwara, A., and Arita, M. (2014). MRMPROBS suite for metabolomics using large-scale MRM assays. Bioinformatics 30,
2379-2380.

811.

Tsugawa, H., Kind, T., Nakabayashi, R., Yukihira, D., Tanaka, W., Cajka, T., Saito, K., Fiehn, O., and Arita, M. (2016) Hydrogen Rearrangement Rules:
Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. Anal Chem 88, 7946-7958.

812.

Tsugawa, H., Ohta, E., Izumi, Y., Ogiwara, A., Yukihira, D., Bamba, T., Fukusaki, E., and Arita, M. (2015). MRM-DIFF: data processing strategy for
differential analysis in large scale MRM-based lipidomics studies. Front Genet 5, 471.

813.

Tsuji, T., Gotoh, H., Morita, S., Hirata, J., Minakuchi, Y., Yaginuma, T., Toyoda, A., and Niimi, T. (2018). Molecular Characterization of Eye PigmentationRelated ABC Transporter Genes in the Ladybird Beetle Harmonia axyridis Reveals Striking Gene Duplication of the white Gene. Zoolog. Sci. 35, 260-267.

814.

Tsujimura, T., Takase, O., Yoshikawa, M., Sano, E., Hayashi, M., Takato, T., Toyoda, A., Okano, H., and Hishikawa, K. (2018). Control of directionalityof chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus. Epigenetics Chromatin 11, 51.

815.

Tsukahara, T., Iwase, N., Kawakami, K., Iwasaki, M., Yamamoto, C., Ohmine, K., Uchibori, R., Teruya, T., Ido, H., Saga, Y., Urabe, M., Mizukami, H.,
Kume, A., Nakamura, M., Brentjens, R., and Ozawa, K. (2015) The Tol2 transposon system mediates the genetic engineering of T-cells with CD19-specificchimeric antigen receptors for B-cell malignancies. Gene Ther 22,209-215.

816.

Tsukiji, N., Amano, T., and Shiroishi, T. (2014). A novel regulatory element for Shh expression in the lung and gut of mouse embryos. Mech. Dev. 131,
127-136.

817.

Tsunaka, Y., Fujiwara, Y., Oyama, T., Hirose, S., and Morikawa, K. (2016) Integrated molecular mechanism directing nucleosome reorganization by human
FACT. Genes Dev 30, 673-686.

818.

Uchimura, A., Higuchi, M., Minakuchi, Y., and Ohno, M., Toyoda, A., Fujiyama, A., Miura, I., Wakana, S., Nishino, J., Yagi, T. (2015) Germline mutation
rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice. Genome Res 25,1125-1134.

819.

Uchiyama, J., Asakura, R., Moriyama, A., Kubo, Y., Shibata, Y., Yoshino, Y., Tahara, H., Matsuhashi, A., Sato, S., Nakamura, Y., Tabata, S., and Ohta, H.
(2014). Sll0939 is induced by Slr0967 in the cyanobacterium Synechocystis sp. PCC6803 and is essential for growth under various stress conditions. Plant
Physiol. Biochem. 81, 36-43.

820.

Ujisawa, T., Ohta, A., Ii, T., Minakuchi, Y., Toyoda, A., Ii, M., and Kuhara, A. (2018). Endoribonuclease ENDU-2 regulates multiple traits including cold
tolerance via cell autonomous and nonautonomous controls in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U. S. A. 115, 8823-8828.

821.

Uno, Y., Osada, N., Sakurai, S., Shimozawa, N., Iwata, T., Ikeo, K., and Yamazaki, H. (2018). Development of genotyping method for functionally relevant
variants of cytochromes P450 in cynomolgus macaques. J. Vet. Pharmacol. Ther. 41, e30-e34.

822.

Uno, Y., Uehara, S., Kohara, S., Osada, N., Murayama, N., and Yamazaki, H. (2015) CYP2D44 polymorphisms in cynomolgus and rhesus macaques. Mol
Biol Rep 42,1149-1155.

823.

Ursell, T., Lee, T.K., Shiomi, D., Shi, H., Tropini, C., Monds, R.D., Colavin, A., Billings, G., Bhaya-Grossman, I., Broxton, M., Huang, B.E., Niki, H., and
Huang, K.C. (2017). Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. BMC Biol 15, 17.

824.

Urushihara, H., Kuwayama, H., Fukuhara, K., Itoh, T., Kagoshima, H., Shin-I, T., Toyoda, A., Ohishi, K., Taniguchi, T., Noguchi, H., Kuroki, Y., Hata, T.,
Uchi, K., Mohri, K., King, J.S., Insall, R.H., Kohara, Y., and Fujiyama, A. (2015) Comparative genome and transcriptome analyses of the social amoeba
Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation. BMC Genomics 16,80.

‑88‑

825.

Ushida, K., Tsuchida, S., Ogura, Y., Toyoda, A., and Maruyama, F. (2016) Domestication and cereal feeding developed domestic pig-type intestinal
microbiota in animals of suidae. Anim Sci J 87, 835-841.

826.

van, 't Hof F.N., Ruigrok, Y.M., Lee, C.H., Ripke, S., Anderson, G., de, Andrade M., Baas, A.F., Blankensteijn, J.D., Bottinger, E.P., Bown, M.J., Broderick,J., Bijlenga, P., Carrell, D.S., Crawford, D.C., Crosslin, D.R., Ebeling, C., Eriksson, J.G., Fornage, M., Foroud, T., von, Und Zu Fraunberg M., Friedrich,
C.M., Gaal, E.I., Gottesman, O., Guo, D.C., Harrison, S.C., Hernesniemi, J., Hofman, A., Inoue, I., Jaaskelainen, J.E., Jones, G.T., Kiemeney, L.A., Kivisaari,R., Ko, N., Koskinen, S., Kubo, M., Kullo, I.J., Kuivaniemi, H., Kurki, M.I., Laakso, A., Lai, D., Leal, S.M., Lehto, H., LeMaire, S.A., Low, S.K.,
Malinowski, J., McCarty, C.A., Milewicz, D.M., Mosley, T.H., Nakamura, Y., Nakaoka, H., Niemela, M., Pacheco, J., Peissig, P.L., Pera, J., RasmussenTorvik, L., Ritchie, M.D., Rivadeneira, F., van, Rij A.M., Santos-Cortez, R.L., Saratzis, A., Slowik, A., Takahashi, A., Tromp, G., Uitterlinden, A.G., Verma,
S.S., Vermeulen, S.H., Wang, G.T., Han, B., Rinkel, G.J., and de, Bakker P.I. (2016) Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic
Aneurysms. J Am Heart Assoc 5, e002603.

827.

Venero, Galanternik M., Castranova, D., Gore, A.V., Blewett, N.H., Jung, H.M., Stratman, A.N., Kirby, M.R., Iben, J., Miller, M.F., Kawakami, K., Maraia,
R.J., and Weinstein, B.M. (2017). A novel perivascular cell population in the zebrafish brain. Elife 6, e24369.

828.

Vukasinovic, N., Oda, Y., Pejchar, P., Synek, L., Pecenkova, T., Rawat, A., Sekeres, J., Potocky, M., and Zarsky, V. (2017). Microtubule-dependent targetingof the exocyst complex is necessary for xylem development in Arabidopsis. New Phytol 213, 1052-1067.

829.

Wada, H., and Kawakami, K. (2015) Size control during organogenesis: Development of the lateral line organs in zebrafish. Dev Growth Differ 57,169-178.

830.

Wada, H., Iwasaki, M., and Kawakami, K. (2014). Development of the lateral line canal system through a bone remodeling process in zebrafish. Dev. Biol.
392, 1-14.

831.

Wada, K., Wada, Y., Iwasaki, Y., and Ikemura, T. (2017). Time-series oligonucleotide count to assign antiviral siRNAs with long utility fit in the big dataera. Gene Ther 24, 668-673.

832.

Wai, H.A., Kawakami, K., Wada, H., Muller, F., Vernallis, A.B., Brown, G., and Johnson, W.E. (2015) The development and growth of tissues derived from
cranial neural crest and primitive mesoderm is dependent on the ligation status of retinoic acid receptor gamma: evidence that retinoic acid receptor gammafunctions to maintain stem/progenitor cells in the absence of retinoic acid. Stem Cells Dev 24,507-519.

833.

Wang, X.F., Shen, Y., Cheng, Q., Fu, C.L., Zhou, Z.Z., Hirose, S., and Liu, Q.X. (2017). Apontic directly activates hedgehog and cyclin E for proper organ
growth and patterning. Sci Rep 7, 12470.

834.

Watanabe, H., Goto, S., Mori, H., Higashi, K., Hosomichi, K., Aizawa, N., Takahashi, N., Tsuchida, M., Suzuki, Y., Yamada, T., Horii, A., Inoue, I.,
Kurokawa, K., and Narita, I. (2017). Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy. Nephrol Dial Transplant 32, 2072-2079.

835.

Watanabe, H., Nakamura, I., Mizutani, S., Kurokawa, Y., Mori, H., Kurokawa, K., and Yamada, T. (2018). Minor taxa in human skin microbiome contributeto the personal identification. PLoS One 13, e0199947.

836.

Watanabe, S., Noda, A., Ohbayashi, R., Uchioke, K., Kurihara, A., Nakatake, S., Morioka, S., Kanesaki, Y., Chibazakura, T., and Yoshikawa, H. (2018).
ParA-like protein influences the distribution of multi-copy chromosomes in cyanobacterium Synechococcus elongatus PCC 7942. Microbiology 164, 4556.

837.

Watanabe, T., Shimazaki, T., Mishiro, A., Suzuki, T., Hirata, H., Tanimoto, M., and Oda, Y. (2014). Coexpression of auxiliary Kvbeta2 subunits with Kv1.1
channels is required for developmental acquisition of unique firing properties of zebrafish Mauthner cells. J. Neurophysiol. 111, 1153-1164.

838.

White, M.A., Kitano, J., and Peichel, C.L. (2015) Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback
Y Chromosome. Mol Biol Evol 32,1981-1995.

839.

Wohlgemuth, G., Mehta, S.S., Mejia, R.F., Neumann, S., Pedrosa, D., Pluskal, T., Schymanski, E.L., Willighagen, E.L., Wilson, M., Wishart, D.S., Arita,M., Dorrestein, P.C., Bandeira, N., Wang, M., Schulze, T., Salek, R.M., Steinbeck, C., Nainala, V.C., Mistrik, R., Nishioka, T., and Fiehn, O. (2016)
SPLASH, a hashed identifier for mass spectra. Nat Biotechnol 34, 1099-1101.

840.

Wollmann, H., Stroud, H., Yelagandula, R., Tarutani, Y., Jiang, D., Jing, L., Jamge, B., Takeuchi, H., Holec, S., Nie, X., Kakutani, T., Jacobsen, S.E., andBerger, F. (2017). The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana. Genome Biol 18, 94.

841.

Wu, L., McCluskey, K., Desmeth, P., Liu, S., Hideaki, S., Yin, Y., Moriya, O., Itoh, T., Kim, C.Y., Lee, J.-S., et al. (2018). The global catalogue of
microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species. Gigascience 7, giy026.

842.

Wu, L., Sun, Q., Desmeth, P., Sugawara, H., Xu, Z., McCluskey, K., Smith, D., Alexander, V., Lima, N., Ohkuma, M., Robert, V., Zhou, Y., Li, J., Fan, G.,Ingsriswang, S., Ozerskaya, S., and Ma, J. (2017). World data centre for microorganisms: an information infrastructure to explore and utilize preserved
microbial strains worldwide. Nucleic Acids Res 45, D611-D618.

843.

Wu, Q., Fukuda, K., Kato, Y., Zhou, Z., Deng, C.X., and Saga, Y. (2016) Sexual Fate Change of XX Germ Cells Caused by the Deletion of SMAD4 andSTRA8 Independent of Somatic Sex Reprogramming. PLoS Biol 14, e1002553.

844.

Wu, Q., Fukuda, K., Weinstein, M., Graff, J.M., and Saga, Y. (2015) SMAD2 and p38 signaling pathways act in concert to determine XY primordial germ
cell fate in mice. Development 142,575-586.

845.

Xiao, Y., Faucherre, A., Pola-Morell, L., Heddleston, J.M., Liu, T.L., Chew, T.L., Sato, F., Sehara-Fujisawa, A., Kawakami, K., and Lopez-Schier, H. (2015)
High-resolution live imaging reveals axon-glia interactions during peripheral nerve injury and repair in zebrafish. Dis Model Mech 8,553-564.

846.

Yabuzaki, J. (2017). Carotenoids Database: structures, chemical fingerprints and distribution among organisms. Database (Oxford) 2017, bax004.

847.

Yagisawa, F., Kuroiwa, H., Fujiwara, T., and Kuroiwa, T. (2016) Intracellular Structure of the Unicellular Red Alga Cyanidioschyzon merolae in Response
to Phosphate Depletion and Resupplementation CYTOLOGIA 81, 341-347.

848.

Yamada, O., Machida, M., Hosoyama, A., Goto, M., Takahashi, T., Futagami, T., Yamagata, Y., Takeuchi, M., Kobayashi, T., Koike, H., Abe, K., Asai, K.,
Arita, M., Fujita, N., Fukuda, K., Higa, K.I., Horikawa, H., Ishikawa, T., Jinno, K., Kato, Y., Kirimura, K., Mizutani, O., Nakasone, K., Sano, M., Shiraishi,‑89‑Y., Tsukahara, M., and Gomi, K. (2016) Genome sequence of Aspergillus luchuensis NBRC 4314. DNA Res 23, 507-515.
849.

Yamagata, N., Hiroi, M., Kondo, S., Abe, A., and Tanimoto, H. (2016) Suppression of Dopamine Neurons Mediates Reward. PLoS Biol 14, e1002586.

850.

Yamaguchi, T., Hosomichi, K., Yano, K., Kim, Y.I., Nakaoka, H., Kimura, R., Otsuka, H., Nonaka, N., Haga, S., Takahashi, M., Shirota, T., Kikkawa, Y.,
Yamada, A., Kamijo, R., Park, S.B., Nakamura, M., Maki, K., and Inoue, I. (2017). Comprehensive genetic exploration of selective tooth agenesis ofmandibular incisors by exome sequencing. Hum Genome Var 4, 17005.

851.

Yamaguchi, T., Nakaoka, H., Yamamoto, K., Fujikawa, T., Kim, Y.I., Yano, K., Haga, S., Katayama, K., Shibusawa, T., Park, S.B., Maki, K., Kimura, R.,
and Inoue, I. (2014). Genome-wide association study of degenerative bony changes of the temporomandibular joint. Oral Dis. 20, 409-415.

852.

Yamamoto-Hino, M., Katsumata, E., Suzuki, E., Maeda, Y., Kinoshita, T., and Goto, S. (2018). Nuclear envelope localization of PIG-B is essential for GPIanchor synthesis in Drosophila. J. Cell Sci. 131, jcs218024.

853.

Yamamoto-Hino, M., Muraoka, M., Kondo, S., Ueda, R., Okano, H., and Goto, S. (2015) Dynamic regulation of innate immune responses in Drosophila by
Senju-mediated glycosylation. Proc Natl Acad Sci U S A 112,5809-5814.

854.

Yamamoto-Hino, M., Yoshida, H., Ichimiya, T., Sakamura, S., Maeda, M., Kimura, Y., Sasaki, N., Aoki-Kinoshita, K.F., Kinoshita-Toyoda, A., Toyoda,
H., Ueda, R., Nishihara, S., and Goto, S. (2015) Phenotype-based clustering of glycosylation-related genes by RNAi-mediated gene silencing. Genes Cells
20,521-542.

855.

Yamamoto, A., Yoshii, M., Murase, S., Fujita, M., Kurata, N., Hobo, T., Kagaya, Y., Takeda, S., and Hattori, T. (2014). Cell-by-cell developmental transition
from embryo to post-germination phase revealed by heterochronic gene expression and ER-body formation in Arabidopsis leafy cotyledon mutants. Plant
Cell Physiol. 55, 2112-2125.

856.

Yamamoto, K., and Kimura, A. (2017). An asymmetric attraction model for the diversity and robustness of cell arrangement in nematodes. Development
144, 4437-4449.

857.

Yamamoto, K., Makino, N., Nagai, M., Araki, H., and Ushimaru, T. (2018). CDK phosphorylation regulates Mcm3 degradation in budding yeast. Biochem.
Biophys. Res. Commun. 506, 680-684.

858.

Yamamoto, K., Makino, N., Nagai, M., Honma, Y., Araki, H., and Ushimaru, T. (2018). TORC1 signaling regulates DNA replication via DNA replication
protein levels. Biochem. Biophys. Res. Commun. 505, 1128-1133.

859.

Yamano, K., Wang, C., Sarraf, S.A., Münch, C., Kikuchi, R., Noda, N.N., Hizukuri, Y., Kanemaki, M.T., Harper, W., Tanaka, K., et al. (2018). Endosomal
Rab cycles regulate Parkin-mediated mitophagy. Elife 7, e31326.

860.

Yamauchi, K., Yamazaki, M., Abe, M., Sakimura, K., Lickert, H., Kawasaki, T., Murakami, F., and Hirata, T. (2017). Netrin-1 Derived from the VentricularZone, but not the Floor Plate, Directs Hindbrain Commissural Axons to the Ventral Midline. Sci Rep 7, 11992.

861.

Yamazaki, T., Endo, M., Ito, K., Suzuki, R., Ota, S., Kuwano, K., Miyamura, S., Toyoda, A., and Kawano, S. (2014). HAP2/GCS1 is involved in the sexual
reproduction system of the marine macroalga Ulva compressa (Ulvales, Chlorophyta). Cytologia 79, 575-584.

862.

Yamazaki, T., Ichihara, K., Suzuki, R., Oshima, K., Miyamura, S., Kuwano, K., Toyoda, A., Suzuki, Y., Sugano, S., Hattori, M., and Kawano, S. (2017).
Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita. Sci Rep 7, 11679.

863.

Yang, L., Paul, S., Trieu, K.G., Dent, L.G., Froldi, F., Fores, M., Webster, K., Siegfried, K.R., Kondo, S., Harvey, K., Cheng, L., Jimenez, G., Shvartsman,
S.Y., and Veraksa, A. (2016) Minibrain and Wings apart control organ growth and tissue patterning through down-regulation of Capicua. Proc Natl Acad
Sci U S A 113, 10583-10588.

864.

Yang, W.-T., Li, Y.-C., Lin, C.-M., Tang, W.-C., Chen, B.-C., Suzuki, E., and Hsu, J.-C. (2018). Adherens junction-associated pores mediate the intercellulartransport of endosomes and cytoplasmic proteins. Biochem. Biophys. Res. Commun. 505, 664-670.

865.

Yang, Y.-X., Wei, L., Zhang, Y.-J., Hayano, T., Piñeiro Pereda, M.D.P., Nakaoka, H., Li, Q., Barragán Mallofret, I., Lu, Y.-Z., Tamagnone, L., et al. (2018).
Long non-coding RNA p10247, high expressed in breast cancer (lncRNA-BCHE), is correlated with metastasis. Clin. Exp. Metastasis 35, 109-121.

866.

Yang, Y.H.C., Kawakami, K., and Stainier, D.Y. (2018). A new mode of pancreatic islet innervation revealed by live imaging in zebrafish. Elife 7, e34519.

867.

Yano, K., and Niki, H. (2017). Multiple cis-Acting rDNAs Contribute to Nucleoid Separation and Recruit the Bacterial Condensin Smc-ScpAB. Cell Rep
21, 1347-1360.

868.

Yano, K., Masuda, K., Akanuma, G., Wada, T., Matsumoto, T., Shiwa, Y., Ishige, T., Yoshikawa, H., Niki, H., Inaoka, T., and Kawamura, F. (2016) Growthand sporulation defects in Bacillus subtilis mutants with a single rrn operon can be suppressed by amplification of the rrn operon. Microbiology 162, 35-45.

869.

Yesbolatova, A., and Kanemaki, M.T. (2018). TAGing for destruction. Nat. Chem. Biol. 14, 414-415.

870.

Yokota, Y., Nakajima, H., Wakayama, Y., Muto, A., Kawakami, K., Fukuhara, S., and Mochizuki, N. (2015) Endothelial Ca(2+) oscillations reflect VEGFR
signaling-regulated angiogenic capacity in vivo. Elife 4,e08817.

871.

Yokouchi, K., Onuma, R., and Horiguchi, T. (2018). Ultrastructure and phylogeny of a new species of mixotrophic dinoflagellate, Paragymnodinium
stigmaticum sp. nov. (Gymnodiniales, Dinophyceae). Phycologia 57, 539-554.

872.

Yokoyama, S., Furukawa, S., Kitada, S., Mori, M., Saito, T., Kawakami, K., Belmonte, J.C.I., Kawakami, Y., Ito, Y., Sato, T., and Asahara, H. (2017).
Analysis of transcription factors expressed at the anterior mouse limb bud. PLoS One 12, e0175673.

873.

Yonezawa T, Segawa T, Mori H, Campos PF, Hongoh Y, Endo H, Akiyoshi A, Manabe M, Kohno N, Nishida S, Wu J, Jin H, Kishino H, Kurokawa K,
Yoshifumi N, Tanabe H, Mukoyama H, Yoshida K, Rasoamiaramanana A, Yamagishi S, Hayashi Y, Yoshida A, Koike H, Akishinonomiya F, Willerslev
E, Hasegawa M (2017) Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites. Current Biology, 27, 66-77.

874.

Yoo, S.K., Pascoe, H.G., Pereira, T., Kondo, S., Jacinto, A., Zhang, X., and Hariharan, I.K. (2016) Plexins function in epithelial repair in both Drosophila‑90‑and zebrafish. Nat Commun 7, 12282.
875.

Yoshiba, S., and Hamada, H. (2014). Roles of cilia, fluid flow, and Ca2+ signaling in breaking of left-right symmetry. Trends Genet. 30, 10-17.

876.

Yoshida, K., Go, Y., Kushima, I., Toyoda, A., Fujiyama, A., Imai, H., Saito, N., Iriki, A., Ozaki, N., and Isoda, M. (2016) Single-neuron and genetic
correlates of autistic behavior in macaque. Sci Adv 2, e1600558.

877.

Yoshida, K., Makino, T., and Kitano, J. (2017). Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus
nipponicus). J Hered 108, 63-68.

878.

Yoshida, K., Makino, T., Yamaguchi, K., Shigenobu, S., Hasebe, M., Kawata, M., Kume, M., Mori, S., Peichel, C.L., Toyoda, A., Fujiyama, A., and Kitano,J. (2014). Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. PLoS Genet 10, e1004223.

879.

Yoshida, K., Miyagi, R., Mori, S., Takahashi, A., Makino, T., Toyoda, A., Fujiyama, A., and Kitano, J. (2016) Whole-genome sequencing reveals small
genomic regions of introgression in an introduced crater lake population of threespine stickleback. Ecol Evol 6, 2190-2204.

880.

Yoshida, M. (2015) Genomic studies of the cephalopods. NIPPON SUISAN GAKKAISHI 81, 137-137.

881.

Yoshida, M., Nakanaga, K., Ogura, Y., Toyoda, A., Ooka, T., Kazumi, Y., Mitarai, S., Ishii, N., Hayashi, T., and Hoshino, Y. (2016) Complete Genome
Sequence of Mycobacterium ulcerans subsp. shinshuense. Genome Announc 4, e01050-01016.

882.

Yoshida, M.A., Ogura, A., Ikeo, K., Shigeno, S., Moritaki, T., Winters, G.C., Kohn, A.B., and Moroz, L.L. (2015) Molecular Evidence for Convergenceand Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems. Integr Comp Biol 55,1070-1083.

883.

Yoshida, M.A., Yamada, L., Ochi, H., Iwata, Y., Tamura-Nakano, M., Sawada, H., Sauer, W.H., Ogura, A., and Hirohashi, N. (2014). Integrative omics
analysis reveals differentially distributed proteins in dimorphic euspermatozoa of the squid, Loligo bleekeri. Biochem. Biophys. Res. Commun. 450, 12181224.

884.

Yoshida, M.A., Yura, K., and Ogura, A. (2014). Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Sci. Rep. 4, 4256.

885.

Yoshida, Y., Kuroiwa, H., Shimada, T., Yoshida, M., Ohnuma, M., Fujiwara, T., Imoto, Y., Yagisawa, F., Nishida, K., Hirooka, S., Misumi, O., Mogi, Y.,
Akakabe, Y., Matsushita, K., and Kuroiwa, T. (2017). Glycosyltransferase MDR1 assembles a dividing ring for mitochondrial proliferation comprising
polyglucan nanofilaments. Proc Natl Acad Sci U S A 114, 13284-13289.

886.

Yoshimi, K., Kunihiro, Y., Kaneko, T., Nagahora, H., Voigt, B., and Mashimo, T. (2016) ssODN-mediated knock-in with CRISPR-Cas for large genomic
regions in zygotes. Nat Commun 7, 10431.

887.

Yu, Q., Li, X.T., Zhao, X., Liu, X.L., Ikeo, K., Gojobori, T., and Liu, Q.X. (2014). Coevolution of axon guidance molecule Slit and its receptor Robo. PLoS
One 9, e94970.

888.

Yu, W., Zheng, H., Lin, W., Tajima, A., Zhang, Y., Zhang, X., Zhang, H., Wu, J., Han, D., Rahman, N.A., Korach, K.S., Gao, G.F., Inoue, I., and Li, X.
(2014). Estrogen promotes Leydig cell engulfment by macrophages in male infertility. J. Clin. Invest. 124, 2709-2721.

889.

Yun, K., Ajima, R., Sharma, N., Costantini, F., Mackem, S., Lewandoski, M., Yamaguchi, T.P., and Perantoni, A.O. (2014). Non-canonical Wnt5a/Ror2
signaling regulates kidney morphogenesis by controlling intermediate mesoderm extension. Hum. Mol. Genet. 23, 6807-6814.

890.

Yuyama, I., Higuchi, T., and Takei, Y. (2016) Sulfur utilization of corals is enhanced by endosymbiotic algae. Biol Open 5, 1299-1304.

891.

Yuyama, I., Ishikawa, M., Nozawa, M., Yoshida, M.-A., and Ikeo, K. (2018). Transcriptomic changes with increasing algal symbiont reveal the detailed
process underlying establishment of coral-algal symbiosis. Sci. Rep. 8, 16802.

892.

Zhai, Z., Kondo, S., Ha, N., Boquete, J.P., Brunner, M., Ueda, R., and Lemaitre, B. (2015) Accumulation of differentiating intestinal stem cell progenies
drives tumorigenesis. Nat Commun 6,10219.

893.

Zhang, B.B., Yao, Y.Y., Zhang, H.F., Kawakami, K., and Du, J.L. (2017). Left Habenula Mediates Light-Preference Behavior in Zebrafish via an
Asymmetrical Visual Pathway. Neuron 93, 914-928.e4.

894.

Zhang, R.W., Li, X.Q., Kawakami, K., and Du, J.L. (2016) Stereotyped initiation of retinal waves by bipolar cells via presynaptic NMDA autoreceptors.
Nat Commun 7, 12650.

895.

Zhao, W., Ajima, R., Ninomiya, Y., and Saga, Y. (2015) Segmental border is defined by Ripply2-mediated Tbx6 repression independent of Mesp2. Dev
Biol 400,105-117.

896.

Zhao, W., Oginuma, M., Ajima, R., Kiso, M., Okubo, A., and Saga, Y. (2018). Ripply2 recruits proteasome complex for Tbx6 degradation to define segment
border during murine somitogenesis. Elife 7, e33068.

897.

Zhou, M., Kawashima, N., Suzuk, N., Yamamoto, M., Ohnishi, K., Katsube, K., Tanabe, H., Kudo, A., Saito, M., and Suda, H. (2015) Periostin is a negative
regulator of mineralization in the dental pulp tissue. Odontology 103,152-159.

898.

Zhou, Z., Kawabe, H., Suzuki, A., Shinmyozu, K., and Saga, Y. (2017). NEDD4 controls spermatogonial stem cell homeostasis and stress response by
regulating messenger ribonucleoprotein complexes. Nat Commun 8, 15662.

899.

Zhou, Z., Shirakawa, T., Ohbo, K., Sada, A., Wu, Q., Hasegawa, K., Saba, R., and Saga, Y. (2015) RNA Binding Protein Nanos2 Organizes Posttranscriptional Buffering System to Retain Primitive State of Mouse Spermatogonial Stem Cells. Dev Cell 34,96-107.

900.

Zhu, Y., Matsumoto, T., Nagasawa, T., Mackay, F., and Murakami, F. (2015) Chemokine Signaling Controls Integrity of Radial Glial Scaffold in Developing
Spinal Cord and Consequential Proper Position of Boundary Cap Cells. J Neurosci 35,9211-9224.

901.

Zitouni, S., Francia, M.E., Leal, F., Montenegro, Gouveia S., Nabais, C., Duarte, P., Gilberto, S., Brito, D., Moyer, T., Kandels-Lewis, S., Ohta, M.,
Kitagawa, D., Holland, A.J., Karsenti, E., Lorca, T., Lince-Faria, M., and Bettencourt-Dias, M. (2016) CDK1 Prevents Unscheduled PLK4-STIL Complex
Assembly in Centriole Biogenesis. Curr Biol 26, 1127-1137.

‑91‑