Research outline（Updated: November 1st, 2021）
Department/Center
Department ofInformatics

Laboratory

Gene- Expression
Analysis

Faculty

OKUBO, Kousaku / Professor

Genetic Informatics KAWAMOTO, Shoko /Associate Professor

Genome Evolution

Genome Diversity

KUROKAWA, Ken / Professor
HIGASHI, Koichi / Assistant Professor

MORI, Hiroshi / Associate Professor

BiologicalNetworks

ARITA, Masanori / Professor

GenomeInformatics

NAKAMURA, Yasukazu / Professor

KAWASHIMA, Takeshi / Assistant Professor

TANIZAWA, Yasuhiro / Assistant Professor

Research outline“How can we make use of data and information at ourfinger-tip in making smarter decisions in our own
contexts?” Without solving this question, all analytical anddescriptive efforts that digitalize the reality end up in vain.
Our tentative answer/goal for this is to develop method toenhance “fluidity” and “utility"of medical knowledge among
humans and machines.
We are working on research and development of databases
and information retrieval system for the national
bio-resource project (NBRP).
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 an
integrated database “MicrobeDB.jp”, II. Microbialcommunity dynamics.
Our main research goal is to understand the relationships
between the habitat of organisms and genome diversity. To
facilitate the studies using comparative genomics andmetagenomics, we arealso developing various
bioinformatics methodologies.
Network analysis of metabolic pathways based oncomprehensive identification and quantification ofmetabolites (metabolomics); Bioinformatics related to plantsecondary metabolism and lipid metabolism
Intelligent information technology for structural andfunctional annotations of large-scale nucleotide sequences.

Department ofGenomics andEvolutionary Biology

DNA Data Analysis

Population
Genetics

IKEO, Kazuho / Associate Professor

SAITOU, Naruya / Professor※To be retired on March 31st,2022

JINAM, Timothy / Assistant Professor
SATO, Yutaka / Professor

Plant Genetics

NOSAKA (TAKAHASHI), Misuzu / AssistantProfessor
SUZUKI, Toshiya / Assistant Professor

EvolutionaryGenetics

Human Genetics

Ecological Genetics
Comparative
Genomics
Molecular Life
History

AKASHI, Hiroshi / Professor
MATSUMOTO, Tomotaka / Assistant Professor

INOUE, Ituro /Professor
KITANO, Jun / Professor

Evolutionary study of genomic structure and gene
expression pattern to elucidate the evolutionary
mechanism of central nervous system and sensory organs.
Evolutionary genomics analysis of various species.
Metagenome analysis.Developing databases and computer
software for biological research.
We study evolution of genes and genomes, in particular
human evolution. We also develop methods for study ofgenome evolution.
The goal of our research is to understand molecularmechanisms governing early processes of plantdevelopment using a series of rice embryogenesis defective
mutants. Currently we are focusing on the mechanism of
regulating the cell division pattern and plasticity incellular differentiation in rice embryo.
We infer mechanisms of genome evolution using population
genetic andcomparative genomic approaches. Current interests
include global
forces such as biosynthetic constraints that underlie weakselection.
Medical genomic study using high-throughput sequencing
data is a promising procedure to create an innovate
healthcare system and open a new aspect of population
genetics.

YAMASAKI, Yo / Assistant Professor

We use threespine stickleback fishes to investigate thegenetic and molecular mechanisms underlying adaptationand speciation.

TOYODA, Atsushi / Project Professor

We have been conducting advanced genomics research on
the plasticity of genome structure and functions using mostadvanced genome technology such as New-Generation
Sequencers.

KURAKU, Shigehiro / Professor

We focus on vertebrates and bridge molecular-level
laboratory approaches and genome informatics, in order todocument genome evolution and elucidate its mechanism.

Symbiosis and CellEvolution

Model FishGenetics
Cell Dynamics andSignaling

Department of Gene
Function andPhenomicsPlant Cytogenetics

MIYAGISHIMA, Shin-ya / Professor
FUJIWARA, Takayuki / Assistant Professor

SAKAI, Noriyoshi / Associate Professor
KAWASAKI, Toshihiro / Assistant Professor
ODA, Yoshihisa / Professor
SASAKI, Takema / Assistant Professor
NONOMURA, Ken-ichi / Associate Professor
TSUDA, Katsutoshi / Assistant Professor

Mammalian Neural IWASATO, Takuji / Professor
Circuits
NAKAGAWA, Naoki / Assistant Professor
Multiscale Sensory
Structure
Multicellular
Organization
Brain Function
Molecular andDevelopmentalBiology

YONEHARA, Keisuke / Professor
SAWA, Hitoshi / Professor
NEGISHI, Takefumi / Assistant Professor
HIRATA, Tatsumi / Professor
KAWASAKI, Takahiko / Assistant Professor
ZHU, Yan / Assistant Professor
KAWAKAMI, Koichi / Professor

In order to understand endosymbiotic evolution of
eukaryotes, we are studying coordinating mechanisms ofeukaryotic cell and organelle/endosymbiont proliferation
using algae, plants, and protists.
We establish reliable protocols for genetically modificationof zebrafish using sperm, and analyze the molecularmechanisms of spermatogenesis and early development inzebrafish.
We study the dynamic behavior of cortical cytoskeletonsand small GTPases during cell differentiation and celldivision to understand the mechanism underlying cell wall
patterning in plant cells.
We aim to elucidate the regulatory system of plant
germ-cell development and chromosome kinetics, mainly
using seed-sterile rice mutants.
We are studying molecular and cellular mechanisms ofneuronal circuit development in the mammals, using
mouse genetics and other related methods.
We use mice and marmosets to understand the structure,function, development, disease, and environmental
adaptation of visual neural circuits at multi-levels,
including genes, neural circuit physiology, and behavior.
We are studying the mechanisms that produce a variety ofcell types through asymmetric cell divisions using thenematode C.elegans.
Development of the vertebrate nervous system with special
focus on neuronal network formation.
Genetic studies on development, morphogenesis andbehaviors by using a model vertebrate zebrafish.

SAGA, Yumiko / Professor
Mammalian
Development※To be retired on March 31st,2022

KATO, Yuzuru / Assistant Professor
AJIMA, Rieko / Assistant Professor

Microbial
Physiology
Mouse Genomics
Resource

Genome DynamicsNIKI, Hironori / Professor

KOIDE, Tsuyoshi / Associate Professor
TAKANAMI, Keiko /Assistant Professor

MAESHIMA, Kazuhiro / Professor
IDE, Satoru / Assistant Professor
HIBINO, Kayo / Assistant Professor

Cell Architecture

KIMURA, Akatsuki / Professor
TORISAWA, Takayuki / Assistant Professor

Department ofChromosome Science
Physics and Cell
Biology

Molecular Cell
Engineering

SHIMAMOTO, Yuta / Associate Professor
SAITO, Kei / Assistant Professor

KANEMAKI, Masato / Professor

We study the early developmental events and theregulatory mechanisms during mouse embryogenesis
through generation and analyses of gene-knockout andtransgenic mice. We are especially interested in the organs
derived from mesoderm (heart, lung, somite), and the germ
cell system.
We investigate higher order structure of chromosomes andtheir dynamics in yeast and bacteria through genetic andcell biological analysis.
For understanding genetic basis of behavioral diversity,behavioral and genetic analyses are applied on a variety ofmouse resources including wild-derived strains. We aredeveloping genome editing methods in mice for analyzing
function of genes.
Our research interest lies in determining how a long stringof genomic DNA is three-dimensionally organized in living
cells, and how the organized genome functions duringcellular proliferation, differentiation, and development. We
are using a novel combination of molecular cell biology andbiophysics to elucidate 3D-organization and dynamics ofhuman genome chromatin.
To understand the three-dimensional architecture of thecell and its dynamics, quantitative imaging and modelingapproaches are employed. Specific targets of the research
are size and shape of organelles, the mechanics ofcytokinesis, and cytoplasmic streaming in the C. elegans
embryo.
Our laboratory uses a combination of biophysics,
biochemistry, cell biology, and materials science to study
how the mitotic spindle properly assembles and segregateschromosomes in cell division.
To understand DNA transactions in human cells, we
generate conditional cells using the auxin-inducible degron
technology for genetic and cytological analyses. We also
develop new technologies for construction of mutant humancells.

Invertebrate
Genetics

SAITO, Kuniaki / Professor
MIYOSHI, Keita / Assistant Professor

We investigate molecular mechanisms of Drosophila geneexpression and repression through biochemical and genetic
techniques. Especially, we are focusing on the small RNA
pathways and chromatin regulation during germ celldevelopment.

KUBO, Fumi / Associate Professor

We study how visual information generates goal-directedbehavior. We aim to understand the neural circuitmechanisms underlying this process using a combination ofgenetic, optic and behavioral approaches in zebrafish.

MURAYAMA, Yasuto / Associate Professor

We investigate molecular mechanism underling regulationof chromosome organization and dynamics byrecapitulating their biochemical reactions using purified
proteins. We now especially focus on SMC complexes.

Advanced Genomics
CenterNOGUCHI, Hideki / Project Professor

Development of new algorithms for de novo sequenceassemblies, and analytical tools for comparative genomics
employing massive data produced from next generation
sequencers.

Radioisotope Unit

ANDACHI, Yoshiki / Assistant Professor

We study microRNA-mediated post-transcriptional
regulation in C. elegans using our original methods for thedetection of microRNAs and target genes.

Center for Frontier
ResearchSystems
Neuroscience

Chromosome
Biochemistry