Research Outline（Updated: April 1st, 2024）
Department/Center
Department ofInformatics

Laboratory

Gene- Expression
Analysis

Faculty

OKUBO, Kousaku / Professor

Genetic Informatics KAWAMOTO, Shoko /Associate Professor

Genome Evolution

Genome Diversity

Department ofGenomics andEvolutionary Biology

KUROKAWA, Ken / Professor
HIGASHI, Koichi / Assistant Professor

MORI, Hiroshi / Associate Professor

Biological
Networks

ARITA, Masanori / Professor

GenomeInformatics

NAKAMURA, Yasukazu / Professor

DNA Data Analysis

KOSHIMIZU, Shizuka / Assistant Professor

TANIZAWA, Yasuhiro / Assistant Professor

IKEO, Kazuho / Associate 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 analyticaland descriptive efforts that digitalize the reality end up invain. Our tentative answer/goal for this is to develop
method to enhance “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 bioresource 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 toplant secondary metabolism and lipid metabolism
Intelligent information technology for structural andfunctional annotations of large-scale nucleotide sequences.
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.

Plant Genetics

SATO, Yutaka / Professor

Evolutionary
Genetics

AKASHI, Hiroshi / Professor

Ecological Genetics
ComparativeGenomics
Molecular Life
History
Symbiosis and Cell
Evolution

Department of GeneFunction andPhenomics

Model FishGenetics

Plant Cytogenetics

KITANO, Jun / Professor
YAMASAKI, Yo / Assistant Professor
TOYODA, Atsushi / Project Professor
KURAKU, Shigehiro / Professor
KAWAGUCHI, Akane / Assistant Professor
MIYAGISHIMA, Shin-ya / Professor
FUJIWARA, Takayuki / Assistant Professor

SAKAI, Noriyoshi / Associate Professor

NONOMURA, Ken-ichi / Associate Professor
TSUDA, Katsutoshi / Assistant Professor

Mammalian Neural IWASATO, Takuji / Professor
Circuits
NAKAGAWA, Naoki / Assistant Professor

The goal of our research is to understand molecularmechanisms governing early processes of plantdevelopment using a series of rice embryogenesis defectivemutants. Currently we are focusing on the mechanism ofregulating 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 weak
selection.
We use threespine stickleback fishes to investigate thegenetic and molecular mechanisms underlying adaptationand speciation.
We have been conducting advanced genomics research on
the plasticity of genome structure and functions using
most advanced genome technology such as NewGeneration Sequencers.
We focus on vertebrates and bridge molecular-level
laboratory approaches and genome informatics, in order todocument genome evolution and elucidate its mechanism.
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 aim to elucidate the regulatory system of plant germcell 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.

Neurobiology andPathology

Multiscale Sensory
Structure
MulticellularOrganization
Brain Function
Molecular andDevelopmentalBiology
Microbial
Physiology
Mouse Genomics
Resource
Department ofChromosome Science
Genome Dynamics

ASAKAWA, Kazuhide / Associate Professor

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

Using zebrafish as a primary model, we study the biology
and disease of the motor system at the behavioral, circuit,
cellular, and molecular levels. The ultimate goal is toidentify the root causes of ALS and to develop therapeuticstrategies through comprehensive and multidimensional
basic research.
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.

KAWAKAMI, Koichi / Professor

Genetic studies on development, morphogenesis andbehaviors by using a model vertebrate zebrafish.

NIKI, Hironori / ProfessorWe 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.

KOIDE, Tsuyoshi / Associate Professor

MAESHIMA, Kazuhiro / Professor
HIBINO, Kayo / Assistant Professor

Cell Architecture

Chromosome
Biochemistry
Physics and Cell
Biology

Center for Frontier
Research

KIMURA, Akatsuki / Professor
TORISAWA, Takayuki / Assistant Professor

MURAYAMA, Yasuto / Associate Professor
KUROKAWA, Yumiko / Assistant Professor
SHIMAMOTO, Yuta / Associate Professor
SAITO, Kei / Assistant Professor

Molecular CellEngineering

KANEMAKI, Masato / Professor

Invertebrate
Genetics

SAITO, Kuniaki / Professor

YAMAGUCHI, Kosuke / Assistant Professor

MIYOSHI, Keita / Assistant Professor

Gene Quantity
Biology

SASAKI, Mariko / Associate Professor

Plant Evolution

FUKUSHIMA, Kenji / Associate Professor

Theoretical Ecology
YAMAMICHI, Masato / Associate Professor
and Evolution

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.
We investigate molecular mechanism underling regulationof chromosome organization and dynamics byrecapitulating their biochemical reactions using purified
proteins. We now especially focus on SMC complexes.
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, wegenerate conditional cells using the auxin-inducible degron
technology for genetic and cytological analyses. We also
develop new technologies for construction of mutant
human cells.
We investigate molecular mechanisms of Drosophila gene
expression and repression through biochemical and genetic
techniques. Especially, we are focusing on the small RNA
pathways and chromatin regulation during germ cell
development.
We study molecular mechanisms underlying genomicchanges in eukaryotic cells. We mainly use budding yeast
and human cell cultures and analyze genomic changes that
result in changes to DNA quantity, using genetic andmolecular biology tools. We specialize in isolating Mbpsized DNA and separating it by Pulsed-Field Gel
Electrophoresis.
Our research aims to demystify evolutionary innovations byintegrating computational and experimental approaches tostudy a wide range of organisms, with a particular focus onplants.
We combine mathematical models, microcosm experiments,and meta-analyses to investigate complex feedbacks
between rapid evolution and ecological processes.

Chemical andRadioisotope
Management 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.