Laboratory of Interdisciplinary Biology (Theoretical Biology)



Associate Professor
Koichi Fujimoto
Specially-appointed Associate Professor
Thorsten Henrich
Assistant Professor
Miho S. Kitazawa
mail kitazawa @
Specially-appointed Assistant Professor
Katsuyoshi Matsushita
mail kmatsu @

Interdisciplinary Biology


Department of Biological Sciences


School of Science

Research Theme

Using physics, mathematics and bioinformatics, our laboratory tries to understand the underlying mechanisms of biological processes using computer simulations and data analysis.


Living systems are highly complex where huge number of dynamic elements (genes and cells) interact each other to perform various functions. Recent development of highly quantitative experiments has clarified that the structure of the gene networks can affect the spatiotemporal gene expression. However, the structure-function relationship is little examined. By mutual feedback between the experiment and mathematical analyses, a design principle of living systems might be discovered. Currently, we are mainly studying how gene networks regulate animal and plant morphogenesis, and chemical and mechanical communications of cell populations. Through the physical and mathematical analyses of the models consistently with molecular genetic data, our missions are to uncover the function of the network-structure-function relationship, the logic of the network evolution, and the collective decision making of cells (Left figure).


Recently a number of orphan genes where identified in several organisms that have no homologues in any other species. The mechanisms, however of how new genes emerge has not yet been understood. To approach this question we start with well-annotated genomes and use genes without any homology assignment as a candidate list for gene emergence. We will screen this candidate list by using gene expression data and sequence comparisons to other genomes. This way we can study the changes that have occurred to bring a gene into existence (Right figure).

0Fujimoto research

1Henrich research


M.S. Kitazawa and K. Fujimoto. Relationship between the species-representative phenotype and intraspecific variation in Ranunculaceae floral organ and Asteraceae flower numbers Annals of Botany 117(5) , 925 - 935 (2016)

M.S. Kitazawa and K. Fujimoto. A Dynamical Phyllotaxis Model to Determine Floral Organ Number PLOS Comp. Biol. 11(5): e1004145 , (2015)

M.S. Kitazawa and K. Fujimoto. A developmental basis for stochasticity in floral organ numbers. Frontiers Plant Sci. 5: 545 , (2014)

K. Fujimoto and S. Sawai. A Design Principle of Group-level Decision Making in Cell Populations. PLOS Comp. Biol. 9(6): e1003110 , (2013)

T. Gregor, K. Fujimoto, N. Masaki, S. Sawai. The Onset of Collective Behavior in Social Amoebae. Science 328 (5981) , 1021 - 1025 (2010)

K. Fujimoto, S. Ishihara and K. Kaneko. Network evolution of body plans. PLoS ONE 3(7): e2772 , (2008)


Dr. Koichi Fujimoto
Osaka University, Graduate School of Science
1-1, Machikaneyama-cho, Toyonaka, Osaka 560-0043
TEL/FAX: +81-6-6850-5822

Thorsten Henrich, Ph.D., Associate Professor
Osaka University, Chemistry Biology Combined Major Program, International College
5th floor of Interdisciplinary Research Building, room 509
1-2 Machikaneyama-cho, Toyonaka,
Osaka 560-0043, Japan

Tel: +81-6-6850-5578
Fax: +81-6-6850-5961