Theoretical Cell Science

kao Wataru Fujibuchi, Ph.D. Professor   btn

As the first informatics laboratory at CiRA, we are engaging in 1) spatio-temporal analysis of cell differentiations to construct fundamental theories, 2) design of 3D tissues derived from iPS cells by single-cell analysis, 3) development of a human cell database and its medical application, and 4) establishment of drug screening system for cell therapy based on artificial intelligence.  To enhance quality control of engineered cells, we are further developing a reference database of all human cell types at single-cell levels. Using this database, we will construct a “cell periodic table” with which we will theoretically find unknown cell types or elucidate the natural history of cell type generation.

Research and Education

Our laboratory directs Japanese Society for Bioinformatics (JSBi) as a board member and leads “SIG on Biological Systems Theory” of JSBi, thus students are encouraged to give a few presentations in a year. Our laboratory has a new system; the wet group conducts demonstration experiments to verify theories, which is uncommon for informatics laboratories. Therefore, students may take a part in either wet or dry group and perform researches. The wet group develops advanced single-cell analysis technologies, measuring omics data from whole human cell types. With the obtained data, the dry group constructs a human cell database (SHOGoiN), developing algorithms and tools to analyze it. Both groups collaborate to challenge the birth mechanisms of cell types or diseased cells.
As educational activities, we have a meeting for journal news and research seminar once a week to polish up speed-reading and presentation skills. From this fiscal year, we started a student exchange program with Berlin-Brandenburg Center for Regenerative Therapies, and enthusiastic students may be allowed to stay in a couple of months even if they are in the first year. Importantly, we have options to hire students in our laboratory to support his or her school expenses.

1) Database for human cell information for cell studies and differentiation analyses

2) Photo of laboratory members (April of 2018)

Recent Publications

  1. Aiba T, Saito T, Hayashi A, Sato S, Yunokawa H, Maruyama T, Fujibuchi W, Kurita H, Ohsako S. Does the prenatal bisphenol A exposure alter DNA methylation levels in the mouse hippocampus? : An analysis using a high-sensitivity methylome technique Genes and Environment (accepted 2018)
  2. Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH. A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.
    Stem Cell Reports 10(1):1-6, 2018.
  3. Sakurai, K., Kurtz, A., Stacey, G., Sheldon, M., and Fujibuchi, W.
    First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine.
    Stem Cells Transl Med. 5(10): 1345-1361 (2016).
  4. Yamane, J., Aburatani, S., Imanishi, S., Akanuma, H., Nagano, R., Kato, T., Sone, H., Ohsako, S. and Fujibuchi, W.
    Prediction of Developmental Chemical Toxicity based on Gene Networks of Human Embryonic Stem Cells.
    Nucleic Acids Res. 44(12): 5515-5528 (2016).
  5. Tanaka, T., Maeda, Y., Veluchamy, A., Tanaka, M., Abida, H., Maréchal, E., Bowler, C., Muto, M., Sunaga, Y., Tanaka, M., Yoshino, T., Taniguchi, T., Fukuda, Y., Nemoto, M., Matsumoto, M., Wong, P.S., Aburatani, S., and Fujibuchi, W.
    Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome.
    Plant Cell. 27(1): 162-176 (2015).

Theoretical Cell Science

Professor: Wataru Fujibuchi
Researcher: Junko Yamane