Education:

B.A.        University of Tokyo, Dept. of Mathematical Engineering (Mar 1999)

Ph.D.        Tokyo Medical and Dental University, Dept. of Bioinformatics (Mar 2005)

Professional experiences:

Jan 2006 - present

1. Assistant Professor, Dept. of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University
   

Aug 2009 - Sep 2009

1. Visiting Researcher, BIOQUANT, Heidelberg University
   

May 2008 - Nov 2008

1. Visiting Researcher, BIOQUANT, Heidelberg University
   

Apr 2006 - Dec 2006

1. Project Assistant Professor, Center for Information Medicine, Tokyo Medical and Dental University
   

Apr 2005 - Mar 2006

1. Postdoctoral Researcher, Dept. of Bioinformatics, Tokyo Medical and Dental University
   

Selected publications:

1. 1.Human mesenchymal stem cells in synovial fluid increase in the knee with degenerated cartilage and osteoarthritis.
   Sekiya I, Ojima M, Suzuki S, Yamaga M, Horie M, Koga H, Tsuji K, Miyaguchi K, Ogishima S, Tanaka H, Muneta T.
   J Orthop Res. 2011 (accepted).
   

2. 2.The 2nd DBCLS BioHackathon: interoperable bioinformatics web services for integrated applications.
   

3. Katayama T†, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Knjo AR, Konishi F, Kovarskaya Y, Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.
   

4. J Biomed Semantics. 2011;2:4.
   

3. 3. Omics-based identification of pathophysiological processes.
   

4. Tanaka H†, Ogishima S.
   

5. Methods Mol Biol. 2011;719:499-509.
   

4. 4. Suppression of the novel ER protein Maxer by mutant ataxin-1 in Bergman glia contributes to non-cell-autonomous toxicity.
   

5. Shiwaku H, Yoshimura N, Tamura T, Sone M, Ogishima S, Watase K, Tagawa K, Okazawa H†.
   

6. EMBO J. 2010 Jul 21;29(14):2446-60.
   

5. 5. Prognostic value of matrix Gla protein in breast cancer.
   

6. Yoshimura K, Takeuchi K, Nagasaki K, Ogishima S, Tanaka H, Iwase T, Akiyama F, Kuroda Y, Miki Y†.
   

7. Mol Med Report. 2009 Jul-Aug;2(4):549-53.
   

6. 6. Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation.
   

7. Ota MS, Kaneko Y, Kondo K, Ogishima S, Tanaka H, Eto K, Kondo T†.
   

8. PLoS Genet. 2009 Apr;5(4):e1000443.
   

7. 7. BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network.
   

8. Ishiwata RR*, Morioka MS*, Ogishima S†, Tanaka H.
   

9. Bioinformatics. 2009 Feb 15;25(4):543-4.
   

8. 8. Missing link in the evolution of Hox clusters.
   

9. Ogishima S, Tanaka H†.
   

10. Gene. 2007 Jan 31;387(1-2):21-30.
    

9. 9. Standardized phylogenetic tree: a reference to discover functional evolution.
   

10. Endo T†, Ogishima S, Tanaka H.
    

11. J Mol Evol. 2003;57 Suppl 1:S174-81.
    

10. 10. Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method.
    

11. Ren F, Ogishima S, Tanaka H†.
    

12. Gene. 2003 Oct 23;317(1-2):89-95.
    

11. 11. Inference and prediction of courses of the diseases caused by pathologic viruses by estimating molecular evolution of within-host virus.
    

12. Ren F, Ogishima S, Tanaka H†.
    

13. Stud Health Technol Inform. 2001;84(Pt 2):979-83.
    

12. 12. A new algorithm for analysis of within-host HIV-1 evolution.
    

13. Ren F, Ogishima S, Tanaka H†.
    

14. Pac Symp Biocomput. 2001:595-605.
    

As Waddington proposed a metaphor for development and differentiation as "epigenetic landscape" (Waddington, 1953), understanding of developmental and differentiation processes as state transition of attractors of cells along with "valley" where a "marble" rolls down to the point of lowest local elevation has been a holy grail in developmental biology.

        Half a century later, Kauffman proposed the idea that a cell type is an attractor of the gene regulatory network (Kauffman, 1993). As gene regulatory network, the Boolean K=N network model was proposed, and then 2N/2 was estimated as the number of attractors for K=N networks. The number of attractor for 100,000 genes regulatory network was estimated to be 317 states. Gene expression states regulated by gene regulatory network should reflect cell types, that is "system attractors" on epigenetic landscape.

        Not only development and differentiation but also disease pathogenesis and progression can be understood by trajectories of "systems attractors" on epigenetic landscape determined by gene regulatory networks. A disease is believed to be an aberration of biological system. However, disease is not a temporal aberration but a stable aberration of biological system. That is, a "disease type" is also an attractor of the gene regulatory network.

        Nowadays, vast amounts of so-called omics data has been accumulating, molecular mechanisms of iPS/ES differentiation, disease pathogenesis and progression, have been growing understanding rapidly. Attempts to understand differentiation and disease pathogenesis/progression process as state transition of "systems attractors" have just started. We developed a novel method to estimate a “expression potential filed” determined by a gene regulatory network, and estimated an expression potential on a gene expression states plane as for iPS/ES differentiation, disease pathogenesis and progression. We then calculated gradients on an expression potential field for showing “expression trajectories” among gene expression states, that is, "systems attractors" as cell types and disease types. “Expression trajectories” on expression potential field enable us to elucidate iPS/ES differentiation, disease pathogenesis and progression process and their molecular mechanisms.