Research and Education for Biomedical Informatics at Tokyo Medical and Dental University

Summary

Objectives

Based on a basic concept of “Systems Life Science: understanding life and disease as a unified system”, we move forward in research, empirical implementation, and making contributions to healthcare policy.

Methods

We integrate bioinformatics and medical informatics for identifying critical issues in biological science and solving medical challenges with a concept of “Systems Life Science” which consists of “Systems Evolutionary Biology” for basic science, “Systems Pathology” for clinical sciences, and an empirical medical informatics for future medicine.

Results

Our laboratory is an integrated laboratory consisting of a computational biology group in the School of Biomedical Sciences (SBS), a bioinformatics group in the Medical Research Institute (MRI), and a medical informatics group in the Information Center for Medical Sciences (ICMS) with a philosophy of “Empirical Systems Life Science”.

Conclusions

Based on the philosophy of “Empirical Systems Life Science”, we continue to forward our research, education, systems implementations, and international standardization efforts. We believe that this approach will become a fundamental and effective way to uncover many of the secrets of life processes, and to help/solve complex issues for future medicine in this post genomic era with exceedingly rapidly growing amounts of -omics data and knowledge.

 

MissingLinkText

Keywords

Empirical systems life science - systems evolutionary biology - systems pathology - systems medical informatics - translational research informatics

 

 

MissingLinkText

• References

• 1 Niimura Y, Nei M. Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci USA 2005; 102: 6039-44.
• 2 Niimura Y, Nei M. Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 2005; 346: 13-21.
• 3 International Rice Genome Sequencing Project. The map based sequence of the rice genome. Nature 2005; 436: 793-800.
• 4 Ogishima S, Tanaka H. The missing link in the evolution of Hox clusters. Gene. 2006 accepted
• 5 Ren F, Tsubota A, Hirokawa T, Kumada H, Yang Z, Tanaka H. A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. Gene 2006; 383: 43-51.
• 6 Ren F, Tanaka H, Yang Z. An empirical examination of the utility of codon-substitution models in phylo geny reconstruction. Syst Biol 2005; 54: 808-18.
• 7 Construction of exhaustive molecular pathological database, outlays for promoting Japanese Science and Technology, Japan Science and Technology Agency. http://www.jst.go.jp/EN/index.html 2007 [accessed 05.02.06]
• 8 Bio-Medical-Omics Informatics Education Program, outlays for promoting Japanese Science and Technology, Japan Science and Technology Agency. http://www.jst.go.jp/EN/index.html 2007 [accessed 05.02.06]
• 9 Hasegawa N, Sugiura W, Matsuda M, Mogushi K, Tanaka H, Ren F. Inference of evolutionary gorces driving HIV-1 drug-ersistance acquisition under HAART using longitudinal HIV-1 protease gene samples. Antivir Ther 2005; S10: 114.
• 10 Experimental use of electronic tags in medical field, outlays for promoting Japanese Science and Technology, Japan Science and Technology Agency. http://www.jst.go.jp/EN/index.html 2007 [accessed 05.02.06]
• 11 International Organization for Standardization, TC215. Genomic Sequence Variation Markup Language. http://www.iso.org/iso/en/CatalogueDetailPage.CatalogueDetail?CSNUMBER=43182&scopelist=PROGRAMME 2006 [accessed 11.07.06]
• 12 Nakaya J, Ido K, Hiroi K, Yang W, Kimura M. (Best Paper Award) Genomic Sequence Variation Markup Language (GSVML) for Global Interoperability of Clinical Genomics Data. Asia Pacific Association for Medical Informatics 2006 Proceedings 2006; 1-8.
• 13 Hiroi K, Ido K, Yang W, Nakaya J. Interface Analysis between GSVML and HL7 version3. J Biomed Inform. In press 2007
• 14 Nakaya J, Shimizu T, Tanaka H. Knowledge Platform to use BioMedical Semantic WEBs individually: Bridging Gene Ontologies and Clinical Ontologies at individual site (Leadoff Article). International Journal of Computer Science and Network Security 2006; 06 (2A): 1-9.
• 15 Nakaya J, Shimizu T, Tanaka H. e-protocol - A Translational Research (TR) protocol generator and monitor -. Communication Network, International Journal of Computer Science and Network Security. 2006; 06 (7B): 18-23.