Toshiro Ohsumi

Molbio Department


Bioinformatics Scientist

Department of Molecular Biology
Simches Research Center
Boston, MA 02114


Email

About Toshiro Ohsumi

Toshiro Ohsumi develops fast, memory efficient algorithms for sequencing alignment, ChIP-seq, polymorphism detection, and other data- processing applications for next-generation sequencer data, primarily in C++0x. His current research focus is on developing a C++0x framework for common sequence tasks and develop new algorithms for polymorphism detection and ChIP-Seq binding location prediction. Prior to MGH, Toshiro has worked at the Broad Institute as a computational biologist and Colgate University as an assistant professor of computer science. Toshiro earned a B.A. in mathematics and physics (University of California at Santa Cruz), a M.A. in applied mathematics (University of California at Irvine), and a Ph.D. in computer science (Rensselaer Polytechnic Institute) on efficiently solving time-dependent partial differential equations in moving domains arising in simulating formation and healing of artificial and natural [biphasic] tissue.

Publications
    2012
  1. Chou J, Ohsumi TK, Geha RS. Use of whole exome and genome sequencing in the identification of genetic causes of primary immunodeficiencies. Curr Opin Allergy Clin Immunol 2012 Dec; 12(6):623-8.

  2. Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res. 2012 Oct; 22(10):1864-76.

  3. Ohsumi TK, Borowsky ML. MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks. Bioinformatics 2012 Oct 1; 28(19):2412-6.

  4. Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren AM, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris DJ, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF. Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries. Cell 2012 Apr 27; 149(3):525-37.

  5. Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat. Genet. 2012 Apr; 44(4):390-7, S1.

  6. Yuan CC, Matthews AG, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA. Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell Rep 2012 Feb 23; 1(2):83-90.

  7. 2011
  8. Sharp JA, Plant JJ, Ohsumi TK, Borowsky M, Blower MD. Functional analysis of the microtubule-interacting transcriptome. Mol. Biol. Cell 2011 Nov; 22(22):4312-23.

  9. Talkowski ME, Ernst C, Heilbut A, Chiang C, Hanscom C, Lindgren A, Kirby A, Liu S, Muddukrishna B, Ohsumi TK, Shen Y, Borowsky M, Daly MJ, Morton CC, Gusella JF. Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research. Am. J. Hum. Genet. 2011 Apr 8; 88(4):469-81.

  10. 2010
  11. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 2010 Dec 22; 40(6):939-53.

  12. 2009
  13. Lau NC, Ohsumi T, Borowsky M, Kingston RE, Blower MD. Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi. EMBO J. 2009 Oct 7; 28(19):2945-58.

  14. Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat. Methods 2009 Jan; 6(1):67-9.

  15. 2008
  16. Ohsumi TK, Flaherty JE, Evans MC, Barocas VH. Three-dimensional simulation of anisotropic cell-driven collagen gel compaction. Biomech Model Mechanobiol 2008 Feb; 7(1):53-62.

  17. 2002
  18. Caraco T, Glavanakov S, Chen G, Flaherty JE, Ohsumi TK, Szymanski BK. Stage-structured infection transmission and a spatial epidemic: a model for Lyme disease. Am. Nat. 2002 Sep; 160(3):348-59.

  19. 2000
  20. Ohsumi TK, Flaherty JE, Barocas VH, Adjerid S, Aiffa M. Adaptive Finite Element Analysis of the Anisotropic Biphasic Theory of Tissue-Equivalent Mechanics. Comput Methods Biomech Biomed Engin 2000; 3(3):215-229.

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