Taku A. Tokuyasu, PhD

Taku A. Tokuyasu, PhD

Computational Biology Core, UCSF Helen Diller Family Comprehensive Cancer Center


Phone: (415) 514-1530 (voice)
Box 0128, UCSF
San Francisco, CA 94143-0128


University of California, Berkeley, CA, PhD, 2001, Computer Science
Princeton University, Princeton, NJ, PhD, 1989, Physics
Pomona College, Claremont, CA, BA, 1984, Physics

Professional Experience

  • 1989-1991
    Postdoctoral researcher, Physics, IBM T.J. Watson Research Center, Yorktown Heights, NY
  • 1991-1993
    Postdoctoral researcher, Physics, Boston University, Boston, MA
  • 1998-2000
    Consultant, Xerox PARC Research Center, Palo Alto, CA
  • 2001-2006
    Informatics Research Scientist, UCSF Cancer Center, San Francisco, CA
  • 2006-2009
    Informatics Core Manager, UCSF Cancer Center, San Francisco, CA
  • 2009 - present
    Computational Biologist, UCSF Cancer Center, San Francisco, CA

Honors & Awards

  • 1984
    Phi Beta Kappa
  • 1984 -1986
    NSF Graduate Research Fellow
  • 2007
    UCSF STAR Tier One Award for Outstanding Performance

Selected Publications

  • Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RC, Olshen AB, Pinkel D, Schmidt BL, Albertson DG. Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis. Clin Cancer Res. 2011 Nov 15;17(22):7024-34.
  • Nabavizadeh N, Klifa C, Newitt D, Lu Y, Chen YY, Hsu H, Fisher C, Tokayasu T, Olshen AB, Spellman P, Gray JW, Hylton N, Park CC. Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI. Integr Biol (Camb). 2011 Apr;3(4):490-6.
  • Paquette J, Tokuyasu T. EGAN: exploratory gene association networks. Bioinformatics. 2010 Jan 15;26(2):285-6.
  • Chen YY, Hwang ES, Roy R, DeVries S, Anderson J, Wa C, Fitzgibbons PL, Jacobs TW, MacGrogan G, Peterse H, Vincent-Salomon A, Tokuyasu T, Schnitt SJ, Waldman FM. Genetic and phenotypic characteristics of pleomorphic lobular carcinoma in situ of the breast. Am J Surg Pathol. 2009 Nov;33(11):1683-94.
  • Snijders AM, Hermsen MA, Baughman J, Buffart TE, Huey B, Gajduskova P, Roydasgupta R, Tokuyasu T, Meijer GA, Fridlyand J, Albertson DG. Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instability. Genes Chromosomes Cancer. 2008 Jan;47(1):71-83.
  • Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG. Genome position and gene amplification. Genome Biol. 2007;8(6):R120.
  • Tokuyasu TA, Cotter PD, Segraves R, Harris J, Elder ME, Gonzales M, Pinkel D, Albertson DG, Rauen KA. Detection of single clone deletions using array CGH: identification of submicroscopic deletions in the 22q11.2 deletion syndrome as a model system. Am J Med Genet A. 2007 May 1;143A(9):925-32.
  • Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec;10(6):529-41.
  • Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006 Apr 18;6:96.
  • Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM. Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clin Cancer Res. 2005 Mar 1;11(5):1791-7.
  • Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res. 2005 Feb;15(2):302-11.
  • Tokuyasu TA, Albertson D, Pinkel D, Jain A. Wavelet Transforms for the Analysis of Microarray Experiments.Proceedings of the Computational Systems Bioinformatics Conference (CSB2003), Stanford, CA, IEEE, 2003.
  • Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D. Fully automatic quantification of microarray image data. Genome Res. 2002 Feb;12(2):325-32.
  • Tokuyasu TA, Chou PA. Turbo recognition: a statistical approach to layout analysis. Document Recognition VIII, Proceedings of the SPIE 4307:123-129, 2001.
  • Tokuyasu TA, Chou PA. An iterative approach to document image analysis. DLIA99 workshop, Bangalore, India, 1999.
  • Tokuyasu TA, O'Gorman L. Document analysis versus understanding. DAS '96 Working Group Report, in Document Analysis Systems II, J.J. Hull and S.L. Taylor, eds, Singapore: World Scientific, 1997.
  • Fateman RJ, Tokuyasu T, Berman BP, Mitchell N. Optical Character Recognition and Parsing of Typeset Mathematics. J. of Visual Communication and Image Representation 7(1):2-15 , 1996.
  • Tokuyasu T, Kamal M, Murthy G. Numerical renormalization group for finite Fermi systems. Phys Rev Lett. 1993 Dec 20;71(25):4202-4205.
  • Tokuyasu TA, Toner J. Anomalous elasticity and symmetry breaking fields in tethered membranes. Phys Rev Lett. 1992 Jun 22;68(25):3721-3724.
  • Reger JD, Tokuyasu TA, Young AP, Fisher MP. Vortex-glass transition in three dimensions. Phys Rev B Condens Matter. 1991 Oct 1;44(13):7147-7150
  • Fisher MP, Tokuyasu TA, Young AP. Vortex variable-range-hopping resistivity in superconducting films. Phys Rev Lett. 1991 Jun 3;66(22):2931-2934.
  • Tokuyasu TA, Hess DW, Sauls JA. Vortex states in an unconventional superconductor and the mixed phases of UPt3. Phys Rev B Condens Matter. 1990 May 1;41(13):8891-8903.
  • Tokuyasu T, Sauls JA, Rainer D. Proximity effect of a ferromagnetic insulator in contact with a superconductor. Phys Rev B Condens Matter. 1988 Nov 1;38(13):8823-8833.