University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Adam Olshen, PhD

Adam Olshen, PhD

Professor, Dept. of Epidemiology and Biostatistics, UCSF
Director, Computational Biology and Informatics Core, UCSF Helen Diller Family Comprehensive Cancer Center

Cancer Center Program Memberships

Non-aligned

Education

University of Washington, Seattle, WA, Ph.D., 1997, Biostatistics
University of Washington, Seattle, WA, M.S., 1994, Biostatistics
University of California, Berkeley, CA, M.A., 1992, Statistics
University of California, Berkeley, CA, B.A., 1990, Statistic


Professional Experience

  • 1990-1992
    Teaching Assistant, University of California at Berkeley, Berkeley, CA
  • 1992-1997
    Assistant, University of Washington, Seattle, WA
  • 1995
    Teaching Assistant, University of Washington, Seattle, WA
  • 1995
    Statistical Consultant, The Research Group, Seattle, WA
  • 1997-1999
    Biostatistician, Stanford Human Genome Center, Stanford University, Palo Alto, CA
  • 2000-2001
    Informatics Research Scientist, UCSF Cancer Center, Univ. of California, San Francisco, CA
  • 2001-2007
    Assistant Attending Biostatistician, Memorial Sloan-Kettering Cancer Center, New York, NY
  • 2007-2009
    Associate Attending Biostatistician, Memorial Sloan-Kettering Cancer Center, New York, NY
  • 2009-2013
    Associate Professor, Dept. of Epidemiology and Biostatistics, Univ. of California, San Francisco, CA
  • 2009-2011
    Director, Biostatistics and Computational Biology Core, UCSF Helen Diller Family Comprehensive Cancer Center
  • 2011-present
    Director, Computational Biology Core, UCSF Helen Diller Family Comprehensive Cancer Center
  • 2013-present
    Professor, Dept. of Epidemiology and Biostatistics, Univ. of California, San Francisco, CA

Selected Publications

  • Thompson EA, Lin S, Olshen AB, Wijsman EM. Monte Carlo analysis on a large pedigree. Genet Epidemiol. 1993;10(6):677-82.
  • Olshen AB, Wijsman EM. Pedigree analysis package vs. MIXD: fitting the mixed model on a large pedigree. Genet Epidemiol. 1996; 13: 91-106.
  • Olshen AB, O'Sullivan F. Camouflaged deconvolution with application to blood curve modeling in FDG PET Studies. Journal of the American Statistical Association 1997; 92: 1293-1303.
  • Eubank WB, Mankoff DA, Schmiedl UP, Winter TC 3rd, Fisher ER, Olshen AB, Graham MM, Eary JF. Imaging of oncologic patients: benefit of combined CT and FDG PET in the diagnosis of malignancy. AJR American Journal of Roentgenol. 1998, 171:1103-10.
  • Eary JF, Mankoff DA, Spence AM, Berger MS, Olshen AB, Link JM, O'Sullivan F,Krohn KA. 2-[C-11]thymidine imaging of malignant brain tumors.Cancer Research. 1999;59:615-21.
  • Olivier M, Aggarwal A, Allen J, Almendras AA, Bajorek ES, Beasley EM, Brady SD, Bushard JM, Bustos VI, Chu A, Chung TR, De Witte A, Denys ME, Dominguez R, Fang NY, Foster BD, Freudenberg RW, Hadley D, Hamilton LR, Jeffrey TJ, Kelly L, Lazzeroni L, Levy MR, Lewis SC, Liu X, Lopez FJ, Louie B, Marquis JP, Martinez RA, Matsuura MK, Misherghi NS, Norton JA, Olshen AB, Perkins SM, Perou AJ, Piercy C, Piercy M, Qin F, Reif T, Sheppard K, Shokoohi V, Smick GA, Sun WL, Stewart EA, Fernando J, Tejeda, Tran NM, Trejo T, Vo NT, Yan SC, Zierten DL, Zhao S,Sachidanandam R, Trask BJ, Myers RM, Cox DR. A high-resolution radiation hybrid map of the human genome draft sequence. Science. 2001;291:1298-302.
  • Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Kovacs G, Presti JC, Waldman FM. Array based CGH for the differential diagnosis of renal cell cancer. Cancer Research 62: 957-960. 2002.
  • Olshen AB, Jain AN. Deriving quantitative conclusion from microarray expression data. Bioinformatics 2002; 18: 961-970.
  • Massion PP, Kuo W-L, Stokoe D, Olshen AB, Treseler PA, Chin K, Chen C, Polifoff D, Jain AN, Pinkel D, Albertson DG, Jablons DM, Gray JW. Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: Implications of the PI3-Kinase pathway. Cancer Research 2002; 62: 3636-3640.
  • Solit DB, Basso AD, Olshen AB, Scher HI, Rosen N. Inhibition of heat shock protein 90 function down-regulates AKT kinase and sensitizes tumors to taxol. Cancer Research 2003; 63: 2139-2144.
  • Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo W-L, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Research 2003; 63: 2872-2880.
  • Hedvat CV, Comenzo RL, Teruya-Feldstein J, Ely SA, Olshen AB, Osman K, Zhang Y, Kalakonda N, Nimer SD. Insights into extramedullary tumour cell growth revealed by expression profiling of human plasmacytomas and multiple myeloma. British Journal of Haematology 2003; 122: 728-744.
  • Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, West J, Rostan S, Nguyen KCQ, Powers S, Ye KQ, Venkatraman E, Olshen AB, Norton L, Wigler M. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003 Oct; 13(10): 2291-305. Epub 2003 Oct 2.
  • DeCandia P, Solit DB, Giri D, Brogi E, Siegel PM, Olshen AB, Muller WJ, Rosen N, Benezra R. Angiogenesis impairment in Id-deficient mice cooperates with an Hsp90 inhibitor to completely suppress HER2/neu-dependent breast tumors. Proceedings of the National Science USA 2003; 100: 12337-12342.
  • Westermark UK, Reyngold M, Olshen AB, Baer R, Jasin,M, Moynahan ME. BARD1 participates with BRCA-1 in homology-directed repair of chromosome breaks. Molecular Cell Biology 2003; 23: 7926-7936.
  • Bastian BC, Olshen AB, LeBoit PE, Pinkel D. Classifying melanocytic tumors based on DNA copy number changes. American Journal of Pathol. 2003,163:1765-70.
  • Houldsworth J, Olshen AB, Cattoretti G, Donnelly GB, Teruya-Feldstein J, Qin J, Palanisamy N, Shen Y, Dyomina K, Petlakh M, Pan Q, Zelenetz AD, Dalla-Favera R, Chaganti R. Relationship between REL amplification, REL function, and clinical and biologic features in diffuse large B-cell lymphomas. Blood. 2004; 103: 1862-1868.
  • Ferguson SE, Olshen AB, Viale A, Awtrey CS, Barakat RR, Boyd J. Gene expression profiling of tamoxifen-associated uterine cancers: evidence for two molecular classes of endometrial carcinoma. Gynecology Oncology 2004; 92: 719-725.
  • Couedel C, Mills KD, Barchi M, Shen L, Olshen AB, Johnson RD, Nussenzweig A, Essers J, Kanaar R, Li GC, Alt FW, Jasin M. Collaboration of homologous recombination and nonhomologous end-joining factors for the survival and integrity of mice and cells. Genes & Development 2004;18:1293-1304.
  • Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5:557-572.
  • Olshen AB, Cosman PC, Rodrigo AG, Bickel PJ, Olshen RA. Vector quantization of amino acids: Analysis of the HIV V3 loop region. Journal of Statistical Planning and Inference. 2005;130:277-298.
  • Chadalavada RS, Houldsworth J, Olshen AB, Bosl GJ, Studer L, Chagnati RS. Transcriptional program of bone morphogenetic protein-2 induced epithelial and smooth muscle differentiation of pluripotent human embryonal carcinon cells. Functional & Integrative Genomics, 2005; 5: 59-69.
  • Ferguson SE, Olshen AB, Viale A, Barakat RR, Boyd J. Stratification of intermediate-risk endometrial cancer patients into groups at high risk or low risk for recurrence based on tumor gene expression profiles. Clinical Cancer Research 2005; 11: 2252-2257
  • Korkola JE, Houldsworth J, Dobrzynski D, Olshen AB, Reuter VE, Bosl GJ, Chaganti RS. Gene expression-based classification of nonseminomatous male germ cell tumors. Oncogene. 2005 Jul 28;24(32):5101-7.
  • Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD, Viale A, Olshen AB,Gerald WL, Massague J. Genes that mediate breast cancer metastasis to lung. Nature 2005;436:518-24.
  • Huang S, Li Y, Chen Y, Podsypanina K, Chamorro M, Olshen AB, Desai KV, Tann A, Petersen D, Green JE, Varmus HE. Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice. Genome Biology. 2005;6:R84.
  • Gupta GP, Minn AJ, Kang Y, Siegel PM, Serganova I, Cordon-Cardo C, Olshen AB, Gerald WL, Massague J. Identifying Site-specific Metastasis Genes and Functions. Cold Spring Harbor Symposia Quantitative Biology. 2005;70:1-10.
  • Chen W, Houldsworth J, Olshen AB, Nabjangud G, Chaganti S, Venkatraman ES, Halaas J, Teruya-Feldstein J, Zelenetz AD, Chaganti RS. Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas. Blood. 2006;15;107:2477-2785. Epub 2005.
  • Ferguson SE, Olshen AB, Levine DA, Viale A, Barakat RR, Boyd J. Molecular profiling of endometrial cancers from African-American and Caucasian women. Gynecology Oncology. 2005 Dec
  • Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. Journal of Clinical Investigation 2006;116:271-84.
  • Korkola JE, Houldsworth J, Chadalavada RS, Olshen AB, Dobrzynski D, Reuter VE, Bosl GJ, Chaganti RS. Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31 is associated with in vivo differentiation of human male germ cell tumors. Cancer Research. 2006; 66: 820-827
  • Lopez-Rios F, Chuai S, Flores R, Shimizu S, Ohno T, Wakahara K, Illei PB, Hussain S, Krug L, Zakowski MF, Rusch V, Olshen AB, Ladanyi M. Global gene expression profiling of pleural mesotheliomas: overexpression of aurora kinases and P16/CDKN2A deletion as prognostic factors and critical evaluation of microarray-based prognostic prediction. Cancer Research. 2006; 66: 2970-2979.
  • Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen AB, 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;6:96.
  • Chadalavada RS, Korkola JE, Houldsworth J, Olshen AB, Bosl GJ, Studer L, Chaganti RS. Constitutive Gene Expression Predisposes Morphogen-Mediated Cell Fate Responses of NT2/D1 and 27X-1 Human Embryonal Carcinoma Cells. Stem Cells. 2007, 25:771-8.
  • Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007; 15;23:657-63.
  • Lae M, Ahn E, Mercado G, Chuai S, Edgar M, Pawel B, Olshen AB, Barr F, Ladanyi M. Global gene expression profiling of PAX-FKHR fusion-positive alveolar and PAX-FKHR fusion-negative embryonal rhabdomyosarcomas. Journal of Pathology. 2007;212:143-151
  • Korkola JE, Heck S, Olshen AB, Reuter VE, Bosl GJ, Houldsworth J, Chaganti RS. In vivo differentiation and genomic evolution in adult male germ cell tumors. Genes Chromosomes Cancer. 2008 Jan;47(1):43-55.
  • Assimes TL, Olshen AB, Narasimhan B, Olshen RA. Associations among multiple markers and complex disease: models, algorithms, and applications. Adv Genet. 2008;60:437-64. Review.
  • Olshen AB, Gold B, Lohmueller KE, Struewing JP, Satagopan J, Stefanov SA, Eskin E, Kirchhoff T, Lautenberger JA, Klein RJ, Friedman E, Norton L, Ellis NA, Viale A, Lee CS, Borgen PI, Clark AG, Offit K, Boyd J. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping. BMC Genet. 2008 Feb 5;9:14.
  • Gold B, Kirchhoff T, Stefanov S, Lautenberger J, Viale A, Garber J, Friedman E, Narod S, Olshen AB, Gregersen P, Kosarin K, Olsh A, Bergeron J, Ellis NA, Klein RJ, Clark AG, Norton L, Dean M, Boyd J, Offit K. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4340-5. Epub 2008 Mar 7.
  • Houldsworth J, Petlakh M, Olshen AB, Chaganti RS. Pathway activation in large B-cell non-Hodgkin lymphoma cell lines by doxorubicin reveals prognostic markers of in vivo response. Leuk Lymphoma. 2008 Nov;49(11):2170-80.
  • Filion C, Motoi T, Olshen AB, Laé M, Emnett RJ, Gutmann DH, Perry A, Ladanyi M, Labelle Y. The EWSR1/NR4A3 fusion protein of extraskeletal myxoid chondrosarcoma activates the PPARG nuclear receptor gene. J Pathol. 2009 Jan;217(1):83-93.