 Adam Olshen, PhD
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| Title | Associate Professor in Residence |
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| School | UCSF School of Medicine |
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| Department | Epidemiology & Biostatistics |
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| Address | 1450 3rd Street
San Francisco CA 94158
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| Phone | 415-514-9406 |
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 Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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Sadanandam A, Lyssiotis CA, Homicsko K, Collisson EA, Gibb WJ, Wullschleger S, Ostos LC, Lannon WA, Grotzinger C, Del Rio M, Lhermitte B, Olshen AB, Wiedenmann B, Cantley LC, Gray JW, Hanahan D. A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med. 2013 Apr 14.
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Kobos R, Nagai M, Tsuda M, Merl MY, Saito T, Laé M, Mo Q, Olshen A, Lianoglou S, Leslie C, Ostrovnaya I, Antczak C, Djaballah H, Ladanyi M. Combining integrated genomics and functional genomics to dissect the biology of a cancer-associated, aberrant transcription factor, the ASPSCR1-TFE3 fusion oncoprotein. J Pathol. 2013 Apr; 229(5):743-54.
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Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, Shen R. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci U S A. 2013 Mar 12; 110(11):4245-50.
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Magbanua MJ, Sosa EV, Roy R, Eisenbud LE, Scott JH, Olshen A, Pinkel D, Rugo HS, Park JW. Genomic profiling of isolated circulating tumor cells from metastatic breast cancer patients. Cancer Res. 2013 Jan 1; 73(1):30-40.
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Shen R, Mo Q, Schultz N, Seshan VE, Olshen AB, Huse J, Ladanyi M, Sander C. Integrative subtype discovery in glioblastoma using iCluster. PLoS One. 2012; 7(4):e35236.
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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.
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Oricchio E, Nanjangud G, Wolfe AL, Schatz JH, Mavrakis KJ, Jiang M, Liu X, Bruno J, Heguy A, Olshen AB, Socci ND, Teruya-Feldstein J, Weis-Garcia F, Tam W, Shaknovich R, Melnick A, Himanen JP, Chaganti RS, Wendel HG. The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma. Cell. 2011 Oct 28; 147(3):554-64.
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Wang L, Motoi T, Khanin R, Olshen A, Mertens F, Bridge J, Dal Cin P, Antonescu CR, Singer S, Hameed M, Bovee JV, Hogendoorn PC, Socci N, Ladanyi M. Identification of a novel, recurrent HEY1-NCOA2 fusion in mesenchymal chondrosarcoma based on a genome-wide screen of exon-level expression data. Genes Chromosomes Cancer. 2012 Feb; 51(2):127-39.
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Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics. 2011 Aug 1; 27(15):2038-46.
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Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, Creaney J, Lake RA, Zakowski MF, Reva B, Sander C, Delsite R, Powell S, Zhou Q, Shen R, Olshen A, Rusch V, Ladanyi M. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet. 2011 Jul; 43(7):668-72.
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Ostrovnaya I, Seshan VE, Olshen AB, Begg CB. Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles. Bioinformatics. 2011 Jun 15; 27(12):1698-9.
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Brevet M, Shimizu S, Bott MJ, Shukla N, Zhou Q, Olshen AB, Rusch V, Ladanyi M. Coactivation of receptor tyrosine kinases in malignant mesothelioma as a rationale for combination targeted therapy. J Thorac Oncol. 2011 May; 6(5):864-74.
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Collisson EA, Sadanandam A, Olson P, Gibb WJ, Truitt M, Gu S, Cooc J, Weinkle J, Kim GE, Jakkula L, Feiler HS, Ko AH, Olshen AB, Danenberg KL, Tempero MA, Spellman PT, Hanahan D, Gray JW. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat Med. 2011 Apr; 17(4):500-3.
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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.
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Affer M, Dao S, Liu C, Olshen AB, Mo Q, Viale A, Lambek CL, Marr TG, Clarkson BD. Gene Expression Differences between Enriched Normal and Chronic Myelogenous Leukemia Quiescent Stem/Progenitor Cells and Correlations with Biological Abnormalities. J Oncol. 2011; 2011:798592.
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Bachleitner-Hofmann T, Sun MY, Chen CT, Liska D, Zeng Z, Viale A, Olshen AB, Mittlboeck M, Christensen JG, Rosen N, Solit DB, Weiser MR. Antitumor activity of SNX-2112, a synthetic heat shock protein-90 inhibitor, in MET-amplified tumor cells with or without resistance to selective MET Inhibition. Clin Cancer Res. 2011 Jan 1; 17(1):122-33.
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Moltzahn F, Olshen AB, Baehner L, Peek A, Fong L, Stöppler H, Simko J, Hilton JF, Carroll P, Blelloch R. Microfluidic-based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in the sera of prostate cancer patients. Cancer Res. 2011 Jan 15; 71(2):550-60.
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Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105.
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Rose AE, Satagopan JM, Oddoux C, Zhou Q, Xu R, Olshen AB, Yu JZ, Dash A, Jean-Gilles J, Reuter V, Gerald WL, Lee P, Osman I. Copy number and gene expression differences between African American and Caucasian American prostate cancer. J Transl Med. 2010; 8:70.
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Ostrovnaya I, Olshen AB, Seshan VE, Orlow I, Albertson DG, Begg CB. A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data. Stat Med. 2010 Jul 10; 29(15):1608-21.
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Ostrovnaya I, Nanjangud G, Olshen AB. A classification model for distinguishing copy number variants from cancer-related alterations. BMC Bioinformatics. 2010; 11:297.
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Pothuri B, Leitao MM, Levine DA, Viale A, Olshen AB, Arroyo C, Bogomolniy F, Olvera N, Lin O, Soslow RA, Robson ME, Offit K, Barakat RR, Boyd J. Genetic analysis of the early natural history of epithelial ovarian carcinoma. PLoS One. 2010; 5(4):e10358.
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Korkola JE, Houldsworth J, Feldman DR, Olshen AB, Qin LX, Patil S, Reuter VE, Bosl GJ, Chaganti RS. Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumors. J Clin Oncol. 2009 Nov 1; 27(31):5240-7.
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Shen R, Olshen AB, Ladanyi M. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics. 2009 Nov 15; 25(22):2906-12.
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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.
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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.
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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.
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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; 9:14.
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Zhou P, Comenzo RL, Olshen AB, Bonvini E, Koenig S, Maslak PG, Fleisher M, Hoffman J, Jhanwar S, Young JW, Nimer SD, Boruchov AM. CD32B is highly expressed on clonal plasma cells from patients with systemic light-chain amyloidosis and provides a target for monoclonal antibody-based therapy. Blood. 2008 Apr 1; 111(7):3403-6.
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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.
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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.
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Zhou P, Teruya-Feldstein J, Lu P, Fleisher M, Olshen A, Comenzo RL. Calreticulin expression in the clonal plasma cells of patients with systemic light-chain (AL-) amyloidosis is associated with response to high-dose melphalan. Blood. 2008 Jan 15; 111(2):549-57.
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Laé M, Ahn EH, Mercado GE, Chuai S, Edgar M, Pawel BR, Olshen A, Barr FG, Ladanyi M. Global gene expression profiling of PAX-FKHR fusion-positive alveolar and PAX-FKHR fusion-negative embryonal rhabdomyosarcomas. J Pathol. 2007 Jun; 212(2):143-51.
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Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007 Mar 15; 23(6):657-63.
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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 Mar; 25(3):771-8.
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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; 6:96.
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López-Ríos 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 Res. 2006 Mar 15; 66(6):2970-9.
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Anderson SE, Nonaka D, Chuai S, Olshen AB, Chi D, Sabbatini P, Soslow RA. p53, epidermal growth factor, and platelet-derived growth factor in uterine leiomyosarcoma and leiomyomas. Int J Gynecol Cancer. 2006 Mar-Apr; 16(2):849-53.
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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 Res. 2006 Jan 15; 66(2):820-7.
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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. J Clin Invest. 2006 Jan; 116(1):271-84.
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Ferguson SE, Olshen AB, Levine DA, Viale A, Barakat RR, Boyd J. Molecular profiling of endometrial cancers from African-American and Caucasian women. Gynecol Oncol. 2006 May; 101(2):209-13.
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Chen W, Houldsworth J, Olshen AB, Nanjangud 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 Mar 15; 107(6):2477-85.
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Leiser AL, Anderson SE, Nonaka D, Chuai S, Olshen AB, Chi DS, Soslow RA. Apoptotic and cell cycle regulatory markers in uterine leiomyosarcoma. Gynecol Oncol. 2006 Apr; 101(1):86-91.
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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 Biol. 2005; 6(10):R84.
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Moskowitz CH, Zelenetz AD, Kewalramani T, Hamlin P, Lessac-Chenen S, Houldsworth J, Olshen A, Chaganti R, Nimer S, Teruya-Feldstein J. Cell of origin, germinal center versus nongerminal center, determined by immunohistochemistry on tissue microarray, does not correlate with outcome in patients with relapsed and refractory DLBCL. Blood. 2005 Nov 15; 106(10):3383-5.
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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.
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Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD, Viale A, Olshen AB, Gerald WL, Massagué J. Genes that mediate breast cancer metastasis to lung. Nature. 2005 Jul 28; 436(7050):518-24.
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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. Clin Cancer Res. 2005 Mar 15; 11(6):2252-7.
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Chadalavada RS, Houldsworth J, Olshen AB, Bosl GJ, Studer L, Chaganti RS. Transcriptional program of bone morphogenetic protein-2-induced epithelial and smooth muscle differentiation of pluripotent human embryonal carcinoma cells. Funct Integr Genomics. 2005 Apr; 5(2):59-69.
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Gupta GP, Minn AJ, Kang Y, Siegel PM, Serganova I, Cordón-Cardo C, Olshen AB, Gerald WL, Massagué J. Identifying site-specific metastasis genes and functions. Cold Spring Harb Symp Quant Biol. 2005; 70:149-58.
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Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004 Oct; 5(4):557-72.
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Leitao MM, Soslow RA, Nonaka D, Olshen AB, Aghajanian C, Sabbatini P, Dupont J, Hensley M, Sonoda Y, Barakat RR, Anderson S. Tissue microarray immunohistochemical expression of estrogen, progesterone, and androgen receptors in uterine leiomyomata and leiomyosarcoma. Cancer. 2004 Sep 15; 101(6):1455-62.
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Yoon SS, Segal NH, Olshen AB, Brennan MF, Singer S. Circulating angiogenic factor levels correlate with extent of disease and risk of recurrence in patients with soft tissue sarcoma. Ann Oncol. 2004 Aug; 15(8):1261-6.
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Couëdel C, Mills KD, Barchi M, Shen L, Olshen A, 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 Dev. 2004 Jun 1; 18(11):1293-304.
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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. Gynecol Oncol. 2004 Feb; 92(2):719-25.
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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 RS. Relationship between REL amplification, REL function, and clinical and biologic features in diffuse large B-cell lymphomas. Blood. 2004 Mar 1; 103(5):1862-8.
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Westermark UK, Reyngold M, Olshen AB, Baer R, Jasin M, Moynahan ME. BARD1 participates with BRCA1 in homology-directed repair of chromosome breaks. Mol Cell Biol. 2003 Nov; 23(21):7926-36.
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Bastian BC, Olshen AB, LeBoit PE, Pinkel D. Classifying melanocytic tumors based on DNA copy number changes. Am J Pathol. 2003 Nov; 163(5):1765-70.
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de Candia 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. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12337-42.
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Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, West JA, Rostan S, Nguyen KC, Powers S, Ye KQ, Olshen A, Venkatraman E, 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.
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Hedvat CV, Comenzo RL, Teruya-Feldstein J, Olshen AB, Ely SA, Osman K, Zhang Y, Kalakonda N, Nimer SD. Insights into extramedullary tumour cell growth revealed by expression profiling of human plasmacytomas and multiple myeloma. Br J Haematol. 2003 Sep; 122(5):728-44.
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Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, 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 Res. 2003 Jun 1; 63(11):2872-80.
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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 Res. 2003 May 1; 63(9):2139-44.
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Staack A, Kassis AP, Olshen A, Wang Y, Wu D, Carroll PR, Grossfeld GD, Cunha GR, Hayward SW. Quantitation of apoptotic activity following castration in human prostatic tissue in vivo. Prostate. 2003 Feb 15; 54(3):212-9.
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Olshen AB, Jain AN. Deriving quantitative conclusions from microarray expression data. Bioinformatics. 2002 Jul; 18(7):961-70.
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Massion PP, Kuo WL, Stokoe D, Olshen AB, Treseler PA, Chin K, Chen C, Polikoff 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 phosphatidylinositol 3-kinase pathway. Cancer Res. 2002 Jul 1; 62(13):3636-40.
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Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Kovacs G, Waldman FM. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 2002 Feb 15; 62(4):957-60.
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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 A, Perkins SM, Perou AJ, Piercy C, Piercy M, Qin F, Reif T, Sheppard K, Shokoohi V, Smick GA, Sun WL, Stewart EA, Fernando J. A high-resolution radiation hybrid map of the human genome draft sequence. Science. 2001 Feb 16; 291(5507):1298-302.
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Eary JF, Mankoff DA, Spence AM, Berger MS, Olshen A, Link JM, O'Sullivan F, Krohn KA. 2-[C-11]thymidine imaging of malignant brain tumors. Cancer Res. 1999 Feb 1; 59(3):615-21.
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Eubank WB, Mankoff DA, Schmiedl UP, Winter TC, 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 Am J Roentgenol. 1998 Oct; 171(4):1103-10.
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Olshen AB, Wijsman EM. Pedigree analysis package vs. MIXD: fitting the mixed model on a large pedigree. Genet Epidemiol. 1996; 13(1):91-106.
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Thompson EA, Lin S, Olshen AB, Wijsman EM. Monte Carlo analysis on a large pedigree. Genet Epidemiol. 1993; 10(6):677-82.
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