Adam Olshen, PhD, MA
Professor
Epidemiology & Biostatistics
School of Medicine

Websites

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• Profile at UCSF Cancer Center (cancer.ucsf.edu)

Publications (133)

Top publication keywords:
Quantitative Trait LociProtein BiosynthesisCluster AnalysisDNA MethylationGene Expression ProfilingSoftwareChromosomesNeoplasmsChromatinGenome, HumanLeukemia, Myelomonocytic, JuvenileOligonucleotide Array Sequence AnalysisRibosomesGene DosageSequence Analysis, DNA

• Perturbations in inflammatory pathways are associated with shortness of breath profiles in oncology patients receiving chemotherapy.
  Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer 2024 Shin J, Miaskowski C, Wong ML, Yates P, Olshen AB, Roy R, Dokiparthi V, Cooper B, Paul S, Conley YP, Levine JD, Hammer MJ, Kober K
• Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units.
  BMC bioinformatics 2024 Kober KM, Berger L, Roy R, Olshen A
• Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data.
  bioRxiv : the preprint server for biology 2024 Ve K, R R, Cac P, A K, E T, Cc S, Ab O
• Effect of a Home-based Walking Intervention on Cardiopulmonary Fitness and Quality of Life Among Men with Prostate Cancer on Active Surveillance: The Active Surveillance Exercise Randomized Controlled Trial.
  European urology oncology 2023 Van Blarigan EL, Kenfield SA, Olshen A, Panchal N, Encabo K, Tenggara I, Graff RE, Bang AS, Shinohara K, Cooperberg MR, Carroll PR, Jones LW, Winters-Stone K, Luke A, Chan JM
• Multiomic Single Cell Sequencing Identifies Stemlike Nature of Mixed Phenotype Acute Leukemia and Provides Novel Risk Stratification.
  bioRxiv : the preprint server for biology 2023 Peretz CAC, Kennedy VE, Walia A, Delley CL, Koh A, Tran E, Clark IC, Hayford CE, D'Amato C, Xue Y, Fontanez KM, Roy R, Logan AC, Perl AE, Abate A, Olshen A, Smith CC

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• Venetoclax and dinaciclib elicit synergistic preclinical efficacy against hypodiploid acute lymphoblastic leukemia.
  Haematologica 2023 Pariury H, Fandel J, Bachl S, Ang KK, Markossian S, Wilson CG, Braun BS, Popescu B, Wohlfeil M, Beckman K, Xirenayi S, Roy RP, Olshen AB, Smith C, Arkin MR, Loh ML, Diaz-Flores E
• Prediction of morning fatigue severity in outpatients receiving chemotherapy: less may still be more.
  Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer 2023 Kober KM, Roy R, Conley Y, Dhruva A, Hammer MJ, Levine J, Olshen A, Miaskowski C
• Epigenetic Regulation of Inflammatory Mechanisms and a Psychological Symptom Cluster in Patients Receiving Chemotherapy.
  Nursing research 2023 Harris CS, Miaskowski CA, Conley YP, Hammer MJ, Dunn LB, Dhruva AA, Levine JD, Olshen AB, Kober KM
• Torch-eCpG: A fast and scalable eQTM mapper for thousands of molecular phenotypes with graphical processing units.
  bioRxiv : the preprint server for biology 2023 Kober KM, Berger L, Roy R, Olshen A
• Therapeutic implications of transcriptomics in head and neck cancer patient-derived xenografts.
  PloS one 2023 Lee RH, Roy R, Li H, Hechmer A, Zhu TR, Izgutdina A, Olshen AB, Johnson DE, Grandis JR
• Does multi-way, long-range chromatin contact data advance 3D genome reconstruction?
  BMC bioinformatics 2023 Olshen AB, Segal MR
• Sleep disturbance is associated with perturbations in immune-inflammatory pathways in oncology outpatients undergoing chemotherapy.
  Sleep medicine 2022 Calvo-Schimmel A, Kober KM, Paul SM, Cooper BA, Harris C, Shin J, Hammer MJ, Conley YP, Dokiparthi V, Olshen A, Levine JD, Miaskowski C
• Perturbations in common and distinct inflammatory pathways associated with morning and evening fatigue in outpatients receiving chemotherapy.
  Cancer medicine 2022 Kober KM, Harris C, Conley YP, Dhruva A, Dokiparthi V, Hammer MJ, Levine JD, Oppegaard K, Paul S, Shin J, Sucher A, Wright F, Yuen B, Olshen AB, Miaskowski C
• Perturbations in Neuroinflammatory Pathways Are Associated With a Worst Pain Profile in Oncology Patients Receiving Chemotherapy.
  The journal of pain 2022 Shin J, Kober KM, Harris C, Oppegaard K, Calvo-Schimmel A, Paul SM, Cooper BA, Olshen A, Dokiparthi V, Conley YP, Hammer M, Levine JD, Miaskowski C
• Gastrointestinal Symptom Cluster is Associated With Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy.
  Biological research for nursing 2022 Harris CS, Miaskowski CA, Conley YP, Hammer MJ, Dhruva AA, Levine JD, Olshen AB, Kober KM
• Association between Ancestry-Specific 6q25 Variants and Breast Cancer Subtypes in Peruvian Women.
  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2022 Zavala VA, Casavilca-Zambrano S, Navarro-Vásquez J, Castañeda CA, Valencia G, Morante Z, Calderón M, Abugattas JE, Gómez H, Fuentes HA, Liendo-Picoaga R, Cotrina JM, Monge C, Neciosup SP, Huntsman S, …
• COVIDNearTerm: A simple method to forecast COVID-19 hospitalizations.
  Journal of clinical and translational science 2022 Olshen AB, Garcia A, Kapphahn KI, Weng Y, Vargo J, Pugliese JA, Crow D, Wesson PD, Rutherford GW, Gonen M, Desai M
• Ferrous iron-activatable drug conjugate achieves potent MAPK blockade in KRAS-driven tumors.
  The Journal of experimental medicine 2022 Jiang H, Muir RK, Gonciarz RL, Olshen AB, Yeh I, Hann BC, Zhao N, Wang YH, Behr SC, Korkola JE, Evans MJ, Collisson EA, Renslo AR
• Molecular and phenotypic diversity of CBL-mutated juvenile myelomonocytic leukemia.
  Haematologica 2022 Hecht A, Meyer JA, Behnert A, Wong E, Chehab F, Olshen A, Hechmer A, Aftandilian C, Bhat R, Choi SW, Chonat S, Farrar JE, Fluchel M, Frangoul H, Han JH, Kolb EA, Kuo DJ, MacMillan ML, Maese L, Maloney…
• Discovering dominant tumor immune archetypes in a pan-cancer census.
  Cell 2021 Combes AJ, Samad B, Tsui J, Chew NW, Yan P, Reeder GC, Kushnoor D, Shen A, Davidson B, Barczak AJ, Adkisson M, Edwards A, Naser M, Barry KC, Courau T, Hammoudi T, Argüello RJ, Rao AA, Olshen AB, …
• Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer.
  JCI insight 2021 Bouhaddou M, Lee RH, Li H, Bhola NE, O'Keefe RA, Naser M, Zhu TR, Nwachuku K, Duvvuri U, Olshen AB, Roy R, Hechmer A, Bolen J, Keysar SB, Jimeno A, Mills GB, Vandenberg S, Swaney DL, Johnson DE, …
• Exploring the genetic and epigenetic origins of juvenile myelomonocytic leukemia using newborn screening samples.
  Leukemia 2021 Behnert A, Meyer J, Parsa JY, Hechmer A, Loh ML, Olshen A, de Smith AJ, Stieglitz E
• In utero and early-life exposure to thirdhand smoke causes profound changes to the immune system.
  Clinical science (London, England : 1979) 2021 Snijders AM, Zhou M, Whitehead TP, Fitch B, Pandey P, Hechmer A, Huang A, Schick SF, de Smith AJ, Olshen AB, Metayer C, Mao JH, Wiemels JL, Kogan SC
• The role of HER2 and HER3 in HER2-amplified cancers beyond breast cancers.
  Scientific reports 2021 Majumder A, Sandhu M, Banerji D, Steri V, Olshen A, Moasser MM
• Prediction of evening fatigue severity in outpatients receiving chemotherapy: less may be more.
  Fatigue : biomedicine, health & behavior 2021 Kober KM, Roy R, Dhruva A, Conley YP, Chan RJ, Cooper B, Olshen A, Miaskowski C
• Pan-cancer identification of clinically relevant genomic subtypes using outcome-weighted integrative clustering.
  Genome medicine 2020 Arora A, Olshen AB, Seshan VE, Shen R
• International Consensus Definition of DNA Methylation Subgroups in Juvenile Myelomonocytic Leukemia.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2020 Schönung M, Meyer J, Nöllke P, Olshen AB, Hartmann M, Murakami N, Wakamatsu M, Okuno Y, Plass C, Loh ML, Niemeyer CM, Muramatsu H, Flotho C, Stieglitz E, Lipka DB
• Human pediatric B-cell acute lymphoblastic leukemias can be classified as B-1 or B-2-like based on a minimal transcriptional signature.
  Experimental hematology 2020 Fitch B, Roy R, Geng H, Montecino-Rodriguez E, Bengtsson H, Gaillard C, Hiam K, Casero D, Olshen AB, Dorshkind K, Kogan SC
• Ribosome profiling reveals a functional role for autophagy in mRNA translational control.
  Communications biology 2020 Goldsmith J, Marsh T, Asthana S, Leidal AM, Suresh D, Olshen A, Debnath J
• Glucocorticoids paradoxically facilitate steroid resistance in T cell acute lymphoblastic leukemias and thymocytes.
  The Journal of clinical investigation 2020 Meyer LK, Huang BJ, Delgado-Martin C, Roy RP, Hechmer A, Wandler AM, Vincent TL, Fortina P, Olshen AB, Wood BL, Horton TM, Shannon KM, Teachey DT, Hermiston ML
• Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain.
  Molecular pain 2020 Kober KM, Lee MC, Olshen A, Conley YP, Sirota M, Keiser M, Hammer MJ, Abrams G, Schumacher M, Levine JD, Miaskowski C
• Next-Generation Sequencing of Retinoblastoma Identifies Pathogenic Alterations beyond RB1 Inactivation That Correlate with Aggressive Histopathologic Features.
  Ophthalmology 2019 Afshar AR, Pekmezci M, Bloomer MM, Cadenas NJ, Stevers M, Banerjee A, Roy R, Olshen AB, Van Ziffle J, Onodera C, Devine WP, Grenert JP, Bastian BC, Solomon DA, Damato BE
• Targeted Genomic Profiling of Acral Melanoma.
  Journal of the National Cancer Institute 2019 Yeh I, Jorgenson E, Shen L, Xu M, North JP, Shain AH, Reuss D, Wu H, Robinson WA, Olshen A, von Deimling A, Kwok PY, Bastian BC, Asgari MM
• Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis.
  Translational vision science & technology 2019 Afshar AR, Damato BE, Stewart JM, Zablotska LB, Roy R, Olshen AB, Joseph NM, Bastian BC
• Identifying a potential biomarker for primary focal segmental glomerulosclerosis and its association with recurrence after transplantation.
  Clinical transplantation 2019 Harel E, Shoji J, Abraham V, Miller L, Laszik Z, Thurison T, King A, Olshen A, Leung J, Szabo G, Hann B, Høyer-Hansen G, Craik CS, Vincenti F
• A Pilot Study Using a Multistaged Integrated Analysis of Gene Expression and Methylation to Evaluate Mechanisms for Evening Fatigue in Women Who Received Chemotherapy for Breast Cancer.
  Biological research for nursing 2019 Flowers E, Flentje A, Levine J, Olshen A, Hammer M, Paul S, Conley Y, Miaskowski C, Kober KM
• Magnetic resonance spectroscopy (MRS) can identify painful lumbar discs and may facilitate improved clinical outcomes of lumbar surgeries for discogenic pain.
  European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society 2019 Gornet MG, Peacock J, Claude J, Schranck FW, Copay AG, Eastlack RK, Benz R, Olshen A, Lotz JC
• Expression of mitochondrial dysfunction-related genes and pathways in paclitaxel-induced peripheral neuropathy in breast cancer survivors.
  Molecular pain 2018 Kober KM, Olshen A, Conley YP, Schumacher M, Topp K, Smoot B, Mazor M, Chesney M, Hammer M, Paul SM, Levine JD, Miaskowski C
• Phenotypic Characterization of Paclitaxel-Induced Peripheral Neuropathy in Cancer Survivors.
  Journal of pain and symptom management 2018 Kober KM, Mazor M, Abrams G, Olshen A, Conley YP, Hammer M, Schumacher M, Chesney M, Smoot B, Mastick J, Paul SM, Levine JD, Miaskowski C
• ABVD Without Radiation for Newly Diagnosed Pediatric and Young Adult Patients With Hodgkin Lymphoma: A Single Center Retrospective Analysis of 28 Consecutive Patients.
  Journal of pediatric hematology/oncology 2018 Stieglitz E, Dinh T, Phelps AS, Pampaloni MH, Olshen AB, Robbins E
• Disease burden and conditioning regimens in ASCT1221, a randomized phase II trial in children with juvenile myelomonocytic leukemia: A Children's Oncology Group study.
  Pediatric blood & cancer 2018 Dvorak CC, Satwani P, Stieglitz E, Cairo MS, Dang H, Pei Q, Gao Y, Wall D, Mazor T, Olshen AB, Parker JS, Kahwash S, Hirsch B, Raimondi S, Patel N, Skeens M, Cooper T, Mehta PA, Grupp SA, Loh ML
• Features of MRI stromal enhancement with neoadjuvant chemotherapy: a subgroup analysis of the ACRIN 6657/I-SPY TRIAL.
  Journal of medical imaging (Bellingham, Wash.) 2017 Olshen A, Wolf D, Jones EF, Newitt D, van ‘t Veer LJ, Yau C, Esserman L, Wulfkuhle JD, Gallagher RI, Singer L, Petricoin EF, Hylton N, Park CC
• Genome-wide DNA methylation is predictive of outcome in juvenile myelomonocytic leukemia.
  Nature communications 2017 Stieglitz E, Mazor T, Olshen AB, Geng H, Gelston LC, Akutagawa J, Lipka DB, Plass C, Flotho C, Chehab FF, Braun BS, Costello JF, Loh ML
• Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Mazor T, Chesnelong C, Pankov A, Jalbert LE, Hong C, Hayes J, Smirnov IV, Marshall R, Souza CF, Shen Y, Viswanath P, Noushmehr H, Ronen SM, Jones SJM, Marra MA, Cairncross JG, Perry A, Nelson SJ, …
• Heterogeneous resistance to quizartinib in acute myeloid leukemia revealed by single-cell analysis.
  Blood 2017 Smith CC, Paguirigan A, Jeschke GR, Lin KC, Massi E, Tarver T, Chin CS, Asthana S, Olshen A, Travers KJ, Wang S, Levis MJ, Perl AE, Radich JP, Shah NP
• Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient.
  Oral oncology 2017 Wang SJ, Asthana S, van Zante A, Heaton CM, Phuchareon J, Stein L, Higuchi S, Kishimoto T, Chiu CY, Olshen AB, McCormick F, Tetsu O
• Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Williams KE, Lemieux GA, Hassis ME, Olshen AB, Fisher SJ, Werb Z
• Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia.
  Nature genetics 2016 Stieglitz E, Taylor-Weiner AN, Chang TY, Gelston LC, Wang YD, Mazor T, Esquivel E, Yu A, Seepo S, Olsen SR, Rosenberg M, Archambeault SL, Abusin G, Beckman K, Brown PA, Briones M, Carcamo B, Cooper T,…
• Development and Validation of a Gene-Based Model for Outcome Prediction in Germ Cell Tumors Using a Combined Genomic and Expression Profiling Approach.
  PloS one 2015 Korkola JE, Heck S, Olshen AB, Feldman DR, Reuter VE, Houldsworth J, Bosl GJ, Chaganti RS
• Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity.
  Nature biotechnology 2015 Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, Gao J, Socci ND, Solit DB, Olshen AB, Schultz N, Taylor BS
• The genomic landscape of juvenile myelomonocytic leukemia.
  Nature genetics 2015 Stieglitz E, Taylor-Weiner AN, Chang TY, Gelston LC, Wang YD, Mazor T, Esquivel E, Yu A, Seepo S, Olsen S, Rosenberg M, Archambeault SL, Abusin G, Beckman K, Brown PA, Briones M, Carcamo B, Cooper T, …
• DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors.
  Cancer cell 2015 Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJA, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers MLM, Bollen AW, Taylor BS, Molinaro AM, Olshen AB…
• Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway.
  Nature genetics 2015 Shain AH, Garrido M, Botton T, Talevich E, Yeh I, Sanborn JZ, Chung J, Wang NJ, Kakavand H, Mann GJ, Thompson JF, Wiesner T, Roy R, Olshen AB, Gagnon A, Gray JW, Huh N, Hur JS, Busam KJ, Scolyer RA, …
• DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.
  Genome research 2014 Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B
• Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib.
  Haematologica 2014 Olshen A, Tang M, Cortes J, Gonen M, Hughes T, Branford S, Quintás-Cardama A, Michor F
• Changes in abundance of oral microbiota associated with oral cancer.
  PloS one 2014 Schmidt BL, Kuczynski J, Bhattacharya A, Huey B, Corby PM, Queiroz EL, Nightingale K, Kerr AR, DeLacure MD, Veeramachaneni R, Olshen AB, Albertson DG, Muy-Teck Teh
• Recurrent epimutations activate gene body promoters in primary glioblastoma.
  Genome research 2014 Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF
• Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.
  Science (New York, N.Y.) 2013 Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS…
• The translational landscape of the mammalian cell cycle.
  Molecular cell 2013 Stumpf CR, Moreno MV, Olshen AB, Taylor BS, Ruggero D
• Assessing gene-level translational control from ribosome profiling.
  Bioinformatics (Oxford, England) 2013 Olshen AB, Hsieh AC, Stumpf CR, Olshen RA, Ruggero D, Taylor BS
• A colorectal cancer classification system that associates cellular phenotype and responses to therapy.
  Nature medicine 2013 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
• Combining integrated genomics and functional genomics to dissect the biology of a cancer-associated, aberrant transcription factor, the ASPSCR1-TFE3 fusion oncoprotein.
  The Journal of pathology 2013 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
• Pattern discovery and cancer gene identification in integrated cancer genomic data.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M, Shen R
• β1-Integrin via NF-κB signaling is essential for acquisition of invasiveness in a model of radiation treated in situ breast cancer.
  Breast cancer research : BCR 2013 Nam JM, Ahmed KM, Costes S, Zhang H, Onodera Y, Olshen AB, Hatanaka KC, Kinoshita R, Ishikawa M, Sabe H, Shirato H, Park CC
• Genomic profiling of isolated circulating tumor cells from metastatic breast cancer patients.
  Cancer research 2012 Magbanua MJ, Sosa EV, Roy R, Eisenbud LE, Scott JH, Olshen A, Pinkel D, Rugo HS, Park JW
• Integrative subtype discovery in glioblastoma using iCluster.
  PloS one 2012 Shen R, Mo Q, Schultz N, Seshan VE, Olshen AB, Huse J, Ladanyi M, Sander C
• Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2011 Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RC, Olshen AB, Pinkel D, Schmidt BL, Albertson DG
• The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma.
  Cell 2011 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, …
• 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 2011 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
• Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.
  Bioinformatics (Oxford, England) 2011 Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE
• The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma.
  Nature genetics 2011 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
• Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.
  Bioinformatics (Oxford, England) 2011 Ostrovnaya I, Seshan VE, Olshen AB, Begg CB
• Coactivation of receptor tyrosine kinases in malignant mesothelioma as a rationale for combination targeted therapy.
  Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2011 Brevet M, Shimizu S, Bott MJ, Shukla N, Zhou Q, Olshen AB, Rusch V, Ladanyi M
• Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy.
  Nature medicine 2011 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
• Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI.
  Integrative biology : quantitative biosciences from nano to macro 2011 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
• Gene Expression Differences between Enriched Normal and Chronic Myelogenous Leukemia Quiescent Stem/Progenitor Cells and Correlations with Biological Abnormalities.
  Journal of oncology 2011 Affer M, Dao S, Liu C, Olshen AB, Mo Q, Viale A, Lambek CL, Marr TG, Clarkson BD
• 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.
  Clinical cancer research : an official journal of the American Association for Cancer Research 2011 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
• Microfluidic-based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in the sera of prostate cancer patients.
  Cancer research 2010 Moltzahn F, Olshen AB, Baehner L, Peek A, Fong L, Stöppler H, Simko J, Hilton JF, Carroll P, Blelloch R
• Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
  Nature biotechnology 2010 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…
• Copy number and gene expression differences between African American and Caucasian American prostate cancer.
  Journal of translational medicine 2010 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
• A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data.
  Statistics in medicine 2010 Ostrovnaya I, Olshen AB, Seshan VE, Orlow I, Albertson DG, Begg CB
• A classification model for distinguishing copy number variants from cancer-related alterations.
  BMC bioinformatics 2010 Ostrovnaya I, Nanjangud G, Olshen AB
• Genetic analysis of the early natural history of epithelial ovarian carcinoma.
  PloS one 2010 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
• Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumors.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2009 Korkola JE, Houldsworth J, Feldman DR, Olshen AB, Qin LX, Patil S, Reuter VE, Bosl GJ, Chaganti RS
• Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis.
  Bioinformatics (Oxford, England) 2009 Shen R, Olshen AB, Ladanyi M
• The EWSR1/NR4A3 fusion protein of extraskeletal myxoid chondrosarcoma activates the PPARG nuclear receptor gene.
  The Journal of pathology 2009 Filion C, Motoi T, Olshen AB, Laé M, Emnett RJ, Gutmann DH, Perry A, Ladanyi M, Labelle Y
• Pathway activation in large B-cell non-Hodgkin lymphoma cell lines by doxorubicin reveals prognostic markers of in vivo response.
  Leukemia & lymphoma 2008 Houldsworth J, Petlakh M, Olshen AB, Chaganti RS
• Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33.
  Proceedings of the National Academy of Sciences of the United States of America 2008 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, …
• Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.
  BMC genetics 2008 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…
• 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 Zhou P, Comenzo RL, Olshen AB, Bonvini E, Koenig S, Maslak PG, Fleisher M, Hoffman J, Jhanwar S, Young JW, Nimer SD, Boruchov AM
• Associations among multiple markers and complex disease: models, algorithms, and applications.
  Advances in genetics 2008 Assimes TL, Olshen AB, Narasimhan B, Olshen RA
• In vivo differentiation and genomic evolution in adult male germ cell tumors.
  Genes, chromosomes & cancer 2008 Korkola JE, Heck S, Olshen AB, Reuter VE, Bosl GJ, Houldsworth J, Chaganti RS
• Calreticulin expression in the clonal plasma cells of patients with systemic light-chain (AL-) amyloidosis is associated with response to high-dose melphalan.
  Blood 2007 Zhou P, Teruya-Feldstein J, Lu P, Fleisher M, Olshen A, Comenzo RL
• Global gene expression profiling of PAX-FKHR fusion-positive alveolar and PAX-FKHR fusion-negative embryonal rhabdomyosarcomas.
  The Journal of pathology 2007 Laé M, Ahn EH, Mercado GE, Chuai S, Edgar M, Pawel BR, Olshen A, Barr FG, Ladanyi M
• A faster circular binary segmentation algorithm for the analysis of array CGH data.
  Bioinformatics (Oxford, England) 2007 Venkatraman ES, Olshen AB
• Constitutive gene expression predisposes morphogen-mediated cell fate responses of NT2/D1 and 27X-1 human embryonal carcinoma cells.
  Stem cells (Dayton, Ohio) 2006 Chadalavada RS, Korkola JE, Houldsworth J, Olshen AB, Bosl GJ, Studer L, Chaganti RS
• Breast tumor copy number aberration phenotypes and genomic instability.
  BMC cancer 2006 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
• 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 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
• p53, epidermal growth factor, and platelet-derived growth factor in uterine leiomyosarcoma and leiomyomas.
  International journal of gynecological cancer : official journal of the International Gynecological Cancer Society 2006 Anderson SE, Nonaka D, Chuai S, Olshen AB, Chi D, Sabbatini P, Soslow RA
• 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 Korkola JE, Houldsworth J, Chadalavada RS, Olshen AB, Dobrzynski D, Reuter VE, Bosl GJ, Chaganti RS
• Differential exoprotease activities confer tumor-specific serum peptidome patterns.
  The Journal of clinical investigation 2006 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
• Molecular profiling of endometrial cancers from African-American and Caucasian women.
  Gynecologic oncology 2005 Ferguson SE, Olshen AB, Levine DA, Viale A, Barakat RR, Boyd J
• Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas.
  Blood 2005 Chen W, Houldsworth J, Olshen AB, Nanjangud G, Chaganti S, Venkatraman ES, Halaas J, Teruya-Feldstein J, Zelenetz AD, Chaganti RS
• Apoptotic and cell cycle regulatory markers in uterine leiomyosarcoma.
  Gynecologic oncology 2005 Leiser AL, Anderson SE, Nonaka D, Chuai S, Olshen AB, Chi DS, Soslow RA
• Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice.
  Genome biology 2005 Huang S, Li Y, Chen Y, Podsypanina K, Chamorro M, Olshen AB, Desai KV, Tann A, Petersen D, Green JE, Varmus HE
• 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 Moskowitz CH, Zelenetz AD, Kewalramani T, Hamlin P, Lessac-Chenen S, Houldsworth J, Olshen A, Chaganti R, Nimer S, Teruya-Feldstein J
• Gene expression-based classification of nonseminomatous male germ cell tumors.
  Oncogene 2005 Korkola JE, Houldsworth J, Dobrzynski D, Olshen AB, Reuter VE, Bosl GJ, Chaganti RS
• Genes that mediate breast cancer metastasis to lung.
  Nature 2005 Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD, Viale A, Olshen AB, Gerald WL, Massagué 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 : an official journal of the American Association for Cancer Research 2005 Ferguson SE, Olshen AB, Viale A, Barakat RR, Boyd J
• Transcriptional program of bone morphogenetic protein-2-induced epithelial and smooth muscle differentiation of pluripotent human embryonal carcinoma cells.
  Functional & integrative genomics 2005 Chadalavada RS, Houldsworth J, Olshen AB, Bosl GJ, Studer L, Chaganti RS
• Identifying site-specific metastasis genes and functions.
  Cold Spring Harbor symposia on quantitative biology 2005 Gupta GP, Minn AJ, Kang Y, Siegel PM, Serganova I, Cordón-Cardo C, Olshen AB, Gerald WL, Massagué J
• Circular binary segmentation for the analysis of array-based DNA copy number data.
  Biostatistics (Oxford, England) 2004 Olshen AB, Venkatraman ES, Lucito R, Wigler M
• Tissue microarray immunohistochemical expression of estrogen, progesterone, and androgen receptors in uterine leiomyomata and leiomyosarcoma.
  Cancer 2004 Leitao MM, Soslow RA, Nonaka D, Olshen AB, Aghajanian C, Sabbatini P, Dupont J, Hensley M, Sonoda Y, Barakat RR, Anderson S
• Circulating angiogenic factor levels correlate with extent of disease and risk of recurrence in patients with soft tissue sarcoma.
  Annals of oncology : official journal of the European Society for Medical Oncology 2004 Yoon SS, Segal NH, Olshen AB, Brennan MF, Singer S
• Collaboration of homologous recombination and nonhomologous end-joining factors for the survival and integrity of mice and cells.
  Genes & development 2004 Couëdel C, Mills KD, Barchi M, Shen L, Olshen A, Johnson RD, Nussenzweig A, Essers J, Kanaar R, Li GC, Alt FW, Jasin M
• Gene expression profiling of tamoxifen-associated uterine cancers: evidence for two molecular classes of endometrial carcinoma.
  Gynecologic oncology 2004 Ferguson SE, Olshen AB, Viale A, Awtrey CS, Barakat RR, Boyd J
• Relationship between REL amplification, REL function, and clinical and biologic features in diffuse large B-cell lymphomas.
  Blood 2003 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
• BARD1 participates with BRCA1 in homology-directed repair of chromosome breaks.
  Molecular and cellular biology 2003 Westermark UK, Reyngold M, Olshen AB, Baer R, Jasin M, Moynahan ME
• Classifying melanocytic tumors based on DNA copy number changes.
  The American journal of pathology 2003 Bastian BC, Olshen AB, LeBoit PE, Pinkel D
• Angiogenesis impairment in Id-deficient mice cooperates with an Hsp90 inhibitor to completely suppress HER2/neu-dependent breast tumors.
  Proceedings of the National Academy of Sciences of the United States of America 2003 de Candia P, Solit DB, Giri D, Brogi E, Siegel PM, Olshen AB, Muller WJ, Rosen N, Benezra R
• Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation.
  Genome research 2003 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
• Insights into extramedullary tumour cell growth revealed by expression profiling of human plasmacytomas and multiple myeloma.
  British journal of haematology 2003 Hedvat CV, Comenzo RL, Teruya-Feldstein J, Olshen AB, Ely SA, Osman K, Zhang Y, Kalakonda N, Nimer SD
• Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.
  Cancer research 2003 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
• Inhibition of heat shock protein 90 function down-regulates Akt kinase and sensitizes tumors to Taxol.
  Cancer research 2003 Solit DB, Basso AD, Olshen AB, Scher HI, Rosen N
• Quantitation of apoptotic activity following castration in human prostatic tissue in vivo.
  The Prostate 2003 Staack A, Kassis AP, Olshen A, Wang Y, Wu D, Carroll PR, Grossfeld GD, Cunha GR, Hayward SW
• Deriving quantitative conclusions from microarray expression data.
  Bioinformatics (Oxford, England) 2002 Olshen AB, Jain AN
• Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway.
  Cancer research 2002 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
• Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer.
  Cancer research 2002 Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Kovacs G, Waldman FM
• A high-resolution radiation hybrid map of the human genome draft sequence.
  Science (New York, N.Y.) 2001 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,…
• 2-[C-11]thymidine imaging of malignant brain tumors.
  Cancer research 1999 Eary JF, Mankoff DA, Spence AM, Berger MS, Olshen A, Link JM, O'Sullivan F, Krohn KA
• Imaging of oncologic patients: benefit of combined CT and FDG PET in the diagnosis of malignancy.
  AJR. American journal of roentgenology 1998 Eubank WB, Mankoff DA, Schmiedl UP, Winter TC, Fisher ER, Olshen AB, Graham MM, Eary JF
• Pedigree analysis package vs. MIXD: fitting the mixed model on a large pedigree.
  Genetic epidemiology 1996 Olshen AB, Wijsman EM
• Monte Carlo analysis on a large pedigree.
  Genetic epidemiology 1993 Thompson EA, Lin S, Olshen AB, Wijsman EM