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Eliezer Van Allen, MD


Medical Oncology

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Physician

  • Physician
  • Instructor in Medicine, Harvard Medical School

Centers/Programs

Clinical Interests

  • Genitourinary oncology

Contact Information

  • Appointments617-582-9725 (follow-up)
    877-332-4294 (new)
  • Office Phone Number617-632-4524
  • Fax617-632-2165

Board Certification:

  • Internal Medicine, 2010

Fellowship:

  • Dana-Farber/Partners CancerCare, Medical Oncology

Residency:

  • University of California, San Francisco, Internal Medicine

Medical School:

  • University of California, Los Angeles

Research

Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun. 2021 10 01; 12(1):5775.
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RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics. J Clin Invest. 2021 Sep 23.
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Biologically informed deep neural network for prostate cancer discovery. Nature. 2021 Oct; 598(7880):348-352.
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Molecular correlates of response to eribulin and pembrolizumab in hormone receptor-positive metastatic breast cancer. Nat Commun. 2021 09 21; 12(1):5563.
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Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer. Cell Rep. 2021 Sep 07; 36(10):109665.
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Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: a phase II and biomarker study. NPJ Breast Cancer. 2021 Aug 25; 7(1):110.
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Discovery and Features of an Alkylating Signature in Colorectal Cancer. Cancer Discov. 2021 Oct; 11(10):2446-2455.
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Transcriptional profiling of primary prostate tumor in metastatic hormone-sensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED trial. Ann Oncol. 2021 09; 32(9):1157-1166.
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Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Cancer Res. 2021 Aug 01; 81(15):3971-3984.
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Clinical Inflection Point Detection on the Basis of EHR Data to Identify Clinical Trial-Ready Patients With Cancer. JCO Clin Cancer Inform. 2021 06; 5:622-630.
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Evolution of delayed resistance to immunotherapy in a melanoma responder. Nat Med. 2021 06; 27(6):985-992.
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Impact of Pathogenic Germline DNA Damage Repair alterations on Response to Intense Neoadjuvant Androgen Deprivation Therapy in High-risk Localized Prostate Cancer. Eur Urol. 2021 Sep; 80(3):295-303.
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Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance. Clin Cancer Res. 2021 Jul 01; 27(13):3610-3619.
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Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity. Cancer Discov. 2021 Aug; 11(8):1952-1969.
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Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. Cancer Cell. 2021 May 10; 39(5):649-661.e5.
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Transcriptional mediators of treatment resistance in lethal prostate cancer. Nat Med. 2021 03; 27(3):426-433.
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Dissecting the immunogenomic biology of cancer for biomarker development. Nat Rev Clin Oncol. 2021 03; 18(3):133-134.
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Systematic auditing is essential to debiasing machine learning in biology. Commun Biol. 2021 02 10; 4(1):183.
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Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. Nat Commun. 2021 02 05; 12(1):808.
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Evaluating the molecular diagnostic yield of joint genotyping-based approach for detecting rare germline pathogenic and putative loss-of-function variants. Genet Med. 2021 05; 23(5):918-926.
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Beyond conventional immune-checkpoint inhibition - novel immunotherapies for renal cell carcinoma. Nat Rev Clin Oncol. 2021 04; 18(4):199-214.
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Integrated Analysis of Germ Cell Tumors. Methods Mol Biol. 2021; 2195:181-187.
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Predicting immunotherapy response through genomics. Curr Opin Genet Dev. 2021 02; 66:1-9.
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Clinical Efficacy and Molecular Response Correlates of the WEE1 Inhibitor Adavosertib Combined with Cisplatin in Patients with Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2021 02 15; 27(4):983-991.
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Integrated molecular drivers coordinate biological and clinical states in melanoma. Nat Genet. 2020 12; 52(12):1373-1383.
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Re: Russell E.N. Becker, Alexa R. Meyer, Aaron Brant, et al. Clinical Restaging and Tumor Sequencing are Inaccurate Indicators of Response to Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.07.016. Eur Urol. 2021 02; 79(2):e56-e57.
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Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer. Clin Cancer Res. 2021 Apr 01; 27(7):2011-2022.
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Accelerating precision medicine in metastatic prostate cancer. Nat Cancer. 2020 Nov; 1(11):1041-1053.
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Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma. JAMA. 2020 11 17; 324(19):1957-1969.
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Germ Cell Tumor Molecular Heterogeneity Revealed Through Analysis of Primary and Metastasis Pairs. JCO Precis Oncol. 2020; 4.
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Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer Res. 2020 12 01; 80(23):5393-5407.
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Effect of Eribulin With or Without Pembrolizumab on Progression-Free Survival for Patients With Hormone Receptor-Positive, ERBB2-Negative Metastatic Breast Cancer: A Randomized Clinical Trial. JAMA Oncol. 2020 10 01; 6(10):1598-1605.
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Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non-Muscle-Invasive Bladder Cancer. Cancer Res. 2020 10 15; 80(20):4476-4486.
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A phase 2 trial of buparlisib in patients with platinum-resistant metastatic urothelial carcinoma. Cancer. 2020 10 15; 126(20):4532-4544.
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Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy. J Clin Invest. 2020 08 03; 130(8):4266-4281.
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Natural Language Processing to Ascertain Cancer Outcomes From Medical Oncologist Notes. JCO Clin Cancer Inform. 2020 08; 4:680-690.
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CoMut: visualizing integrated molecular information with comutation plots. Bioinformatics. 2020 08 01; 36(15):4348-4349.
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Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2020 Jul; 26(7):1147.
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FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues. Nat Protoc. 2020 08; 15(8):2503-2518.
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Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant. Nat Commun. 2020 06 12; 11(1):2996.
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Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. J Immunother Cancer. 2020 06; 8(1).
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Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med. 2020 06; 26(6):909-918.
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Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression. J Clin Oncol. 2020 07 20; 38(21):2380-2389.
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Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas. Ann Oncol. 2020 08; 31(8):1011-1020.
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Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade. Cancer Discov. 2020 09; 10(9):1296-1311.
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Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma. Nat Cancer. 2020 May; 1(5):493-506.
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Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors. Cancer Immunol Res. 2020 08; 8(8):1075-1084.
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Engaging Patients in Precision Oncology: Development and Usability of a Web-Based Patient-Facing Genomic Sequencing Report. JCO Precis Oncol. 2020; 4.
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Germline Features Associated with Immune Infiltration in Solid Tumors. Cell Rep. 2020 03 03; 30(9):2900-2908.e4.
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ATM Loss Confers Greater Sensitivity to ATR Inhibition Than PARP Inhibition in Prostate Cancer. Cancer Res. 2020 06 01; 80(11):2094-2100.
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Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2020 06 01; 26(11):2565-2572.
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Identification of cancer driver genes based on nucleotide context. Nat Genet. 2020 02; 52(2):208-218.
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The role of site-specific therapy for cancers of unknown of primary: A meta-analysis. Eur J Cancer. 2020 03; 127:118-122.
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A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma. Br J Cancer. 2020 02; 122(4):555-563.
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Prevalence of pathogenic germline cancer risk variants in high-risk urothelial carcinoma. Genet Med. 2020 04; 22(4):709-718.
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Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2019 12; 25(12):1916-1927.
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CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. Cell Rep. 2019 11 19; 29(8):2355-2370.e6.
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Results of a Multicenter Phase II Study of Atezolizumab and Bevacizumab for Patients With Metastatic Renal Cell Carcinoma With Variant Histology and/or Sarcomatoid Features. J Clin Oncol. 2020 01 01; 38(1):63-70.
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Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer. JCO Precis Oncol. 2019; 3.
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Scaling computational genomics to millions of individuals with GPUs. Genome Biol. 2019 11 01; 20(1):228.
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Clinical Validation of PBRM1 Alterations as a Marker of Immune Checkpoint Inhibitor Response in Renal Cell Carcinoma. JAMA Oncol. 2019 Nov 01; 5(11):1631-1633.
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Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes From Radiology Reports. JAMA Oncol. 2019 Oct 01; 5(10):1421-1429.
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Metabolomic adaptations and correlates of survival to immune checkpoint blockade. Nat Commun. 2019 09 25; 10(1):4346.
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Finding the edge of the seat. Nat Med. 2019 09; 25(9):1328.
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Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2019 Jul; 51(7):1194.
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Integrative Molecular Characterization of Resistance to Neoadjuvant Chemoradiation in Rectal Cancer. Clin Cancer Res. 2019 09 15; 25(18):5561-5571.
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Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer. Cancer Immunol Res. 2019 08; 7(8):1230-1236.
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Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma. Clin Cancer Res. 2019 08 15; 25(16):5135-5142.
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Mechanisms of Resistance to Immune Checkpoint Blockade: Why Does Checkpoint Inhibitor Immunotherapy Not Work for All Patients? Am Soc Clin Oncol Educ Book. 2019 Jan; 39:147-164.
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Genomic correlates of clinical outcome in advanced prostate cancer. Proc Natl Acad Sci U S A. 2019 06 04; 116(23):11428-11436.
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Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group. Br J Cancer. 2019 Apr; 120(8):869.
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Association of Inherited Pathogenic Variants in Checkpoint Kinase 2 (CHEK2) With Susceptibility to Testicular Germ Cell Tumors. JAMA Oncol. 2019 Apr 01; 5(4):514-522.
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Genomic correlates of response to immune checkpoint blockade. Nat Med. 2019 03; 25(3):389-402.
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Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites. Clin Cancer Res. 2019 04 15; 25(8):2458-2470.
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Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer. Eur Urol. 2019 07; 76(1):89-97.
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Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine. Genome Med. 2018 11 29; 10(1):93.
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Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest. 2018 11 01; 128(11):5185.
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A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 11 01; 175(4):984-997.e24.
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Everolimus and pazopanib (E/P) benefit genomically selected patients with metastatic urothelial carcinoma. Br J Cancer. 2018 09; 119(6):707-712.
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Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest. 2018 10 01; 128(10):4441-4453.
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A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Ann Oncol. 2018 09 01; 29(9):1895-1902.
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Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nat Genet. 2018 09; 50(9):1271-1281.
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Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group. Br J Cancer. 2018 08; 119(5):615-621.
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Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018 12; 36(11):1056-1058.
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Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 08 09; 174(4):1034-1035.
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ERCC2 Helicase Domain Mutations Confer Nucleotide Excision Repair Deficiency and Drive Cisplatin Sensitivity in Muscle-Invasive Bladder Cancer. Clin Cancer Res. 2019 02 01; 25(3):977-988.
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Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors. JCO Precis Oncol. 2018; 2018.
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LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade. Cell. 2018 07 26; 174(3):549-563.e19.
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Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations. Cancer Res. 2018 08 15; 78(16):4716-4730.
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Early loss of mitochondrial complex I and rewiring of glutathione metabolism in renal oncocytoma. Proc Natl Acad Sci U S A. 2018 07 03; 115(27):E6283-E6290.
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Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19.
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Enrichment of FGFR3-TACC3 Fusions in Patients With Bladder Cancer Who Are Young, Asian, or Have Never Smoked. JCO Precis Oncol. 2018; 2.
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The Clinical Activity of PD-1/PD-L1 Inhibitors in Metastatic Non-Clear Cell Renal Cell Carcinoma. Cancer Immunol Res. 2018 07; 6(7):758-765.
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Interactive or static reports to guide clinical interpretation of cancer genomics. J Am Med Inform Assoc. 2018 05 01; 25(5):458-464.
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Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun. 2018 04 27; 9(1):1691.
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Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell. 2018 04 19; 173(3):624-633.e8.
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Integrated genomic characterization of oral carcinomas in post-hematopoietic stem cell transplantation survivors. Oral Oncol. 2018 06; 81:1-9.
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Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 04 05; 173(2):321-337.e10.
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Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 04 05; 173(2):371-385.e18.
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The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2018 05; 50(5):645-651.
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Phase I Trial of a Tablet Formulation of Pilaralisib, a Pan-Class I PI3K Inhibitor, in Patients with Advanced Solid Tumors. Oncologist. 2018 04; 23(4):401-e38.
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Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018 03 01; 102(3):401-414.
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Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in BRAFV600E Colorectal Cancer. Cancer Discov. 2018 04; 8(4):417-427.
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Change in Neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma. J Immunother Cancer. 2018 01 22; 6(1):5.
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Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018 Feb 16; 359(6377):801-806.
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Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer. Nat Commun. 2017 12 19; 8(1):2193.
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Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol. 2017; 1.
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Tumor Evolution: A Problem of Histocompatibility. Cell. 2017 11 30; 171(6):1252-1253.
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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017 11 06; 8(1):1324.
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Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids. Cancer Discov. 2018 02; 8(2):196-215.
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The Potential and Challenges of Expanded Germline Testing in Clinical Oncology. JAMA. 2017 09 05; 318(9):801-803.
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Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 08 23; 5(2):105-118.e9.
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Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance. Sci Transl Med. 2017 Aug 09; 9(402).
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Transforming the Perioperative Treatment Paradigm in Non-Metastatic RCC-A Possible Path Forward. Kidney Cancer. 2017 Jul 26; 1(1):31-40.
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In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature. 2017 07 27; 547(7664):413-418.
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Systematic genomic and translational efficiency studies of uveal melanoma. PLoS One. 2017; 12(6):e0178189.
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Toward Molecularly Driven Precision Medicine in Lung Adenocarcinoma. Cancer Discov. 2017 06; 7(6):555-557.
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Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017 09; 7(9):973-983.
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The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell Rep. 2017 04 04; 19(1):218-224.
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Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2017 03 01; 18(1):46.
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Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma. Immunity. 2017 02 21; 46(2):197-204.
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Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma. Michaelson MD, McKay RR, Werner L, Atkins MB, Van Allen EM, Olivier KM, Song J, Signoretti S, McDermott DF, Choueiri TK.Cancer. 2015 Oct 1;121(19):3435-43. [Epub 2015 Jun 8]. doi: 10.1002/cncr.29503. Urol Oncol. 2017 03; 35(3):117-118.
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Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study. Genet Med. 2017 07; 19(7):787-795.
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The fuzzy world of precision medicine: deliberations of a precision medicine tumor board. Per Med. 2017 Jan; 14(1):37-50.
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Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. Cancer Immunol Res. 2017 01; 5(1):84-91.
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Genomic evolution and chemoresistance in germ-cell tumours. Nature. 2016 11 30; 540(7631):114-118.
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Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2016 11 17; 17(1):231.
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Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma. Clin Cancer Res. 2017 Jun 15; 23(12):3214-3222.
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Somatic cancer variant curation and harmonization through consensus minimum variant level data. Genome Med. 2016 11 04; 8(1):117.
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Delivering on the promise of precision cancer medicine. Genome Med. 2016 10 25; 8(1):110.
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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 10 18; 17(4):1206.
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Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017 May 01; 23(9):2367-2373.
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Genomic Approaches to Understanding Response and Resistance to Immunotherapy. Clin Cancer Res. 2016 Dec 01; 22(23):5642-5650.
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Tumor Mutational Load and Immune Parameters across Metastatic Renal Cell Carcinoma Risk Groups. Cancer Immunol Res. 2016 10; 4(10):820-822.
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A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine. Oncotarget. 2016 Aug 16; 7(33):52888-52899.
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Clinical Validation of Chemotherapy Response Biomarker ERCC2 in Muscle-Invasive Urothelial Bladder Carcinoma. JAMA Oncol. 2016 Aug 01; 2(8):1094-6.
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The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. Genome Med. 2016 07 26; 8(1):79.
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Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer. N Engl J Med. 2016 Aug 04; 375(5):443-53.
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Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma. J Natl Compr Canc Netw. 2016 07; 14(7):820-4.
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Genomic determinants of cancer immunotherapy. Curr Opin Immunol. 2016 08; 41:32-38.
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A phase 1 study of buparlisib and bevacizumab in patients with metastatic renal cell carcinoma progressing on vascular endothelial growth factor-targeted therapies. Cancer. 2016 Aug 01; 122(15):2389-98.
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Precision medicine for advanced prostate cancer. Curr Opin Urol. 2016 May; 26(3):231-9.
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Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer. Bladder Cancer. 2016 Apr 27; 2(2):165-202.
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Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat Genet. 2016 06; 48(6):600-606.
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Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 05; 34(5):539-46.
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Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 Apr 26; 15(4):857-865.
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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016 Apr 08; 352(6282):189-96.
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Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016 Mar 25; 351(6280):1463-9.
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Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia. Blood. 2016 05 26; 127(21):2598-606.
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Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study. Genet Med. 2016 10; 18(10):1011-9.
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Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Mar; 22(3):298-305.
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Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma. Clin Cancer Res. 2016 05 15; 22(10):2445-2452.
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Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors. Clin Cancer Res. 2016 05 01; 22(9):2183-9.
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Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov. 2015 Nov; 5(11):1164-1177.
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Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015 Oct 09; 350(6257):207-211.
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Next-generation sequencing to guide cancer therapy. Genome Med. 2015; 7(1):80.
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Integrative Clinical Genomics of Advanced Prostate Cancer. Cell. 2015 Jul 16; 162(2):454.
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Characterization of Clinical Cases of Collecting Duct Carcinoma of the Kidney Assessed by Comprehensive Genomic Profiling. Eur Urol. 2016 09; 70(3):516-21.
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CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc. 2015 Nov; 22(6):1231-42.
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Phase II study of tivantinib (ARQ 197) in patients with metastatic triple-negative breast cancer. Invest New Drugs. 2015 Oct; 33(5):1108-14.
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Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma. Cancer. 2015 Oct 01; 121(19):3435-43.
View in: PubMed

Somatic Copy Number Abnormalities and Mutations in PI3K/AKT/mTOR Pathway Have Prognostic Significance for Overall Survival in Platinum Treated Locally Advanced or Metastatic Urothelial Tumors. PLoS One. 2015; 10(6):e0124711.
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Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation. Cancer Immunol Res. 2015 Aug; 3(8):855-63.
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Integrative clinical genomics of advanced prostate cancer. Cell. 2015 May 21; 161(5):1215-1228.
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Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma. JAMA Oncol. 2015 May; 1(2):238-44.
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PLZF, a tumor suppressor genetically lost in metastatic castration-resistant prostate cancer, is a mediator of resistance to androgen deprivation therapy. Cancer Res. 2015 May 15; 75(10):1944-8.
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Re: Floris H. Groenendijk, Jeroen de Jong, Elisabeth E. Fransen van de Putte, et al. ERBB2 Mutations Characterize a Subgroup of Muscle-invasive Bladder Cancers with Excellent Response to Neoadjuvant Chemotherapy. Eur Urol. In press. http://dx.doi.org/10.1016/j.eururo.2015.01.014. Eur Urol. 2015 Aug; 68(2):e31-2.
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A functional landscape of resistance to ALK inhibition in lung cancer. Cancer Cell. 2015 Mar 09; 27(3):397-408.
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Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations. Cancer Discov. 2015 Apr; 5(4):358-67.
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Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci U S A. 2014 Dec 23; 111(51):E5564-73.
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Kinome-wide functional screen identifies role of PLK1 in hormone-independent, ER-positive breast cancer. Cancer Res. 2015 Jan 15; 75(2):405-14.
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RNF43 is frequently mutated in colorectal and endometrial cancers. Nat Genet. 2014 Dec; 46(12):1264-6.
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Response and acquired resistance to everolimus in anaplastic thyroid cancer. N Engl J Med. 2014 Oct 09; 371(15):1426-33.
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Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov. 2014 Oct; 4(10):1140-53.
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Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nat Biotechnol. 2014 Jul; 32(7):644-52.
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Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014 Jun; 20(6):682-8.
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Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014 May; 32(5):479-84.
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Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib. Cancer Discov. 2014 May; 4(5):546-53.
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Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy. Prostate Cancer Prostatic Dis. 2014 Mar; 17(1):23-7.
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The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 2014 Jan; 4(1):94-109.
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MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov. 2014 Jan; 4(1):61-8.
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A phase II trial of AS1411 (a novel nucleolin-targeted DNA aptamer) in metastatic renal cell carcinoma. Invest New Drugs. 2014 Feb; 32(1):178-87.
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Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium. Genet Med. 2013 Nov; 15(11):860-7.
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A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record. Genet Med. 2013 Oct; 15(10):824-32.
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Punctuated evolution of prostate cancer genomes. Cell. 2013 Apr 25; 153(3):666-77.
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Clinical analysis and interpretation of cancer genome data. J Clin Oncol. 2013 May 20; 31(15):1825-33.
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A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov. 2013 Mar; 3(3):350-62.
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Moving toward personalized medicine in castration-resistant prostate cancer. Urol Clin North Am. 2012 Nov; 39(4):483-90.
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Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet. 2012 May 20; 44(6):685-9.
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A Common Language for Transformative Healthcare Networking. New England Journal of Medicine. 2012.

A piece of my mind. Paracentesis by moonlight. JAMA. 2011 Apr 27; 305(16):1635-6.
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The paradox of positive thinking. J Clin Oncol. 2011 Jul 01; 29(19):2730-1.
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Off-label use of rituximab in a multipayer insurance system. J Oncol Pract. 2011 Mar; 7(2):76-9.
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One day later. Continuing psychological stress after a cardiac intensive care rotation. J Gen Intern Med. 2010 Aug; 25(8):882-3.
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A role in transition. Ann Intern Med. 2009 Sep 15; 151(6):427-8.
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Comments on the recent clinical guidance statement on HIV screening. Ann Intern Med. 2009 Aug 18; 151(4):286; author reply 287.
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Novel secondary hormonal therapy in advanced prostate cancer: an update. Curr Opin Urol. 2009 May; 19(3):315-21.
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