John PaulYing-ChingShenMD

PubMed

• 1975 citations
  Integrated Genomic Characterization of Papillary Thyroid Carcinoma
  Nishant Agrawal, Rehan Akbani, B. Arman Aksoy, Adrian Ally, Harindra Arachchi
  Cell. 2014-10-23
• 10 citations
  Oncogene addiction to GNAS in GNASmutant tumors.
  Aditya More, Ichiaki Ito, Valsala Haridas, Saikat Chowdhury, Yue Gu
  Oncogene. 2022-08-01
• 490 citations
  Network based stratification of tumor mutations
  Trey Ideker, Matan Hofree, John Paul Shen
  Nature Methods. 2015-04-29

Journal Articles

• Evans syndrome  
  Ghashghaei R, Popa R, Shen JP, American Journal of Medicine, 1/1/2013

Abstracts/Posters

• Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interaction networks to identify clinically relevant subtypes in high grade...
  Shen JP, Hofree M, Bojorquez-Gomez A, Saenz C, Ideker T, Marsha Rivkin 10th Biannual Ovarian Cancer Research Symposium, 1/8/2014
• A prognostic model of head and neck cancer ties TP53 mutation to 3p loss.
  Gross A, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T, AACR Annual Meeting, 1/8/2014
• Network-based stratification of thyroid cancer.
  Hofree M, Shen JP, Ideker T, AACR Annual Meeting, 1/6/2014
• Molecular profiles of gastric cancer: The UCSD experience.
  McGee DM, Shen JP, Fanta PT, Lowy AM, J Clin Oncol (ASCO-GI Meeting Abstracts), 1/30/2013
• Molecular profiles of appendiceal adenocarcinoma: The UCSD experience.
  Shen JP, McGee DM, Lowy AM, Fanta PT, J Clin Oncol (ASCO-GI Meeting Abstracts), 1/30/2013
• Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interaction networks to identify clinically relevant subtypes in high grade...
  Hofree M, Shen JP, Carter H, Gross A, Ideker T, AACR Advances in Ovarian Cancer Research: From Concept to Clinic, 1/18/2013
• Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma.
  Gross A, Choueiri M, Shen JP, Randall JM, Ideker T, Hofree M, J Clin Oncol (ASCO Meeting Abstracts), 1/17/2013
• Cross-species synthetic lethal interaction screening as a strategy for the identification of novel therapeutic targets in cancer.
  Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Li JF, Sobol RW, Ideker T, J Clin Oncol (ASCO Meeting Abstracts), 1/17/2013
• High-Throughput Synthetic Lethal Interaction Screening in Model Organisms as a Strategy for the Identification of Novel Therapeutic Targets in Cancer.
  Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Xu J, Wang ZZ, Li JF, Gross A, Bean G, Sobol RW, Ideker T, AACR Translational Impact of Model Organisms, 1/7/2013
• Network-based stratification of tumor mutations.
  Hofree M, Shen JP, Carter H, Gross A, Ideker T, Annual International Conference on Intelligent Systems for Molecular Biology, 1/1/2013
• Molecular predictors of treatment response in colon and gastric cancer.
  Shen JP, Roeland E, Hwang M, Shimabukuro KA, Sicklick JK, Ramamoorthy S, McLemore EC, Reid TR, Lowy A, Fanta P, J Clin Oncol (ASCO Meeting Abstracts), 1/30/2012
• Network-based stratification of tumor mutations.
  Hofree M, Shen JP, Ideker T, The 13th International Conference on Systems Biology, 1/1/2012
• Network-based stratification of tumor mutations.
  Hofree M, Shen JP, Ideker T, mutations, The Cancer Genome Atlas 2nd Annual Scientific Symposium, 1/1/2012
• Molecular predictors of treatment response in colon and gastric cancer.
  Fanta PT, Roeland E, Shen JP, Shimabukuro KA, Hwang M, Ramamoorthy S, Lowy A, J Clin Oncol (ASCO-GI Meeting Abstracts), 1/1/2012
• The rational for combined proteasome and autophagy inhibition in multiple myeloma established using novel translational platforms.
  Shen JP, Divakaran S, Ponduro S, Vogl DT, Amaravadi RK, Bradner JE, Blood (ASH Annual Meeting Abstracts), 1/1/2008
• Autophagy as a Target Pathway in Multiple Myeloma: a Forward Chemical Genetic Approach.
  Shen JP, Divakaran S, Kuai LT, Wang X, Ong SE, Amaravadi R, Wood J, Carr S, Haggarty S, Bradner JE, Blood (ASH Annual Meeting Abstracts), 1/1/2007
• Discovery and Characterization of Small Molecule Inhibitors of Autophagy for Cancer Therapy.
  Bradner JE, Shen JP, Perlstein EO, Divakaran S, Greenberg EF, Amaravadi R, Schreiber SL, Blood (ASH Annual Meeting Abstracts), 1/1/2006
• Targeting the Protein Degradation Pathway in Multiple Myeloma with Synergistic, Selective Small Molecules.
  Shen JP, Greenberg EF, Hideshima T, Anderson KC, Schreiber SL, Bradner JE, Blood (ASH Annual Meeting Abstracts), 1/1/2005
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Lectures

• Hematology & Oncology Board Review. 
  University of California, San Diego, 2013, 2014 - 1/18/2014
• Basics of Chemotherapy. 
  University of California, San Diego - 1/26/2013
• Applying systems biology techniques to address both diagnostic and therapeutic challenges in oncology. 
  1/24/2013
• Biomarkers in Clinical Oncology. 
  University of California, San Diego - 1/9/2013
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