John PaulYing-ChingShenMD

PubMed

• 24 citations
  Survival improvement for patients with metastatic colorectal cancer over twenty years.
  Fadl A Zeineddine, Mohammad A Zeineddine, Abdelrahman Yousef, Yue Gu, Saikat Chowdhury, Arvind Dasari, Ryan W Huey, Benny Johnson, Bryan Kee, Michael S Lee, Maria Pia ...> ;NPJ Precision Oncology. 2023 Feb 13
• 13 citations
  Resistance Mechanisms to Anti-Epidermal Growth Factor Receptor Therapy inWild-Type Colorectal Cancer Vary by Regimen and Line of Therapy.
  Christine M Parseghian, Ryan Sun, Melanie Woods, Stefania Napolitano, Hey Min Lee, Jumanah Alshenaifi, Jason Willis, Shakayla Nunez, Kanwal P Raghav, Van K Morris, Joh...> ;Journal of Clinical Oncology. 2023 Jan 20
• Association of Prediagnosis Obesity and Postdiagnosis Aspirin With Survival From Stage IV Colorectal Cancer.
  Jennifer S Davis, Janelle C Chavez, Melissa Kok, Yazmin San Miguel, Hwa Young Lee, Henry Henderson, Michael J Overman, Van Morris, Bryan Kee, David Fogelman, Shailesh ...> ;JAMA Network Open. 2022 Oct 3
• 5 citations
  Oncogene addiction to GNAS in GNASmutant tumors.
  Ichiaki Ito, Valsala Haridas, Saikat Chowdhury, Yue Gu, Princess Dickson, Natalie Fowlkes, John Paul Shen, Aditya More> ;Oncogene. 2022 Aug 1
• 25 citations
  Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
  Shaolong Cao, Jennifer R Wang, Shuangxi Ji, Peng Yang, Yaoyi Dai, Shuai Guo, Matthew D Montierth, John Paul Shen, Xiao Zhao, Jingxiao Chen, Jaewon James Lee, Paola A G...> ;Nature Biotechnology. 2022 Nov 1
• 44 citations
  Patient-derived micro-organospheres enable clinical precision oncology.
  Shengli Ding, Carolyn Hsu, Zhaohui Wang, Naveen R Natesh, Rosemary Millen, Marcos Negrete, Nicholas Giroux, Grecia O Rivera, Anders Dohlman, Shree Bose, Tomer Rotstein...> ;Cell Stem Cell. 2022 Jun 2
• 4 citations
  What is the Risk for Peritoneal Metastases and Survival Afterwards in T4 Colon Cancers?
  Abhineet Uppal, Beth Helmink, Travis E Grotz, Tsuyoshi Konishi, Keith F Fournier, Sa Nguyen, Melissa W Taggart, John Paul Shen, Brian K Bednarski, Yi-Qian N You, Georg...> ;Annals of Surgical Oncology. 2022 Mar 19
• 4 citations
  Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective.
  David G Menter, Vahid Afshar-Kharghan, John Paul Shen, Stephanie L Martch, Anirban Maitra, Scott Kopetz, Kenneth V Honn, Anil K Sood> ;Cancer Metastasis Reviews. 2022 Mar 1
• 27 citations
  Clinical and Molecular Characterization ofMutations as Predictive Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Cancers.
  Garmezy, B., Gheeya, J., Lin, H., Huang, Y., Kim, T., Jiang, X., Thein, K., Pilié, P., Zeineddine, F., Wang, W., Shaw, K., Rodon, J., Shen, J., Yuan, Y., Meric-Bernsta...> ;JCO Precision Oncology. 2022 Feb 1
• Artificial intelligence, molecular subtyping, biomarkers, and precision oncology.
  John Paul Shen> ;Emerging Topics in Life Sciences. 2021 Dec 21
• 14 citations
  Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer
  Saikat Chowdhury, Matan Hofree, Kangyu Lin, Dipen M. Maru, Scott Kopetz, John Paul Shen> ;Cancers. 2021 Sep 30
• 13 citations
  Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis.
  Lihua Wang, Ergang Wang, Jorge Prado Balcazar, Zhenzhen Wu, Kun Xiang, Yi Wang, Qiang Huang, Marcos Negrete, Kai-Yuan Chen, Wei Li, Yujie Fu, Anders Dohlman, Robert Mi...> ;Advanced Science. 2021 Aug 10
• 7 citations
  The Provocative Roles of Platelets in Liver Disease and Cancer.
  Preeti Kanikarla Marie, Natalie W. Fowlkes, Vahid Afshar-Kharghan, Stephanie L. Martch, Alexey V. Sorokin, John Paul Shen, Van K. Morris, Arvind Dasari, Nancy You, Ani...> ;Frontiers in Oncology. 2021 Jul 21
• 33 citations
  Comprehensive Clinical and Molecular Characterization of KRASG12C-Mutant Colorectal Cancer.
  Jason Henry, Oluwadara Coker, Saikat Chowdhury, John Paul Shen, Van K. Morris, Arvind Dasari, Kanwal Pratap Singh Raghav, Maliha Nusrat, Bryan K. Kee, Christine Megerd...> ;JCO Precision Oncology. 2021 Apr 6
• 54 citations
  Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients
  Jianzhu Ma, Samson Fong, Yunan Luo, Christopher J. Bakkenist, John Paul Shen, Soufiane Mourragui, Lodewyk F. A. Wessels, Marc Hafner, Roded Sharan, Jian Peng, Trey Ideker> ;Nature Cancer. 2021 Jan 25
• 477 citations
  Network based stratification of tumor mutations
  Trey Ideker, Matan Hofree, John Paul Shen> ;Nature Methods. 2015 Apr 29
• 1867 citations
  Integrated Genomic Characterization of Papillary Thyroid Carcinoma
  , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,...> ;Cell. 2014 Oct 23
• 95 citations
  Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss
  Andrew M. Gross, Ryan K. Orosco, John Paul Shen, Ann Marie Egloff, Hannah Carter, Matan Hofree, Michel Choueiri, Charles S. Coffey, Scott M. Lippman, D. Neil Hayes, Ez...> ;Nature Genetics. 2014 Sep 1
• 155 citations
  Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease
  James E. Bradner, Raymond H. Mak, Shyam K. Tanguturi, Ralph Mazitschek, Stephen J. Haggarty, Kenneth N. Ross, Cindy Y. Chang, Jocelyn Bosco, Nathan West, Elizabeth M. ...> ;Proceedings of the National Academy of Sciences of the United States of America. 2010 Jul 13
• 97 citations
  A robust small-molecule microarray platform for screening cell lysates
  James E. Bradner, Olivia M. McPherson, Ralph Mazitschek, David Barnes-Seeman, John Paul Shen, Jasmeet Dhaliwal, Kristen E. Stevenson, Jay L. Duffner, Seung Bum Park, D...> ;Chemistry & Biology. 2006 May 1
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Journal Articles

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

Abstracts/Posters

• 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: 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
• Network-based stratification of thyroid cancer.
  Hofree M, Shen JP, Ideker T, AACR Annual Meeting, 1/6/2014
• 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
• 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
• 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
• 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
• 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
• 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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