University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Bin Chen, PhD

Bin Chen, PhD

Assistant Professor, Dept. of Pediatrics and Institute for Computational Health Sciences, UCSF

Cancer Center Program Memberships

Breast Oncology | Experimental Therapeutics

Education

Chongqing University, China, B.S., 07/2004, Chemistry
Indiana University, Bloomington, M.S., 08/2009, Chemical Informatics
Indiana University, Bloomington, Ph.D., 08/2012, Informatics
Stanford University, Postdoc, 03/2015, Systems Medicine


Professional Experience

  • 2004-2007
    Research Assistant, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, China
  • 2007-2012
    Research Assistant, Indiana University, Bloomington, IN
  • 2008-2008
    Intern, Novartis Institutes of Biomedical Research, Cambridge, MA
  • 2009-2009
    Intern, Pfizer Global Research & Development, Groton, CT
  • 2010-2010
    Intern, Pfizer Global Research & Development, Groton, CT
  • 2011-2011
    Intern, Merck, Rahway, NJ
  • 2012-2012
    Semantic Web developer, Novartis Institutes of Biomedical Research, Cambridge, MA
  • 2015-2017
    Instructor, Dept. of Pediatrics and Institute for Computational Health Sciences, UCSF
  • 2017-present
    Assistant Professor, Dept. of Pediatrics and Institute for Computational Health Sciences, UCSF

Honors & Awards

  • 2009
    Symyx Ph.D. Fellowship
  • 2010
    First place in poster competition, Center for Bioinformatics Research Industry Collaboration Workshop on Life Sciences Informatics, Indiana University
  • 2010
    CINF Scholarship for Scientific Excellence, ACS Chemical Information Division
  • 2012
    Student travel fellowship, Semantic in Healthcare and Life Science
  • 2012
    Lucille Wert Scholarship, ACS Chemical Information Division
  • 2014
    Jason Morrow Trainee Award 2014, ASCPT
  • 2014
    Presidential Trainee Award 2014, ASCPT
  • 2015
    Presidential Poster of Distinction, 2015, the Liver Meeting
  • 2016
    Travel fellowship, LINCS meeting at UC Irvine

Selected Publications

  1. Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun. 2017 Jul 12; 8:16022.
    View on PubMed
  2. Chen B, Wei W, Ma L, Yang B, Gill RM, Chua MS, Butte AJ, So S. Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling. Gastroenterology. 2017 Jun; 152(8):2022-2036.
    View on PubMed
  3. Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte AJ, Godwin AK. In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma. Oncotarget. 2017 Jan 17; 8(3):4079-4095.
    View on PubMed
  4. Paik H, Chen B, Sirota M, Hadley D, Butte AJ. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol. 2016 Nov; 5(11):599-607.
    View on PubMed
  5. Fu G, Ding Y, Seal A, Chen B, Sun Y, Bolton E. Predicting drug target interactions using meta-path-based semantic network analysis. BMC Bioinformatics. 2016 Apr 12; 17:160.
    View on PubMed
  6. Chen B, Butte AJ. Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther. 2016 Mar; 99(3):285-97.
    View on PubMed
  7. Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT Pharmacometrics Syst Pharmacol. 2015 Oct; 4(10):576-84.
    View on PubMed
  8. Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ. Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research. BMC Med Genomics. 2015; 8 Suppl 2:S5.
    View on PubMed
  9. Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Brief Bioinform. 2016 Jan; 17(1):2-12.
    View on PubMed
  10. Wu M, Sirota M, Butte AJ, Chen B. Characteristics of drug combination therapy in oncology by analyzing clinical trial data on ClinicalTrials.gov. Pac Symp Biocomput. 2015; 68-79.
    View on PubMed
  11. Fan-Minogue H, Chen B, Sikora-Wohlfeld W, Sirota M, Butte AJ. A systematic assessment of linking gene expression with genetic variants for prioritizing candidate targets. Pac Symp Biocomput. 2015; 383-94.
    View on PubMed
  12. Chen B. Ten simple rules for internship in a pharmaceutical company. PLoS Comput Biol. 2014 May; 10(5):e1003600.
    View on PubMed
  13. Chen B, Wang H, Ding Y, Wild D. Synthesis Lectures on the Semantic Web: Theory and Technology. Semantic Breakthrough in Drug Discovery. 2014.
    View on PubMed
  14. Chen B, Butte AJ. Network medicine in disease analysis and therapeutics. Clin Pharmacol Ther. 2013 Dec; 94(6):627-9.
    View on PubMed
  15. Bin Chen, David J Wild. Practice and Challenges of Building a Semantic Framework for Chemogenomics Research. Molecular Informatics. 2013; 32(11-12):1000-1008.
    View on PubMed
  16. Auerbach RK, Chen B, Butte AJ. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool. Bioinformatics. 2013 Aug 01; 29(15):1922-4.
    View on PubMed
  17. Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, Hastings J, Chen B, Wild DJ. The ChEMBL database as linked open data. J Cheminform. 2013 May 08; 5(1):23.
    View on PubMed
  18. Chen B, Ding Y, Wild DJ. Assessing drug target association using semantic linked data. PLoS Comput Biol. 2012; 8(7):e1002574.
    View on PubMed
  19. Chen B, Sheridan RP, Hornak V, Voigt JH. Comparison of random forest and Pipeline Pilot Naïve Bayes in prospective QSAR predictions. J Chem Inf Model. 2012 Mar 26; 52(3):792-803.
    View on PubMed
  20. Chen B, Ding Y, Wild DJ. Improving integrative searching of systems chemical biology data using semantic annotation. J Cheminform. 2012 Mar 08; 4(1):6.
    View on PubMed

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