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Bin Chen, PhD

TitleAssistant Professor
SchoolUCSF School of Medicine
DepartmentPediatrics
Address550 16th. Street
San Francisco CA 94158
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    Collapse Biography 
    Collapse Education and Training
    Stanford UniversityPostdoctoral Scholar2015School of Medicine
    Indiana University at BloomingtonPhD2012School of Informatics
    Collapse Awards and Honors
    NIH2017  - 2021BD2K K01 award

    Collapse Overview 
    Collapse Overview
    The long-term goal of Dr. Bin Chen's lab is to develop computational methods and tools to discover new or better therapeutic candidates for cancers through collaborating with bench scientists and clinicians. Rapidly decreasing costs of molecular measurement technologies not only enable profiling of disease sample molecular features (e.g., transcriptome, proteome, metabolome) at different levels (e.g., tissues, single cells), but also enable measuring of cellular signatures of individual drugs in clinically relevant models. Our lab is interested in leveraging these data and artificial intelligence to connect different components (patients, tissues, in vitro models and in vivo models) in translational research. We currently focus on liver cancer, breast cancer and a few pediatric cancers.


    Collapse Research 
    Collapse Research Activities and Funding
    I-SPY2 +: Evolving the I-SPY 2 TRIAL to include MRI-directed, adaptive sequential treatment to optimize breast cancer outcomes
    NIH/NCI P01CA210961Sep 8, 2017 - Aug 31, 2022
    Role: Co-Investigator
    Targeting glucose metabolism for the treatment of Hepatocellular Carcinoma
    NIH R21TR001743Aug 15, 2017 - Jul 31, 2019
    Role: Principal Investigator
    Integrating transcriptomic, proteomic and pharmacogenomic data to inform individualized therapy in cancers
    NIH K01ES028047May 1, 2017 - Apr 30, 2021
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, Chen B, Lee A, Brown AS, Aasi SZ, Hollmig T, Ator MA, Dorsey BD, Ruggeri BR, Zificsak CA, Sirota M, Tang JY, Butte A, Epstein E, Sarin KY, Oro AE. Combined inhibition of atypical PKC and histone deacetylase 1 is cooperative in basal cell carcinoma treatment. JCI Insight. 2017 Nov 02; 2(21). PMID: 29093271.
      View in: PubMed
    2. Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S, Sirota M, Musen MA, Butte AJ. Precision annotation of digital samples in NCBI's gene expression omnibus. Sci Data. 2017 Sep 19; 4:170125. PMID: 28925997.
      View in: PubMed
    3. 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. PMID: 28699633.
      View in: PubMed
    4. 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. PMID: 28284560.
      View in: PubMed
    5. 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. PMID: 27863422.
      View in: PubMed
    6. 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. PMID: 27860440.
      View in: PubMed
    7. 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. PMID: 27071755; PMCID: PMC4830032.
    8. Chen B, Butte AJ. Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther. 2016 Mar; 99(3):285-97. PMID: 26659699; PMCID: PMC4785018.
    9. 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. PMID: 26535158; PMCID: PMC4625862.
    10. 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. PMID: 26043652; PMCID: PMC4460709.
    11. 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. PMID: 25832646; PMCID: PMC4719067 [Available on 01/01/17].
    12. 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. PMID: 25592569; PMCID: PMC4361221.
    13. 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. PMID: 25592598; PMCID: PMC4299914.
    14. Chen B. Ten simple rules for internship in a pharmaceutical company. PLoS Comput Biol. 2014 May; 10(5):e1003600. PMID: 24811706; PMCID: PMC4014388.
    15. Chen B, Wang H, Ding Y, Wild D. Synthesis Lectures on the Semantic Web: Theory and Technology. Semantic Breakthrough in Drug Discovery. 2014.
    16. Bin Chen, David J Wild. Practice and Challenges of Building a Semantic Framework for Chemogenomics Research. Molecular Informatics. 2013; 32(11-12):1000-1008.
    17. Chen B, Butte AJ. Network medicine in disease analysis and therapeutics. Clin Pharmacol Ther. 2013 Dec; 94(6):627-9. PMID: 24241637.
      View in: PubMed
    18. 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. PMID: 23732275; PMCID: PMC3712221.
    19. 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. PMID: 23657106; PMCID: PMC3700754.
    20. Chen B, Ding Y, Wild DJ. Assessing drug target association using semantic linked data. PLoS Comput Biol. 2012; 8(7):e1002574. PMID: 22859915; PMCID: PMC3390390.
    21. 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. PMID: 22360769.
      View in: PubMed
    22. 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. PMID: 22401035; PMCID: PMC3320537.
    23. Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Bin Chen, David Wild. Browsing large-scale cheminformatics data with dimension reduction. 2011.
    24. He B, Tang J, Ding Y, Wang H, Sun Y, Shin JH, Chen B, Moorthy G, Qiu J, Desai P, Wild DJ. Mining relational paths in integrated biomedical data. PLoS One. 2011; 6(12):e27506. PMID: 22162991; PMCID: PMC3232205.
    25. Chen B, McConnell KJ, Wale N, Wild DJ, Gifford EM. Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology. Bioinformatics. 2011 Nov 01; 27(21):3044-9. PMID: 21903625.
      View in: PubMed
    26. Bin Chen, David J Wild, Qian Zhu, Ying Ding, Xiao Dong, Madhuvanthi Sankaranarayanan, Huijun Wang, Yuyin Sun. Chem2bio2rdf: A linked open data portal for chemical biology. 2010.
    27. Ying Ding, Yuyin Sun, Bin Chen, Katy Borner, Li Ding, David Wild, Melanie Wu, Dominic DiFranzo, Alvaro Graves Fuenzalida, Daifeng Li, Stasa Milojevic, ShanShan Chen, Madhuvanthi Sankaranarayanan, Ioan Toma. Semantic web portal: a platform for better browsing and visualizing semantic data. 2010.
    28. Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y, Wild DJ. Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics. 2010 May 17; 11:255. PMID: 20478034; PMCID: PMC2881087.
    29. Chen B, Wild DJ. PubChem BioAssays as a data source for predictive models. J Mol Graph Model. 2010 Jan; 28(5):420-6. PMID: 19897391.
      View in: PubMed
    30. Chen B, Wild D, Guha R. PubChem as a source of polypharmacology. J Chem Inf Model. 2009 Sep; 49(9):2044-55. PMID: 19708682.
      View in: PubMed
    31. Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S, Hamon J, Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL. Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis. J Chem Inf Model. 2009 Feb; 49(2):308-17. PMID: 19434832.
      View in: PubMed
    32. Shi LW, Chen B, Zhou JH, Zhang T, Kang Q, Chen MB. Structure and relative stability of drum-like C4nN2n n = 3-8) cages and their hydrogenated products C4nH4nN2n (n = 3-8) cages. J Phys Chem A. 2008 Nov 20; 112(46):11724-30. PMID: 18947219.
      View in: PubMed
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