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.
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  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.
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  3. Bin Chen#*, Li Ma#, Hyojung Paik, Marina Sirota, Mei-Sze Chua*,Samuel So, Atul J. Butte*. Reversal of cancer gene expression correlates with drug efficacy and suggests therapeutic targets, accepted in principle, Nature Communications, #co-first, *co-corresponding
    NEWS
    New Computational Method to Aid Cancer Drug Discovery (Genetic Engineering & Biotechnology News)
    Using LINCS and other Big Data to Find New Cancer Treatments (Program highlight @NIH The Common Fund)
  4. Bin Chen#, Wei Wei#, Li Ma, Bin Yang, Ryan M. Gill, Mei-Sze Chua, Atul J. Butte, Samuel So. Computational Discovery of Niclosamide Ethanolamine, A Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells in Vitro and in Mice by Inhibiting CDC37 Signaling, Gastroenterology (IF: 18), #co-first
    NEWS
  5. Ziyan Pessetto, Bin Chen, Hani Alturkmani, Stephen Hyter, Colleen Flynn, Micheal Baltezor, Yan Ma, Howard Rosenthal, Kathleen Neville, Scott Weir, Atul Butte, Andrew Godwin. In Silico and In Vitro Drug Screening Identifies New Therapeutic Approaches for Ewing Sarcoma, oncotarget, 2016 Nov 16. PMID: 27863422.
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  6. H Paik, B Chen, M Sirota, D Hadley and AJ Butte. Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses. CPT Pharmacometrics Syst Pharmacol. 2016 Nov 14. PMID: 27860440.
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  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; 17(1):160. PMID: 27071755.
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  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. #corresponding
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  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.
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  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 [Available on 01/01/16].
  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.
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  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 1; 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; 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.
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  22. Chen B, Ding Y, Wild DJ. Improving integrative searching of systems chemical biology data using semantic annotation. J Cheminform. 2012; 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 1; 27(21):3044-9. PMID: 21903625.
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  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; 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.
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  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.
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  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.
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  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.
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