1. #Billy Zeng, #Benjamin S. Glicksberg, #Patrick Newbury, Jing Xing, Ke Liu, Anita Wen, Caven Chow, Bin Chen, OCTAD: an open workplace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features
    View in: bioRxiv
  2. Rama Shankar, Mara L. Leimanis, Patrick A. Newbury, Ke Liu, Jing Xing, Derek Nedveck, Eric J. Kort, Jeremy W Prokop, Guoli Zhou, André S Bachmann, Bin Chen*, Surender Rajasekaran*, Gene expression signatures identify pediatric patients with multiple organ dysfunction who require advanced life support in the intensive care unit
    View in: submitted to medRxiv,
  3. Sean A Misek, Patrick A Newbury, Evgenii Chekalin, Shreya Paithankar, Andrea I Doseff, Bin Chen*, Kathleen A Gallo*, Richard R Neubig*, Ibrutinib blocks YAP1 activation and reverses BRAFi resistance in melanoma cells
    View in: submitted to bioRxiv,

  1. Rohrberg J, Van de Mark D, Amouzgar M, Lee JV, Taileb M, Corella A, Kilinc S, Williams J, Jokisch ML, Camarda R, Balakrishnan S, Shankar R, Zhou A, Chang AN, Chen B, Rugo HS, Dumont S, Goga A. MYC Dysregulates Mitosis, Revealing Cancer Vulnerabilities, Cell Rep. 2020 Mar 10;30(10):3368-3382.e7. doi: 10.1016/j.celrep.2020.02.041. PMID: 32160543 PMCID: PMC7085414
    View in: PubMed
  2. Chen B#, Garmire L, Calvisi DF, Chua M-S, Kelley RK, Chen X. Harnessing big ‘omics’ data and AI for drug discovery in hepatocellular carcinoma, Nat Rev Gastroenterol Hepatol. 2020 Jan 3. doi: 10.1038/s41575-019-0240-9. PMID: 31900465
    View in: Web , MSU Today,
  3. Hyojung Paik, Matthew J. Kan, Nadav Rappoport, Dexter Hadley, Marina Sirota, Bin Chen, Udi Manber, Seong Beom Cho & Atul J. Butte, Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia, Scientific Data volume 6, Article number: 201 (2019)
    View in: Web
  4. McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK, Gordan JD, Gill RM, Blanchard SC, Ruggero D. A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS. Elife. 2019 Sep 3;8. pii: e48847. doi: 10.7554/eLife.48847. PMID: 31478838
    View in: Web
  5. K. Yu, B. Chen, D. Aran, J. Charalel, C. Yau, D. M. Wolf, L. J. van ‘t Veer, A. J. Butte, T. Goldstein & M. Sirota, Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types, Nature Communicationsvolume 10, Article number: 3574 (2019). PMID:31395879
    View in: Web
  6. Liu K, Newbury PA, Glicksberg BS, Zeng WZD, Paithankar S, Andrechek ER, Chen B., Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic data Nat Commun. 2019 May 15;10(1):2138. doi: 10.1038/s41467-019-10148-6. PMID: 31092827
    View in: Web
    Tweeted by NCI Genomices, NatRevClinOncol and many others.
  7. Benjamin S. Glicksberg, Li Li, Rong Chen, Joel Dudley, Bin Chen. Book Chapter: Leveraging Big Data to Transform Drug Discovery (Bioinformatics in Drug Discovery 3rd Ed. Editors: Richard Larson, MD, PhD & Tudor Opera, MD, PhD). PMID:30848458
  8. William Zeng, Benjamin Glicksberg, Yangyan Li, Bin Chen, Selecting precise reference normal tissue samples for cancer research using a deep learning approach,BMC Med Genomics. 2019 Jan 31;12(Suppl 1):21. doi: 10.1186/s12920-018-0463-6. PMID: 30704474
    View in: PubMed, BMC medical genomics (transferred from BMC genomics to BMC medical genomics).
  9. Zhiyue Tom Hu, Yuting Ye, Patrick Newbury, Haiyan Huang#, Bin Chen#, AICM: A Genuine Framework for Correcting Inconsistency Between Large Pharmacogenomics Datasets, Pac Symp Biocomput. 2019;24:248-259. PMID: 30864327 , #:corresponding
  10. Sharpnack MF, Chen B, Aran D, Kosti I, Sharpnack DD, Carbone DP, Mallick P, Huang K. Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma. EBioMedicine. 2018 Jan; 27:167-175. PMID: 29273356.
    View in: PubMed
  11. Zhang S, Wang J, Wang H, Fan L, Fan B, Zeng B, Tao J, Li X, Che L, Cigliano A, Ribback S, Dombrowski F, Chen B, Cong W, Wei L, Calvisi DF, Chen X. Hippo Cascade Controls Lineage Commitment of Liver Tumors in Mice and Humans. Am J Pathol. 2018 Jan 31. PMID: 29378174.
    View in: PubMed
  12. 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
  13. 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
  14. 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 reveals therapeutic targets. , Nature Communications, 2017 Jul 12;8:16022. doi: 10.1038/ncomms16022, PMID:28699633, #co-first, *co-corresponding
    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)
  15. 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), 2017 Jun;152(8):2022-2036. doi: 10.1053/j.gastro.2017.02.039. Epub 2017 Mar 8. PMID:28284560 #co-first
  16. 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.
    View in: PubMed
  17. 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.
    View in: PubMed
  18. 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.
    View in: PubMed
  19. 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
    View in: PubMed
  20. 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.
  21. 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.
  22. 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.
    View in: PubMed
  23. Wu M, Sirota M, Butte AJ, Chen B.Characteristics of drug combination therapy in oncology by analyzing clinical trial data on Pac Symp Biocomput. 2015; 68-79. PMID: 25592569; PMCID: PMC4361221.
  24. 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].
  25. Chen B. Ten simple rules for internship in a pharmaceutical company. PLoS Comput Biol. 2014 May; 10(5):e1003600. PMID: 24811706; PMCID: PMC4014388.
  26. Chen B, Wang H, Ding Y, Wild D. Synthesis Lectures on the Semantic Web: Theory and Technology. Semantic Breakthrough in Drug Discovery. 2014.
  27. Bin Chen, David J Wild. Practice and Challenges of Building a Semantic Framework for Chemogenomics Research. Molecular Informatics. 2013; 32(11-12):1000-1008.
  28. 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
  29. 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.
  30. 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.
  31. 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.
  32. 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
  33. 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.
  34. Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Bin Chen, David Wild. Browsing large-scale cheminformatics data with dimension reduction. 2011.
  35. 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.
  36. 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.
    View in: PubMed
  37. 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.
  38. 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.
  39. 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.
  40. 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
  41. 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
  42. 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
  43. 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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