Print (since 2020, only partial publications are listed, see (full list)
  1. Ruoqiao Chen, Jiayu Zhou, Bin Chen*, Imputing abundance of over 2500 surface proteins from single-cell transcriptomes with context-agnostic zero-shot deep ensembles, Cell Systems, 2024
    View in: Web page

  2. Evgenii Chekalin, Shreya Paithankar, Rama Shankar, Jing Xing, Wenfeng Xu, Bin Chen*, Computational discovery of co-expressed antigens as dual targeting candidates for cancer therapy through bulk, single-cell, and spatial transcriptomics, Bioinformatics advances, 2024
    View in: Web page

  3. Xiaodan Zhang, Martin Witteveen-Lane, Christine Skovira, Aakash A. Dave, Jeffrey S Jones, Erin R. McNeely, Michael R. Lawrence, David G. Morgan, Dave Chesla and Bin Chen*, Incidence and Risk Factors for Mild Cognitive Impairment in West Michigan: A Rural-Urban Comparison Utilizing Electronic Health Records, Alzheimer’s & Dementia: Translational Research & Clinical Interventions, 2024
    View in: Web page

    Mild Cognitive Impairment could be going unreported in rural areas of West Michigan, study suggests (MSU Today release)

    Study: Rural Michiganders are being underdiagnosed for cognitive impairment (NPR)
  4. Xiaodan Zhang, Nabasmita Talukdar, Sandeep Vemulapalli, Sumyeong Ahn, Jiankun Wang, Han Meng, Sardar Mehtab Bin Murtaza, Dmitry Leshchiner, Aakash Ajay Dave, Dimitri F. Joseph, Martin Witteveen-Lane, Dave Chesla, Jiayu Zhou, and Bin Chen*, Comparison of Prompt Engineering and Fine-Tuning Strategies in Large Language Models in the Classification of Clinical Notes, AMIA 2024 Informatics Summit
    View in: Web page

  5. Ruihua Liu, Shang Su, Jing Xing, Ke Liu, Yawei Zhao, Mary Stangis, Diego P Jacho, Eda D Yildirim-Ayan, Cara M Gatto-Weis, Bin Chen*, Xiaohong Li*, Tumor removal limits prostate cancer cell dissemination in bone and osteoblasts induce cancer cell dormancy through focal adhesion kinase, J Exp Clin Cancer Res, 2023 Oct 11;42(1):264. doi: 10.1186/s13046-023-02849-0. PMID: 37821954 PMCID: PMC10566127
    View in: Web page

  6. Shan-Ju Yeh, Shreya Paithankar, Ruoqiao Chen, Jing Xing, Mengying Sun, Ke Liu, Jiayu Zhou, Bin Chen*, TransCell: In silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning, Genomics, Proteomics and Bioinformatics, 2023
    View in: Web page

  7. Guisheng Zhao#, Patrick Newbury#, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides1 Bin Chen* and Rintaro Hashizume*, Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma, Acta Neuropathol Commun 2022 Oct 23;10(1):150. doi: 10.1186/s40478-022-01463-z. PMID: 36274161
    View in: Web page

  8. Ke Liu, Martin Witteveen-Lane, Benjamin S Glicksberg, Omkar Kulkarni, Rama Shankar, Evgeny Chekalin, Shreya Paithankar, Jeanne Yang, Dave Chesla, Bin Chen, BGLM: big data-guided LOINC mapping with multi-language support, JAMIA Open . 2022 Nov 25;5(4):ooac099. doi: 10.1093/jamiaopen/ooac099. PMID: 36448022 PMCID: PMC9696745
    View in: Web page

  9. Guisheng Zhao#, Patrick Newbury#, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides1 Bin Chen* and Rintaro Hashizume*, Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma, Acta Neuropathol Commun 2022 Oct 23;10(1):150. doi: 10.1186/s40478-022-01463-z. PMID: 36274161
    View in: Web page

  10. Jing Xing,#, Rama Shankar,#, Meehyun Ko,#, Keke Zhang, Sulin Zhang, Aleksandra Drelich, Shreya Paithankar, Eugene Chekalin, Mei-Sze Chua, Surender Rajasekaran, Chien-Te Kent Tseng, Mingyue Zheng, Seungtaek Kim*, Bin Chen*, Deciphering COVID-19 host transcriptomic complexity and variations for therapeutic discovery against new variants, iScience (Cell publishing group), 2022 Oct 21;25(10):105068. doi: 10.1016/j.isci.2022.105068., PMID: 36093376 PMCID: PMC9439871
    View in: Web page

    Repurposing existing drugs to fight new COVID-19 variants (MSU Today release)
  11. Mengying Sun, Jing Xing, Han Meng, Huijun Wang, Bin Chen, Jiayu Zhou, MolSearch: Search-based Multi-objective Molecular Generation and Property Optimization. KDD Health Day 2022 (Best Paper Award, First place)
    View in: Proceedings
  12. Ke Liu#, Omkar Kulkarni#,, Martin Witteveen-Lane, Bin Chen*, Dave Chesla*, MetBERT: a generalizable and pre-trained deep learning model for the prediction of metastatic cancer from clinical notes, AMIA 2022, PMID: 35854741, PMC9285138
    View in: Proceedings
  13. 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, Mol Pharmacol . 2022 Jan;101(1):1-12. doi: 10.1124/molpharm.121.000331. PMID: 34732527
    View in: Website (Cover)
  14. Alice Taubes, Phil Nova, Kelly A. Zalocusky, Idit Kosti, Mesude Bicak, Misha Y. Zilberter, Yanxia Hao, Seo Yeon Yoon, Tomiko Oskotsky, Silvia Pineda, Bin Chen, Emily A. Aery Jones, Krishna Choudhary, Brian Grone, Maureen E. Balestra, Fayzan Chaudhry, Ishan Paranjpe, Jessica De Freitas, Nicole Koutsodendris, Nuo Chen, Celine Wang, William Chang, Alice An, Benjamin S. Glicksberg, Marina Sirota & Yadong Huang, Experimental and real world evidence supporting the computational repurposing of bumetanide to prevent or treat APOE4-related Alzheimer’s disease, Nature Aging
    View in: Website
  15. Jing Xing, Shreya Paithankar, Ke Liu, Katie Uhl, Xiaopeng Li, Meehyun Ko, Seungtaek Kim, Jeremy Haskins, Bin Chen, Published Anti-SARS-CoV-2 In Vitro Hits Share Common Mechanisms of Action that Synergize with Antivirals, Briefings in Bioinformatics
    View in: Website
  16. Mengying Sun, Jing Xing, Huijun Wang, Bin Chen, Jiayu Zhou,MoCL: Contrastive Learning on Molecular Graphs with Multi-level Domain Knowledge, KDD 2021
    View in: arXiv
  17. Mengying Sun, Jing Xing, Bin Chen, Jiayu Zhou, Robust Collaborative Learning with Noisy Labels, ICDM 2020, acceptance rate (19.76%)
    View in: arXiv
  18. #Billy Zeng, #Benjamin S. Glicksberg, #Patrick Newbury, #Evgenii Chekalin, Jing Xing, Ke Liu, Anita Wen, Caven Chow, Bin Chen, OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features, Nat Protoc., 2020 Dec 23. doi: 10.1038/s41596-020-00430-z. PMID:33361798
    View in: Nature Protocols, 2020
  19. 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, EBioMedicine (The Lancet), VOLUME 62, 103122, DECEMBER 01, 2020.
    View in: website
  20. Zhou G, Holzman C, Chen B, Wang P, Heng YJ, Kibschull M, Lye SJ, Kasten EP. EBF1-correlated long non-coding RNA transcript levels in 3rd trimester maternal blood and risk of spontaneous preterm birth. Reproductive Sciences. 2020; PMID: 32959224. DOI: 10.1007/s43032-020-00320-5.
    View in: PubMed
  21. Jeremy W Prokop, Rama Shankar, Ruchir Gupta, Mara L Leimanis, Derek Nedveck, Katie Uhl, Bin Chen, Nicholas L Hartog, Jason Van Veen, Joshua S Sisco, Olivia Sirpilla, Todd Lydic, Brian Boville, Angel Hernandez, Chi Braunreiter, ChiuYing Cynthia Kuk, Varinder Singh, Joshua Mills, Marc Wegener, Marie Adams, Mary Rhodes, Andre S Bachmann, Wenjing Pan, Miranda L Byrne-Steele, D Casey Smith, Mollye Depinet, Brittany E Brown, Mary Eisenhower, Jian Han, Marcus Haw, Casey Madura, Dominic J Sanfilippo, Laurie H Seaver, Caleb Bupp, Surender Rajasekaran, Translational and Precision Medicine: Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19, Physiol Genomics. 2020 Jun 1; 52(6): 255–268, PMID: 32437232
    View in: PubMed
  22. 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
  23. 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. (IF = 30) 2020 Jan 3. doi: 10.1038/s41575-019-0240-9. PMID: 31900465
    View in: Web , MSU Today,
  24. 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
  25. 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
  26. 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
  27. 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
    NEWS
    Big data helps identify better way to research breast cancer’s spread (MSU press release, Science Daily, EurekAlert )
    Breast Cancer Cell Lines Get Big Data Assistance (GEN News)
    Are Cell Lines the Best Model to Analyze Breast Cancer Biology? (I3Health News)
    Big data helps determine better research models to fight the spread of breast cancer (The Medical News)
    Using Big Data to Improve Metastatic Breast Cancer Research (Specialty Pharmacy Times)
    Genomic Analysis Reveals Differences Between Cancer Cell Lines and Human Cancers (Breast Cancer News)
    Genetic databases provide solutions for breast cancer research (Scientific American Arabic)
    Tweeted by NCI Genomices, NatRevClinOncol and many others.
    Selected as an NIEHS Extramural Paper of the Month.
  28. 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
    View in: Methods in Molecular Biology , PubMed .
  29. 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).
  30. 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
    View in: PSB 2019 Proceedings
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
    link
    NEWS
    Big-Data Analysis Points Toward New Drug Discovery Method (UCSF press release, Science Daily, EurekAlert )
    Database sleuths turn up a surprising new drug to test against cancer (STAT)
    Systems Study Taps Cancer Gene Expression Reversal to Predict Drug Response (genomeweb)
    How Big Data Is Transforming Medicine (HuffPost)
    New Computational Method to Aid Cancer Drug Discovery (Genetic Engineering & Biotechnology News)
    UCSF-led research produces method for probing new drug use (XINHUA)
    Using LINCS and other Big Data to Find New Cancer Treatments (Program highlight @NIH The Common Fund)
    大数据分析助跑抗癌新药发现 (ebiotrade)
  36. 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
    link
    NEWS
    Deworming Pill May Be Effective in Treating Liver Cancer (UCSF press release, 中文)
    Bioinformatic Search Identifies Tapeworm Drug for Treatment of Hepatocellular Carcinoma (Featured in Gastro journal)
    New Approach to Drug Discovery Finds Veterinary Pill Helps Mice Fight Liver Cancer (LIVER DISEASE NEWS)
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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.
    View in: PubMed, PubMed Central
  42. 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.
    View in: PubMed, PubMed Central
  43. 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
  44. 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.
    View in: PubMed, PubMed Central
  45. 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].
    View in: PubMed, PubMed Central
  46. Chen B. Ten simple rules for internship in a pharmaceutical company. PLoS Comput Biol. 2014 May; 10(5):e1003600. PMID: 24811706; PMCID: PMC4014388.
    View in: PubMed, PubMed Central
  47. Chen B, Wang H, Ding Y, Wild D. Synthesis Lectures on the Semantic Web: Theory and Technology. Semantic Breakthrough in Drug Discovery. 2014.
    ***Amazon***,
  48. Bin Chen, David J Wild. Practice and Challenges of Building a Semantic Framework for Chemogenomics Research. Molecular Informatics. 2013; 32(11-12):1000-1008.
  49. 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
  50. 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.
    View in: PubMed, PubMed Central
  51. 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.
    View in: PubMed, PubMed Central
  52. 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.
    View in: PubMed, PubMed Central
  53. 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
  54. 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.
    View in: PubMed, PubMed Central
  55. Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Bin Chen, David Wild. Browsing large-scale cheminformatics data with dimension reduction. 2011.
  56. 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.
    View in: PubMed, PubMed Central
  57. 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
  58. 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.
  59. 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.
  60. 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.
    View in: PubMed, PubMed Central
  61. 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
  62. 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
  63. 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
  64. 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