- Jing Xing#, Mingdian Tan#, Dmitry Leshchiner#, Mengying Sun#, Mohamed Abdelgied#, Li Huang, Shreya Paithankar, Katie Uhl, Rama Shankar, Erika Lisabeth, Bilal Aleiwi, Tara Jager, Cameron Lawson, Reda Girgis, Richard R. Neubig, Samuel So, Edmund Ellsworth, Xiaopeng Li*, Mei-Sze Chua*, Jiayu Zhou*, Bin Chen*, Deep learning-based screening and design of novel therapeutics that reverse disease-associated transcriptional phenotypes, Cell, Accepted
- Nabasmita Talukdar, Xiaodan Zhang, Shreya Paithankar, Hui Wang, Bin Chen, A survey of using EHR as real-world evidence for discovering and validating new drug indications, Drug Discovery Today, 2025 Dec;30(12):104552.
- Zhiyue Tom Hu, Yaodong Yu, Ruoqiao Chen, Shan-Ju Yeh, Bin Chen*, Haiyan Huang*, Large-Scale Information Retrieval and Correction of Noisy Pharmacogenomic Datasets through Residual Thresholded Deep Matrix Factorization, Brief Bioinform 2025 May 1;26(3):bbaf226. doi: 10.1093/bib/bbaf226.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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)
- 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
- 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
- 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
- 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
- Mengying Sun, Jing Xing, Huijun Wang, Bin Chen, Jiayu Zhou,MoCL: Contrastive Learning on Molecular Graphs with Multi-level Domain Knowledge, KDD 2021
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#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
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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.
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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
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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
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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
NEWS
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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
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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
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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
NEWS
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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
NEWS