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publication.html
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<html><head>
<meta charset="utf-8">
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<div id="underReviewList">
<ol reversed="reversed" style="font-size:130%;">
</ol>
</div>
<b>Preprint for COVID</b>
<div id="publicationList">
<ol reversed="reversed" style="font-size:130%;">
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">Mengying Sun, Christopher Daniel Chang, Shan-Ju Yeh, Shilong Li, Ke Liu, Guoli Zhou, Rama Shankar, Jing Xing, Austin VanVelsen, Tyler VanVelsen, Benjamin Feng, Krista Young, Michael Strug, Lauren Turco, Zichen Wang, Eric Schadt, Rong Chen, Xiaohong Li, Li Li, Jiayu Zhou, and Bin Chen, Analysis of 220,000 human transcriptome samples reveals that differential expression of virus entry proteins is associated with sex differences in COVID-19
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: submitted https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7654875/
</div>
</span>
</div>
</li>
</ol>
</div>
<hr class="featurette-divider">
<b>Print (since 2020, only partial publications are listed, see </b> (<a href = "https://scholar.google.com/citations?user=K7MBJlwAAAAJ&hl=en" target = '_blank'>full list</a>)
<div id="publicationList">
<ol reversed="reversed" style="font-size:130%;">
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid=""> 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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://academic.oup.com/jamiaopen/article/5/4/ooac099/6847193?login=false" target = '_blank'>Web page</a>
<p></p>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid=""> 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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://doi.org/10.1186/s40478-022-01463-z" target = '_blank'>Web page</a>
<p></p>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="">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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://www.cell.com/iscience/fulltext/S2589-0042(22)01340-2" target = '_blank'>Web page</a>
<p></p>
<a href="https://msutoday.msu.edu/news/2022/repurposing-existing-drugs-to-fight-new-covid-19-variants" target="_blank">Repurposing existing drugs to fight new COVID-19 variants</a> (MSU Today release)
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="">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)
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://dl.acm.org/doi/10.1145/3534678.3542676" target = '_blank'>Proceedings</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9285138/" target = '_blank'>Proceedings</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://molpharm.aspetjournals.org/content/101/1" target = '_blank'>Website (Cover)</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://www.nature.com/articles/s43587-021-00122-7" target = '_blank'>Website</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">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
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://academic.oup.com/bib/article/22/6/bbab249/6318177" target = '_blank'>Website</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287"> Mengying Sun, Jing Xing, Huijun Wang, Bin Chen, Jiayu Zhou,MoCL: Contrastive Learning on Molecular Graphs with Multi-level Domain Knowledge, KDD 2021
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://arxiv.org/abs/2106.04509" target = '_blank'>arXiv</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287"> Mengying Sun, Jing Xing, Bin Chen, Jiayu Zhou, Robust Collaborative Learning with Noisy Labels, ICDM 2020, acceptance rate (19.76%)
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">
<div class="viewIn">
View in: <a href = "https://arxiv.org/abs/2012.13670" target = '_blank'>arXiv</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> #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
<div class="viewIn">
View in: <a href='https://www.nature.com/articles/s41596-020-00430-z' target='_blank'> Nature Protocols, 2020</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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.
<div class="viewIn">
View in: <a href = "https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(20)30498-9/fulltext" target = "_blank">website</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="32437232">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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.
<div class="viewIn">
View in: <a href='https://www.ncbi.nlm.nih.gov/pubmed/32959224' target='_blank'>PubMed</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="32437232">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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
<div class="viewIn">
View in: <a href='https://www.ncbi.nlm.nih.gov/pubmed/32437232' target='_blank'>PubMed</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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
<div class="viewIn">
View in: <a href='https://www.ncbi.nlm.nih.gov/pubmed/32160543' target='_blank'>PubMed</a>
</div>
</span>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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
</span>
<div class="viewIn">
View in: <a href='https://www.nature.com/articles/s41575-019-0240-9' target='_blank'>Web</a>
, <a href="https://msutoday.msu.edu/news/2020/big-data-targets-deadly-liver-cancer/" target="_blank">MSU Today</a>,
</div>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="31478838">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">Hyojung Paik, Matthew J. Kan, Nadav Rappoport, Dexter Hadley, Marina Sirota, <b>Bin Chen</b>, 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)
</span>
</div>
<div class="viewIn">
View in: <a href='https://rdcu.be/bUk3Q' target='_blank'>Web</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="31478838">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, <b>Chen B</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
</span>
</div>
<div class="viewIn">
View in: <a href='https://elifesciences.org/articles/48847' target='_blank'>Web</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="29378174">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">K. Yu, <b>B. Chen</b>, 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
</span>
</div>
<div class="viewIn">
View in: <a href='https://www.nature.com/articles/s41467-019-11415-2' target='_blank'>Web</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" >
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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</span>
</div>
<div class="viewIn">
View in: <a href='https://www.nature.com/articles/s41467-019-10148-6' target='_blank'>Web</a>
</div>
<div class="viewIn">
<b>NEWS</b>
</div>
<div class="viewIn">
<a href="https://msutoday.msu.edu/news/2019/big-data-helps-identify-better-way-to-research-breast-cancers-spread/" target="_blank">Big data helps identify better way to research breast cancer’s spread</a> (MSU press release,
<a href="https://www.sciencedaily.com/releases/2019/05/190515085440.htm" target="_blank">Science Daily</a>,
<a href="https://www.eurekalert.org/pub_releases/2019-05/msu-bdh051419.php" target="_blank">EurekAlert</a>
)
</div>
<div class="viewIn">
<a href="https://www.genengnews.com/news/breast-cancer-cell-lines-get-big-data-assistance/" target="_blank">Breast Cancer Cell Lines Get Big Data Assistance</a> (GEN News)
</div>
<div class="viewIn">
<a href="https://www.i3health.us/news/are-cell-lines-the-best-model-to-analyze-breast-cancer-biology" target="_blank">Are Cell Lines the Best Model to Analyze Breast Cancer Biology?
</a> (I3Health News)
</div>
<div class="viewIn">
<a href="https://www.news-medical.net/news/20190515/Big-data-helps-determine-better-research-models-to-fight-the-spread-of-breast-cancer.aspx" target="_blank">Big data helps determine better research models to fight the spread of breast cancer
</a> (The Medical News)
</div>
<div class="viewIn">
<a href="https://www.specialtypharmacytimes.com/news/using-big-data-to-improve-metastatic-breast-cancer-research" target="_blank">Using Big Data to Improve Metastatic Breast Cancer Research
</a> (Specialty Pharmacy Times)
</div>
<div class="viewIn">
<a href="https://breastcancer-news.com/2019/07/19/genomic-analysis-shows-cancer-cell-lines-different-human-cancers/" target="_blank">Genomic Analysis Reveals Differences Between Cancer Cell Lines and Human Cancers
</a> (Breast Cancer News)
</div>
<div class="viewIn">
<a href="https://www.scientificamerican.com/arabic/articles/news/genetic-databases-provide-solutions-for-breast-cancer-research/" target="_blank">Genetic databases provide solutions for breast cancer research
</a> (Scientific American Arabic)
</div>
<div class="viewIn">
Tweeted by <a href="https://twitter.com/NCIgenomics/status/1132296267378380800" target="_blank">NCI Genomices</a>, <a href="https://twitter.com/NatRevClinOncol/status/1131205575461806082" target="_blank">NatRevClinOncol</a> and many others.
</div>
<div class="viewIn">
Selected as <a href="https://factor.niehs.nih.gov/2019/7/papers/dert/index.htm" target="_blank">an NIEHS Extramural Paper of the Month</a>.
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl09_lblPublication"></span>
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</div>
<div class="viewIn">
View in: <a href='https://link.springer.com/protocol/10.1007%2F978-1-4939-9089-4_6' target='_blank'>Methods in Molecular Biology </a>, <a href='//www.ncbi.nlm.nih.gov/pubmed/30848458' target='_blank'>PubMed</a> .
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="336909">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication"> 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
</span>
</div>
<div class="viewIn">
View in: <a href='//www.ncbi.nlm.nih.gov/pubmed/30704474' target='_blank'>PubMed</a>, <a href='https://rdcu.be/bjyiV' target='_blank'>BMC medical genomics</a> (transferred from BMC genomics to BMC medical genomics).
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="337287">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">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</span>
</div>
<div class="viewIn">
View in: <a href='http://psb.stanford.edu/psb-online/proceedings/psb19/hu.pdf' target='_blank'>PSB 2019 Proceedings</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="29273356">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">Sharpnack MF, <b>Chen B</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.</span>
</div>
<div class="viewIn">
View in: <a href='//www.ncbi.nlm.nih.gov/pubmed/29273356' target='_blank'>PubMed</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="29378174">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">Zhang S, Wang J, Wang H, Fan L, Fan B, Zeng B, Tao J, Li X, Che L, Cigliano A, Ribback S, Dombrowski F, <b>Chen B</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.</span>
</div>
<div class="viewIn">
View in: <a href='//www.ncbi.nlm.nih.gov/pubmed/29378174' target='_blank'>PubMed</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl01_liPublication" data-pmid="29093271">
<div>
<span id="ctl01_rpPublication_ctl01_lblPublication">Mirza AN, Fry MA, Urman NM, Atwood SX, Roffey J, Ott GR, <b>Chen B</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.</span>
</div>
<div class="viewIn">
View in: <a href='//www.ncbi.nlm.nih.gov/pubmed/29093271' target='_blank'>PubMed</a>
</div>
</li>
<li id="ctl01_rpPublication_ctl02_liPublication" data-pmid="28925997">
<div>
<span id="ctl01_rpPublication_ctl02_lblPublication">Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, <b>Chen B</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.</span>
</div>
<div class="viewIn">
View in: <a href='//www.ncbi.nlm.nih.gov/pubmed/28925997' target='_blank'>PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl01_lblPublication">
<b>Bin Chen</b>#*, 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
<div class="viewIn">
<a href="https://www.nature.com/articles/ncomms16022" target="_blank">link</a>
</div>
<div class="viewIn">
<b>NEWS</b>
</div>
<div class="viewIn">
<a href="https://www.ucsf.edu/news/2017/07/407696/big-data-analysis-points-toward-new-drug-discovery-method" target="_blank">Big-Data Analysis Points Toward New Drug Discovery Method</a> (UCSF press release,
<a href="https://www.sciencedaily.com/releases/2017/07/170714072222.htm" target="_blank">Science Daily</a>,
<a href="https://www.eurekalert.org/pub_releases/2017-07/uoc--bap071117.php" target="_blank">EurekAlert</a>
)
</div>
<div class="viewIn">
<a href="https://t.co/fIbAh6BMJp" target="_blank">Database sleuths turn up a surprising new drug to test against cancer</a> (STAT)
</div>
<div class="viewIn">
<a href="https://www.genomeweb.com/sequencing/systems-study-taps-cancer-gene-expression-reversal-predict-drug-response" target="_blank">Systems Study Taps Cancer Gene Expression Reversal to Predict Drug Response</a> (genomeweb)
</div>
<div class="viewIn">
<a href="http://www.huffingtonpost.com/entry/how-big-data-is-transforming-medicine_us_59673813e4b07b5e1d96ed79" target="_blank">How Big Data Is Transforming Medicine</a> (HuffPost)
</div>
<div class="viewIn">
<a href="http://www.genengnews.com/gen-news-highlights/new-computational-method-to-aid-cancer-drug-discovery/81254661" target="_blank">New Computational Method to Aid Cancer Drug Discovery</a> (Genetic Engineering &
Biotechnology News)
</div>
<div class="viewIn">
<a href="http://news.xinhuanet.com/english/2017-07/13/c_136439385.htm" target="_blank">UCSF-led research produces method for probing new drug use</a> (XINHUA)
</div>
<div class="viewIn">
<a href="https://commonfund.nih.gov/LINCS/programhighlights#Cancer" target="_blank">Using LINCS and other Big Data to Find New Cancer Treatments</a> (Program highlight @NIH The Common Fund)
</div>
<div class="viewIn">
<a href="http://www.ebiotrade.com/newsf/2017-7/2017713224257119.htm" target="_blank">大数据分析助跑抗癌新药发现</a> (ebiotrade)
</div>
</span>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl01_lblPublication">
<b>Bin Chen</b>#, 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
<div class="viewIn">
<a href="http://www.gastrojournal.org/article/S0016-5085(17)30264-0/abstract" target="_blank">link</a>
</div>
<div class="viewIn">
<b>NEWS</b>
</div>
<div class="viewIn">
<a href="http://www.ucsf.edu/news/2017/03/406321/deworming-pill-may-be-effective-treating-liver-cancer" target="_blank">Deworming Pill May Be Effective in Treating Liver Cancer </a> (UCSF press release,
<a href="http://www.bioon.com/3g/id/6701223/" target="_blank">中文</a>)
</div>
<div class="viewIn">
<a href="http://journalsblog.gastro.org/bioinformatic-search-identifies-tapeworm-drug-for-treatment-of-hepatocellular-carcinoma/" target="_blank">Bioinformatic Search Identifies Tapeworm Drug for Treatment of Hepatocellular Carcinoma</a> (Featured in Gastro journal)
</div>
<div class="viewIn">
<a href="https://liverdiseasenews.com/2017/04/05/deworming-pill-nexavar-mice-liver-cancer/" target="_blank">New Approach to Drug Discovery Finds Veterinary Pill Helps Mice Fight Liver Cancer</a> (LIVER DISEASE NEWS)
</div>
</span>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl01_lblPublication">Ziyan Pessetto,
<b>Bin Chen</b>, 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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/27863422" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl01_lblPublication">H Paik,
<b>B Chen</b>, 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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/27860440" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl01_lblPublication">Fu G, Ding Y, Seal A,
<b>Chen B</b>, Sun Y, Bolton E. Predicting drug target interactions using
meta-path-based semantic network analysis. BMC Bioinformatics. 2016; 17(1):160.
PMID: 27071755.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/27071755" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl02_lblPublication">
<b>Chen B#</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</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/26659699" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl03_lblPublication">
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/26535158" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC4625862" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl04_lblPublication"></span>
<b>Chen B</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.</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/26043652" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC4460709" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl05_lblPublication">Li J, Zheng S,
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/25832646" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl06_lblPublication">Wu M, Sirota M, Butte AJ,
<b>Chen B.</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/25592569" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC4361221" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl07_lblPublication">Fan-Minogue H,
<b>Chen B</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].</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/25592598" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC4299914" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl08_lblPublication">
<b>Chen B</b>. Ten simple rules for internship in a pharmaceutical company.
PLoS Comput Biol. 2014 May; 10(5):e1003600. PMID: 24811706; PMCID: PMC4014388.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/24811706" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC4014388" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl09_lblPublication"></span>
<b>Chen B</b>, Wang H, Ding Y, Wild D. Synthesis Lectures on the Semantic
Web: Theory and Technology. Semantic Breakthrough in Drug Discovery. 2014.</div>
<div class="viewIn">
<a href="https://www.amazon.com/Semantic-Breakthrough-Discovery-Synthesis-Lectures/dp/1627054502" target="_blank">***Amazon***</a>,</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl10_lblPublication">
<b>Bin Chen</b>, David J Wild. Practice and Challenges of Building a Semantic
Framework for Chemogenomics Research. Molecular Informatics. 2013; 32(11-12):1000-1008.</span>
</div>
<div class="viewIn"></div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl11_lblPublication">
<b>Chen B</b>, Butte AJ. Network medicine in disease analysis and therapeutics.
Clin Pharmacol Ther. 2013 Dec; 94(6):627-9. PMID: 24241637.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/24241637" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl12_lblPublication">Auerbach RK,
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/23732275" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC3712221" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl13_lblPublication">Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko
V, Hastings J,
<b>Chen B</b>, Wild DJ. The ChEMBL database as linked open data. J Cheminform.
2013; 5(1):23. PMID: 23657106; PMCID: PMC3700754.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/23657106" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC3700754" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl14_lblPublication">
<b>Chen B</b>, Ding Y, Wild DJ. Assessing drug target association using semantic
linked data. PLoS Comput Biol. 2012; 8(7):e1002574. PMID: 22859915; PMCID:
PMC3390390.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/22859915" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC3390390" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl15_lblPublication">
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/22360769" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl16_lblPublication">
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/22401035" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC3320537" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl17_lblPublication">Jong Youl Choi, Seung-Hee Bae, Judy Qiu,
<b>Bin Chen</b>, David Wild. Browsing large-scale cheminformatics data with
dimension reduction. 2011.</span>
</div>
<div class="viewIn"></div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl18_lblPublication">He B, Tang J, Ding Y, Wang H, Sun Y, Shin JH,
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/22162991" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC3232205" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl19_lblPublication">
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/21903625" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl20_lblPublication">
<b>Bin Chen</b>, 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.</span>
</div>
<div class="viewIn"></div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl21_lblPublication">Ying Ding, Yuyin Sun,
<b>Bin Chen</b>, 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.</span>
</div>
<div class="viewIn"></div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl22_lblPublication">
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/20478034" target="_blank">PubMed</a>,
<a href="//www.ncbi.nlm.nih.gov/pmc/articles/PMC2881087" target="_blank">PubMed Central</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl23_lblPublication">
<b>Chen B</b>, Wild DJ. PubChem BioAssays as a data source for predictive
models. J Mol Graph Model. 2010 Jan; 28(5):420-6. PMID: 19897391.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/19897391" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl24_lblPublication">
<b>Chen B</b>, Wild D, Guha R. PubChem as a source of polypharmacology. J
Chem Inf Model. 2009 Sep; 49(9):2044-55. PMID: 19708682.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/19708682" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl25_lblPublication">Scheiber J,
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/19434832" target="_blank">PubMed</a>
</div>
</li>
<li>
<div>
<span id="ctl00_rpPublication_ctl26_lblPublication">Shi LW,
<b>Chen B</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.</span>
</div>
<div class="viewIn">View in:
<a href="//www.ncbi.nlm.nih.gov/pubmed/18947219" target="_blank">PubMed</a>
</div>
</li>
</ol>
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