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Repurposing existing drugs to fight new COVID-19 variants (MSU Today release)

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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

View in: Nature Protocols, 2020

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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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.

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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

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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

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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

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)

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

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

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

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

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

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

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.

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.

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.

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.

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

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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)

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

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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)

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.

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.

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.

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

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.

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.

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.

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.

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].

Chen B. Ten simple rules for internship in a pharmaceutical company. PLoS Comput Biol. 2014 May; 10(5):e1003600. PMID: 24811706; PMCID: PMC4014388.

Chen B, Wang H, Ding Y, Wild D. Synthesis Lectures on the Semantic Web: Theory and Technology. Semantic Breakthrough in Drug Discovery. 2014.

Bin Chen, David J Wild. Practice and Challenges of Building a Semantic Framework for Chemogenomics Research. Molecular Informatics. 2013; 32(11-12):1000-1008.

Chen B, Butte AJ. Network medicine in disease analysis and therapeutics. Clin Pharmacol Ther. 2013 Dec; 94(6):627-9. PMID: 24241637.

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.

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.

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.

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.

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.

Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Bin Chen, David Wild. Browsing large-scale cheminformatics data with dimension reduction. 2011.

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.

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.

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.

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.

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.

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.

Chen B, Wild D, Guha R. PubChem as a source of polypharmacology. J Chem Inf Model. 2009 Sep; 49(9):2044-55. PMID: 19708682.

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.

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.