Last updated: 11-20-2020

Publications

See publications from:

Some publications may require a subscription to access full manuscripts.

Featured Publications

Tong ZB, Braisted J, Chu PH, Gerhold D. The MT1G gene in LUHMES neurons is a sensitive biomarker of neurotoxicity. Neurotox Res. 2020;38(4):967-978. doi:10.1007/s12640-020-00272-3. PMID:32870474.

Zhu Q, Nguyen D, Grishagin I, et al. An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). J Biomed Semantics. 2020;11(1):13. doi: 10.1186/s13326-020-00232-y. PMID:. PMCID:PMC7663894

Sheils T, Mathias S, Kelleher K, et al. TCRD and Pharos 2020: Mining the human proteome for disease biology. Nucleic Acids Res. 2020;gkaa993. doi:10.1093/nar/gkaa993. PMID:33156327

2020

Tong ZB, Braisted J, Chu PH, Gerhold D. The MT1G gene in LUHMES neurons is a sensitive biomarker of neurotoxicity. Neurotox Res. 2020;38(4):967-978. doi:10.1007/s12640-020-00272-3. PMID:32870474.

Zhu Q, Nguyen D, Grishagin I, et al. An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD). J Biomed Semantics. 2020;11(1):13. doi: 10.1186/s13326-020-00232-y. PMID:. PMCID:PMC7663894

Sheils T, Mathias S, Kelleher K, et al. TCRD and Pharos 2020: Mining the human proteome for disease biology. Nucleic Acids Res. 2020;gkaa993. doi:10.1093/nar/gkaa993. PMID:33156327

Zhu Q, Nguyen DT, Sid E, Pariser A. Leveraging the UMLS as a data standard for rare disease data normalization and harmonization. Methods Inf Med. 2020. doi:10.1055/s-0040-1718940

Peryea, T, Southall, N, Miller, M, et al. Global Substance Registration System: consistent scientific descriptions for substances related to health. Nucleic Acids Res. 2020;gkaa962. doi:10.1093/nar/gkaa962. PMID:33137173.

Zhu Q, Nguyen DT, Alyea G, Hanson K, Sid E, Pariser A. Phenotypically similar rare disease identification from an integrative knowledge graph for data harmonization: Preliminary study. JMIR Med Inform. 2020;8(10):e18395. doi:10.2196/18395. PMID:33006565.

Patt A, Demoret B, Stets C, et al. MDM2-dependent rewiring of metabolomic and lipidomic profiles in dedifferentiated liposarcoma models. Cancers (Basel). 2020;12(8):2157. doi:10.3390/cancers12082157. PMID:32759684. PMCID:PMC7463633.

Tristan CA, Ormanoglu P, Slamecka J, et al. Robotic high-throughput biomanufacturing and functional differentiation of human pluripotent stem cells. bioRxiv. Preprint posted online 2020;2020.08.03.235242. doi:10.1101/2020.08.03.235242. PMID:32793899. PMCID:PMC7418713.

Zhao Y, Man-Un Ung P, Zahoránszky-Kőhalmi G, et al. Identification of a G-protein-independent activator of GIRK channels. Cell Rep. 2020;31(11):107770. doi:10.1016/j.celrep.2020.107770.

Brimacombe KR, Zhao T, Eastman RT, et al. An OpenData portal to share COVID-19 drug repurposing data in real time. bioRxiv. Preprint posted online 2020;2020.06.04.135046. doi:10.1101/2020.06.04.135046. PMID:32511420. PMCID:PMC7276055.

Eicher T, Kinnebrew G, Patt A, et al. Metabolomics and multi-omics integration: A survey of computational methods and resources. Metabolites. 2020;10(5):202. doi:10.3390/metabo10050202. PMID:32429287. PMCID:PMC7281435.

Siramshetty VB, Nguyen DT, Martinez NJ, Simeonov A, Southall NT, Zakharov A. Critical assessment of artificial intelligence methods for prediction of hERG channel inhibition in the “big data” era. ChemRxiv. Epub April 16, 2020. doi:10.26434/chemrxiv.12119040.v1.

Shah P, Siramshetty VB, Zakharov AV, Southall NT, Xu X, Nguyen DT. Predicting liver cytosol stability of small molecules. J Cheminform. 2020;12:21. Published online 2020 April 7. doi:10.1186/s13321-020-00426-7. PMCID:PMC7140498.

Chu PH, Chen G, Kuo D, et al. Stem cell-derived endothelial cell model that responds to tobacco smoke like primary endothelial cells. Chem Res Toxicol. 2020;33(3):751-763. doi:10.1021/acs.chemrestox.9b00363. PMID:32119531.

Ellis CR, Racz R, Kruhlak NL, et al. Evaluating kratom alkaloids using PHASE. PLoS One. 2020;15(3):e0229646. doi:10.1371/journal.pone.0229646. eCollection 2020. PMID:32126112.

Sheils T, Mathias SL, Siramshetty VB, et al. How to illuminate the druggable genome using Pharos. Curr Protoc Bioinformatics. 2020;69(1):e92. doi:10.1002/cpbi.92. PMID:31898878.

Zahoranszky-Kohalmi G, Wan KK, Godfrey AG. (2020): Hilbert-curve assisted structure embedding method. ChemRxiv. Preprint posted online Feb 28, 2020. doi:10.26434/chemrxiv.11911296.v1.

Godfrey AG, Michael SG, Sittampalam GS, Zahoránszky-Köhalmi G. A perspective on innovating the chemistry lab bench. Front Robot AI. 2020;7:24. doi:10.3389/frobt.2020.00024.

Zahoránszky-Kőhalmi G, Sheils T, Oprea TI. SmartGraph: A network pharmacology investigation platform. J Cheminform. 2020;12:5. doi:10.1186/s13321-020-0409-9.

2019

Peryea T, Katzel D, Zhao T, Southall N, Nguyen DT. MOLVEC: Open source library for chemical structure recognition. In Abstracts of Papers of the American Chemical Society. Vol. 258. Washington, D.C.: American Chemical Society; 2019.

Fecho K, Ahalt SC, Arunachalam S, et al.; Biomedical Data Translator Consortium. Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon. J Biomed Inform. 2019;100:103325. doi:10.1016/j.jbi.2019.103325. PMID:31676459. PMCID:PMC6953386.

Huang R, Zhu H, Shinn P, et al. The NCATS Pharmaceutical Collection: A 10-year update. Drug Discov Today. 2019;24(12):2341-2349. doi:10.1016/j.drudis.2019.09.019. PMID:31585169.

Zakharov AV, Zhao T, Nguyen DT, et al. Novel consensus architecture to improve performance of large-scale multitask deep learning QSAR models. J Chem Inf Model. 2019;59(11):4613-4624. doi:10.1021/acs.jcim.9b00526. PMID:31584270.

Chen Y, Tristan CA, Chen L, et al. A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells. bioRxiv. Preprint posted online Oct 22, 2019. doi:10.1101/815761.

Southall NT, Natarajan M, Lau LPL, et al.; IRDiRC Data Mining and Repurposing Task Force. The use or generation of biomedical data and existing medicines to discover and establish new treatments for patients with rare diseases — recommendations of the IRDiRC Data Mining and Repurposing Task Force. Orphanet J Rare Dis. 2019;14(1):225. doi:10.1186/s13023-019-1193-3. PMID:31615551.

Southall NT. Freedom of Information Act access to an investigational new drug application. ACS Pharmacol Transl Sci. 2019;2(6):497-500. doi:10.1021/acsptsci.9b00056. eCollection 2019 Dec 13. PMID:32259081.

Solinski HJ, Dranchak P, Oliphant E, et al. Inhibition of natriuretic peptide receptor 1 reduces itch in mice. Sci Transl Med. 2019;11(500):eaav5464. doi:10.1126/scitranslmed.aav5464. PMID:31292265. PMCID:PMC7218920.

Huang R, Grishagin I, Wang Y, et al. The NCATS BioPlanet — An integrated platform for exploring the universe of cellular signaling pathways for toxicology, systems biology, and chemical genomics. Front Pharmacol. 2019;10:445. doi:10.3389/fphar.2019.00445. eCollection 2019. PMID:31133849.

Austin CP, Colvis CM, Southall NT. Deconstructing the translational Tower of Babel. Clin Transl Sci. 2019;12(2):85. doi:10.1111/cts.12595. Epub 2018 Nov 9. PMID:30412342.

Gorshkov K, Chen CZ, Marshall RE, et al. Advancing precision medicine with personalized drug screening. Drug Discov Today. 2019;24(1):272-278. doi:10.1016/j.drudis.2018.08.010. PMID:30125678.

2018 and Earlier

Kearney SE, Zahoránszky-Kőhalmi G, Brimacombe KR, et al. Canvass: A crowd-sourced, natural-product screening library for exploring biological space. ACS Central Science. 2018;4(12):1727-1741. doi:10.1021/acscentsci.8b00747. PMID:30648156.

Zhou W, Sun W, Yung MMH, et al. Autocrine activation of JAK2 by IL-11 promotes platinum drug resistance. Oncogene. 2018;37(29):3981-3997. doi:10.1038/s41388-018-0238-8. PMID:29662190. PMCID:PMC6054535.

Oprea TI, Bologa CG, Brunak S, et al. Unexplored therapeutic opportunities in the human genome. Nat Rev Drug Discov. 2018;17(5):317-332. doi:10.1038/nrd.2018.14. PMID:29472638.

Tong ZB, Huang R, Wang Y, et al. The Toxmatrix: Chemo-genomic profiling identifies interactions that reveal mechanisms of toxicity. Chem Res Toxicol. 2018;31(2):127-136. doi:10.1021/acs.chemrestox.7b00290. PMID:29156121.

Coussens NP, Braisted JC, Peryea T, Sittampalam GS, Simeonov A, Hall MD. Small-molecule screens: A gateway to cancer therapeutic agents with case studies of Food and Drug Administration–approved drugs. Pharmacol Rev. 2017;69(4):479-496. doi:10.1124/pr.117.013755. PMID:28931623. PMCID:PMC5612261.

Nguyen DT, Mathias S, Bologa C, et al. Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 2017;45(D1):D995-D1002. doi:10.1093/nar/gkw1072. PMID:27903890. PMCID:PMC5210555.