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William J. Welsh, Ph.D.

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Selected Recent Publications: (from over 450 total)

Osimitz TG, Welsh WJ, Ai N, Toole C. Polyester monomers lack ability to bind and activate both androgenic and estrogenic receptors as determined by In Vitro and In Silico methods.   Food Chem Toxicol. 2015 Jan;75:128-38. Epub 2014 Oct 28.


Ai N, Welsh WJ, Santhanam U, Hu H, Lyga J. Novel virtual screening approach for the discovery of human tyrosinase inhibitors. PLoS One. 2014 Nov 26;9(11):e112788. eCollection 2014.


Helsley RN, Sui Y, Ai N, Park SH, Welsh WJ, Zhou C. Pregnane X Receptor Mediates Dyslipidemia Induced by the HIV Protease Inhibitor Amprenavir in Mice. Mol Pharmacol. 2013 Jun;83(6):1190-9. Epub 2013 Mar 21.

Meng Q, Richmond-Bryant J, Lu SE, Buckley B, Welsh WJ, Whitsel EA, Hanna A, Yeatts KB, Warren J, Herring AH, Xiu A. Cardiovascular Outcomes and the Physical and Chemical Properties of Metal Ions Found in Particulate Matter Air Pollution: a QICAR Study. Environ Health Perspect. 2013 May;121(5):558-64.

Duan P, Li S, Ai N, Hu L, Welsh WJ, You G. Potent inhibitors of human organic anion transporters 1 and 3 from clinical drug libraries: discovery and molecular characterization. Mol Pharm. 2012 Nov 5;9(11):3340-6.

Fomovska A, Wood RD, Mui E, Dubey JP, Ferreira LR, Hickman MR, Lee PJ, Leed SE, Auschwitz JM, Welsh WJ, Sommerville C, Woods S, Roberts C, McLeod R. Salicylanilide inhibitors of Toxoplasma gondii. J Med Chem. 2012 Oct 11;55(19):8375-91.

Hehir S, Plourde NM, Gu L, Poree DE, Welsh WJ, Moghe PV, Uhrich KE. Carbohydrate composition of amphiphilic macromolecules influences physicochemical properties and binding to atherogenic scavenger receptor A. Acta Biomater. 2012 Nov;8(11):3956-62.

Osimitz TG, Eldridge ML, Sloter E, Welsh W, Ai N, Sayler GS, Menn F, Toole C. Lack of androgenicity and estrogenicity of the three monomers used in Eastman's Tritan™ copolyesters. Food Chem Toxicol. 2012 Jun;50(6):2196-205.

Sui Y, Ai N, Park SH, Rios-Pilier J, Perkins JT, Welsh WJ, Zhou C. Bisphenol A and its analogues activate human pregnane X receptor. Environ Health Perspect. 2012 Mar;120(3):399-405.

Zang Q, Keire DA, Buhse LF, Wood RD, Mital DP, Haque S, Srinivasan S, Moore CM, Nasr M, Al-Hakim A, Trehy ML, Welsh WJ. Identification of heparin samples that contain impurities or contaminants by chemometric pattern recognition analysis of proton NMR spectral data. Anal Bioanal Chem. 2011 Aug;401(3):939-55.

Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, Grishina M, Gasteiger J, Schwab C, Baskin II, Palyulin VA, Radchenko EV, Welsh WJ, Kholodovych V, Chekmarev D, Cherkasov A, Aires-de-Sousa J, Zhang QY, Bender A, Nigsch F, Patiny L, Williams A, Tkachenko V, Tetko IV. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J Comput Aided Mol Des. 2011 Jun;25(6):533-54.

Kortagere S, Mui E, McLeod R, Welsh WJ. Rapid discovery of inhibitors of Toxoplasma gondii using hybrid structure-based computational approach. J Comput Aided Mol Des. 2011 May;25(5):403-11.

Zang Q, Keire DA, Wood RD, Buhse LF, Moore CM, Nasr M, Al-Hakim A, Trehy ML, Welsh WJ. Combining (1)H NMR spectroscopy and chemometrics to identify heparin samples that may possess dermatan sulfate (DS) impurities or oversulfated chondroitin sulfate (OSCS) contaminants. J Pharm Biomed Anal. 2011 Apr 5;54(5):1020-9.

Passic SR, Ferguson ML, Catalone BJ, Kish-Catalone T, Kholodovych V, Zhu W, Welsh W, Rando R, Howett MK, Wigdahl B, Labib M, Krebs FC. Structure-activity relationships of polybiguanides with activity against human immunodeficiency virus type 1. Biomed Pharmacother. 2010 Dec;64(10):723-32.

Zang Q, Keire DA, Wood RD, Buhse LF, Moore CM, Nasr M, Al-Hakim A, Trehy ML, Welsh WJ. Determination of galactosamine impurities in heparin samples by multivariate regression analysis of their (1)H NMR spectra. Anal Bioanal Chem. 2011 Jan;399(2):635-49.

Fernández JR, Sweet ES, Welsh WJ, Firestein BL. Identification of small molecule compounds with higher binding affinity to guanine deaminase (cypin) than guanine. Bioorg Med Chem. 2010 Sep 15;18(18):6748-55.

Peng Y, Zhang Q, Snyder GL, Zhu H, Yao W, Tomesch J, Papke RL, O'Callaghan JP, Welsh WJ, Wennogle LP. Discovery of novel alpha7 nicotinic receptor antagonists. Bioorg Med Chem Lett. 2010 Aug 15;20(16):4825-30.

Li CW, Ai N, Dinh GK, Welsh WJ, Chen JD. Human ADA3 regulates RARalpha transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. Nucleic Acids Res. 2010 Sep;38(16):5291-303.

Thakkar N, Pirrone V, Passic S, Keogan S, Zhu W, Kholodovych V, Welsh W, Rando R, Labib M, Wigdahl B, Krebs FC. Persistent interactions between biguanide-based compound NB325 and CXCR4 result in prolonged inhibition of human immunodeficiency virus type 1 infection. Antimicrob Agents Chemother. 2010 May;54(5):1965-72.

Oelschlaeger P, Ai N, Duprez KT, Welsh WJ, Toney JH. Evolving carbapenemases: can medicinal chemists advance one step ahead of the coming storm? J Med Chem. 2010 Apr 22;53(8):3013-27.

Delker DA, Geter DR, Roop BC, Ward WO, Ahlborn GJ, Allen JW, Nelson GM, Ouyang M, Welsh W, Chen Y, O'Brien T, Kitchin KT. Oncogene expression profiles in K6/ODC mouse skin and papillomas following a chronic exposure to monomethylarsonous acid. J Biochem Mol Toxicol. 2009 Nov-Dec;23(6):406-18.

Peng Y, Zhang Q, Arora S, Keenan SM, Kortagere S, Wannemacher KM, Howells RD, Welsh WJ. Novel delta opioid receptor agonists exhibit differential stimulation of signaling pathways. Bioorg Med Chem. 2009 Sep 1;17(17):6442-50.

Chekmarev D, Kholodovych V, Kortagere S, Welsh WJ, Ekins S. Predicting inhibitors of acetylcholinesterase by regression and classification machine learning approaches with combinations of molecular descriptors. Pharm Res. 2009 Sep;26(9):2216-24.

Kim C, Choi J, Lee SJ, Welsh WJ, Yoon S. NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation. Nucleic Acids Res.2009 Jul;37(Web Server issue):W469-73.

Ai N, Krasowski MD, Welsh WJ, Ekins S. Understanding nuclear receptors using computational methods. Drug Discov Today. 2009 May;14(9-10):486-94.

Plourde NM, Kortagere S, Welsh W, Moghe PV. Structure-activity relations of nanolipoblockers with the atherogenic domain of human macrophage scavenger receptor A. Biomacromolecules. 2009 Jun 8;10(6):1381-91.

Chen M, Martin J, Fang H, Isukapalli S, Georgopoulos PG, Welsh WJ, Tong W. ebTrack: an environmental bioinformatics system built upon ArrayTrack. BMC Proc. 2009 Mar 10;3 Suppl 2:S5.

Lin YS, Yasuda K, Assem M, Cline C, Barber J, Li CW, Kholodovych V, Ai N, Chen JD, Welsh WJ, Ekins S, Schuetz EG. The major human pregnane X receptor (PXR) splice variant, PXR.2, exhibits significantly diminished ligand-activated transcriptional regulation. Drug Metab Dispos. 2009 Jun;37(6):1295-304.

Arora S, Wang XI, Keenan SM, Andaya C, Zhang Q, Peng Y, Welsh WJ. Novel microtubule polymerization inhibitor with potent antiproliferative and antitumor activity. Cancer Res. 2009 Mar 1;69(5):1910-5.

Kortagere S, Chekmarev D, Welsh WJ, Ekins S. Hybrid scoring and classification approaches to predict human pregnane X receptor activators. Pharm Res. 2009 Apr;26(4):1001-11.

Schnackenberg LK, Chen M, Sun J, Holland RD, Dragan Y, Tong W, Welsh W, Beger RD. Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies. Toxicol Appl Pharmacol. 2009 Feb 15;235(1):25-32.

Thakkar N, Pirrone V, Passic S, Zhu W, Kholodovych V, Welsh W, Rando RF, Labib ME, Wigdahl B, Krebs FC. Specific interactions between the viral coreceptor CXCR4 and the biguanide-based compound NB325 mediate inhibition of human immunodeficiency virus type 1 infection. Antimicrob Agents Chemother. 2009 Feb;53(2):631-8.

Ekins S, Kholodovych V, Ai N, Sinz M, Gal J, Gera L, Welsh WJ, Bachmann K, Mani S. Computational discovery of novel low micromolar human pregnane X receptor antagonists. Mol Pharmacol. 2008 Sep;74(3):662-72.

Kortagere S, Ekins S, Welsh WJ. Halogenated ligands and their interactions with amino acids: implications for structure-activity and structure-toxicity relationships. J Mol Graph Model. 2008 Sep;27(2):170-7.

Chekmarev DS, Kholodovych V, Balakin KV, Ivanenkov Y, Ekins S, Welsh WJ. Shape signatures: new descriptors for predicting cardiotoxicity in silico. Chem Res Toxicol. 2008 Jun;21(6):1304-14.

Kortagere S, Chekmarev D, Welsh WJ, Ekins S. New predictive models for blood-brain barrier permeability of drug-like molecules. Pharm Res. 2008 Aug;25(8):1836-45.

Reschly EJ, Ai N, Welsh WJ, Ekins S, Hagey LR, Krasowski MD. Ligand specificity and evolution of liver X receptors. J Steroid Biochem Mol Biol. 2008 May;110(1-2):83-94.

Reschly EJ, Ai N, Ekins S, Welsh WJ, Hagey LR, Hofmann AF, Krasowski MD. Evolution of the bile salt nuclear receptor FXR in vertebrates. J Lipid Res. 2008 Jul;49(7):1577-87.

Gubskaya AV, Kholodovych V, Knight D, Kohn J, Welsh WJ. Prediction of Fibrinogen Adsorption for Biodegradable Polymers: Integration of Molecular Dynamics and Surrogate Modeling. Polymer (Guildf). 2007 Sep 10;48(19):5788-5801.

Fernández JR, Welsh WJ, Firestein BL. Structural characterization of the zinc binding domain in cytosolic PSD-95 interactor (cypin): Role of zinc binding in guanine deamination and dendrite branching. Proteins. 2008 Feb 15;70(3):873-81.

Yoon S, Welsh WJ, Jung H, Yoo YD. CSSP2: an improved method for predicting contact-dependent secondary structure propensity. Comput Biol Chem. 2007 Oct;31(5-6):373-7.

Kohn J, Welsh WJ, Knight D. A new approach to the rationale discovery of polymeric biomaterials. Biomaterials. 2007 Oct;28(29):4171-7.

Woodard CL, Keenan SM, Gerena L, Welsh WJ, Geyer JA, Waters NC. Evaluation of broad spectrum protein kinase inhibitors to probe the architecture of the malarial cyclin dependent protein kinase Pfmrk. Bioorg Med Chem Lett. 2007 Sep 1;17(17):4961-6.

Zhang Q, Peng Y, Wang XI, Keenan SM, Arora S, Welsh WJ. Highly potent triazole-based tubulin polymerization inhibitors. J Med Chem. 2007 Feb 22;50(4):749-54.

Wang CY, Ai N, Arora S, Erenrich E, Nagarajan K, Zauhar R, Young D, Welsh WJ. Identification of previously unrecognized antiestrogenic chemicals using a novel virtual screening approach. Chem Res Toxicol. 2006 Dec;19(12):1595-601.

Kortagere S, Welsh WJ. Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors.  J Comput Aided Mol Des. 2006 Dec;20(12):789-802.