Publications

Research publications acknowledging COBRE CBID grant funding (NIH P20GM113117)

How (and when) should I credit CBID CoBRE in my publications?

Research Publications

  1. Fehr A, Pfannenstiel J, Cluff D. Discovery of 2-Amide-3-methylester Thiophenes that Target SARS-CoV-2 Mac1 and Repress Coronavirus Replication Validating Mac1 as an Antiviral Target. J Med Chem. 2024 67(8):6519-6536. PMC10793406.
  2. Fehr A, Pfannenstiel J. SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling. Proc Natl Acad Sci. 2024 121(15):e2320194121. PMC11009620.
  3. Garcia MB, Singh M, Miller E, Neuenswander S, Douglas J, Boskovic Z. Twisted Intramolecular Charge-Transfer (TICT) State Addition to Electron-Poor Olefins. J Org Chem. 2024 Mar 1;89(5):3058-3064. Epub 2024 Feb 14. PMID: 38354334; PMC11006016.
  4. Glatthardt T, Lima RD, de Mattos RM, Ferreira RBR. Microbe Interactions within the Skin Microbiome. Antibiotics (Basel). 2024 Jan 4;13(1):pii:49. PMID:38247608; PMC10812674.
  5. Hall KT, Kenedy MR, Johnson DK, Hefty PS, Akins DR. A conserved C-terminal domain of TamB interacts with multiple BamA POTRA domains in Borreliella burgdorferi. PLoS One. 2024 Aug 29; 19(8):e0304839. PMID: 39208212; PMC11361582.
  6. Ikujuni AP, Dhar R, Cordova A, Bowman AM, Noga S, Slusky JSG. Discovery and Characterization of Two Folded Intermediates for Outer Membrane Protein TolC Biogenesis. J Mol Biol. 2024 Aug 15; 436(16):168652. PMID: 38871177.
  7. >Kerr CM, Pfannenstiel JJ, Alhammad YM, Roy A, O'Connor JJ, Ghimire R, Khattabi R, Shrestha R, McDonald PR, Gao P, Johnson DK, More S, Channappanavar R, Fehr AR. Mutation of highly conserved residues in loop 2 of the coronavirus macrodomain demonstrates that enhanced ADP-ribose binding is detrimental to infection. bioRxiv. 2024 Jan 4;pii:2024.01.03.574082. PMID: 38260573; PMC10802294.
  8. Kim Y, Pool E, Kim E, Dampalla CS, Nguyen HN, Johnson DK, Lovell S, Groutas WC, Chang K-O. Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus. Microbiol Spectr. 2024 Apr; 12(4):e03372-23. Epub Mar 11. PMID: 38466127; PMC10986521.
  9. Li P, Kim Y, Dampalla CS, Nhat Nguyen H, Meyerholz DK, Johnson DK, Lovell S, Groutas WC, Perlman S, Chang K-O. Potent 3CLpro inhibitors effective against SARS-CoV-2 and MERS-CoV in animal models by therapeutic treatment. mBio. 2024 Feb 14;15(2):e0287823. Epub 2023 Dec 21. PMID:38126789; PMC10865860.
  10. McCloskey E, Kashipathy M, Cooper A, Gao P, Johnson DK, Battaile KP, Lovell S, Davido DJ. HSV-1 ICP0 dimer domain adopts a novel β-barrel fold. Proteins. 2024 Jul;92(7):830-841. Epub 2024 Feb 19. PMID:38372168; PMC10827139.
  11. McGuinness KN, Fehon N, Feehan R, Miller M, Mutter AC, Rybak LA, Nam J, AbuSalim JE, Atkinson JT, Heidari H, Losada N, Kim JD, Koder RL, Lu Y, Silberg JJ, Slusky JSG, Falkowski PG, Nanda V. The energetics and evolution of oxidoreductases in deep time. Proteins. 2024 92(1): 52-59. PMID:37596815.
  12. Oakley B, Woods K, Akhter S, Rodriguez B, Townsend K, Smith N, Smith B, Wambua A, Craddock V, Abisado-Duque R, Hancock L, Miao Y, Chandler J. Characterization of natural product inhibitors of quorum sensing reveals competitive inhibition of Pseudomonas aeruginosa RhlR by ortho-vanillin. Microbiol Spectr. 2024 July 24;0:e00681-24. PMID: 39046261.
  13. Weeramange C, Menjivar C, O'Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton A, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. J Biol Chem. 2024 Jun; 300(6):107352. PMID: 38723750; PMC11157272.
  1. Adhikari S, Baral P. Protocol for neonatal respiratory syncytial virus infection in mice and immune analysis of infected lungs and bronchoalveolar lavage fluid. STAR Protoc. 2023 Sep 15;4(3):102434. Epub 2023 Jul 9. PMID: 37432860; PMC10362174.
  2. Alhammad YM, Parthasarathy S, Ghimire R, Kerr CM, O'Connor JJ, Pfannenstiel JJ, Chanda D, Miller CA, Baumlin N, Salathe M, Unckless RL, Zuñiga S, Enjuanes L, More S, Channappanavar R, Fehr AR. SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in cell culture and in mice. Proc Natl Acad Sci U S A. 2023 Aug 29;120(35):e2302083120. Epub 2023 Aug 22. PMID:37607224; PMC10468617.
  3. Alhammad YM, Parthasarathy S, Ghimire R, Kerr CM, O'Connor JJ, Pfannenstiel JJ, Chanda D, Miller CA, Baumlin N, Salathe M, Unckless RL, Zuñiga S, Enjuanes L, More S, Channappanavar R, Fehr AR. SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in mice. bioRxiv. 2023 Apr 6;pii:2023.04.06.535927. PMC10104158.
  4. Apley KD, Griffith AS, Downes GM, Ross P, Farrell MP, Kendall P, Berkland CJ. CD22L Conjugation to Insulin Attenuates Insulin-Specific B Cell Activation. Bioconjug Chem. 2023 Nov 15;34(11):2077-2088. Epub 2023 Oct 26. PMID:37883211; PMC11034786.
  5. Bowen HG, Kenedy MR, Johnson DK, MacKerell AD, Akins DR. Identification of a novel transport system in Borrelia burgdorferi that links the inner and outer membranes. Pathog Dis. 2023 Jan 17;81. pii: ftad014. PMID: 37385817; PMC10353723.
  6. Chacha WE, Tran H, Scarlett WR, Hutchison JM. Extraction of active, contaminant degrading enzymes from soil. Applied soil ecology: a section of Agriculture, Ecosystems & Environment. 2023 Jul;187:104841. PMC10544838.
  7. Crean RM, Slusky JSG, Kasson PM, Kamerlin SCL. KIF-Key Interactions Finder: A program to identify the key molecular interactions that regulate protein conformational changes. Chem Phys. 2023 Apr 14; 158(14):144114. PMID: 37061494; PMC not required.
  8. Davies AM, Londhe SS, Smith ER, Tunge JA. Single-Step Synthesis of γ-Ketoacids through a Photoredox-Catalyzed Dual Decarboxylative Coupling of α-Oxo Acids and Maleic Anhydrides. Org Lett. 2023 Dec 8;25(48):8634-8639. Epub 2023 Nov 22. PMID: 37991504.
  9. Dhar R, Bowman AM, Hatungimana B, Slusky JSG. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol. 2023 Sep 26; 435(22):168292. PMID: 37398247; PMC10312768.
  10. Feehan R, Copeland M, Franklin MW, Slusky JSG. MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. Protein Sci. 2023 Apr;32(4):e4626. PMC10044107.
  11. Ferreira RBR, Antunes C. Development: Unlocking the microbiome. eLife. 2023 Oct 11; 12:e92482.
  12. He H, Pramanik AS, Swanson SK, Johnson, DK, Florens L, Zückert WR. A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane. Mol Microbiol. 2023 June;119(6)752-767. PMID:37170643; PMC10330739.
  13. Ho KV, Hsieh HY, Roy A,Foote S, McDonald P, Coggeshall MV, Ito H, Lei Z, Sumner LW, Stewart GC, Lin CH. Quantification and characterization of biological activities of glansreginin A in black walnuts (Juglans nigra). Sci Rep. 2023 Nov 1;13(1):18860. PMID: 37914763; PMC10620390.
  14. Höcker B, Lu P, Glasgow A, Marks DS, Chatterjee P, Slusky JSG, Schueler-Furman O, Huang P. How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design? Cell Syst. 2023 Aug 16;14(8):629-632. Opinion. PMID: 37591202.
  15. Ikujuni AP, Budiardjo SJ, Dhar R, Slusky JSG. Detergent headgroups control TolC folding in vitro. Biophys J. 2023 Apr 4;122(7):1185-1197. Epub 2023 Feb 10. Feb 10:S0006-3495(23)00099-1. PMID: 36772796; PMC10111266.
  16. Jin Y, Basu S, Feng M, Ning Y, Munasinghe I, Joachim AM, Li J, Madden R, Burks H, Gao P, Perera C, Werbovetz KA, Zhang K, Wang MZ. CYP5122A1 encodes an essential sterol C4-methyl oxidase in Leishmania donovani and determines the antileishmanial activity of antifungal azoles. Res Sq. 2023 Jul 27. pii: rs.3.rs-3185204. PMID:37546914: PMC10402201.
  17. Johnson SN, Brucks SD, Apley KD, Farrell MP, Berkland CJ. Multivalent Scaffolds to Promote B cell Tolerance. Mol Pharm. 2023 Aug 7;20(8):3741-3756. Epub 2023 Jul 6. Review. PMID:37410969; PMC pending.
  18. Joseph E, Hernandez RD, Tunge JA. Cobalt-Catalyzed Decarboxylative Allylations: Development and Mechanistic Studies. Chemistry. 2023 Oct 18;29(58):e202302174. Epub 2023 Sep 7. PMID: 37467152; PMC10592299.
  19. Joseph E, Smith I, Tunge JA. Cobalt-catalyzed decarboxylative difluoroalkylation of nitrophenylacetic acid salts. Chem Sci. 2023 Nov 16; 14(47):13902-13907. PMID:38075641; PMC10699560.
  20. Kerr CM, Parthasarathy S, Schwarting N, O'Connor JJ, Pfannenstiel JJ, Giri E, More S, Orozco RC, Fehr AR. PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell- and tissue-specific manner. J Virology. 2023 Sept 28; 97(9): e00885-23. Epub 2023 Sep 11. PMID: 37695054; PMC10537751.
  21. Ly CY, Pfannenstiel J, Pant A, Yang Z, Fehr AR, Rodzkin MS, Davido DJ. Inhibitors of One or More Cellular Aurora Kinases Impair the Replication of Herpes Simplex Virus 1 and Other DNA and RNA Viruses with Diverse Genomes and Life Cycles. Microbiol Spectr. 2023 Jan-Feb; 11(1): e01943-22. Published online 2022 Dec 20. PMC9927324.
  22. Montezano D, Bernstein R, Copeland MM, Slusky JSG. General features of transmembrane beta barrels from a large database. Proc Natl Acad Sci U S A. 2023 July 11, 120 (29) e2220762120. PMID:37432995; PMC10629564.
  23. O'Connor JJ, Ferraris D, Fehr AR. An Update on the Current State of SARS-CoV-2 Mac1 Inhibitors. Pathogens. 2023 Oct 7; 12(10):1221. PMC10610136.
  24. O'Connor JJ, Voth L, Athmer J, George NM, Connelly CM, Fehr AR. Two Commercially Available Blood-Stabilization Reagents Serve as Potent Inactivators of Coronaviruses. Pathogens. 2023 Aug 25; 12(9):1082. PMC10534660.
  25. Otter CJ, Bracci N, Parenti NA, Ye C, Tan LH, Asthana A, Pfannenstiel JJ, Jackson N, Fehr AR, Silverman RH, Cohen NA, Martinez-Sobrido L, Weiss SR. SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling. bioRxiv. 2023 Nov 15. pii: 2023.11.15.566945. PMID:38014074; PMC10680701.
  26. Rodriguez Ugalde AA, Bloom S. Teaching water new tricks through boron coordination: Applications to green and sustainable synthesis. Curr. Opin. Green Sustain. Chem. 2023 40, 100776. NIHMS1887145.
  27. Samanta S, Akhter F, Roy A, Chen D, Turner B, Wang Y, Clemente N, Wang C, Swerdlow RH, Battaile KP, Lovell S, Yan SF, Yan SS. New cyclophilin D inhibitor rescues mitochondrial and cognitive function in Alzheimer's disease. Brain. 2023; Dec 26;pii:awad432. Epub ahead of print. PMID: 38146639l; PMCID pending.
  28. Boskovic Z. Photochemical Decarbonylation of Oxetanone and Azetidinone: Spectroscopy, Computational Models, and Synthetic Applications**. Angewandte Chemie International Edition. 2023 62(3),e202215856. PMID: 36399366; PMC9839639.
  29. Thapa P, Upadhyay SP, Singh V, Boinpelly VP, Zhou J, Johnson DK, Gurung P, Lee ES, Sharma R, Sharma M. Chalcone: A potential scaffold for NLRP3 inflammasome inhibitors. Eur J Med Chem Rep. 2023 Apr;7:100100. PMC10081147.
  1. Antillon K, Ross PA, Farrell MP. Directing CAR NK Cells via the Metabolic Incorporation of CAR Ligands into Malignant Cell Glycans. ACS Chem Biol. 2022 Jun 17;17(6):1505-1512. Epub 2022 Jun 1. PMID: 35648806; PMC10061155.
  2. Baid S, Hefty PS, Morgan, DE. A CURE for the COVID-19 Era: A Vaccine-Focused Online Immunology Laboratory. J Microbiol Biol Educ. 2022 Aug; 23(2): e00311-21. Published online 2022 May 16. PMC9429876.
  3. Chilamari M, Immel JR, Chen PH, Alghafli BM, Bloom S. Flavin Metallaphotoredox Catalysis: Synergistic Synthesis in Water. ACS Catal. 2022 Apr 1;12(7):4175-4181. Epub 2022 Mar 22. PMID: 35865831; PMC9299445.
  4. Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. Proc Natl Acad Sci U S A. 2022 May 24;119(21):e2123208119. Epub 2022 May 20.PMID: 35594398; PMC8722591.
  5. Dasovich M, Zhuo J, Goodman JA, Thomas A, McPherson RL, Jayabalan AK, Busa VF, Cheng SJ, Murphy BA, Redinger KR, Alhammad YMO, Fehr AR, Tsukamoto T, Slusher BS, Bosch J, Wei H, Leung AKL. High-Throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain. ACS Chem Biol. 2022 Jan 21;17(1):17-23. Epub 2021 Dec 14.PMID: 34904435; PMC8691451.
  6. Do N, Ackley BD, Lansdon P. Draft Genome Sequence of Novel Staphylococcus epidermidis Strain EVL2000, Exhibiting Pathogenicity against Caenorhabditis elegans. Microbiol Resour Announc.. 2022 Apr 21;11(4):e0123921. Epub 2022 Mar 14.PMID: 35286161; PMC9022524.
  7. Feng M, Jin Y, Yang S, Joachim AM, Ning Y, Mori-Quiroz LM, Fromm J, Perera C, Zhang K, Werbovetz KA, Wang MZ. Sterol profiling of Leishmania parasites using a new HPLC-tandem mass spectrometry-based method and antifungal azoles as chemical probes reveals a key intermediate sterol that supports a branched ergosterol biosynthetic pathway. Int J Parasitol Drugs Drug Resist. 2022 Aug 15;20:27-42. Epub ahead of print. PMID: 35994895; PMC9418051.
  8. Gary S, Bloom S. Peptide Carbocycles: From -SS- to -CC- via a Late-stage ‘Snip-and-Stitch’. ACS Cent. Sci. 2022 8, 1537-1547. Article featured in Synform, 2023, A51-A53.  PMC9686213.
  9. Hasan MK, El Qaidi S, McDonald P, Roy A, Hardwidge PR. Repurposing Avasimibe to Inhibit Bacterial Glycosyltransferases. Pathogens. 2022 Mar 17;11(3). pii:370. PMID: 35335693; PMC8953086.
  10. Henderson IM, Marez C, Dokladny K, Smoake J, Martinez M, Johnson DK, Uhl GR. Substrate-selective positive allosteric modulation of PTPRD's phosphatase by flavonols. Biochemical Pharmacology. 2022 202:115109. PMC10184881.
  11. Henderson IM, Zeng F, Bhuiyan NH, Luo D, Martinez M, Smoake J, Bi F, Perera C, Johnson D, Prisinzano TE, Wang W, Uhl GR. Structure-activity studies of PTPRD phosphatase inhibitors identify a 7-cyclopentymethoxy illudalic acid analog candidate for development. Biochem Pharmacol. 2022 Jan;195:114868. Epub 2021 Dec 2. PMID: 34863978; PMC9248268.
  12. Hutchison JM, Li Z, Chang CN, Hiripitiyage Y, Wittman M, Sturm BSM. Improving correlation of wastewater SARS-CoV-2 gene copy numbers with COVID-19 public health cases using readily available biomarkers. FEMS Microbes. 2022; 3: xtac010. Epub 2022 Apr 1. PMID: 36118159; PMC9480869.
  13. Immel JR, Bloom S. carba-Nucleopeptides (cNPs): A Biopharmaceutical Modality Formed through Aqueous Rhodamine B Photoredox Catalysis. Angew Chem Int Ed Engl. 2022 Jul 11;61(28):e202205606. Epub 2022 May 17. PMID: 35507689; PMC9256812.
  14. Kapadia K, Trojniak AE, Guzmán Rodríguez KB, Klus NJ, Huntley C, McDonald P, Roy A, Frankowski KJ, Aubé J, Muma NA. Small-Molecule Disruptors of Mutant Huntingtin-Calmodulin Protein-Protein Interaction Attenuate Deleterious Effects of Mutant Huntingtin. ACS Chem Neurosci. 2022 Aug 3;13(15):2315-2337. Epub 2022 Jul 14. PMID: 35833925; PMC11005818.
  15. Kaur S, Nieto NS, McDonald P, Beck JR, Honzatko RB, Roy A, Nelson SW. Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase. J Enzyme Inhib Med Chem. 2022 Dec;37(1):1320-1326. PMID: 35514163; PMC9090415.
  16. Kurhade SE, Ross P, Gao FP, Farrell MP. Lectin Drug Conjugates Targeting High Mannose N-Glycans. Chembiochem. 2022 Oct 6;23(19):e202200266. Epub 2022 Jul 27. PMID: 35816406; PMC9738879.
  17. Leung AKL, Griffin DE, Bosch J, Fehr AR. The Conserved Macrodomain Is a Potential Therapeutic Target for Coronaviruses and Alphaviruses. Pathogens. 2022 Jan 14;11(1):94. PMID: 35056042; PMC8780475.
  18. Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler1. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J. 2022 Dec;289(23):7399-7410. Epub 2021 Sep 13. PMID: 34323016; PMC9027952.
  19. Ning K, Roy A, Cheng F, Xu P, Kleiboeker S, Escalante CR, Wang J, Qiu J. High-Throughput Screening Identifies Inhibitors for Parvovirus B19 Infection of Human Erythroid Progenitors. J Virol. 2022 Jan 26;96(2):e0132621. Epub 2021 Oct 20. PMID: 34669461; PMC8791288.
  20. Nishikawa S, Kaida A, Parrales A, Ranjan A, Alalem M, Ren H, Schoenen FJ, Johnson DK, Iwakuma T. DNAJA1- and conformational mutant p53-dependent inhibition of cancer cell migration by a novel compound identified through a virtual screen. Cell Death Discov. 2022 8:437. PMID: 36316326; PMC9622836.
  21. Pantelopulos GA, Matsuoka D, Hutchison JM, Sanders CR, Sugita Y, Straub JE, Thirumalai D. Formation of extramembrane β-strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proc Natl Acad Sci U S A. 2022 Dec 27;119(52):e2212207119. PMID: 36538482; PMC9907117.
  22. Parthasarathy S, Fehr AR. PARP14: A key ADP-ribosylating protein in host-virus interactions?PLoS Pathog. 2022 Jun 9;18(6):e1010535. eCollection 2022 Jun. PMID: 35679255; PMC9182250.
  23. Perera KD, Johnson DK, Lovell S, Groutas WC, Chang KO, Kim Y. Potent Protease Inhibitors of Highly Pathogenic Lagoviruses: Rabbit Hemorrhagic Disease Virus and European Brown Hare Syndrome Virus. Microbiol Spectr. 2022 Aug 31;10(4):e0014222. Epub 2022 Jun 29. PMID: 35766511; PMC9430360.
  24. Roy A, Alhammad YM, McDonald P, Johnson DK, Zhuo J, Wazir S, Ferraris D, Lehtiö L, Leung AKL, Fehr AR. Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening. Antiviral Res. 2022 Jul;203:105344. Epub 2022 May 19. PMID: 35598780; PMC9119168.
  25. Sharma VK, Hutchison JM, Allgeier AM. Redox Biocatalysis: Quantitative Comparisons of Nicotinamide Cofactor Regeneration Methods. ChemSusChem. 2022 Nov 22;15(22):e202200888. Epub 2022 Oct 26. Review. PMID: 36129761; PMC10029092.
  26. Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain. Bioorg Med Chem. 2022 Aug 1;67:116788. Epub 2022 May 11. PMID: 35597097; PMC9093066.
  27. Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain. bioRxiv. 2022 Feb 28;2022.06.27.497816. PMID: 35262078; PMC8902877.
  28. Singh M, Gaskins B, Johnson DR, Elles CG, Boskovic Z. Synthesis of Cycloheptatriene-Containing Azetidine Lactones. J Org Chem. 2022 Nov 18;87(22): 15001-15010. Online ahead of print 2022 May 23. PMID: 35605105; PMC10091648.
  29. Tetteh JT, Pham A, Peltier E, Hutchison JM, Ghahfarokhi RB. Predicting the electrokinetic properties on an outcrop and reservoir composite carbonate surfaces in modified salinity brines using extended surface complexation models. Fuel(Lond). 2022 Feb 1;309. Epub 2021 Oct 5. PMID: 35722593; PMC9202652.
  30. Tran HT, Nguyen MK, Hoang HG, Hutchison JM, Vu CT. Composting and green technologies for remediation of phthalate (PAE)-contaminated soil: Current status and future perspectives. Chemosphere. 2022 Nov;307(Pt 4):135989. Epub 2022 Aug 18. Review. PMID: 35988768; PMC10052775.
  31. Upadhyay SP, Singh V, Sharma R, Zhou J, Thapa P, Johnson DK, Keightley A, Chen M, Suo W, Sharma M. Influence of ligand geometry on cholinesterase enzyme - A comparison of 1-isoindolinone based structural analog with Donepezil. J Mol Struct. 2022 Jan 5;1247. Epub 2021 Aug 31. PMID: 34776532; PMC8589283.
  32. Yusuf IO, Qiao T, Parsi S, Tilvawala R, Thompson PR, Xu Z. Protein citrullination marks myelin protein aggregation and disease progression in mouse ALS models. Acta Neuropathol Commun. 2022 10:135. Epub 2022 Sep 8. PMID: 36076282; PMC9458309.
  1. Abisado RG, Kimbrough JH, McKee BM, Craddock VD, Smalley NE, Dandekar AA, Chandler JR. Tobramycin adaptation enhances policing of social cheaters in Pseudomonas aeruginosa. Appl Environ Microbiol AEM. 2021 87(12):e0002921. PMID: 3383701; PMC8174604.
  2. Alhammad YMO, Kashipathy MM, Roy A, Gagné JP, McDonald P, Gao P, Nonfoux L, Battaile KP, Johnson DK, Holmstrom ED, Poirier GG, Lovell S, Fehr AR. The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase. J Virol. 2021 Jan 13;95(3):e01969-20. PMID: 33158944; PMC7925111. 
  3. Bawa S, Gameros S, Baumann K, Brooks DS, Kollhoff JA, Zolkiewski M, David Re Cecconi A, Panini N, Russo M, Piccirillo R, Johnson DK, Kashipathy MM, Battaile KP, Lovell S, Bouyain SEA, Kawakami J, Geisbrecht ER. Costameric integrin and Sarcoglycan protein levels are altered in a Drosophila model for Limb Girdle Muscular Dystrophy type 2H. Mol Biol Cell. Feb 1 2021; 32(3):260-27. Epub ahead of print. PMID:33296226; PMC8098830.
  4. Budiardjo SJ, Ikujuni AP, Firlar E, Cordova A, Kaelber JT, Slusky JSG. High-Yield Preparation of Outer Membrane Protein Efflux Pumps byin Vitro Refolding is Concentration Dependent. J Membr Biol. Feb 2021, 254(1):41-50. PMID: 33462665; PMC8101038.
  5. Chitsike L, Yuan CH, Roy A, Boyle K, Duerksen-Hughes PJ. A high-content AlphaScreen™ identifies E6-specific small molecule inhibitors as potential therapeutics for HPV+ head and neck squamous cell carcinomas. Oncotarget. 2021 Mar 16;12(6):549-561. eCollection 2021 Mar 16. PMID: 33796223; PMC798482. 
  6. Dhokale RA, Seidl FJ, Shinde AH, Mague JT, Sathyamoorthi S. Tethered Silanoxyiodination of Alkenes. J Org Chem. 2021 Jul 2;86(13):9233-9243. Epub 2021 Jun 15. PMID: 34128664; PMC9012987.
  7. Dhokale RA, Seidl FJ, Sathyamoorthi S. A Formal Rearrangement of Allylic Silanols. Molecules. 2021 Jul 23;26(13):3829. PMID: 34201779; PMC8270268.
  8. Dimond ZE, Suchland RJ, Baid S, LaBrie SD, Soules KR, Stanley J, Carrell S, Kwong F, Wang Y, Rockey DD, Hybiske K, Hefty PS. Inter-species lateral gene transfer focused on the Chlamydia plasticity zone identifies loci associated with immediate cytotoxicity and inclusion stability. Mol Microbiol. 2021 Dec;116(6):1433-1448. Epub 2021 Nov 16.PMID: 34738268; PMC9119408.
  9. Dimond ZE, Hefty PS. Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors. Pathog Dis. 2021 Mar 10;79(2):ftaa035. PMID: 32639528; PMC7948067.
  10. Dogrammatzis C, Saleh S, Deighan C, Kalamvoki M. Diverse Populations of Extracellular Vesicles with Opposite Functions during Herpes Simplex Virus 1 Infection. J Virol. 2021 Feb 24;95(6):e02357-20. PMID: 33361424; PMC8094966.
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  15. Grunewald ME, Shaban MG, Mackin SR, Fehr AR, Perlman S. Murine Coronavirus Infection Activates the Aryl Hydrocarbon Receptor in an Indoleamine 2,3-Dioxygenase-Independent Manner, Contributing to Cytokine Modulation and Proviral TCDD-Inducible-PARP Expression. J Virol. 2020 Jan 17;94(3):e01743-19. PMID: 31694960; PMC7000979.
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  17. Ho KV, Roy A, Foote S, Vo PH, Lall N, Lin CH. Profiling Anticancer and Antioxidant Activities of Phenolic Compounds Present in Black Walnuts (Juglans nigra) Using a High-Throughput Screening Approach. Molecules. 2020 Oct 2;25(19). PMID: 33023106; PMC7583942.
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  13. Roy A, McDonald P, Timmermann BN, Gupta M, Chaguturu R. Bioactivity Profiling of Plant Biodiversity of Panama by High Throughput Screening. Nat Prod Commun. 2019 Jan; 14(1): 71–74. PMID: 31938081; PMC6959481.
  14. Roy A. Challenges with risk mitigation in academic drug discovery: finding the best solution. Expert Opin Drug Discov. Feb 2019, 14(2):95-100. PMID: 30513005; PMC6467222.
  15. Waisner H, Kalamvoki M. The ICP0 Protein of Herpes Simplex Virus 1 (HSV-1) Downregulates Major Autophagy Adaptor Proteins Sequestosome 1 and Optineurin during the Early Stages of HSV-1 Infection. J Virol. 2019 Oct 15;93(21):pii:e01258-19. PMID: 31375597; PMC6803258.
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  2. El Qaidi S, Zhu C, McDonald P, Roy A, Maity PK, Rane D, Perera C, Hardwidge PR. High-Throughput Screening for Bacterial Glycosyltransferase Inhibitors. Front Cell Infect Microbiol. 2018;8:435. eCollection 2018. PMID: 30619781; PMC6305410.
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  1. Cao S, Dhungel P, Yang Z. Going against the Tide: Selective Cellular Protein Synthesis during Virally Induced Host Shutoff. J Virol. 2017 Aug 10;91(17). PMID: 28637757; PMC5553178.
  2. Cao S, Realegeno S, Pant A, Satheshkumar PS, Yang Z. Suppression of poxvirus replication by resveratrol. Front Microbiol. 2017 Nov 17;8:2196. PMID: 29204136; PMC5698801.
  3. Dai A, Cao S, Dhungel P, Luan Y, Liu Y, Xie Z, Yang, Z. Ribosome Profiling Reveals Translational Upregulation of Cellular Oxidative Phosphorylation mRNAs during Vaccinia Virus-Induced Host Shutoff. Journal of Virology Mar 2017, 14:91(5):pii:JVI.00071-17. PMID: 28003488; PMC5309933. 
  4. Deschamps T, Kalamvoki M. Impaired STING Pathway in Human Osteosarcoma U2OS Cells Contributes to the Growth of ICP0-Null Mutant Herpes Simplex Virus. Journal of Virology Apr 2017, 13:91(9):pii:e00006-17. PMID: 28179534. PMC5391473.
  5. Deschamps T, Dogrammatzis C, Mullick R, Kalamvoki M. Cbl E3 Ligase Mediates the Removal of Nectin-1 from the Surface of Herpes Simplex Virus 1-Infected Cells.  J Virol. 2017 May 26;91(12). PMID: 28381567; PMC5446655.
  6. Deschamps T, Kalamvoki M. Evasion of the STING DNA-Sensing Pathway by VP11/12 of Herpes Simplex Virus 1. J Virol. 2017 Jul 27;91(16). PMID: 28592536; PMC5533902.
  7. Dhungel P, Cao S, Yang Z.The 5'-poly(A) leader of poxvirus mRNA confers a translational advantage that can be achieved in cells with impaired cap-dependent translation. PLoS Pathog. 2017 Aug 30;13(8):e1006602. PMID: 28854224; PMC5595341.
  8. Girinathan BP, Monot M, Boyle D, McAllister KN, Sorg JA, Dupuy B, Govind R. Effect of tcdR mutation on sporulation in the epidemic Clostridium difficile strain R20291. mSphere2017 Feb 15;2(1). PMID: 28217744; PMC531115.
  9. Komiya T, Yamamoto S, Roy A, McDonald P, Perez RP. Drug screening to target nuclear orphan receptor NR4A2 for cancer therapeutics. Transl Lung Cancer Res. 2017 Oct;6(5):600-610. PMID: 29114475; PMC5653521.
  10. Roy A, Mir MA. Development of High-Throughput Screening Assay for Antihantaviral Therapeutics. SLAS Discov. 2017 Jul;22(6):767-774. PMID: 28340538; PMC5854180.
  1. Budiardjo SJ, Licknack TJ, Cory MB, Kapros D, Roy A, Lovell S, Douglas J, Karanicolas J. Full and Partial Agonism of a Designed Enzyme Switch. ACS Synthetic Biology Dec 2016, 16:5(12):1475-84. PMID: 27389009; PMC5161622.
  2. Gowthaman R, Miller SA, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J. DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites. Journal of Medicinal Chemistry May 2016, 12:59(9):4152-70. PMID: 26126123; PMC4707132.
  3. Kim S, Patel DS, Park S, Slusky J, Klauda JB, Widmalm G, Im W. Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophysical Journal Oct 2016, 18:111(8):1750-60. PMID: 27760361; PMC5071556.
  4. Lee MM, Peterson BR. Quantification of Small Molecule-Protein Interactions using FRET between Tryptophan and the Pacific Blue Fluorophore. ACS Omega Dec 2016, 31:1(6):1266-76. PMID: 28058293; PMC5204206.
  5. Meneely KM, Ronnebaum TA, Riley AP, Prisinzano TE, Lamb AL. Holo Structure and Steady State Kinetics of the Thiazolinyl Imine Reductases for Siderophore Biosynthesis. Biochemistry Sept. 27 2016, pp.5423-33. PMID: 27601130; PMC5046821.
  6. Parrales A, Ranjan A, Iyer SV, Padhye S, Weir SJ, Roy A, Iwakuma T. DNAJA1 controls the fate of misfolded mutant p53 through the mevalonate pathway. Nature Cell Biology Nov 2016, 18(11):1233-1243. PMID: 27775703; PMC5340314.
  7. Phaniraj S, Gao Z, Rane D, Peterson BR. Hydrophobic resorufamine derivatives: potent and selective red fluorescent probes of the endoplasmic reticulum of mammalian cells. Dyes and pigments: an international journal Dec 2016, 135:127-33. PMID: 27765999; PMC5066811.
  8. Polireddy K, Dong R, McDonald PR, Wang T, Luke B, Chen P, Broward M, Roy A, Chen Q. Targeting Epithelial-Mesenchymal Transition for Identification of Inhibitors for Pancreatic Cancer Cell Invasion and Tumor Spheres Formation. PLoS one Oct 2016, 20:11(10):e0164811. PMID: 27764163; PMC5072586.
  9. Roy A, Patwardhan B, Chaguturu R. Reigniting pharmaceutical innovation through holistic drug targeting. Drug Discovery World Summer 2016, pp.45-55.
  10. Salim NN, Ganaie SS, Roy A, Jeeva S, Mir MA. Targeting a Novel RNA-Protein Interaction for Therapeutic Intervention of Hantavirus Disease. Journal of Biological Chemistry Nov 2016, 18:291(47):24702-14. PMID: 27733686; PMCID: PMC5114419.
  11. Slusky JS. Outer membrane protein design. Current Opinion in Structural Biology Nov 2016, 25:45:45-52. PMID: 27894013; PMC5445000.
  12. Valasani KR, Sun Q, Fang D, Zhang Z, Yu Q, Guo Y, Li J, Roy A, ShiDu Yan S. Identification of a Small Molecule Cyclophilin D Inhibitor for Rescuing Aβ-Mediated Mitochondrial Dysfunction. ACS Medicinal Chemistry Letters Jan 2016, 6:7(3):294-9. PMID: 26985318; PMC4789676.