Publications

Research publications acknowledging COBRE CBID grant funding (NIH P20GM113117)

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

Phase 1 Publications

  1. Budiardjo SJ, Ikujuni AP, Firlar E, Cordova A, Kaelber JT, Slusky JSG. High-Yield Preparation of Outer Membrane Protein Efflux Pumps by in Vitro Refolding is Concentration DependentJ Membr Biol. Feb 2021, 254(1):41-50. PMID: 33462665. PMC pending. 
  2. Fahad AS, Timm MR, Madan B, Burgomaster KE, Dowd KA, Normandin E, Gutiérrez-González MF, Pennington JM, De Souza MO, Henry AR, Laboune F, Wang L, Ambrozak DR, Gordon IJ, Douek DC, Ledgerwood JE, Graham BS, Castilho LR, Pierson TC, Mascola JR, DeKosky BJ. Comprehensive Functional Profiling of Anti-Zika Virus Antibodies in Convalescent PatientsFrontiers in Immunology. Feb 24 2021, 12:615102. PMID pending. PMC pending. 
  3. Farrell MP, Kurhade SE, Weiner JD, Gao FP. Functionalized High Mannose‐Specific Lectins for the Discovery of Type I Mannosidase InhibitorsAngewandte Chemie. Mar 16 2021. PMID: 33728787. PMC pending. 
  4. Lockbaum GJ, Reyes AC, Lee JM, Tilvawala R, Nalivaika EA, Ali A, Kurt Yilmaz N, Thompson PR, Schiffer CA. Crystal Structure SARS-CoV-2 main protease in complex with the non-covalent inhibitor ML188Viruses2021, 13(2): 174. PMID:33503819. PMC pending.
  5. Ly CY, Yu C, McDonald PRoy AJohnson DDavido DJ. Simple and Rapid High-Throughput Assay to Identify HSV-1 ICP0 Transactivation InhibitorsbioRXiv. Jan 13 2021
  6. Voth LS, O'Connor JJ, Kerr CM, Doerger E, Schwarting N, Sperstad P, Johnson DKFehr AR. Unique mutations in the MHV macrodomain differentially attenuate virus replication, indicating multiple roles for the macrodomain in coronavirus replicationJ Virol May 19 2021
  7. Yang Y, Borel T, de Azambuja F, Johnson DK, Sorrentino JP, Udokwu C, Davis I, Liu A, Altman RA. Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine PathwayJ Med Chem. Jan 14 2021, 64(1):797-811. PMID:33369426. PMC pending.
  8. Zhu C, El Qaidi S, McDonald PRoy AHardwidge PR. YM155 inhibits NleB and SseK arginine glycosyltransferase activity. Pathogens. Feb 23 2021, 10(2):253. PMID pending. PMC pending.
  1. Alhammad YMO, Fehr AR. The Viral Macrodomain Counters Host Antiviral ADP-RibosylationViruses. Apr 2020, 12(4):384. PMID:32244383. PMC7232374. 
  2. Alhammad YMO, Kashipathy MM, Roy A, Gagne JP, Nonfoux L, McDonald P, Gao P, Battaile KP, Johnson DK, Poirier GG, Lovell S, Fehr AR. The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolasebioRxiv. Preprint. May 12 2020, 12(4):384. PMID:32511412. PMC7263559. 
  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 2HMol Biol Cell. Dec 9, 2020, Epub ahead of print. PMID:33296226. PMC pending. 
  4. Benomar S, Bender AM, Peterson BR, Chandler JRAckley BD. The C. elegans CHP1 homolog, pbo-1, functions in innate immunity by regulating the pH of the intestinal lumenPLoS Pathogens Jan 9 2020, 16(1):e1008134. PMID:31917826. PMC6952083. 
  5. Cao S, Lin Y, Yang Z. BVaccinia virus transcriptome analysis by RNA sequencing. Vaccinia Virus: Methods and Protocols. Methods in Molecular Biology. Book chapter. 2020. In press.
  6. Chilamari M, Immel J, Bloom S. General Access to C-Centered Radicals: Combining a Bioinspired Photocatalyst with Boronic Acids in Aqueous MediaACS Catal. 2020 10(21):12727–12737. PMID: in process. PMCID in process. 
  7. DeMars Z, Singh VK, Bose JL. Exogenous fatty acids remodel Staphylococcus aureus lipid composition through fatty acid kinase. J Bacteriol. June 2020, 25(14):e00128-20. PMID:32366591. PMC7317038. 
  8. Dimond ZE, Hefty PS. Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors. [published online ahead of print, 2020 Jul 8]. Pathog Dis. 2020:ftaa035. PMID:32639528. PMCID in progress. 
  9. Fehr AR. Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoVMethods Mol. Bio. 2020, 2099:53-68. PMID:31883087. PMC7121842. 
  10. Fehr AR, Singh SA, Kerr CM, Mukai S, Higashi H, Aikawa, M. The impact of PARPs and ADP-ribosylation on inflammation and host-pathogen interactions. .Genes Dev Feb 6 2020. PMID:32029454. PMC7050484. 
  11. 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 ExpressionJ Virol. Jan 2020, 94(3):e01743-19. PMID:31694960. PMC7000979.
  12. Heer CD, Voth LS, Sanderson DJ, Alhammad YMO, Schmidt MS, Trammell SAJ, Perlman S, Cohen MS, Fehr AR, Brenner C. Coronavirus and PARP expression dysregulate the NAD Metabolome: a potentially actionable component of innate immunityJ Biol Chem. October 13 2020, PMID:32511303. PMCID7217258.
  13. Joseph AM, Pohl AE, Ball TJ, Abram TG, Johnson DK, Geisbrecht BV, Shames SR. The Legionella pneumophila Metaeffector Lpg2505 (MesI) Regulates SidI-Mediated Translation Inhibition and Novel Glycosyl Hydrolase ActivityInfect Immun. Apr 2020, 20:88(5). PMID:32122942. PMC7171249.
  14. Klaus JR, Coulon PML, Koirala P, Seyedsayamdost MR, Deziel E, Chandler JR. Secondary metabolites from the Burkholderia pseudomallei complex: structure, ecology and evolution. Review. Journal of Industrial Microbiology and Biotechnology October 14 2020.
  15. Klaus JR, Majerczyk C, Moon S, Eppler NA, Smith S, Tuma E, Groleau M-C, Asfahl KL, Smalley NE, Hayden HS, Piochon M, Ball P, Dandekar AA, Gauthier C, Deziel E, Chandler JR. Burkholderia thailandensis methylated hydroxy-aklylquinolines: biosynthesis and antimicrobial activity in co-culturesApplied and Environmental Microbiology October 2020. AEM.01452-20. PMID:33008823. PMCID in progress. 
  16. Kurland M, O'Meara B, Tucker DK, Ackley BD. The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt SignalingJ Dev. Biol. March 2020, 8(1):5. PMID: 32138237. PMC7151087. 
  17. Lin Y, Qiao W, Yang Z. Ribosome profiling of vaccinia virus-infected cells. Vaccinia Virus: Methods and Protocols. Methods in Molecular Biology. Book chapter. 2020. In press.
  18. Lin Y, Yang Z, Qiao W. Decipher viral infections by ribosome profiling, a review. Bing Du Xue Bao 2020. In press.
  19. Muthuramalingam M, Whittier SK, Lovell S, Battaile KP, Tachiyama S, Johnson DK, Picking WL, Picking WD. The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting PlatformJ Mol Biol.M December 4 2020, 432(24):166693. PMID: 33122003. PMCID in progress.
  20. Peng C, Zhou Y, Cao S, Pant A, Campos Guerrero ML, McDonald PRoy AYang Z. Identification of Vaccinia Virus Inhibitors and Cellular Functions Necessary for Efficient Viral Replication by Screening Bioactives and FDA-Approved DrugsVaccines (Basel) Jul 2020, 8(3):E401. PMID: 32708182. PMC7564539. 
  21. Ridder MJ, Daly SM, Triplett KD, Seawell NA, Hall PR, Bose JL. Staphylococcus aureus fatty acid kinase FakA modulates pathogenesis during skin infection via proteasesInfect Immun. Jul 2020, 88(8):e00163-20. PMID:32513856. PMC7375762. 
  22. Shinde AH, Sathyamoorthi S. Oxidative Cyclization of Sulfamates onto Pendant AlkenesOrg Lett. 2020, 22:896-901. PMID:31927967. PMC in progress. 
  23. Soules KR, Dmitriev A, LaBrie SD, Dimond ZE, May BH, Johnson DK, Zhang Y, Battaile KP, Lovell S, Hefty PS. Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulationMol Microbiol. Jan 2020, 113(1):68-88. PMID: 31637787. PMC7007330.
  24. Soules KR, LaBrie SD, May BH, Hefty PS. Sigma 54-Regulated Transcription Is Associated with Membrane Reorganization and Type III Secretion Effectors during Conversion to Infectious Forms of Chlamydia trachomatismBio. Sep 2020, 11(5):e01725-20. PMID:32900805. PMC7482065. 
  25. Yang Z, Mattingly B, Hall D, Ackley BD, Buechner M. Terminal Web and Vesicle Trafficking Proteins Mediate Nematode Single-Cell Tubulogenesis. J Cell Biol. 2020, in press. 
  1. Austin CM, Garabaglu S, Krute CN, Ridder MJ, Seawell NA, Markiewicz MA, Boyd JM, Bose JL. Contribution of YjblH to Virulence Factor Expression and Host Colonization in Staphylococcus aureusInfect Immun. May 2019, 87(6):e00155-19. PMID:30885928. PMC6529663. 
  2. Channappanavar R, Fehr AR, Zheng J, Wohlford-Lenane C, Abrahante JE, Mack M, Sompallae R, McCray Jr. PB, Meyerholz DK, Perlman S. IFN-I response timing relative to virus replication determines MERS coronavirus infection outcomesJ Clin Invest. Sep 3 2019, 129(9):3625-3639. PMID: 31355779. PMC6715373. 
  3. Deschamps T, Waisner H, Dogrammatzis C, Roy A, Chacko S, Perera CPrisinzano TEKalamvoki M. Discovery of Small-Molecule Inhibitors Targeting the E3 Ubiquitin Ligase Activity of the Herpes Simplex Virus 1 ICP0 Protein Using an In Vitro High-Throughput Screening AssayJ Virol. Jun 2019, 93(13):619-19. PMID: 30996104. PMC6580980. 
  4. Dogrammatzis C, Deschamps T, Kalamvoki M. Biogenesis of extracellular vesicles during herpes simplex virus type 1 infection: The role of the CD63 tetraspaninJ. Virol. Jan 2019, 93(2):e01850-18. PMID: 30355691. PMC6321934. 
  5. Grunewald ME, Chen Y, Kuny C, Maejima T, Lease R, Ferraris D, Aikawa M, Sullivan CS, Perlman S, Fehr AR. The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expressionPLoS Pathog. May 2019, 15(5):e1007756. PMID: 31095648. PMC6521996.
  6. LaBrie SD, Dimond ZE, Harrison KS, Baid S, Wickstrum J, Suchland RJ, Hefty PS. Transposon Mutagenesis in Chlamydia trachomatis identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene TransfermBiol. Jul-Aug 2019, 10(4):e01343-19. PMID: 31387908. PMC6686042. 
  7. Ngwaga T, Hydock AJ, Ganesan S, Shames SR. Potentiation of Cytokine-Mediated Restriction of Legionella intracellular Replication by a Dot/Icm-Translocated EffectorJ Bacteriol. Jun 2019, 201(14):e00755-18. PMID: 31036725. PMC6597390. 
  8. Roy AMcDonald P, Timmermann BN, Gupta M, Chaguturu R. Bioactivity Profiling of Plant Biodiversity of Panama by High Throughput ScreeningNat Prod Commun. Jan 2019, 14(1):71-74. PMID: 31938081. PMC6959481. 
  9. Roy A. Challenges with risk mitigation in academic drug discovery: finding the best solutionExpert Opin Drug Discov. Feb 2019, 14(2):95-100. PMID: 30513005. PMC6467222. 
  10. Waisner H, Kalamvoki M. The ICP0 protein of herpes simplex virus 1 (HSV-1) down-regulates major autophagy adaptor proteins, sequestosome 1 (SQSTM1/p62) and optineurin (OPTN), during the early stages of HSV-1 infectionJ Virol. October 2019, 93(21):pii:e01258-19. PMID: 31375597. PMC6803258. 
  1. Deschamps T, Kalamvoki M. Extracellular vesicles released by herpes simplex virus 1 infected cells block virus replication in recipient cells in a STING-dependent mannerJ. Virol. Aug 2018, 92(18):e01102-18. PMID: 29976662. PMC6146713.
  2. El Qaidi S, Zhu C, McDonald PRoy A, Maity PK, Rane D, Perera CHardwidge PR. High-throughput screening for bacterial glycosyltransferase inhibitorsFront Cell Infect Microbiol 2018, 8:435. PMID: 30619781. PMC6305410.
  3. Evans KC, Benomar S, Camuy-Velez LA, Nasseri EB, Wang X, Neuenswander BChandler JR. Quorum-sensing control of antibiotic resistance stabilizes cooperation in Chromobacterium violaceumThe ISME Journal Jan 26 2018, 12:1263-1272. PMC5932061. 
  4. Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG. Efflux Pumps Represent Possible Evolutionary convergence onto the β-Barrel FoldStructureSept 42018, 26(9):1266-1274.e2. PMC6125174. 
  5. Franklin MW, Slusky JSG. Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen BondingJ. Mol. Biol. Sept2018, 430(18B):3251-3265. PMC6110081. 
  6. Girinathan BP, Ou J, Durpuy B, Govind R. Pleiotropic roles of Clostridium difficile sin locusPLoS Pathogens Mar 2018, 14(3):e1006940. PMID: 29529083. PMC5864091. 
  7. Kfoury N, Sun T, Yu K, Rockwell N, Tinkum KL, Qi Z, Warrington NM, McDonald PRoy A, Weir SJ, Mohila CA, Deneen B, Rubin JB. Cooperative p16 and p21 action protects female astrocytes from transformationActa Neuropathol Commun Feb 20 2018, 6(1):12. PMID: 29458417. PMC5819173. 
  8. Klaus JR, Deay J, Neuenswander B, Hursh W, Gao Z, Bouddhara T, Williams TD, Douglas J, Monize K, Martins P, Majerczyk C, Seyedsayamdost MR, Peterson BR, Rivera M, Chandler JR. Malleilactone is a Burkholderia pseudomallei virulence factor regulated by antibiotics and quorum sensingJ Bacteriol. May 7 2018, 200:e00008-18. PMID: 29735757. PMC6018353.
  9. Mori-Quiroz LM, Hedrick SL, De Los Santos AR, Clift MD. A Unified Strategy for the Syntheses of the Isoquinolinium Alkaloids Berberine, Coptisine, and JatrorrhizineOrg. Lett. June 28 2018, 20(14):4281-4284. NIHMS1012955.
  10. Parrales A, McDonald P, Ottomeyer M, Roy A, Schoenen FJ, Broward M, Bruns T, Thamm DH, Weir SJ, Neville KA, Iwakuma T, Fulbright JM. Comparative oncology approach to drug repurposing in osteosarcomaPLoS One Mar 2018, 26;13(3)e0194224. PMID: 29579058 PMC5868798. 
  11. Polpitiya Arachchige S, Henke W, Pramanik A, Kalamvoki M; Stephens EB. Analysis of Select Herpes Simplex Virus 1 (HSV-1) Proteins for Restriction of Human Immunodeficiency Virus Type 1 (HIV-1): HSV-1 gM Protein Potently Restricts HIV-1 by Preventing Intracellular Transport and Processing of Env gp160J Virol. Jan 15 2018, 92:2. PMID: 29093081. PMC5752927.
  12. Roy A. Early Probe and Drug Discovery in Academia: A MinireviewHigh Throughput Feb 9 2018, 7(1):4. PMID: 29485615. PMC5876530.
  13. Vaidya A, Roy A, Chaguturu R. How to rekindle drug discovery process through integrative therapeutic targeting? Expert Opin Drug Discov, Oct 2018, 13(10):893-898. PMID: 30146919. PMC6436386.
  1. Cao S, Dhungel P, Yang Z. Going against the Tide: Selective Cellular Protein Synthesis during Virally Induced Host ShutoffJ Virol. Aug 2017, 10:91(17). PMID: 28637757. PMC5553178.
  2. Cao S, Realegeno S, Pant A, Satheshkumar PS, Yang, Z. Suppression of poxvirus replication by resveratrolFront Microbiol. Nov 2017, 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 ShutoffJournal 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 VirusJournal of Virology Apr 2017, 13:91(9):pii:e00006-17. PMID: 28178534. 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 CellsJournal of Virology May 2017, 26:91(12):pii:e00393-17. PMID: 28381567. PMC5446655.
  6. Deschamps T, Kalamvoki M. Evasion of the STING DNA-sensing Pathway by VP11/12 of Herpes Simplex Virus 1Journal of Virology Jul 2017, 27:91(16):pii:e00535-17. 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 translationPLoS Pathog. Aug 2017, 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 R20291mSphere Feb 2017, 2(1):e00383-16. PMID: 28217744. PMC5311115.
  9. Komiya T, Yamamoto S, Roy AMcDonald P, Perez RP. Drug screening to target nuclear orphan receptor NR4A2 for cancer therapeuticsTransl Lung Cancer Res. Oct 2017, 6(5):600-610. PMID: 29114475. PMC5653521. 
  10. Roy A, Mir MA. Development of High-Throughput Screening Assay for Antihantaviral TherapeuticsSLAS Discov. Jul 2017, 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 SwitchACS 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 SitesJournal 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 BacteriaBiophysical 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 FluorophoreACS 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 BiosynthesisBiochemistry 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 pathwayNature 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 cellsDyes 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 FormationPLoS one Oct 2016, 20:11(10):e0164811. PMID:27764163. PMC5072586. 
  9. Roy A, Patwardhan B, Chaguturu R. Reigniting pharmaceutical innovation through holistic drug targetingDrug 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. PMC: PMC5114419. 
  11. Slusky JSOuter membrane protein designCurrent 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 DysfunctionACS Medicinal Chemistry Letters Jan 2016, 6:7(3):294-9. PMID:26985318. PMC4789676.