Publications


MB Research Publications

Glatthardt T, Lima RD, de Mattos RM, Ferreira RBR. Microbe Interactions within the Skin Microbiome. Antibiotics (Basel). 2024 Jan 4; 13(1):49.  PMID: 38247608; PMCID: PMC10812674.

Oakley CE, Barton TS Jr., Oakley BR. Identification of the chaA and fwA Spore Color Genes of Aspergillus nidulansJournal of Fungi. 2024; 10(2):104.

Schedl ME, Nguyen NH, Unckless RL, Perlmutter JI. Maintenance and Evaluation of Wolbachia Male-Killers of Dipterans. Methods Mol Biol. 2024; 2739:29-53. PMID: 38006544.

 

  1. Abisado-Duque RG, Townsend KA, Mckee BM, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen M, Chandler JR. An Amino Acid Substitution in Elongation Factor EF-G1A Alters the Antibiotic Susceptibility of Pseudomonas aeruginosa LasR-Null Mutants. J Bacteriol. 2023 Jun 27; 205(6):e0011423.  Epub 2023 May 16. PMID: 37191503; PMCID: PMC10294626.
  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; PMCID: PMC10468617.
  3. Chen RC, Krebill H, Kennedy T, Douglas S, Neufeld KL, Welch DR, Jernigan C, Kimminau KS, Johnston K, Hughes J, Jensen RA. A community engagement training program for basic and translational cancer researchers. Cancer Causes Control. 2023 Dec; 34(12):1123-1132.  Epub 2023 Jul 28. PMID: 37505316.
  4. Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Opinion: Protein folds vs. protein folding: Differing questions, different challenges. Proc Natl Acad Sci U S A. 2023 Jan 3; 120(1):e2214423119.  Epub 2022 Dec 29. PMID: 36580595; PMCID: PMC9910419.
  5. 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. J Chem Phys. 2023 Apr 14; 158(14):144114. PMID: 37061494.
  6. Dhar R, Bowman AM, Hatungimana B, Sg Slusky J. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol. 2023 Sep 26; 435(22):168292. Epub ahead of print. PMID: 37769963.
  7. Everman ER, Macdonald SJ, Kelly JK. The genetic basis of adaptation to copper pollution in Drosophila melanogaster. Front Genet. 2023 Apr 4; 14:1144221.  PMID: 37082199; PMCID: PMC10110907.
  8. 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.  PMID: 36916762; PMCID: PMC10044107.
  9. Ferreira RBR, Antunes LCM. Unlocking the microbiome. Elife. 2023 Oct 11;12:e92482. PMID: 37819270; PMCID: PMC10567107.
  10. Green LC, Slone S, Anthony SR, Guarnieri AR, Parkins S, Shearer SM, Nieman ML, Roy S, Aube J, Wu X, Xu L, Kanisicak O, Tranter M. HuR-dependent expression of Wisp1 is necessary for TGFβ-induced cardiac myofibroblast activity. J Mol Cell Cardiol. 2023  Jan; 174:38-46. Epub 2022 Nov 11. PMID: 36372279; PMCID: PMC9868076.
  11. Huang Z, Liu S, Tang A, Wu X, Aube J, Xu L, Huang Y. Targeting RNA-binding protein HuR to inhibit the progression of renal tubular fibrosis. J Transl Med. 2023 Jun 30; 21(1):428.  PMID: 37391777; PMCID: PMC10311833.
  12. Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet. 2023 May 5; 19(5):e1010439. PMID: 37146087; PMCID: PMC10191298.
  13. 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. PMID: 36772796; PMCID: PMC10111266.
  14. Jenkinson CB, Podgorny AR, Zhong C, Oakley BR. Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors. J Ind Microbiol Biotechnol. 2023 Feb 17;50(1):kuad045.  PMID: 38061800; PMCID: PMC10734572.
  15. 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 Virol. 2023 Sep 28; 97(9):e0088523.  Epub 2023 Sep 11. PMID: 37695054; PMCID: PMC10537751.
  16. Kim H, Park H, Schulz ET, Azuma Y, Azuma M. EWSR1 prevents the induction of aneuploidy through direct regulation of Aurora B. Front Cell Dev Biol. 2023 Feb 15; 11:987153. PMID: 36875767; PMCID: PMC9975954.
  17. Lialys L, Lialys J, Salandrino A, Ackley BD, Fardad S. Optical trapping of sub-millimeter sized particles and microorganisms. Sci Rep. 2023 May 27; 13(1):8615. PMID: 37244967; PMCID: PMC10224970.
  18. Lin SY, Oakley CE, Jenkinson CB, Chiang YM, Lee CK, Jones CG, Seidler PM, Nelson HM, Todd RB, Wang CCC, Oakley BR. A heterologous expression platform in Aspergillus nidulans for the elucidation of cryptic secondary metabolism biosynthetic gene clusters: discovery of the Aspergillus fumigatus sartorypyrone biosynthetic pathway. Chem Sci. 2023 Jun 26; 14(40):11022-11032.  PMID: 37860661; PMCID: PMC10583710.
  19. Loo C, Koirala P, Smith NC, Evans KC, Benomar S, Parisi IR, Oller A, Chandler JR. Cross-species activation of hydrogen cyanide production by a promiscuous quorum-sensing receptor promotes Chromobacterium subtsugae competition in a dual-species model.Microbiology (Reading). 2023 Feb; 169(2):001294. PMID: 36790401; PMCID: PMC10197875.
  20. 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 Feb 14;11(1):e0194322.  Epub 2022 Dec 20. PMID: 36537798; PMCID: PMC9927324.
  21. Mahadik SS, Burt EK, Lundquist EA. SRC-1 controls growth cone polarity and protrusion with the UNC-6/Netrin receptor UNC-5 in Caenorhabditis elegans. bioRxiv [Preprint]. 2023 May 20:2023.05.20.541322. PMID: 37292733; PMCID: PMC10245697.
  22. Mahadik SS, Lundquist EA. TOM-1/tomosyn acts with the UNC-6/netrin receptor UNC-5 to inhibit growth cone protrusion in Caenorhabditis elegans. Development. 2023 Apr 1; 150(7):dev201031. Epub 2023 Apr 4. PMID: 37014062; PMCID: PMC10112904.
  23. Mahadik SS, Lundquist EA. A short isoform of the UNC-6/Netrin receptor UNC-5 is required for growth cone polarity and robust growth cone protrusion in Caenorhabditis elegans. Front Cell Dev Biol. 2023 Aug 15; 11:1240994. PMID: 37649551; PMCID: PMC10464613.
  24. 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. 2023 Aug 19. Epub ahead of print. PMID: 37596815.
  25. 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 Jul 18; 120(29):e2220762120. Epub 2023 Jul 11. PMID: 37432995.
  26. Nepal S, Holmstrom ED. Single-molecule-binding studies of antivirals targeting the hepatitis C virus core protein. J Virol. 2023 Sep 29:e0089223.  Epub ahead of print. PMID: 37772835.
  27. Neufeld KL. New Immune Role for Axin1 in Colon Cancer Suppression. Cell Mol Gastroenterol Hepatol. 2023; 15(3):799-800. Epub 2022 Dec 20. PMID: 36564008; PMCID: PMC9950923.
  28. Oakley BR. The ring saga: looking back at the discovery of γ-tubulin and γ-tubulin ring complexes. Mol Biol Cell. 2023; 34(1):rt1. PMID: 36520030; PMCID: PMC9816641.
  29. 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.  PMID: 37887737; PMCID: PMC10610136.
  30. 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. PMID: 37764890; PMCID: PMC10534660.
  31. Rabot C, Chen Y, Lin SY, Miller B, Chiang YM, Oakley CE, Oakley BR, Wang CCC, Williams TJ. Polystyrene Upcycling into Fungal Natural Products and a Biocontrol Agent. J Am Chem Soc. 2023; 145(9):5222-5230. Epub 2023 Feb 13. PMID: 36779837.
  32. Smith BR, Patch KB, Gupta A, Knoles EM, Unckless RL. The genetic basis of variation in immune defense against Lysinibacillus fusiformis infection in Drosophila melanogaster.PLoS Pathog. 2023 Aug 7; 19(8):e1010934. PMID: 37549163; PMCID: PMC10434897.
  33. Song Z, Zhou S, Zhang H, Keller NP, Oakley BR, Liu X, Yin WB. Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex. Nat Commun. 2023 Nov 14; 14(1):7351. PMID: 37963872; PMCID: PMC10645843.
  34. Sundararajan S, Park H, Kawano S, Johansson M, Lama B, Saito-Fujita T, Saitoh N, Arnaoutov A, Dasso M, Wang Z, Keifenheim D, Clarke DJ, Azuma Y. Methylated histones on mitotic chromosomes promote topoisomerase IIα function for high fidelity chromosome segregation. iScience. 2023 Apr 25; 26(5):106743. PMID: 37197327; PMCID: PMC10183659.
  35. Vakser IA. Prediction of protein interactions is essential for studying biomolecular mechanisms. Proteomics. 2023 Sep; 23(17):e2300219. PMID: 37667816.
  36. Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol. 2023 Oct 1;13(10):e10506. PMCID: PMC10542623.
  37. Wei L, Zhang Q, Zhong C, He L, Zhang Y, Armaly AM, Aubé J, Welch DR, Xu L, Wu X. Functional inhibition of the RNA-binding protein HuR sensitizes triple-negative breast cancer to chemotherapy. Mol Oncol. 2023 Oct; 17(10):1962-1980.  Epub 2023 Jul 19. PMID: 37357618; PMCID: PMC10552894.
  38. Wu X, Ramesh R, Wang J, Zheng Y, Armaly AM, Wei L, Xing M, Roy S, Lan L, Gao FP, Miao Y, Xu L, Aubé J. Small Molecules Targeting the RNA-Binding Protein HuR Inhibit Tumor Growth in Xenografts. J Med Chem. 2023 Feb 9; 66(3):2032-2053. Epub 2023 Jan 23. PMID: 36690437; PMCID: PMC10101218.
  39. Yang Z, Zhang Q, Wu X, Hao S, Hao X, Jones E, Zhang Y, Qiu J, Xu L. Repurposing Niclosamide as a Novel Anti-SARS-CoV-2 Drug by Restricting Entry Protein CD147Biomedicines. 2023 Jul 18; 11(7):2019.  PMID: 37509657; PMCID: PMC10377517.
  40. Zhang J, Qiu R, Bieger BD, Oakley CE, Oakley BR, Egan MJ, Xiang X. Aspergillus SUMOylation mutants exhibit chromosome-segregation defects including chromatin bridges. Genetics. 2023 Sep 19: iyad169.  Epub ahead of print. PMID: 37724751.
  41. Zhang Q, Yang Z, Hao X, Dandreo LJ, He L, Zhang Y, Wang F, Wu X, Xu L.Niclosamide improves cancer immunotherapy by modulating RNA-binding protein HuR-mediated PD-L1 signaling. Cell Biosci. 2023 Oct 17; 13(1):192.  PMID: 37848943; PMCID: PMC10583380.
  1. Aquino Nunez W, Combs B, Gamblin TC, Ackley BD. Age-dependent accumulation of tau aggregation in Caenorhabditis elegans. Front Aging. 2022 Aug 19; 3:928574. PMID: 36062211; PMCID: PMC9437221.
  2. Bhattarai A, Devkota S, Do HN, Wang J, Bhattarai S, Wolfe MS, Miao Y. Mechanism of Tripeptide Trimming of Amyloid beta-Peptide 49 by gamma-Secretase. J Am Chem Soc. 2022 Apr 13; 144(14):6215-6226. PMID: 35377629. Epub 2022 Apr 4. Erratum in: J Am Chem Soc. 2022 May 25; 144(20):9182. PMID: 35377629; PMCID: PMC9798850.
  3. Brown SZ, McCarthy GA, Carroll JR, Di Niro R, Pelz C, Jain A, Sutton TL, Holly HD, Nevler A, Schultz CW, McCoy MD, Cozzitorto JA Jr, Jiang W, Yeo CJ, Dixon DA, Sears RC, Brody JR. The RNA-Binding Protein HuR Posttranscriptionally Regulates the Protumorigenic Activator YAP1 in Pancreatic Ductal Adenocarcinoma. Mol Cell Biol. 2022 Jul 21; 42(7):e0001822. Epub 2022 Jun 15. PMID: 35703534; PMCID: PMC9302082.
  4. Budiardjo SJ, Stevens JJ, Calkins AL, Ikujuni AP, Wimalasena VK, Firlar E, Case DA, Biteen JS, Kaelber JT, Slusky JSG. Colicin E1 opens its hinge to plug TolC. Elife. 2022 Feb 24; 11:e73297.  PMID: 35199644; PMCID: PMC9020818.
  5. 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; PMCID: PMC9173776.
  6. Collins KW, Copeland MM, Kotthoff I, Singh A, Kundrotas PJ, Vakser IA. Dockground resource for protein recognition studies. Protein Sci. 2022 Dec; 31(12):e4481.  PMID: 36281025; PMCID: PMC9667896.
  7. Copeland MM, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. Gaussian Accelerated Molecular Dynamics in OpenMM. J Phys Chem B. 2022 Aug 11; 126(31):5810-5820. Epub 2022 Jul 27. PMID: 35895977; PMCID: PMC9773147.
  8. Dasovich M, Zhuo J, Goodman JA, Thomas A, McPherson RL, Jayabalan AK, Busa VF, Cheng SJ, Murphy BA, Redinger KR, Alhammad YMOFehr 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. Epub 2021 Dec 14. PMID: 34904435.
  9. Do HN, Wang J, Bhattarai AMiao Y. GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling. J Chem Theory Comput. 2022 Mar 8; 18(3):1423-1436. Epub 2022 Feb 24. PMID: 35200019; PMCID: PMC9773012.
  10. 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; PMCID: PMC9022524.
  11. Felmlee KR, Macdonald SJ, Everman ER. Pre-adult exposure to three heavy metals leads to changes in the head transcriptome of adult fliesMicroPubl Biol. 2022 10.17912/micropub.biology.000591. PMID: 35856016; PMCID: PMC9287740.
  12. Jenkins NW, Kundrotas PJ, Vakser IA.Size of the protein-protein energy funnel in crowded environment.Front Mol Biosci. 2022 Nov 8; 9:1031225.  PMID: 36425657; PMCID: PMC9679368.
  13. Hill T, Unckless RL, Perlmutter JI. Positive Selection and Horizontal Gene Transfer in the Genome of a Male-Killing Wolbachia. Mol Biol Evol. 2022 Jan 7;39(1):msab303. PMID: 34662426; PMCID: PMC8763111.
  14. Kaulich E, Carroll T, Ackley BD, Tang YQ, Hardege I, Nehrke K, Schafer WR, Walker DS. Distinct roles for two Caenorhabditis elegans acid-sensing ion channels in an ultradian clock. Elife. 2022 Jun 6;11:e75837. PMID: 35666106; PMCID: PMC9374441.
  15. Kotthoff I, Kundrotas PJ, Vakser IA. DOCKGROUND membrane protein-protein set. PLoS One. 2022 May 17; 17(5):e0267531. PMID: 35580077; PMCID: PMC9113569.
  16. Kotthoff I, Kundrotas PJ, Vakser IA. Dockground scoring benchmarks for protein docking.Proteins. 2022 Jun; 90(6):1259-1266.  Epub 2022 Feb 5. PMID: 35072956; PMCID: PMC9018566.
  17. Kuhn M, Zhang Y, Favate J, Morita M, Blucher A, Das S, Liang S, Preet R, Parham LR, Williams KN, Molugu S, Armstrong RJ, Zhang W, Yang J, Hamilton KE, Dixon DA, Mills G, Morgan TK, Shah P, Andres SF. IMP1/IGF2BP1 in human colorectal cancer extracellular vesicles. Am J Physiol Gastrointest Liver Physiol. 2022 Dec 1; 323(6):G571-G585. Epub 2022 Oct 4. PMID: 36194131; PMCID: PMC9678429.
  18. Lansdon P, Carlson M, Ackley BD. Wild-type Caenorhabditis elegans isolates exhibit distinct gene expression profiles in response to microbial infection. BMC Genomics. 2022 Mar 23;23(1):229. PMID: 35321659; PMCID: PMC8943956.
  19. Lama J, Srivastav S, Tasnim S, Hubbard D, Hadjipanteli S, Smith BRMacdonald SJ, Green L, Kelleher ES. Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts. PLoS Genet. 2022 Dec 7; 18(12):e1010080. PMID: 36477699; PMCID: PMC9762592.
  20. 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; PMCID: PMC8780475.
  21. Ma WJ, Knoles EM, Patch KB, Shoaib MM, Unckless RL. Hoisted with his own petard: How sex-ratio meiotic drive in Drosophila affinis creates resistance alleles that limit its spread. J Evol Biol.2022 Dec; 35(12):1765-1776. Epub 2022 Aug 23. PMID: 35997297.
  22. Macdonald SJ, Cloud-Richardson KM, Sims-West DJ, Long AD. Powerful, efficient QTL mapping in Drosophila melanogaster using bulked phenotyping and pooled sequencing. Genetics. 2022 Mar 3; 220(3):iyab238. PMID: 35100395; PMCID: PMC8893256.
  23. Macdonald SJ, Long AD. Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach.G3 (Bethesda). 2022 Dec 1; 12(12):jkac279. PMID: 36250804; PMCID: PMC9713458.
  24. Malladi S, Powell HR, David A, Islam SA, Copeland MM, Kundrotas PJ, Sternberg MJE, Vakser IA.GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes. J Mol Biol. 2022 Jun 15; 434(11):167608.  Epub 2022 Apr 27. PMID: 35662458; PMCID: PMC9188266.
  25. Meisel RP, Asgari D, Schlamp F, Unckless RL. Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex. G3 (Bethesda). 2022 Jul 6:jkac165. PMID: 35792851; PMCID: PMC9434221.
  26. Ochs ME, McWhirter RM, Unckless RL, Miller DM 3rd, Lundquist EACaenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration. BMC Genomics. 2022 Jan 6; 23(1):13. PMID: 34986795; PMCID: PMC8734324.
  27. Parthasarathy SFehr AR. PARP14: A key ADP-ribosylating protein in host-virus interactions?PLoS Pathog. 2022 Jun 9;18(6):e1010535. PMID: 35679255; PMCID: PMC9182250.
  28. Pawnikar S, Magenheimer BS, Munoz EN, Maser RL, Miao Y. Mechanism of tethered agonist-mediated signaling by polycystin-1. Proc Natl Acad Sci U S A. 2022 May 10; 119(19):e2113786119. PMID: 35522707; PMCID: PMC9171645.
  29. Pawnikar S, Miao Y. Mechanism of Peptide Agonist Binding in CXCR4 Chemokine Receptor. Front Mol Biosci. 2022 Mar 11; 9:821055. PMID: 35359589; PMCID: PMC8963245.
  30. Perusina Lanfranca M, van Loben Sels JM, Ly CY, Grams TR, Dhummakupt A, Bloom DC, Davido DJ. A 77 Amino Acid Region in the N-Terminal Half of the HSV-1 E3 Ubiquitin Ligase ICP0 Contributes to Counteracting an Established Type 1 Interferon Response. Microbiol Spectr. 2022 Aug 31; 10(4):e0059322. PMID: 35730940; PMCID: PMC9430112.
  31. 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; PMCID: PMC9119168.
  32. Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtio 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; PMCID: PMC9093066.
  33. Su M, Paknejad N, Zhu L, Wang J, Do HNMiao Y, Liu W, Hite RK, Huang XY. Structures of β1-adrenergic receptor in complex with Gs and ligands of different efficacies. Nat Commun. 2022 Jul 14; 13(1):4095. PMID: 35835792; PMCID: PMC9283524.
  34. Tucker DK, Adams CS, Prasad G, Ackley BD. The Immunoglobulin Superfamily Members syg-2 and syg-1 Regulate Neurite Development in C. elegans. J Dev Biol. 2022 Jan 9;10(1):3. PMID: 35076532; PMCID: PMC8788504.
  35. Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. Docking-based long timescale simulation of cell-size protein systems at atomic resolution. Proc Natl Acad Sci U S A. 2022 Oct 11; 119(41):e2210249119. Epub 2022 Oct 3. PMID: 36191203; PMCID: PMC9565162.
  36. Wang J, Bhattarai A, Nguyen Do HMiao Y. Challenges and Frontiers of Computational Modeling of Biomolecular RecognitionQRB Discovery. 2022; 3;E13. Epub 2022 Aug 19. PMID: 37377636; PMCID: PMC10299731.
  37. Wang JMiao Y. Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics. J Chem Theory Comput. 2022 Mar 8; 18(3):1275-1285. Epub 2022 Jan 31. PMID: 35099970; PMCID: PMC9817007.
  38. Wu X, Xu L. The RNA-binding protein HuR in human cancer: A friend or foe?Adv Drug Deliv Rev. 2022 May; 184:114179. Epub 2022 Mar 3. PMID: 35248670; PMCID: PMC9035123.
  39. Xiao H, Ye X, Vishwakarma V, Preet RDixon DACRC-derived exosomes containing the RNA binding protein HuR promote lung cell proliferation by stabilizing c-Myc mRNA. Cancer Biol Ther. 2022 Dec 31; 23(1):139-149. PMID: 35130122; PMCID: PMC8824215.
  40. Yuan B, Keller NP, Oakley BR, Stajich JE, Wang CCC. Manipulation of the Global Regulator mcrA Upregulates Secondary Metabolite Production in Aspergillus wentii Using CRISPR-Cas9 with In Vitro Assembled Ribonucleoproteins. ACS Chem Biol. 2022; 17(10):2828-2835. Epub 2022 Oct 5. PMID: 36197945; PMCID: PMC9624091.
  41. Zhao C, Matalonga J, Lancman JJ, Liu L, Xiao C, Kumar S, Gates KP, He J, Graves A, Huisken J, Azuma M, Lu Z, Chen C, Ding BS, Dong PDS  Regenerative failure of intrahepatic biliary cells in Alagille syndrome rescued by elevated Jagged/Notch/Sox9 signaling. Proc Natl Acad Sci U S A. 2022 Dec 13; 119(50):e2201097119. Epub 2022 Dec 5. PMID: 36469766; PMCID: PMC9897440.

     

  1. 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; PMCID: PMC7925111.
  2. Badal VD, Kundrotas PJ, Vakser IA. Text mining for modeling of protein complexes enhanced by machine learning. Bioinformatics. 2021 May 1; 37(4):497-505.  PMID: 32960948; PMCID: PMC8088328.
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