Publications

MB Research Publications

  1. Ackley BD. Bright lights, big synapses: fluorescent proteins let neurons shine. BMC Biol. 2024 Feb 5;22(1):32.  PMID: 38317212; PMCID: PMC10845595.
  2. Akhter S, Tang Z, Wang J, Haboro M, Holmstrom ED, Wang J, Miao Y. Mechanism of Ligand Binding to Theophylline RNA Aptamer. J Chem Inf Model. 2024 Feb 12;64(3):1017-1029. Epub 2024 Jan 16. PMID: 38226603; PMCID: PMC11058067.
  3. Collins, K.W., Copeland, M.M., Brysbaert, G., Wodak, S.J., Bonvin, A.M.J.J., Kundrotas, P.J., Vakser, I.A., Lensink, M.F. CAPRI-Q: The CAPRI resource for assessment of modeling protein interactions, J. Mol. Biol.2024 Sep 1; 436(17):168540.
  4. Dalton HM, Young NJ, Berman AR, Evans HD, Peterson SJ, Patterson KA, Chow CY. A drug repurposing screen reveals dopamine signaling as a critical pathway underlying potential therapeutics for the rare disease DPAGT1-CDG. PLoS Genet. 2024 Oct 28;20(10):e1011458. Epub ahead of print. PMID: 39466823.
  5. Devkota S, Zhou R, Nagarajan V, Maesako M, Do H, Noorani A, Overmeyer C, Bhattarai S, Douglas JT, Saraf A, Miao Y, Ackley BD, Shi Y, Wolfe MS. Familial Alzheimer mutations stabilize synaptotoxic γ-secretase-substrate complexes. Cell Rep. 2024 Feb 27;43(2):113761. Epub 2024 Feb 13. PMID: 38349793.
  6. Everman ER, Macdonald SJ. Gene expression variation underlying tissue-specific responses to copper stress in Drosophila melanogaster. G3 (Bethesda). 2024 Mar 6;14(3):jkae015. PMID: 38262701.
  7. 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.
  8. Gupta A, Unckless RL. Autosomal suppression of sex-ratio meiotic drive influences the dynamics of X and Y chromosome coevolution. J Hered. 2024 Aug 30:esae048. Epub ahead of print. PMID: 39212686.
  9. 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; PMCID: PMC11361582.
  10. 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. Epub 2024 Jun 11. PMID: 38871177; PMCID: PMC11297670.
  11. Jenkinson CB, Lin SY, Villarreal M, Oakley CE, Sherman DH, Lee CK, Wang CCC, Oakley BR. Discovery of Uncommon Tryptophan-Containing Diketopiperazines from Aspergillus homomorphus CBS 101889 Using an Aspergillus nidulans Heterologous Expression System. J Nat Prod. 2024 Jul 26;87(7):1704-1713. Epub 2024 Jul 11. PMID: 38990199.
  12. Kerr CM, Pfannenstiel JJ, Alhammad YM, O'Connor JJ, Ghimire R, Shrestha R, Khattabi R, Saenjamsai P, Parthasarathy S, McDonald PR, Gao P, Johnson DK, More S, Roy A, Channappanavar R, Fehr AR. Mutation of a highly conserved isoleucine residue in loop 2 of several β-coronavirus macrodomains indicates that enhanced ADP-ribose binding is detrimental for replication. J Virol. 2024 Oct 10:e0131324. Epub ahead of print. PMID: 39387584.
  13. Kywe C, Lundquist EA, Ackley BD, Lansdon P. The MAB-5/Hox family transcription factor is important for Caenorhabditis elegans innate immune response to Staphylococcus epidermidis infection. G3 (Bethesda). 2024 May 7;14(5):jkae054. PMID: 38478633; PMCID: PMC11075571.
  14. López Hernández JF, Rubinstein BY, Unckless RL, Zanders SE. Modeling the evolution of Schizosaccharomyces pombe populations with multiple killer meiotic drivers. G3 (Bethesda). 2024 Sep 4;14(9):jkae142.  PMID: 38938172.
  15. Lou H, Zhang Y, Kuczera K, Hageman MJ, Schöneich C. Molecular Dynamics Simulation of an Iron(III) Binding Site on the Fc Domain of IgG1 Relevant for Visible Light-Induced Protein Fragmentation. Mol Pharm. 2024 Feb 5;21(2):501-512.  Epub 2023 Dec 21. PMID: 38128475.
  16. Lundquist E. The DPY-14 cuticle collagen regulates left-right asymmetric neuronal migration in Caenorhabditis elegans. MicroPubl Biol. 2024 Aug 26;2024:10.17912/micropub.biology.001302. PMID: 39258272; PMCID: PMC11384304.
  17. 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. PLoS One. 2024 May 21;19(5):e0295701. PMID: 38771761; PMCID: PMC11108135.
  18. 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 Feb 19.  Epub ahead of print. PMID: 38372168.
  19. 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 Jan;92(1):52-59.  Epub 2023 Aug 19. PMID: 37596815.
  20. Nüesch MF, Pietrek L, Holmstrom ED, Nettels D, von Roten V, Kronenberg-Tenga R, Medalia O, Hummer G, Schuler B. Nanosecond chain dynamics of single-stranded nucleic acids. Nat Commun. 2024 Jul 17;15(1):6010.  PMID: 39019880; PMCID: PMC11255343.
  21. Oakley CE, Barton TS Jr., Oakley BR. Identification of the chaA and fwA Spore Color Genes of Aspergillus nidulans. Journal of Fungi. 2024; 10(2):104.
  22. Olivar C, Yu Z, Miller B, Tangalos M, Jenkinson CB, Nutt SR, Oakley BR, Wang CCC, Williams TJ. Composite Recycling with Biocatalytic Thermoset Reforming. J Am Chem Soc. 2024 Oct 24. Epub ahead of print. PMID: 39447087.
  23. Orozco RC, Marquardt K, Pratumchai I, Shaikh AF, Mowen K, Domissy A, Teijaro JR, Sherman LA. Autoimmunity-associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity. PLoS Pathog. 2024 Mar 21;20(3):e1012095. PMID: 38512979; PMCID: PMC10987006.
  24. Otter CJ, Bracci N, Parenti NA, Ye C, Asthana A, Blomqvist EK, Tan LH, Pfannenstiel JJ, Jackson N, Fehr AR, Silverman RH, Burke JM, Cohen NA, Martinez-Sobrido L, Weiss SR. SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling. Proc Natl Acad Sci U S A. 2024 Apr 9;121(15):e2320194121. Epub 2024 Apr 3. PMID: 38568967; PMCID: PMC11009620.
  25. Paolillo VK, Ochs ME, Lundquist EA. MAB-5/Hox regulates the Q neuroblast transcriptome, including cwn-1/Wnt, to mediate posterior migration in Caenorhabditis elegans.Genetics. 2024 Apr 23:iyae045. Epub ahead of print. PMID: 38652773.
  26. Perlmutter JI, Chapman JR, Wilkinson MC, Nevarez-Saenz I, Unckless RL. A single amino acid polymorphism in natural Metchnikowin alleles of Drosophila results in systemic immunity and life history tradeoffs. PLoS Genet. 2024 Mar 11;20(3):e1011155. PMID: 38466751; PMCID: PMC10957085.
  27. Rabot C, Grau MF, Entwistle R, Chiang YM, Zamora de Roberts Y, Ahuja M, Oakley CE, Wang CCC, Todd RB, Oakley BR. Transcription Factor Engineering in Aspergillus nidulans Leads to the Discovery of an Orsellinaldehyde Derivative Produced via an Unlinked Polyketide Synthase Gene. J Nat Prod. 2024 Sep 27. Epub ahead of print. PMID: 39334518.
  28. Sanderson BJ, Sims-West DJ, Macdonald SJ.Acute exposure to mercury drives changes in gene expression in Drosophila melanogaster. BMC Res Notes. 2024 Sep 30;17(1):279.  PMID: 39350189.
  29. 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.
  30. Shi J, Barman SC, Cheng S, Zeng Y. Metal-organic framework-interfaced ELISA probe enables ultrasensitive detection of extracellular vesicle biomarkers. J Mater Chem B. 2024 Jul 3;12(26):6342-6350. doi: 10.1039/d4tb00585f. PMID: 38856318; PMCID: PMC11222032.
  31. Singh A, Copeland MM, Kundrotas PJ,Vakser IA. GRAMM Web Server for Protein Docking. Methods Mol Biol. 2024;2714:101-112.  PMID: 37676594.
  32. Singh A, Kundrotas PJ, Vakser IA. Diffusion of proteins in crowded solutions studied by docking-based modeling. J Chem Phys. 2024 Sep 7;161(9):095101. PMID: 39225532.
  33. Sperstad PD, Holmstrom ED. Conformational dynamics of the hepatitis C virus 3'X RNA. RNA. 2024 Aug 16;30(9):1151-1163. PMID: 38834242.
  34. Świątek A, Kuczera K, Szoszkiewicz R. Effects of Proline on Internal Friction in Simulated Folding Dynamics of Several Alanine-Based α-Helical Peptides. J Phys Chem B. 2024 Apr 25;128(16):3856-3869.  Epub 2024 Apr 12. PMID: 38606880; PMCID: PMC11056985.
  35. Wazir S, Parviainen TAO, Pfannenstiel JJ, Duong MTH, Cluff D, Sowa ST, Galera-Prat A, Ferraris D, Maksimainen MM, Fehr AR, Heiskanen JP, Lehtiö L. Discovery of 2-Amide-3-methylester Thiophenes that Target SARS-CoV-2 Mac1 and Repress Coronavirus Replication, Validating Mac1 as an Antiviral Target. J MedChem. 2024 Apr 25;67(8):6519-6536. Epub 2024 Apr 9. PMID: 38592023.
  36. Woods KE, Akhter S, Rodriguez B, Townsend KA, Smith N, Smith B, Wambua A, Craddock V, Abisado-Duque RG, Santa EE, Manson DE, Oakley BR, Hancock LE, Miao Y, Blackwell HE, Chandler JR. Characterization of natural product inhibitors of quorum sensing reveals competitive inhibition of Pseudomonas aeruginosa RhlR by ortho-vanillin. Microbiol Spectr.2024 Jul 24:e0068124. Epub ahead of print. PMID: 39046261.
  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. Finan JM, Sutton TL, Dixon DA, Brody JR. Targeting the RNA-Binding Protein HuR in Cancer. Cancer Res. 2023 Nov 1;83(21):3507-3516. PMID: 37683260.
  11. 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.
  12. Harrell TL, Davido DJ, Bertke AS. Herpes Simplex Virus 1 (HSV-1) Infected Cell Protein 0 (ICP0) Targets of Ubiquitination during Productive Infection of Primary Adult Sensory Neurons. Int J Mol Sci. 2023 Feb 2;24(3):2931. doi: 10.3390/ijms24032931. PMID: 36769256; PMCID: PMC9917815.
  13. 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.
  14. 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.
  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. PMID: 36772796; PMCID: PMC10111266.
  16. 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.
  17. 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.
  18. 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.
  19. Kuczera K, Szoszkiewicz R, Shaffer CL, Jas GS. GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction. J Biomol Struct Dyn. 2023;41(21):11671-11680. Epub 2023 Jan 2. PMID: 36591705.
  20. Lee KH, Kuczera K. Effect of alanine versus serine at position 88 of human transthyretin mutants on the protein stability. Protein Eng Des Sel. 2023 Jan 21;36:gzad001. PMID: 36611015.
  21. Lee KH, Kuczera K. Simulation analysis of selective alanine mutation effect on stability of human prion protein. J Biomol Struct Dyn. 2023 Apr;41(7):2619-2629. Epub 2022 Feb 18. PMID: 35176965.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. Rabot C, Chen Y, Bijlani S, Chiang YM, Oakley CE, Oakley BR, Williams TJ, Wang CCC. Conversion of Polyethylenes into Fungal Secondary Metabolites. Angew Chem Int Ed Engl.2023 Jan 23;62(4):e202214609. Epub 2022 Nov 23. PMID: 36417558; PMCID: PMC10100090.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. Vakser IA. Prediction of protein interactions is essential for studying biomolecular mechanisms. Proteomics. 2023 Sep; 23(17):e2300219. PMID: 37667816.
  41. 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.
  42. 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.
  43. 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.
  44. 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 CD147. Biomedicines. 2023 Jul 18; 11(7):2019.  PMID: 37509657; PMCID: PMC10377517.
  45. 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.
  46. 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.
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