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. Wei L, Kim SH, Armaly AM, Aubé J, Xu L, Wu X. RNA-binding protein HuR inhibition induces multiple programmed cell death in breast and prostate cancer. Cell Commun Signal. 2024 Dec 3;22(1):580.  PMID: 39627778; PMCID: PMC11613925.
  37. Wei L, Kim SH, Armaly AM, Aubé J, Xu L, and Wu X, HuR inhibition overcomes cFLIP-mediated doxorubicin resistance in triple-negative breast cancer.  npj Precision Oncology . 2024;8(1):286. PMID pending.
  38. 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.
  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 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. Epub 2021 Dec 14. PMID: 34904435.
  9. Do HN, Wang J, Bhattarai A, Miao 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 flies. MicroPubl Biol. 2022 10.17912/micropub.biology.000591. PMID: 35856016; PMCID: PMC9287740.
  12. Jas GS, Childs EW, Middaugh CR, Kuczera K. Observing reorientation dynamics with Time-Resolved fluorescence and molecular dynamics in varying periodic boundary conditions. J Biomol Struct Dyn. 2022;40(21):10614-10628. Epub 2021 Jul 24. PMID: 34308794.
  13. 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.
  14. 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.
  15. 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.
  16. Kotthoff I, Kundrotas PJ, Vakser IA. DOCKGROUND membrane protein-protein set. PLoS One. 2022 May 17; 17(5):e0267531. PMID: 35580077; PMCID: PMC9113569.
  17. 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.
  18. 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.
  19. 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.
  20. Lama J, Srivastav S, Tasnim S, Hubbard D, Hadjipanteli S, Smith BR, Macdonald 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.
  21. Lee BL, Kuczera K, Lee KH, Childs EW, Jas GS. Unassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation. J Biomol Struct Dyn. 2022 Mar;40(4):1445-1460. Epub 2020 Oct 9. PMID: 33034537.
  22. Lee KH, Kuczera K. Modulation of human transthyretin stability by the mutations at histidine 88 studied by free energy simulation. Proteins. 2022 Nov;90(11):1825-1836. Epub 2022 May 24. PMID: 35484710.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. Meier AA, Kuczera K, Mure M. A 3D-Predicted Structure of the Amine Oxidase Domain of Lysyl Oxidase-Like 2. Int J Mol Sci. 2022 Nov 2;23(21):13385. PMID: 36362176; PMCID: PMC9659206
  29. 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.
  30. Ochs ME, McWhirter RM, Unckless RL, Miller DM 3rd, Lundquist EA. Caenorhabditis 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.
  31. Parthasarathy S, Fehr AR. PARP14: A key ADP-ribosylating protein in host-virus interactions?PLoS Pathog. 2022 Jun 9;18(6):e1010535. PMID: 35679255; PMCID: PMC9182250.
  32. 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.
  33. 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.
  34. 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.
  35. Picard HR, Schwingen KS, Green LM, Shis DL, Egan SM, Bennett MR, Swint-Kruse L. Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes. Proteins. 2022 Jan;90(1):186-199. Epub 2021 Aug 16. PMID: 34369028; PMCID: PMC8671227.
  36. 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.
  37. Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B. 2022 Apr 14;126(14):2647-2657. Epub 2022 Mar 31. PMID: 35357137; PMCID: PMC9014414.
  38. 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.
  39. Spencer P, Ye Q, Misra A, Chandler JR, Cobb CM, Tamerler C. Engineering peptide-polymer hybrids for targeted repair and protection of cervical lesions. Front Dent Med. 2022;3:1007753. Epub 2022 Nov 25. PMID: 37153688; PMCID: PMC10162700.
  40. Su M, Paknejad N, Zhu L, Wang J, Do HN, Miao 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.
  41. 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.
  42. 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.
  43. Wang H, Davido DJ, Mostafa HH, Morrison LA. Efficacy of an HSV-1 Neuro-Attenuated Vaccine in Mice Is Reduced by Preventing Viral DNA Replication. Viruses. 2022 Apr 22;14(5):869.  PMID: 35632611; PMCID: PMC9144315.
  44. Wang J, Bhattarai A, Nguyen Do H, Miao Y. Challenges and Frontiers of Computational Modeling of Biomolecular Recognition. QRB Discovery. 2022; 3;E13. Epub 2022 Aug 19. PMID: 37377636; PMCID: PMC10299731.
  45. Wang J, Miao 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.
  46. Wosztyl A, Kuczera K, Szoszkiewicz R. Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations. J Phys Chem B. 2022 Nov 10;126(44):8901-8912. Epub 2022 Oct 27. PMID: 36300354; PMCID: PMC9661531.
  47. 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.
  48. Xiao H, Ye X, Vishwakarma V, Preet R, Dixon DA. CRC-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.
  49. Yao H, Soldano A, Fontenot L, Donnarumma F, Lovell S, Chandler JR, Rivera M. Pseudomonas aeruginosa Bacterioferritin Is Assembled from FtnA and BfrB Subunits with the Relative Proportions Dependent on the Environmental Oxygen Availability. Biomolecules. 2022 Feb 25;12(3):366. PMID: 35327558; PMCID: PMC8945002.
  50. 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.
  51. 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. 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. 2021 May 26;87(12):e0002921.  Epub 2021 May 26. PMID: 33837019; PMCID: PMC8174604.
  2. Meier AA, Moon HJ, Toth R 4th, Folta-Stogniew E, Kuczera K, Middaugh CR, Mure M. Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2. Biomolecules. 2021 Dec 8;11(12):1846. PMID: 34944490; PMCID: PMC8699698.
  3. 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.
  4. 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.
  5. 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 Dependent. J Membr Biol. 2021 Feb;254(1):41-50.  Epub 2021 Jan 19. PMID: 33462665; PMCID: PMC8101038.
  6. Chiremba TT,Neufeld KL. Constitutive Musashi1 expression impairs mouse postnatal development and intestinal homeostasis. Mol Biol Cell. 2021 Jan 1; 32(1):28-44. Epub 2020 Nov 11. PMID: 33175598; PMCID: PMC8098822.
  7. Dhar R, Feehan R, Slusky JSG. Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels.J Phys Chem B. 2021 Apr 15; 125(14):3622-3628.  Epub 2021 Apr 2. Erratum in: J Phys Chem B. 2021 Oct 28; 125(42):11784. PMID: 33797916; PMCID: PMC8427218.
  8. Dhar R, Slusky JS. Outer membrane protein evolution. Curr Opin Struct Biol. 2021 Jun ;68:122-128.  Epub 2021 Jan 22. PMID: 33493965; PMCID: PMC8222147.
  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; PMCID: PMC7948067.
  10. 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; PMCID: PMC9119408.
  11. Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O’Sullivan K, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Wendy L I, & Christopoulos A. Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia. Nature. 2021 Sep; 597(7877):571-576. Epub 2021 Sep 8. PMID: 34497422; PMCID: PMC8711093.
  12. Everman ER, Cloud-Richardson KM, Macdonald SJ. Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation. Genetics. 2021 Mar 3;217(1):1-20. PMID: 33683361; PMCID: PMC8045719.
  13. Feehan R, Franklin MW, Slusky JSG. Machine learning differentiates enzymatic and non-enzymatic metals in proteins. Nat Commun. 2021 Jun 17; 12(1):3712. PMID: 34140507; PMCID: PMC8211803.
  14. Feehan R, Montezano D, Slusky JSG. Machine learning for enzyme engineering, selection and design. Protein Eng Des Sel. 2021 Feb 15; 34:gzab019. PMID: 34296736; PMCID: PMC8299298.
  15. Gunawardhana SM,Holmstrom ED. Apolar chemical environments compact unfolded RNAs and can promote folding. Biophys Rep (N Y). 2021 Sep 8; 1(1):100004.  Epub 2021 Jul 21. PMID: 35382036; PMCID: PMC8978554.
  16. Gupta S, Wang M, Azuma Y, Muma NA. Regulation of Serotonin 1A Receptor SUMOylation by SENP2 and PIASxα. Int J Mol Sci. 2021 Dec 7;22(24):13176.  PMID: 34947973; PMCID: PMC8706138.
  17. Hadarovich A, Chakravarty D, Tuzikov AV, Ben-Tal N, Kundrotas PJ, Vakser IA. Structural motifs in protein cores and at protein-protein interfaces are different. Protein Sci. 2021 Feb; 30(2):381-390.  Epub 2020 Nov 20. PMID: 33166001; PMCID: PMC7784743.
  18. He X, Smith SE, Chen S, Li H, Wu D, Meneses-Giles PI, Wang Y, Hembree M, Yi K, Zhao X, Guo F, Unruh JR, Maddera LE, Yu Z, Scott A, Perera A, Wang Y, Zhao C, Bae K, Box A, Haug JS, Tao F, Hu D, Hansen DM, Qian P, Saha S, Dixon DA, Anant S, Zhang D, Lin EH, Sun W, Wiedemann L, Li L. Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche. Cell Rep. 2021 Sep 7; 36(10):109674.  PMID: 34496236; PMCID: PMC8451448.
  19. Hill T, Rosales-Stephens HL, Unckless RL. Rapid divergence of the male reproductive proteins in the Drosophila dunni group and implications for postmating incompatibilities between species. G3 (Bethesda). 2021 Apr 15;11(4):jkab050. PMCID: PMC8759818.
  20. Hill T, Unckless RL. Adaptation, ancestral variation and gene flow in a 'Sky Island' Drosophila species. Mol Ecol.2021 Jan; 30(1):83-99. Epub 2020 Nov 7. PMID: 33089581; PMCID: PMC7945764.
  21. Höring C*, Conrad M, Söldner CA, Wang J, Sticht H, Strasser A, & Miao Y* (2021) Specific Engineered G Protein Coupling to Histamine Receptors Revealed from Cellular Assay Experiments and Accelerated Molecular Dynamics Simulations. Int J Mol Sci. 2021 Sep 17; 22(18):10047. PMID: 34576210; PMCID: PMC8467750.
  22. Ingham DJ, Blankenfeld BR, Chacko S, Perera C, Oakley BR, Gamblin TC. Fungally Derived Isoquinoline Demonstrates Inducer-Specific Tau Aggregation Inhibition. Biochemistry. 2021 Jun 1;60(21):1658-1669. Epub 2021 May 19. PMID: 34009955; PMCID: PMC8173610.
  23. Jas GS, Childs EW, Middaugh CR, Kuczera K. Probing the Internal Dynamics and Shape of Simple Peptides in Urea, Guanidinium Hydrochloride, and Proline Solutions with Time-Resolved Fluorescence Anisotropy and Atomistic Cosolvent Simulations. J Phys Chem B. 2021 Oct 7;125(39):10972-10984. Epub 2021 Sep 24. PMID: 34559968.
  24. Jas GS, Childs EW, Middaugh CR, Kuczera K. Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction. Biomolecules. 2021 Sep 12;11(9):1351. doi: 10.3390/biom11091351. PMID: 34572564; PMCID: PMC8471320.
  25. Johansson M, Azuma Y, Clarke DJ. Role of Aurora B and Haspin kinases in the metaphase Topoisomerase II checkpoint. Cell Cycle. 2021 Feb; 20(4):345-352. Epub 2021 Jan 18. PMID: 33459116; PMCID: PMC7894448.
  26. Keffeler EC, Iyer VS, Henderson AJ, Huck IL, Schwarting N, Cortez A, Hancock LE.  Activity of CcpA-regulated GH18 family glycosyl hydrolases that contribute to nutrient acquisition and fitness in Enterococcus faecalis. Infect Immun. 2021 Oct 15; 89(11):e0034321. Epub 2021 Aug 23. PMID: 34424752; PMCID: PMC8519268.
  27. Keffeler EC, Parthasarathy S, Abdullahi ZH, Hancock LE.  Metabolism of poly-β1,4-N-acetylglucosamine substrates and importation of N-acetylglucosamine and glucosamine by Enterococcus faecalis.  J Bacteriol. 2021 Oct 12; 203(21):e0037121.  Epub 2021 Aug 23. PMID: 34424034; PMCID: PMC8508097.
  28. Kuczera K, Szoszkiewicz R, He J, Jas GS. Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction. Life (Basel). 2021 Apr 24;11(5):385. PMID: 33923197; PMCID: PMC8170890.
  29. Kumamoto S, Nishiyama A, Chiba Y, Miyashita R, Konishi C, Azuma Y, Nakanishi M. HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation. Nucleic Acids Res. 2021 May 21; 49(9):5003-5016. PMID: 33872376; PMCID: PMC8136790.
  30. Lee KH, Kuczera K. Free energy simulations to understand the effect of Met → Ala mutations at positions 205, 206 and 213 on stability of human prion protein. Biophys Chem. 2021 Aug;275:106620.  Epub 2021 May 15. PMID: 34058726.
  31. Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. 2021 Dec; 89(12):1800-1823.  Epub 2021 Sep 13. PMID: 34453465; PMCID: PMC8616814.
  32. Liu JCY, Kühbacher U, Larsen NB, Borgermann N, Garvanska DH, Hendriks IA, Ackermann L, Haahr P, Gallina I, Guérillon C, Branigan E, Hay RT, Azuma Y, Nielsen ML, Duxin JP, Mailand N. Mechanism and function of DNA replication-independent DNA-protein crosslink repair via the SUMO-RNF4 pathway. EMBO J. 2021 Sep 15; 40(18):e107413.  Epub 2021 Aug 4. PMID: 34346517; PMCID: PMC8441304.
  33. 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, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J. 2022 Dec; 289(23):7399-7410. Epub 2021 Sep 13. PMID: 34323016; PMCID: PMC9027952.
  34. Ly CY, Yu C, McDonald PR, Roy A, Johnson DK, Davido DJ.  Simple and rapid high-throughput assay to identify HSV-1 ICP0 transactivation inhibitors.Antiviral Res. 2021 Oct; 194:105160. Epub 2021 Aug 9. PMID: 34384824; PMCID: PMC8686521.
  35. Meier AA, Moon HJ, Toth R 4th, Folta-Stogniew E, Kuczera K, Middaugh CR, Mure M. Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2. Biomolecules. 2021 Dec 8;11(12):1846. PMID: 34944490; PMCID: PMC8699698.
  36. Mintoo M, Chakravarty A, Tilvawala R. N-Terminomics Strategies for Protease Substrates Profiling.Molecules. 2021 Aug 3; 26(15):4699.  PMID: 34361849; PMCID: PMC8348681.
  37. Monnahan PJ, Colicchio J, Fishman L, Macdonald SJ, Kelly JK. Predicting evolutionary change at the DNA level in a natural Mimulus population. PLoS Genet. 2021 Jan 13;17(1):e1008945.  PMID: 33439857; PMCID: PMC7837469.
  38. Park H, Kim H, Hassebroek V, Azuma Y, Slawson C, Azuma M. Chromosomal localization of Ewing sarcoma EWSR1/FLI1 protein promotes the induction of aneuploidy. J Biol Chem. 2021 Jan-Jun; 296:100164.  Epub 2020 Dec 10. PMID: 33293370; PMCID: PMC7857440.
  39. Parthasarathy S, Wang X, Carr KR, Varahan S, Hancock EB, Hancock LE. SigV Mediates Lysozyme Resistance in Enterococcus faecalis via RsiV and PgdA.J Bacteriol. 2021 Sep 23; 203(20):e0025821.  Epub 2021 Aug 9. PMID: 34370556; PMCID: PMC8459761.
  40. Puri D, Ponniah K, Biswas K, Basu A, Dey S, Lundquist EA, Ghosh-Roy A. Wnt signaling establishes the microtubule polarity in neurons through regulation of Kinesin-13. J Cell Biol. 2021 Sep 6; 220(9):e202005080. Epub 2021 Jun 17. PMID: 34137792; PMCID: PMC8217938.
  41. Ryu H, Sun XX, Chen Y, Li Y, Wang X, Dai RS, Zhu HM, Klimek J, David L, Fedorov LM, Azuma Y, Sears RC, Dai MS. The deubiquitinase USP36 promotes snoRNP group SUMOylation and is essential for ribosome biogenesis. EMBO Rep. 2021 Jun 4; 22(6):e50684. Epub 2021 Apr 14. PMID: 33852194; PMCID: PMC8183414.
  42. Schultz CW, McCarthy GA, Nerwal T, Nevler A, DuHadaway JB, McCoy MD, Jiang W, Brown SZ, Goetz A, Jain A, Calvert VS, Vishwakarma V, Wang D, Preet R, Cassel J, Summer R, Shaghaghi H, Pommier Y, Baechler SA, Pishvaian MJ, Golan T, Yeo CJ, Petricoin EF, Prendergast GC, Salvino J, Singh PK, Dixon DA, Brody JR.  The FDA approved anthelmintic Pyrvinium Pamoate inhibits pancreatic cancer cells in nutrient depleted conditions by targeting the mitochondria. Mol Cancer Ther. 2021 Nov; 20(11):2166-2176. Epub 2021 Aug 19. PMID: 34413127; PMCID: PMC8859979.
  43. So J, Kim M, Lee SH, Ko S, Lee DA, Park H, Azuma M, Parsons MJ, Prober D, Shin D. Attenuating the Epidermal Growth Factor Receptor-Extracellular Signal-Regulated Kinase-Sex-Determining Region Y-Box 9 Axis Promotes Liver Progenitor Cell-Mediated Liver Regeneration in Zebrafish. Hepatology. 2021 Apr; 73(4):1494-1508. PMID: 32602149; PMCID: PMC7769917.
  44. Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota SS, Zhao J, Douglas JT, Gao P, Holmstrom ED, Miao Y, Wang J. Recognition of single-stranded nucleic acids by small-molecule splicing modulators. Nucleic Acids Res. 2021 Aug 20;49(14):7870-7883.  PMID: 34283224; PMCID: PMC8373063.
  45. Tilvawala R, Nemmara VV, Reyes AC, Sorvillo N, Salinger AJ, Cherpokova D, Fukui S, Gutch S, Wagner D, Thompson PR. The role of SERPIN citrullination in thrombosis. Cell Chem Biol. 2021 Dec 16; 28(12):1728-1739.e5.  Epub 2021 Aug 4. PMID: 34352225; PMCID: PMC8688209.
  46. Voth LS, O'Connor JJ, Kerr CM, Doerger E, Schwarting N, Sperstad P, Johnson DK, Fehr AR.  Unique Mutations in the Murine Hepatitis Virus Macrodomain Differentially Attenuate Virus Replication, Indicating Multiple Roles for the Macrodomain in Coronavirus Replication. J Virol. 2021 Jul 12; 95(15):e0076621. Epub 2021 Jul 12. PMID: 34011547; PMCID: PMC8274620.
  47. Wang J, Lan L, Wu X, Xu L, Miao Y. Mechanism of RNA recognition by a Musashi RNA-binding protein. Curr Res Struct Biol. 2021 Dec 14; 4:10-20. PMID: 34988468; PMCID: PMC8695263.
  1. Alhammad YMO, Fehr AR. The Viral Macrodomain Counters Host Antiviral ADP-ribosylation. Viruses. 2020 Mar 31;12(4):384.  PMID: 32244383; PMCID: PMC7232374.
  2. Bastos, R.W., Valero, C., Silva, L.P., Schoen, T., Drott, M., Brauer, V., Silva-Rocha, R., Lind, A., Steenwyk, J.L., Rokas, A., Rodrigues, F., Resendiz-Sharpe, A., Lagrou, K., Marcet-Houben, M., Gabaldón, T., McDonnell, E., Reid, I., Tsang, A., Oakley, B.R., Loures, F.V., Almeida, F., Huttenlocher, A., Keller, N.P., Ries, L.N.A. and Goldman, G.H. Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans. mSphere. 2020 Apr 8; 5(2):e00153-20. PMID: 32269156; PMCID: PMC7142298.
  3. Benomar S, Lansdon P, Bender AM, Peterson BR, Chandler JR, Ackley BD. The C. elegans CHP1 homolog, pbo-1, functions in innate immunity by regulating the pH of the intestinal lumen. PLoS Pathog. 2020 Jan 9; 16(1):e1008134. PMID: 31917826; PMCID: PMC6952083.
  4. Bhattarai A, Devkota S, Bhattarai S, Wolfe MS, Miao Y. Mechanisms of γ-Secretase Activation and Substrate Processing. ACS Cent Sci.2020 Jun 24; 6(6):969-983.  Epub 2020 Jun 4. PMID: 32607444; PMCID: PMC7318072.
  5. Bhattarai A, Wang J, Miao Y.  Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor. Biochim Biophys Acta Gen Subj. 2020 Aug;1864(8):129615. Epub 2020 Apr 13. PMID: 32298791; PMCID: PMC7261249.
  6. Bravo Núñez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE. Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers. Elife. 2020 Aug 13; 9:e57936. PMID: 32790622; PMCID: PMC7426094.
  7. Chakravarty D, McElfresh GW, Kundrotas PJ, Vakser IA. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking. Proteins. 2020 Aug; 88(8):1070-1081. Epub 2020 Feb 7. PMID: 31994759; PMCID: PMC7375009.
  8. Chapman JR, Dowell MA, Chan R,Unckless RL. The Genetic Basis of Natural Variation in Drosophila melanogaster Immune Defense against Enterococcus faecalis. Genes (Basel). 2020 Feb 22; 11(2):234. PMID: 32098395; PMCID: PMC7074548.
  9. Conrad M, Söldner CA, Miao Y, Sticht H. Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics Study. Int J Mol Sci. 2020 Sep 12 ;21(18):6693.  PMID: 32932742; PMCID: PMC7554837.
  10. Dong R, Chen P, Polireddy K, Wu X, Wang T, Ramesh R, Dixon DA, Xu L, Aubé J, Chen Q. An RNA-Binding Protein, Hu-antigen R, in Pancreatic Cancer Epithelial to Mesenchymal Transition, Metastasis, and Cancer Stem Cells. Mol Cancer Ther. 2020 Nov; 19(11):2267-2277. Epub 2020 Sep 2. PMID: 32879054; PMCID: PMC7921213.
  11. Efimova N, Yang C, Chia JX, Li N, Lengner CJ, Neufeld KL, Svitkina TM. Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion. J Cell Biol. 2020 Sep 7; 219(9):e202003091. PMID: 32597939; PMCID: PMC7480092.
  12. 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. 2020 Mar 1;34(5-6):341-359.  Epub 2020 Feb 6. PMID: 32029454; PMCID: PMC7050484.
  13. Fehr AR. Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoV. Methods Mol. Biol. 2020; 2099:53-68
  14. Frawley, D., Greco, C., Oakley, B., Alhussain, M.M., Fleming, A.B., Keller, N.P. and Bayram, Ö. The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavus. Cell Microbiol. 2020 Jun; 22(6):e13192.  Epub 2020 Mar 3. PMID: 32068947; PMCID: PMC7202998.
  15. Gao Y, Cao D, Pawnikar S, John KP, Ahn HM, Hill S, Ha JM, Parikh P, Ogilvie C, Swain A, Yang A, Bell A, Salazar A, Miao Y, Liang B. Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA. Structure. 2020 Sep 1; 28(9):979-990.e4.  Epub 2020 Jul 21. PMID: 32697936; PMCID: PMC7484405. (Undergraduate)
  16. Ghosh S, Dellibovi-Ragheb TA, Kerviel A, Pak E, Qiu Q, Fisher M, Takvorian PM, Bleck C, Hsu VW, Fehr AR, Perlman S, Achar SR, Straus MR, Whittaker GR, de Haan CAM, Kehrl J, Altan-Bonnet G, Altan-Bonnet N.  β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway. Cell. 2020 Dec 10; 183(6):1520-1535.e14.  Epub 2020 Oct 27. PMID: 33157038; PMCID: PMC7590812.
  17. Gomez CL, Neufeld KL.  Elevated Adenomatous Polyposis Coli in Goblet Cells is Associated with Inflammation in Mouse and Human Colon. Exp Physiol. 2020 Dec; 105(12):2154-2167.  Epub 2020 Nov 4. PMID: 33150708.
  18. Greenberg EP, Chandler JR, Seyedsayamdost MR. The Chemistry and Biology of Bactobolin: A 10-Year Collaboration with Natural Product Chemist Extraordinaire Jon Clardy.   J Nat Prod. 2020 Mar 27; 83(3):738-743. Epub 2020 Feb 27. PMID: 32105069; PMCID: PMC8118907.
  19. 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; PMCID: PMC7000979.
  20. Hassebroek VA, Park H, Pandey N, Lerbakken BT, Aksenova V, Arnaoutov A, Dasso M, Azuma Y.  PICH regulates the abundance and localization of SUMOylated proteins on mitotic chromosomes.  Mol Biol Cell. 2020 Nov 1; 31(23):2537-2556. Epub 2020 Sep 2. PMID: 32877270; PMCID: PMC7851874.
  21. Heer C.D., Voth L.S., Sanderson D.J. , Alhammad Y.M.O, Schmidt M.S., Trammell S.A.J, Perlman S., Cohen M.S.,  Fehr A.R., and Brenner C. Coronavirus infection and PARP expression dysregulate the NAD metabolome: An actionable component of innate immunity. J Biol Chem. 2020 Dec 25; 295(52):17986-17996. Epub 2020 Oct 13. PMID: 33051211; PMCID: PMC7834058.
  22. Hill, T., Unckless, RL.Recurrent evolution of high virulence in isolated populations of a DNA virus. Elife. 2020 Oct 28; 9:e58931.  PMID: 33112738; PMCID: PMC7685711.
  23. Klaus JR, Coulon PML, Koirala P, Seyedsayamdost MR, Déziel E, Chandler JR.Secondary metabolites from the Burkholderia pseudomallei complex: structure, ecology, and evolution. J Ind Microbiol Biotechnol. 2020 Oct;47(9-10):877-887. Epub 2020 Oct 14. PMID: 33052546; PMCID: PMC7746414.
  24. Klaus JR, Majerczyk C, Moon S, Eppler NA, Smith S, Tuma E, Groleau MC, Asfahl KL, Smalley NE, Hayden HS, Piochon M, Ball P, Dandekar AA, Gauthier C, Déziel E, Chandler JR. Burkholderia thailandensis Methylated Hydroxyalkylquinolines: Biosynthesis and Antimicrobial Activity in Cocultures. Appl Environ Microbiol. 2020 Nov 24; 86(24):e01452-20. PMID: 33008823; PMCID: PMC7688213.
  25. Kundrotas PJ, Kotthoff I, Choi SW, Copeland MM, Vakser IA. Dockground Tool for Development and Benchmarking of Protein Docking Procedures. Methods Mol Biol. 2020; 2165:289-300. PMID: 32621232.
  26. Kurland M, O'Meara B, Tucker DK, Ackley BD. The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt Signaling. J Dev Biol. 2020 Mar 3; 8(1):5.  PMID: 32138237; PMCID: PMC7151087.
  27. Lan L, Liu J, Xing M, Smith AR, Wang J, Wu X, Appelman C, Li K, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Miao Y, De Guzman R, Oakley BR, Neufeld KL, and Xu L.  Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction. Cancers (Basel) 2020; 2020 Aug 8; 12(8):2221. PMID: 32784494; PMCID: PMC7463734.
  28. Lan L, Xing M, Kashipathy MM, Douglas JT, Gao P, Battaile KP, Hanzlik RP, Lovell S, and Xu L. Crystal and solution structures of human oncoprotein musashi-2 N-terminal RNA recognition motif 1. Proteins. 2020 Apr; 88(4):573-583. Epub 2019 Oct 29. PMID: 31603583; PMCID: PMC7079100.
  29. Legrand N, Dixon DA, Sobolewski C. Stress granules in colorectal cancer: Current knowledge and potential therapeutic applications. World J Gastroenterol.  2020 Sep 21;26(35):5223-5247. PMID: 32994684; PMCID: PMC7504244.
  30. Liu S, Huang Z, Tang A, Wu X, Aube J, Xu L, Xing C, and Huang Y. Inhibition of RNA-binding protein HuR reduces glomerulosclerosis in experimental nephritis. Clinical Science (Lond) 2020; 134(12):1433-1448. PMID: 32478392; PMCID: PMC8086301.
  31. Macdonald SJ and Highfill CA. A naturally-occurring 22-bp coding deletion in Ugt86Dd reduces nicotine resistance in Drosophila melanogaster. BMC Res Notes.  2020 Mar 30; 13(1):188.  PMID: 32228671; PMCID: PMC7106894
  32. Miao, Y, Bhattarai, A., and Wang, J.  Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics. J Chem Theory Comput. 2020 Sep 8; 16(9):5526-5547.  Epub 2020 Aug 7. PMID: 32692556; PMCID: PMC7768792.
  33. Ochs ME, Josephson MP, Lundquist EA. The Predicted RNA-Binding Protein ETR-1/CELF1 Acts in Muscles To Regulate Neuroblast Migration in Caenorhabditis elegans. G3 (Bethesda). 2020 Jul 7; 10(7):2365-2376.  PMID: 32398235; PMCID: PMC7341121.
  34. Pandey N, Keifenheim D, Yoshida MM, Hassebroek VA, Soroka C, Azuma Y, Clarke DJ. Topoisomerase II SUMOylation activates a metaphase checkpoint via Haspin and Aurora B kinases. J Cell Biol. 2020 Jan 6;219(1):e201807189.  PMID: 31712254; PMCID: PMC7039214.
  35. Parker TW, Neufeld KL.  APC controls Wnt-induced β-catenin destruction complex recruitment in human colonocytes. Sci Rep. 2020 Feb 19; 10(1):2957 PMID: 32076059; PMCID: PMC7031393.
  36. Parker, TW., Rudeen, AJ., Neufeld, KL. Oncogenic Serine 45-Deleted β-Catenin Remains Susceptible to Wnt Stimulation and APC Regulation in Human Colonocytes. Cancers (Basel) 2020, Jul 30; 12(8):2114.  PMID: 32751567; PMCID: PMC7464804.
  37. Parthasarathy S, Jordan LD, Schwarting N, Woods MA, Abdullahi Z, Varahan S, Passos PMS, Miller B, Hancock LE.  Involvement of Chromosomally Encoded Homologs of the RRNPP Protein Family in Enterococcus faecalis Biofilm Formation and UTI Pathogenesis J Bacteriol. 2020 Aug 10; 202(17):e00063-20. PMID: 32540933; PMCID: PMC7417834.
  38. Pawnikar, S., Miao, Y.* Pathway and Mechanism of Drug Binding to Chemokine Receptors Revealed by Accelerated Molecular Simulations. Future Med Chem. 2020 Jul; 12(13):1213-1225. . Epub 2020 Jun 9. PMID: 32515227; PMCID: PMC7367101.
  39. Price TAR, Windbichler N, Unckless RL, Sutter A, Runge JN, Ross PA, Pomiankowski A, Nuckolls NL, Montchamp-Moreau C, Mideo N, Martin OY, Manser A, Legros M, Larracuente AM, Holman L, Godwin J, Gemmell N, Courret C, Buchman A, Barrett LG, Lindholm AK. Resistance to natural and synthetic gene drive systems. J Evol Biol. 2020 Oct; 33(10):1345-1360.  Epub 2020 Sep 24. PMID: 32969551; PMCID: PMC7796552.
  40. Rice C, Macdonald SJ, Wang X, Ward RE. The Broad Transcription Factor Links Hormonal Signaling, Gene Expression, and Cellular Morphogenesis Events During Drosophila Imaginal Disc Development. Genetics. 2020 Dec; 216(4):1137-1152. Epub 2020 Oct 28. PMID: 33115752; PMCID: PMC7768262.
  41. Rudeen AJ, Douglas JT, Xing M, McDonald WH, Lamb AL, Neufeld KL.The 15-Amino Acid Repeat Region of Adenomatous Polyposis Coli Is Intrinsically Disordered and Retains Conformational Flexibility upon Binding β-Catenin.Biochemistry.2020 Oct 20; 59(41):4039-4050. Epub 2020 Oct 1. PMID: 32941008; PMCID: PMC8771494.
  42. Schuler B, Borgia A, Borgia M, Heidarsson P, Holmstrom E, Nettels D, and Sottini A.  Binding without folding – the biomolecular function of disordered polyelectrolyte complexes.  Curr Opin Struct Biol. 2020 Feb; 60:66-76.  Epub 2019 Dec 23. PMID: 31874413.
  43. Schultz CW, Preet R, Dhir T, Dixon DA, Brody JR. Understanding and targeting the disease-related RNA binding protein human antigen R (HuR). Wiley Interdiscip Rev RNA. 2020 May; 11(3):e1581. Epub 2020 Jan 23. PMID: 31970930; PMCID: PMC7482136.
  44. Sharma R, Kk S, Holmstrom ED, Westerlund F. Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion. Biochem Biophys Res Commun. 2020 Nov 26; 533(1):175-180.  Epub 2020 Sep 18. PMID: 32951838; PMCID: PMC7577930.
  45. Singh A, Dauzhenka T, Kundrotas PJ, Sternberg MJE, Vakser IA. Application of docking methodologies to modeled proteins. Proteins. 2020 Sep; 88(9):1180-1188.  Epub 2020 Mar 20. PMID: 32170770; PMCID: PMC7416493.
  46. Smith BR, Macdonald SJ. Dissecting the Genetic Basis of Variation in Drosophila Sleep Using a Multiparental QTL Mapping Resource. Genes (Basel). 2020 Mar 11; 11(3):294. PMID: 32168738; PMCID: PMC7140804.
  47. Soldano A, Yao H, Chandler JR, Rivera M. Inhibiting Iron Mobilization from Bacterioferritin in Pseudomonas aeruginosa Impairs Biofilm Formation Irrespective of Environmental Iron Availability. ACS Infect Dis. 2020 Mar 13; 6(3):447-458. Epub 2020 Jan 15. PMID: 31898890; PMCID: PMC7076691.
  48. Unckless RL, Orr HA. The Population Genetics of Evolutionary Rescue in Diploids: X Chromosomal versus Autosomal Rescue. Am Nat. 2020 Mar;195(3):561-568. Epub 2020 Jan 15. PMID: 32097044; PMCID: PMC7252526.
  49. Vakser IA.Challenges in protein docking. Curr Opin Struct Biol. 2020 Oct; 64:160-165. d Epub 2020 Aug 21. PMID: 32836051; PMCID: PMC7666046.
  50. Wang, J, Miao, Y.  Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding. J Chem Phys. 2020 Oct 21; 153(15):154109. PMID: 33092378; PMCID: PMC7575327.
  51. Wu X, Gardashova G, Lan L, Han S, Zhong C, Marquez RT, Wei L, Wood S, Roy S, Gowthaman R, Karanicolas J, Gao FP, Dixon DA, Welch DR, Li L, Ji M, Aubé J, Xu L. Targeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasis. Commun Biol. 2020 Apr 24; 3(1):193.  PMID: 32332873; PMCID: PMC7181695.
  52. Yang Z, Mattingly BC, Hall DH, Ackley BD, Buechner M. Terminal web and vesicle trafficking proteins mediate nematode single-cell tubulogenesis. J Cell Biol. 2020 Nov 2; 219(11):e202003152. PMID: 32860501; PMCID: PMC7594493.
  53. Zhang A, Ackley BD, Yan D. Vitamin B12 Regulates Glial Migration and Synapse Formation through Isoform-Specific Control of PTP-3/LAR PRTP Expression. Cell Rep. 2020 Mar 24; 30(12):3981-3988.e3. PMID: 32209461; PMCID: PMC7281833.
  54. Zhang P, Wu X, Gardashova G, Yang Y, Zhang Y, Xu L*, and Zeng Y*.  Molecular and Functional Extracellular Vesicle Analysis using Nanopatterned Microchips Monitors Tumor Progression and Metastasis.  Sci Transl Med. 2020 Jun 10; 12(547):eaaz2878.  PMID: 32522804; PMCID: PMC8024111.
  1. Al-Hashimi, H., Chiarellie, T., Lundquist, E.A., Buechner, M., Novel exc Genes Involved in Formation of the Tubular Excretory Canals of Caenorhabditis elegans. G3: Genes/Genomes/Genetics on May 7. G3 (Bethesda). 2019 May 7;9(5):1339-1353. doi: 10.1534/g3.119.200626. PMID: 30885922
  2. Baker, H.A., Fabian, C.J., Hastings, R.C., Dixon, D.A., Nydegger, J.L., Phillips, T.A., Powers, K.R., Kimler, B.F. (2019) Circulating adipose stromal cells as a response biomarker in phase II energy balance trials of obese breast cancer survivors and high-risk women. Breast Cancer Res. Treat. Apr 30
  3. Benomar S, Evans K, Unckless R and Chandler JR. Efflux pumps in Chromobacterium species increase antibiotic resistance and promote survival in a co-culture competition model. AEM In press.
  4. Chakraborty M, Emerson JJ, Macdonald SJ, Long AD. (2019). Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nature Communications 10: 4872.
  5. Chapman, JR, T Hill and RL Unckless. 2019. Balancing selection drives the maintenance of genetic variation in Drosophila antimicrobial peptides. Genome Biology and Evolution (Early online). doi: 10.1093/gbe/evz191.
  6. Dey S, Chakravarty A, Guha Biswas P, De Guzman RN. The type III secretion system needle, tip, and translocon. Protein Sci. 2019 Sep;28(9):1582-1593.  Epub 2019 Aug 2. PMID: 31301256; PMCID: PMC6699086.
  7. Duxbury, E.ML., Day, J.P., Vespasiani, D.M., Thüringer,Y.,  Tolosana, I., Smith.S.CL., Tagliaferri, L., Kamacioglu, A., Lindsley, I., Love, L., Unckless, R.L., Jiggins, F.M., Longdon, B., (2019) Host-pathogen coevolution increases genetic variation in susceptibility to infection. eLife. Apr 30.
  8. Elramli, N., Karahoda, B., Bayram, Ö. S. Frawley, D., Ulas, M., Oakley, C. E., Oakley, B. R., Seiler, S. and Bayram, Ö. (In Press) Assembly of a heptameric STRPAK complex is required for coordination of light-dependent multicellular fungal development with secondary metabolism in Aspergillus nidulans. In Press: PLoS Genetics. 
  9. Everman, E. R., McNeil, C. L., Hackett, J. L., Bain, C. L. and Macdonald, S. J. (2019) Dissection of complex, fitness-related traits in multiple Drosophila mapping populations offers insight into the genetic control of stress resistance. Genetics 211: 1449-1467.
  10. Grau, M. F., R. Entwistle, C. E. Oakley, C. C. C. Wang, and B. R. Oakley. 2019. Overexpression of an LaeA-like Methyltransferase Upregulates Secondary Metabolite Production in Aspergillus nidulans. ACS Chem Biol 14:1643-1651.
  11. Green LC, Anthony SR, Slone S, Lanzillotta L, Nieman ML, Wu X, Robbins N, Jones SM, Roy S, Owens Iii AP, Aube J, Xu L, Lorenz JN, Blaxall BC, Rubinstein J, Benoit JB, Tranter M. Human antigen R as a therapeutic target in pathological cardiac hypertrophy. JCI Insight. 2019 Jan 22. [Epub ahead of print] PubMed PMID: 30668549.
  12. Gujar MR, Stricker AM, Lundquist EA (2019) RHO-1 and the Rho GEF RHGF-1 interact with UNC-6/Netrin signaling to regulate growth cone protrusion and microtubule organization in Caenorhabditis elegans. PLoS Genet 15(6): e1007960.
  13. Grunewald, M.E., M.G. Shaban, S.R. Mackin, A.R. Fehr, and Stanley Perlman. 2019. Murine coronavirus infection activates AhR in an IDO1-independent manner contributing to cytokine modulation and pro-viral TiPARP expression. J Virol. doi: 10.1128/JVI.01743-19. [Epub ahead of print]
  14. Grunewald, Matthew E., Yating Chen, Chad Kuny, Takashi Maejima, Robert Lease, Dana Ferraris, Masanori Aikawa, Christopher S. Sullivan, Stanley Perlman, Anthony R. Fehr (2019) The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression. PLOS Pathogens. May 16.
  15. Hadarovich A, Anishchenko I, Tuzikov AV, Kundrotas PJ, Vakser IA. Gene ontology improves template selection in comparative protein docking. Proteins. 2019 Mar; 87(3):245-253.  Epub 2018 Dec 27. PMID: 30520123; PMCID: PMC6380947.
  16. Hanson, Mark A., Lemaitre, Bruno, and Unckless, Robert L. (2019). Dynamic evolution of antimicrobial peptides underscores trade-offs between immunity and ecological fitness. Frontiers in Immunology 10.3389.
  17. Hill T, Boryana S. Koseva, Robert L. Unckless. The Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes” in Molecular Biology and Evolution. 2019. Mol.Biol.Evol. 36(7):1405-1417.
  18. Hill T, Unckless RL.  A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data. G3 (Bethesda). 2019 Nov 5;9(11):3575-3582.  PMID: 31455677; PMCID: PMC6829143.
  19. Horio, T., Szewczy, E., Oakley, C. E., Osmani, A. H., Osmani, S. A. and Oakley, B. R. (2019) SUMOlock reveals a more complete Aspergillus nidulans SUMOylome. Fungal Genet. Biol. 127:50-59.
  20. Scott D. LaBrie, Zoë E. Dimond, Kelly S. Harrison, Srishti Baid, Jason Wickstrum, Robert J. Suchland, P. Scott Hefty. (2019) Transposon Mutagenesis in Chlamydia trachomatis Identifies CT339 as a ComEC Homolog Important for DNA Uptake and Lateral Gene Transfer. MBio, 2019, 10(4), e01343-19.
  21. Jas GS, Vallejo-Calzada R, Johnson CK, Kuczera K. Dynamic elements and kinetics: Most favorable conformations of peptides in solution with measurements and simulations. J Chem Phys. 2019 Dec 14;151(22):225102. PMID: 31837693.
  22. Kenjic N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL.  PvdF of pyoverdin biosynthesis is a structurally unique N10-formyltetrahydrofolate-dependent formyltransferase.  Arch Biochem Biophys [Epub ahead of print]
  23. Koseva BS, Hackett JL, Zhou Y, Harris BR, Kelly JK, Greenfield MD, Gleason JM, Macdonald SJ. 2019. Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella. Genes, Genomes, Genetics 9: 2349-2361.
  24. Lea, JK and RL Unckless. 2019. An assessment of the immune costs associated with meiotic drive chromosomes in Drosophila. Proceedings of the Royal Society B. 286: 20191534. doi: 10.1098/rspb.2019.1534.
  25. Legrand N, Dixon DA, Sobolewski C. AU-rich elements-binding proteins in colorectal cancer. World J Gastrointest Oncol 2019; 11(2): 71-90
  26. Liu H, Marquez RT, Wu X, Li K, Vadlamani S, Li S, Wang Y, Xu L, Wu D. A non-intrusive evaluation method for tumor-targeting characteristics of nanomedicines based on in vivo near-infrared fluorescence imaging. J Mater Chem B. 2019 Aug 7;7(31):4751-4757. PMID: 31389969; PMCID: PMC6686867.
  27. McFarlane JS, Ronnebaum TA, Meneely KM, Chilton A, Fenton AW, Lamb AL.  Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-π bond.  Acta Crystallogr F Struct Biol Commun. 75, 461-469.
  28. McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL (2019).  Staphylopine and pseudopaline dehydrogenases catalyze reversible reactions and produce stereospecific metallophores.  Journal of Biological Chemistry. [Epub ahead of print]
  29. Monteleone, N.J., Moore, A.E., Iacona, J.R., Lutz, C.S  and Dixon, D.A. miR-21-mediated regulation of 15-hydroxyprostaglandin dehydrogenase in colon cancer. Scientific Reports, 2019.
  30. Moran GR, Lamb AL. (2019) The tenured itch: ready to treat your midcareer malaise?  ASBMB Today, 18(7), 49-50.
  31. Mutreja Y, Combs B, Gamblin TC (2018) FTDP-17 mutations alter the aggregation and microtubule stabilization propensity of tau in an isoform-specific fashion. Biochemistry. In Press. DOI: 10.1021/acs.biochem.8b01039
  32. New, J., Subramaniam, D., Ramalingam, S., Enders, J., Sayed, A.A.A., Ponnurangam, S., Standing, D. Ramamoorthy, P., O'Neil, M., Dixon, D.A., Umar, S., Jensen, R.A., Thomas, S.M. and Anant, S. Pleotropic role of RNA binding protein CELF2 in Autophagy Induction. Molecular Carcinogenesis. 2019; 1-10.
  33. Pandey N, Keifenheim D, Yoshida MM, Hassebroek VA, Soroka C, Azuma Y, Clarke DJ. Topoisomerase II SUMOylation activates a metaphase checkpoint via Haspin and Aurora B kinases. J Cell Biol. 2019 Nov 11. pii: jcb.201807189. doi: 10.1083/jcb.201807189. [Epub ahead of print]
  34. Perlmutter JI, Bordenstein SR, Unckless RL, LePage DP, Metcalf JA, Hill T, Martinez J, Jiggins FM, Bordenstein SR. The phage gene wmk is a candidate for male killing by a bacterial endosymbiont. PLoS Pathog. 2019 Sep 10;15(9):e1007936. PMID: 31504075; PMCID: PMC6736233.
  35. Ronnebaum TA, McFarlane JS, Prisinzano TE, Booker SJ, Lamb AL. Stuffed Methyltransferase Catalyzes the Penultimate Step of Pyochelin Biosynthesis. Biochemistry. 2019 Feb 12;58(6):665-678. Epub 2018 Dec 27. PMID: 30525512; PMCID: PMC6372355.
  36. Slinger BL, Deay JJ, Chandler JR, Blackwell HE. Potent modulation of the CepR quorum sensing receptor and virulence in a Burkholderia cepacia complex member using non-native lactone ligands. Sci Rep.2019 Sep 17;9(1):13449. PMID: 31530834; PMCID: PMC6748986.
  37. Wang D, Stoveken HM, Zucca S, Dao M, Orlandi C, Song C, Masuho I, Johnston C, Opperman KJ, Giles AC, Gill MS, Lundquist EA, Grill B, Martemyanov KA. (2019) Genetic behavioral screen identifies an orphan anti-opioid system, Science, 15 Aug 2019 first release.
  38. Wang, J., and Miao, Y. (2019) Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors, J. Phys. Chem. B, 123, 6462-6473.
  39. Zanders, SE and RL Unckless. 2019. Fertility costs of meiotic drivers. Current Biology 29: R512-520.
  40. Zeng Y, Ma J, Xu L, Wu D. Natural Product Gossypol and Its Derivatives in Precision Cancer Medicine. Curr Med Chem 2019; 26(10):1849-1873. PMID: 28545375.
  1. Abisado R, Benomar S, Klaus JR, Dandekar AA, Chandler JR. Bacterial quorum sensing and microbial community interactions. MBio2018 May 22;9(3). pii: e02331-17. doi: 10.1128/mBio.02331-17.
  2. Alan JK, Robinson SK, Magsig KL, Demarco RS, Lundquist EA. The Atypical Rho GTPase CHW-1 Works with SAX-3/Robo To Mediate Axon Guidance in Caenorhabditis elegans 2018 Apr 13. pii: g3.200148.2018. doi: 10.1534/g3.118.200148. [Epub ahead of print]
  3. Al-Hashimi H, Hall DH, Ackley BD, Lundquist EA, Buechner M “Intermediate filaments EXC-2 and IFA-4 Maintain Luminal Structure of the Tubular Excretory Canals in Caenorhabditis elegans” Genetics, v. 210, issue 2, pp. 637-652.
  4. Anishchenko I, Kundrotas PJ, Vakser IA. Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model. Biophys J. 2018 Sep 4; 115(5):809-821.  Epub 2018 Aug 8. PMID: 30122295; PMCID: PMC6127504.
  5. Bandyopadhyay A, Wang H, Ray JCJ. Lineage space and the propensity of bacterial cells to undergo growth transitions. PLoS Comput Biol. 2018 Aug 22;14(8):e1006380. doi: 10.1371/journal.pcbi.1006380
  6. Belkin S, Kundrotas PJ, Vakser IA.Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. J Comput Aided Mol Des. 2018 Jul; 32(7):769-779.  Epub 2018 Jul 12. PMID: 30003468; PMCID: PMC6640133.
  7. Bhattarai, A., and Miao, Y.* Gaussian accelerated molecular dynamics for elucidation of drug pathways. Expert Opinion On Drug Discovery. In Press
  8. Bardai FH, Wang L, Mutreja Y, Yenjerla M, Gamblin TC, Feany MB. A conserved cytoskeletal signaling cascade mediates neurotoxicity of FTDP-17 tau mutations in vivo. Journal of Neuroscience, 14 November 2017, 1550-17.
  9. Brody JR, Dixon DA. Complex HuR function in pancreatic cancer cells. Wiley Interdiscip Rev RNA. 2018 Feb 16. DOI: 10.1002/wrna.1469.
  10. Celestrin K, Díaz-Balzac CA, Tang LTH, Ackley BD, Bülow HE. Four specific immunoglobulin domains in UNC-52/Perlecan function with NID-1/Nidogen during dendrite morphogenesis in Caenorhabditis elegans. Development. 2018 May 14;145(10):dev158881. PMID: 29678816; PMCID: PMC6001381.
  11. Dauzhenka T, Kundrotas PJ, Vakser IA. Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking. J Comput Chem. 2018 Sep 15; 39(24):2012-2021.  Epub 2018 Sep 18. PMID: 30226647; PMCID: PMC6186188.
  12. Davido DJ, Tu EM, Wang H, Korom M, Gazquez Casals A, Reddy PJ, Mostafa HH, Combs B, Haenchen SD, Morrison LA. Attenuated HSV-1 expressing a mutant form of ICP6 stimulates a strong immune response that protects mice against HSV-1-induced corneal disease. J Virol. 2018 Jun 27. pii: JVI.01036-18. doi: 10.1128/JVI.01036-18. [Epub ahead of print]
  13. Dohn, J, Grubbs A, Oakley E,  Oakley B. New multi-marker strains and complementing genes for Aspergillus nidulans molecular biology. Fungal Genetics and Biology [Epub ahead of print].
  14. Evans KC, Benomar S, Camuy-Vélez LA, Nasseri EB, Wang X, Neuenswander B, Chandler JR.  Quorum-sensing control of antibiotic resistance stabilizes cooperation in Chromobacterium violaceum. The ISME J 2018 10.1038/s41396-018-0047-7.
  15. Franklin MW, Slusky JSG. Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding. J Mol Biol. 2018 Sep 14;430(18 Pt B):3251-3265. doi: 10.1016/j.jmb.2018.06.013. Epub 2018 Jun 23.
  16. Michelle F. Grau, Ruth Entwistle, Yi-Ming Chiang, Manmeet Ahuja, C. Elizabeth Oakley, Tomohiro Akashi, Clay C. C. Wang, Richard B. Todd, and Berl R. Oakley.  Hybrid Transcription Factor Engineering Activates the Silent Secondary Metabolite Gene Cluster for (+)-Asperlin in Aspergillus nidulans.  ACS Chem Biol, Article ASAP
  17. Gujar MR, Sundararajan L, Stricker A, Lundquist EA. Control of Growth Cone Polarity, Microtubule Accumulation, and Protrusion by UNC-6/Netrin and Its Receptors in Caenorhabditis elegans. Genetics. 2018 Jul 25. pii: genetics.301234.2018. doi: 10.1534/genetics.118.301234. [Epub ahead of print]PMID:30045855
  18. Hill T (Unckless Lab), Betancourt AJ Extensive exchange of transposable elements in the Drosophila pseudoobscura group in Mobile DNA. 2018
  19. Hill T, Unckless RL.The dynamic evolution of Drosophila innubila Nudivirus. Infect Genet Evol. 2018 Jan;57:151-157. Epub 2017 Nov 16. PMID: 29155284; PMCID: PMC5725240.
  20. Huang YM, McCammon JA, Miao Y. Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation. J Chem Theory Comput, 2018 Article ASAP, DOI: 10.1021/acs.jctc.7b01226. 
  21. Jas GS, Kuczera K. Deprotonation of a Single Amino Acid Residue Induces Significant Stability in an α-Helical Heteropeptide. J Phys Chem B. 2018 Dec 13;122(49):11508-11518. Epub 2018 Oct 19. PMID: 30339390.
  22. Kato J, Dey S, Soto JE, Butan C, Wilkinson MC, De Guzman RN, Galan JE. A protein secreted by the Salmonella type III secretion system controls needle filament assembly. eLife, 7, e35886, 2018. 
  23. 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 sensing. Journal of Bacteriology. 2018 May 7. pii: JB.00008-18. doi: 10.1128/JB.00008-18. [Epub ahead of print]
  24. Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA. Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.  Proteins. 2018 Mar; 86 Suppl 1(Suppl 1):302-310.  Epub 2017 Sep 28. PMID: 28905425; PMCID: PMC5820180.
  25. Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA. Dockground: A comprehensive data resource for modeling of protein complexes. Protein Sci. 2018 Jan; 27(1):172-181.  Epub 2017 Oct 10. PMID: 28891124; PMCID: PMC5734278.
  26. Lan L, Liu H, Smith AR, Appelman C, Yu J, Larsen S, Marquez RT, Wu X, Liu FY, Gao P, Gowthaman R, Karanicolas J, De Guzman RN, Rogers S, Aubé J, Neufeld KL, Xu L. Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins. BMC Cancer 2018; 18(1):809.
  27. Li J, Smith AR, Marquez RT, Li J, Li K, Lan L, Wu X, Zhao L, Ren F, Wang Y, Wang Y, Jia B, Xu L, Chang Z. MicroRNA-383 acts as a tumor suppressor in colorectal cancer by modulating CREPT/RPRD1B expression. Molecular Carcinogenesis 2018; 57(10):1408-1420. 
  28. McElfresh GC, Ray JCJ. 2018. Intergenerational Cellular Signal Transfer and Erasure. In: The interplay of thermodynamics and computation in natural and artificial systems. D. Wolpert, C. Kempes, J. Grochow and P. Stadler, Eds. Santa Fe Institute Press.
  29. McFarlane JS, Davis CL, Lamb AL.  Staphylopine, pseudopaline, and yersinopine dehydrogenases: a structural and kinetic analysis of a new functional class of opine dehydrogenase.  J. Biol. Chem.  [Epub ahead of print]
  30. McFarlane JS, Lamb AL. Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosa. Biochemistry 56(45): 5967-5971.
  31. McFarlane JS, Hagen R, Chilton AS, Forbes D, Lamb AL, Ellis HR.. Not as easy as π: an insertional residue does not explain the π-helix gain-of-function in two component FMN reductases. Protein Science [Epub ahead of print]
  32. Miao Y Acceleration of Biomolecular Kinetics in Gaussian Accelerated Molecular Dynamics. Journal of Chemical Physics, 149(7):072308. 2018.
  33. Miao, Y.*, Bhattarai, A., Nguyen, A. T., Christopoulos, A., and May, L. T. (2018) Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor, Scientific Reports, 8:16836.https://doi.org/10.1038/s41598-018-35266-x 
  34. Miao Y, Huang YM, Walker R, McCammon JA, & Chang C-eA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry, DOI: 10.1021/acs.biochem.7b01248.
  35. Miao Y, McCammon JA Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled Receptor. Proc Natl Acad Sci U S A, 2018 In Press, DOI: 10.1073/pnas.1800756115.
  36. Mostafa HH, Thompson TW, Konen AJ, Haenchen SD, Hilliard JG, Macdonald SJ, Morrison LA, Davido DJ. Herpes Simplex Virus 1 Mutant with Point Mutations in UL39 Is Impaired for Acute Viral Replication in Mice, Establishment of Latency, and Explant-Induced Reactivation.J Virol. 2018 Jan 10. pii: JVI.01654-17. doi: 10.1128/JVI.01654-17.
  37. Muralidharan R, Mehta M, Ahmed R, Roy S, Xu L, Aubé J, Chen A, Zhao YD, Herman T, Ramesh R, Munshi A. HuR-targeted small molecule inhibitor exhibits cytotoxicity towards human lung cancer cells. Scientific Reports2017; 7:9694.
  38. Mutreja Y and Gamblin TC. Optimization of in vitro conditions to study the arachidonic acid induction of 4R isoforms of the microtubule-associated protein tau. Methods in Cell Biology 141:65-88.
  39. Ni Z, He J, Wu Y, Hu C, Dai X, Yan X, Li B, Li X, Xiong H, Li Y, Li S, Xu L, Li Y, Lian J, He F. AKT-mediated phosphorylation of ATG4B impairs mitochondrial activity and enhances the Warburg effect in hepatocellular carcinoma cells. Autophagy [Epub ahead of print].
  40. V. Paolillo (Lundquist lab), C.B. Jenkinson, T. Horio, B.R. Oakley Cyclins in aspergilli: Phylogenetic and functional analyses of group I cyclins. in Science Direct June 2018.
  41. Peng W, Furuuchi N, Aslanukova L, Huang YH, Brown SZ, Jiang W, Addya S, Vishwakarma V, Peters E, Brody JR, Dixon DA, Sawicki JA. Elevated HuR in Pancreas Promotes a Pancreatitis-Like Inflammatory Microenvironment That Facilitates Tumor Development. Mol Cell Biol.  2018 Jan 16;38(3). pii: e00427-17. doi: 10.1128/MCB.00427-17.
  42. Pieper KE, Unckless RL, Dyer KA. A fast-evolving X-linked duplicate of importin-α2 is overexpressed in sex-ratio drive in Drosophila neotestacea. Mol Ecol. 2018 Dec;27(24):5165-5179. doi: 10.1111/mec.14928. Epub 2018 Dec 10. PMID: 30411843; PMCID: PMC6312747.
  43. Preet R, Dixon DA. Mutant KRAS Exosomes Influence the Metabolic State of the Colon Microenvironment Cellular and Molecular Gastroenterology and Hepatology, Volume 5, Issue 4, 2018, Pages 627-629.e6.
  44. Ranjan A, Iyer SV, Ward C, Link T, Diaz FJ, Dhar A, Tawfik OW, Weinman SA, Azuma Y, Izumi T, Iwakuma T. MTBP inhibits the Erk1/2-Elk-1 signaling in hepatocellular carcinoma.Oncotarget. 2018 Apr 20;9(30):21429-21443. PMID: 29765550; PMCID: PMC5940416.
  45. Reiner DJ, Lundquist EA. Small GTPases. WormBook. 2018 Aug 16; 2018:1-65. PMID: 27218782; PMCID: PMC6369420.
  46. Ronnebaum TA, Lamb AL.. Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study.  Current Opinion in Structural Biology 53, 1-11.
  47. Shelton CL, Lamb AL.  Unraveling the structure and mechanism of the MST(ery) Enzymes.  Trends Biochem Sci.2018 May;43(5):342-357.  Epub 2018 Mar 21. PMID: 29573882; PMCID: PMC5924575.
  48. Smith, BR, Unckless, RL. Draft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory-Derived Pathogen of Drosophila melanogaster. Genome Announcements 6: e01571-17.
  49. Utesch, T., Catalina, A. d. M., Schattenberg, C., Paege, N., Schmieder, P., Krause, E., Miao, Y., McCammon, J. A., Meyer, V., Jung, S., and Mroginski, M. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif. mSphere, 3(5), e00377-18
  50. Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aube J, Sun B, and Xu L. Identification of novel small molecule Beclin 1 mimetics activating autophagy. Oncotarget 2017; 8(31):51355. PMC5584254.
  51. Y Zeng, J Liu, S Yang, W Liu, L Xu, R Wang. Time-lapse live cell imaging to monitor doxorubicin release from DNA origami nanostructures. Journal of Materials Chemistry B, 2018.
  52. Zhang, J., Wang, N., Miao, Y.*, Hauser, F., Rappel, W.-J., McCammon, J. A., and Schroeder, J.* Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements. Proc Natl Acad Sci, In Press
  1. Ahmed-Braimah YH, Unckless RL, Clark AG. Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup. G3 (Bethesda). 2017 Sep 7;7(9):3145-3155. doi: 10.1534/g3.117.1136. PMID: 28739599; PMCID: PMC5592939.
  2. Akhund-Zade J, Bergland AO, Crowe SO, Unckless RL. The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention. J Insect Sci. 2017 Jan 27;17(1):5. doi: 10.1093/jisesa/iew094. PMID: 28042107; PMCID: PMC5270406.
  3. Alaofi A, Farokhi E, Prasasty VD, Anbanandam A, Kuczera K, Siahaan TJ. Probing the interaction between cHAVc3 peptide and the EC1 domain of E-cadherin using NMR and molecular dynamics simulations. J Biomol Struct Dyn. 2017 Jan;35(1):92-104. Epub 2016 Apr 12. PMID: 26728967; PMCID: PMC5061580.
  4. Bardai FH, Wang L, Mutreja Y, Yenjerla M, Gamblin TC, Feany MB. A conserved cytoskeletal signaling cascade mediates neurotoxicity of FTDP-17 tau mutations in vivo. Journal of Neuroscience, 14 November 2017, 1550-17.
  5. Clarke DJ, Azuma Y. Non-Catalytic Roles of the Topoisomerase IIα C-Terminal Domain. Int J Mol Sci. 2017 Nov 17;18(11):2438. doi: 10.3390/ijms18112438. PMID: 29149026; PMCID: PMC5713405.
  6. Dey S, Anbanandam A, Mumford BE, De Guzman RN. Characterization of Small-Molecule Scaffolds That Bind to the Shigella Type III Secretion System Protein IpaD. ChemMedChem. 2017 Sep 21;12(18):1534-1541. doi: 10.1002/cmdc.201700348. Epub 2017 Aug 31. PMID: 28750143; PMCID: PMC5741093.
  7. de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol. 2017 Feb 14;18(1):28. doi: 10.1186/s13059-017-1151-0. PMID: 28196534; PMCID: PMC5307856.
  8. Eshelman K, Yao H, Punchi Hewage AN, Deay JJ, Chandler JR, Rivera M.  Inhibiting the BfrB:Bfd interaction in Pseudomonas causes irreversible iron accumulation in bacterioferritn and iron deficiency in the bacterial cytosol.  Metallomics [Epub ahead of print]
  9. Gao FJ, Shi L, Hines T, Hebbar S, Neufeld KL, Smith DS.  Insulin signaling regulates a functional interaction between Adenomatous Polyposis Coli (APC) and cytoplasmic dynein.  Molecular Biology of the Cell. [Epub ahead of print]
  10. Gujar MR, Stricker AM, Lundquist EA. Flavin monooxygenases regulate Caenorhabditis elegans axon guidance and growth cone protrusion with UNC-6/Netrin signaling and Rac GTPases.PLoS Genet. 2017 Aug 31;13(8):e1006998. doi: 10.1371/journal.pgen.1006998. eCollection 2017 Aug.
  11. Highfill CA, Tran JH, Nguyen SKT, Moldenhauer TR, Wang X, Macdonald SJ. Naturally Segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster. Genetics 2017, 207:311-325.
  12. Hill T and Unckless RL. Baculovirus molecular evolution via gene turnover and recurrent positive selection of key genes. J Virol. 2017 Oct 27;91(22):e01319-17. doi: 10.1128/JVI.01319-17. PMID: 28814516; PMCID: PMC5660496. 
  13. Josephson MP, Aliani R, Norris ML, Ochs ME, Gujar M, Lundquist EA.  The Caenorhabditis elegans NF2/Merlin Molecule NFM-1 Non-autonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit.  Genetics [Epub ahead of print]
  14. Kaur K, Park H, Pandey N, Azuma Y, De Guzman RN. Identification of a new small ubiquitin-like modifier (SUMO)-interacting motif in the E3 ligase PIASy. J Biol Chem. 2017 Jun 16;292(24):10230-10238. doi: 10.1074/jbc.M117.789982. Epub 2017 Apr 28. PMID: 28455449; PMCID: PMC5473226.
  15. Kaur K, Wu X, Fields JK, Johnson DK, Lan L, Pratt M, Somoza AD, Wang CCC, Karanicolas J, Oakley BR, Xu L, De Guzman RN.  The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro.  PLoS One 12(4):e0175471.
  16. McFarlane JS, Lamb AL. Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosa. Biochemistry 56(45): 5967-5971.
  17. Mutreja Y and Gamblin TC. Optimization of in vitro conditions to study the arachidonic acid induction of 4R isoforms of the microtubule-associated protein tau. Methods in Cell Biology 141:65-88.
  18. Najarro MA, Hackett JL, Macdonald SJ. Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster. G3 (Bethesda) 7(6):1631-1641.
  19. Nussinov R, Papin JA, Vakser I.  Computing the dynamic supramolecular structural proteome.  PLoS Computational Biology 13: e1005290.
  20. Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Russo Wortman J, Wang CC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol. 2017 Jan;103(2):347-365. Epub 2016 Nov 14. PMID: 27775185; PMCID: PMC5218965.
  21. Peterson B, Xu L, Levy M.  Targeting multiple receptors on a cell surface for specific cell targeting.  US Patent No.  US 9,636,419, issued May 2.
  22. Rowland MA, Greenbaum JM, Deeds EJ.  Crosstalk and the evolvability of intracellular communication.  Nature Communications 8: 16009.
  23. Sorger R, Bachman JA, Smith A, Sorger PK, Deeds EJ.  Fundamental trade-offs between information flow in single cells and cellular populations.  Proceedings of the National Academy of Sciences USA 114(22): 555-5760.
  24. Sung CT, Chang S-L, Entwistle R, Ahn G, Lin T-S, Petrova V, Yeh H-H, Praseuth MB, Chiang Y-M, Oakley BR, Wang CCC.  Overexpression of a three-gene conidial pigment biosynthetic pathway in Aspergillus nidulans reveals the first NRPS known to acetylate tryptophan. Fungal Genetics and Biology [Epub ahead of print]
  25. Unckless RL, Clark AG, Messer PW. Evolution of Resistance Against CRISPR/Cas9 Gene Drive. Genetics. 2017 Feb;205(2):827-841. doi: 10.1534/genetics.116.197285. Epub 2016 Dec 10. PMID: 27941126; PMCID: PMC5289854.
  26. Wickell DA, Windham MD, Wang X, Macdonald SJ, Beck JB. Can asexuality confer a short-term advantage? Investigating apparent biogeographic success in the apomictic triploid fern Myriopteris gracilis. Am J Bot. 2017 Aug;104(8):1254-1265. doi: 10.3732/ajb.1700126. PMID: 28814405; PMCID: PMC6013364.
  27. Wolfe AR, Ernlund A, McGuinness W, Lehmann C, Carl K, Balmaceda N, Neufeld KL.  Suppression of intestinal tumorigenesis in Apc mutant mice by Musashi-1 deletion.  Journal of Cell Science [Epub ahead of print]
  28. Yu J, Lan L, Lewin SJ, Rogers SA, Roy A, Wu X, Gao P, Karanicolas J, Aube J, Sun B, and Xu L. Identification of novel small molecule Beclin 1 mimetics activating autophagy. Oncotarget 2017; 8(31):51355. PMC5584254.
  29. Yu J, Zhao X, Zhang N, You C, Yao G, Zhu J, Xu L, and Sun B. Identification of novel 3-nitroacridines as autophagy inducers in gastric cancer cells. New Journal of Chemistry2017; 41(10):4087-4095.
  30. Zeng Y, Ma J, Xu L, Wu D. Natural Product Gossypol and Its Derivatives in Precision Cancer Medicine. Current Medicinal Chemistry. 2017 (in press).
  31. Zhang P, Wang X, Fan A, Zheng Y, Liu X, Wang S, Zou H, Oakley BR, Keller NP, Yin WP.  A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici. Mol Microbiol.  [Epub ahead of print]
  32. Zheng Y-G, Wu X-Q, Su J, Jiang P, Xu L, Gao J, Cai B, and Ji M. Design and synthesis of a novel photoaffinity probe for labelling egf receptor tyrosine kinases. Journal of Enzyme Inhibition and Medicinal Chemistry 2017; 32(1):954-959.
  1. Basha A, Basha F, Ali SK, Hanson PR, Oakley BR, Hajovsky H, Mitscher LA.  Onychomycosis and its Chemotherapy. Curr Med Chem 23: 1609-1624.
  2. Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR.  Ligand binding phenomena that pertain to the metabolic function of renalase.  Arch Biochem Biophys 612, 46-56.
  3. Blanco FF, Preet R, Aguado A, Vishwakarma V, Stevens LE, Vyas A, Padhye S, Xu L, Weir SJ, Anant S, Meisner-Kober N, Brody JR, and Dixon DA. Impact of HuR inhibition by the small molecule MS-444 on colorectal cancer cell tumorigenesis. Oncotarget [Epub ahead of print]
  4. Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl. 2016 Jan 26;55(5):1662-5. Epub 2015 Nov 13. PMID: 26563584; PMCID: PMC4724294.
  5. Gruseendorf KA, Trezza CJ, Salem AT, Al-Hashimi H, Mattingly BC, Kampmeyer DE, Khan L, Hall DH, Gobel V, Ackley BD, Buechner M. Facilitation of Endosomal Recycling by an IRG Protein Homologue Maintains Apical Tubule Structure in Caenorhabditis elegans. Genetics [Epub ahead of print]
  6. Hackett JL, Wang X, Smith BR, Macdonald SJ.  Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.  PLoS One. 11: e0162573
  7. Highfill CA, Reeves GA, Macdonald SJ.  Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population.  BMC Genet.  17:113.
  8. Huang W, Beer RL, Delaspre F, Wang G, Edelman HE, Park H, Azuma M, Parsons MJ.  Sox9b is a mediator of retinoic acid signaling restricting endocrine progenitor differentiation.  Developmental Biology 418, 28-39.
  9. Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA.  Challenges in structural approaches to cell modeling.  J Mol Biol 428: 2943-64.
  10. Jas GS, Middaugh CR, Kuczera K. Probing Selection Mechanism of the Most Favorable Conformation of a Dipeptide in Chaotropic and Kosmotropic Solution. J Phys Chem B. 2016 Jul 21;120(28):6939-50. Epub 2016 Jul 7. PMID: 27328987.
  11. Jas GS, Rentchler EC, Słowicka AM, Hermansen JR, Johnson CK, Middaugh CR, Kuczera K. Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte. J Phys Chem B. 2016 Mar 31;120(12):3089-99. Epub 2016 Mar 21. PMID: 26967551.
  12. Josephson MP, Chai Y, Ou G, Lundquist EA.  EGL-20/Wnt and MAB-5/Hox Act Sequentially to Inhibit Anterior Migration of Neuroblasts in C. elegans.  PLoS One: e0148658.
  13. Josephson MP, Miltner AM, Lundquist EA. Non-autonomous Roles of MAB-5/Hox and the Secreted Basement Membrane Molecule SPON-1/F-spondin in Caenorhabditis elegans Neuronal Migration. Genetics. 2016 May 25. pii: genetics.116.188367. [Epub ahead of print]
  14. Johnson DK, Karanicolas J.  Ultra-high-throughput structure-based virtual screening for small-molecule inhibitors of protein-protein interactions.  J. Chem. Inf. Model. [Epub ahead of print]
  15. Kaur K, Chatterjee S, De Guzman RN. Characterization of the Shigella and Salmonella Type III Secretion System Tip-Translocon Protein-Protein Interaction by Paramagnetic Relaxation Enhancement. Chembiochem. 2016 Apr 15;17(8):745-752. doi: 10.1002/cbic.201500556. Epub 2016 Feb 10. PMID: 26749041; PMCID: PMC4918631.
  16. Lanza C, Tan EP, Zhang Z, Machacek M, Brinker AE, Azuma M,  Slawson C.  Reduced O-GlcNAcase expression promotes mitotic errors and spindle defects.  Cell Cycle 15: 1363-75.
  17. Lee BL, Kuczera K, Middaugh CR, Jas GS. Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study. J Chem Phys. 2016 Jun 28;144(24):245103. PMID: 27369545.
  18. Li J, Wehmeyer G, Lovell S, Battaile KP, Egan SM. 1.65 Å resolution structure of AraC family transcriptional activator ToxT from Vibrio cholera.  Acta Cryst.  F72:726-731.
  19. McShan AC, Anbanandam A, Patnaik S, De Guzman RN. Characterization of the Binding of Hydroxyindole, Indoleacetic acid, and Morpholinoaniline to the Salmonella Type III Secretion System Proteins SipD and SipB. ChemMedChem. 2016 May 6;11(9):963-71. doi: 10.1002/cmdc.201600065. Epub 2016 Mar 18. PMID: 26990667; PMCID: PMC5010876.
  20. McShan AC, Kaur K, Chatterjee S, Knight KM, De Guzman RN. NMR identification of the binding surfaces involved in the Salmonella and Shigella Type III secretion tip-translocon protein-protein interactions. Proteins. 2016 Aug;84(8):1097-107. doi: 10.1002/prot.25055. Epub 2016 May 5. PMID: 27093649; PMCID: PMC5261137.
  21. Meneely KM, Ronnebaum TA, Riley AP, Prisinzano TE, Lamb AL. (2016)  Holo structure and steady state kinetics of the thiazolinyl imine reductases for siderophore biosynthesis.  Biochemistry 55, 5423-33.
  22. Meneely KM, Sundlov JA, Gulick AM, Moran GR, Lamb AL.  An open and shut case: the role of magnesium in MST enzymes.  J. Am. Chem. Soc.  [Epub ahead of print]
  23. Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ.  Identifying loci contributing to natural variation in xenobiotic resistance in Drosophila.  PLoS Genet 11(11): e1005663.
  24. Nariya MK, Israeli J, Shi JJ, Deeds EJ.  Mathematical model for length control by the timing of substrate switching in the type III secreation system.  PLoS Comput Biol: e1004851.
  25. Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Wortman JR, Wang CC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol [Epub ahead of print]
  26. Park H, Galbraith R, Turner T, Mehojah J, Azuma M.  Loss of Ewing sarcoma EWS allele promotes tumorigenesis by inducing chromosomal instability in zebrafish.  Sci Rep doi.10.1038/srep32297.
  27. Ray JCJ.  Survival of Phenotypic Information during Cellular Growth Transitions.  ACS Synth Biol. {Epub ahead of print].
  28. Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G. Cellular Growth Arrest and Persistence from Enzyme Saturation.  PLoS Comput Biol. 12(3):e1004825.
  29. Schwieterman AA, Steves AN, Yee V, Donelson CJ, Bentley MR, Santorella EM, Mehlenbacher TV, Pital A, Howard AM, Wilson MR, Ereddia DE, Effrein KS, McMurry JL, Ackley BD, Chisholm AD, Hudson ML. The Caenorhabditis elegans Ephrin EFN-4 Functions Non-cell Autonomously with Heparan Sulfate Proteoglycans to Promote Axon Outgrowth and Branching. Genetics. 2016 Feb;202(2):639-60. Epub 2015 Dec 8. PMID: 26645816; PMCID: PMC4788240.
  30. Slone S, Anthony SR, Wu X, Benoit JB, Aube J, Xu L, Tranter M.  Activation of HuR downstream of p38 MAPK promotes cardiomyocyte hypertrophy. Cellular Signaling 28, 1735-1741.
  31. Sridharan V, Azuma Y.  SUMO-interacting motifs (SIMs) in Polo-like kinase 1-interacting checkpoint helicase (PICH) ensure proper chromosome segregation during mitosis.  Cell Cycle [Epub ahead of print]
  32. Sun J, Chen Y, Li K, Huang Y, Fu X, Zhang X, Zhao W, Wei Y, Xu L, Zhang P, Venkataramanan R, and Li S. A prodrug micellar carrier assembled from polymers with pendant farnesyl thiosalicylic acid moieties for improved delivery of paclitaxel. Acta Biomaterialia 43, 282-291
  33. Tseng BS, Majerczyk CD, Passos da Silva D, Chandler JR, Greenberg EP, Parsek MR.  Quorum sensing influences Buukholderia thailandensis biofilm development and matric production.  J Bacteriol [Epub ahead of print]
  34. Varahan S, Hancock LE. To Defend or Not To Defend: That's the Question. mSphere. 2016 Jun 1;1(3):e00127-16. doi: 10.1128/mSphere.00127-16. PMID: 27306929; PMCID: PMC4894676.
  35. Wang X, Hinshaw KC, Macdonald SJ, Chandler JR.  Draft genome sequence of Chromobacterium violaceum strain CV017.  Genome Accounc 4(2): e00080-16.
  36. Wiley EO, Fuiten AM, Doosey MH, Lohman BK, Merkes C, Azuma M.  The caudal skeleton of the zebrafish, Danio rerio, from a phylogenetic perspective: a polyural interpretation of homologous structures.  Copeia 103 (4), 740-750.
  37. Wu X, Tang W, Marquez RT, Li K, Highfill CA, He F, Lian J, Lin J, Fuchs JR, Ji M, Li L, Xu L.  Overcoming chem/radio-resistance of pancreatic cancer by inhibiting STAT3 signaling.  Oncotarget [Epub ahead of print].
  38. Xu B-Q, Fu Z-G, Meng Y, Wu X-Q, Wu B, Xu L, Jiang J-L, Li L, and Chen Z-N. Gemcitabine enhances cell invasion via activating HAb18G/CD147-EGFR-pSTAT3 signaling. Oncotarget [Epub ahead of print]
  39. Yeh HH, Ahuja M, Chiang YM, Oakley CE, Moore S, Yoon O, Hajovsky H, Bok JW, Keller NP, Wang CC, Oakley BR.  Resistance gene-guided genomie mining: serial promoter exchanges in Aspergillus nidulans reveal the biosynthetic pathway for fellutamide B, a proteasome inhibitor.  ACS Chem Biol [Epub ahead of print]
  40. Yoshida MM, Azuma Y. Mechanisms behind Topoisomerase II SUMOylation in chromosome segregation. Cell Cycle. 2016 Dec;15(23):3151-3152. doi: 10.1080/15384101.2016.1216928. Epub 2016 Aug 2. PMID: 27484981; PMCID: PMC5176152.
  41. Yoshida MM, Ting L, Gygi SP, Azuma Y.  SUMOylation of DNA topoisomerase IIα regulates histone H3 kinase Haspin and H3 phosphorylation in mitosis.  J. Cell Biol 213: 665-78.
  1. Barta ML, Battaile KP, Lovell S, Hefty PS.  Hypothetical Protein CT398 (CdsZ) Interacts with σ54 (RpoN)-Holoenzyme and the Type III Secretion Export Apparatus in Chlamydia trachomatis.  Protein Sci [Epub ahead of print]
  2. Boutell C, Davido DJ. A quantitative assay to monitor HSV-1 ICP0 ubiquitin ligase activity in vitro. Methods 2015 Apr 8 [Epub ahead of print]
  3. Chaudhury S, Nordhues BA, Kaur K, Zhang N, De Guzman RN. Nuclear Magnetic Resonance Characterization of the Type III Secretion System Tip Chaperone Protein PcrG of Pseudomonas aeruginosa. Biochemistry. 2015 Nov 3;54(43):6576-85. doi: 10.1021/acs.biochem.5b00664. Epub 2015 Oct 21. PMID: 26451841; PMCID: PMC5289745.
  4. Chiang Y-M, Ahuja M., Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CC, Oakley BR. Development of genetic dereplication strain in Aspergillus nidulans results in the discovery of Aspercryptin. Angew Chem Int Ed Eng [Epub ahead of print]
  5. Deng L, Shang L, Bai S, Chen J, He X, Trevino RM, Chen S, Li X, Meng X, Yu B, Wang X, Liu Y, McDermott SP, Ariazi AE, Ginestier C, Ibarra I, Ke J, Luther TK, Clouthier SG, Xu L, Shan G, Song E, Yao H, Hannon GJ, Weiss SJ, Wicha MS, Liu S. microRNA100 inhibits self-renewal of breast cancer stem-like cells and breast tumor development. Cancer Research 74, 6648-6660.
  6. Edgerton H, Paolillo V, Oakley BR.  Spatial regulation of the spindle assembly checkpoint and anaphase promoting complex in Aspergillus nidulans.  Molecular Microbiology.  [Epub ahead of print]
  7. Fowler AM, Shinogle HE, Davido DJ.  Development of a novel cell-based assay to monitor the transactivation activity of the HSV-1 protein ICP0.  Antiviral Res 120: 1-6.
  8. Gilmore MS, Rauch M, Ramsey MM, Himes PR, Varahan S, Manson JM, Lebreton F, Hancock LE.  Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains.  Proc Natl Acad Sci USA [Epub ahead of print]
  9. Gonzalez C, Ray JCJ, Manhard M, Adams RM, Nevozhay D, Morozov AV, Balazsi G.  Stress-response balance drives the evolution of a network module and its host genome.  Mol Systems Biol 11: 827.
  10. Gowthaman R, Lyskov S, Karanicolas J.  DARC 2.0: Improved docking and virtual screening at protein interaction sites.  PLoS One 10(7):e0131612.
  11. Gowthaman R, Miller SA, Robers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aube J, Roy A, Karanicolas J.  DARC: Mapping surface topography by ray-casting for effective virtual screening at protein interaction sites.  J. Med Chem.  [Epub ahead of print]
  12. Guo C-J, Sun W-W, Bruno KS, Oakley BR, Keller NP, Wang CCC.  Spatial regulation of a common precursor from two distinct genes generates metabolite diversity. Chemical Science [In Press]
  13. Hartin SN, Hudson ML, Yingling C, Ackley BD.  A synthetic lethal screen identifies a role for Lin-44/Wnt in C. elegans embryogenesis.  PLoS One: e0121397.
  14. Hinks J, Poh WH, Chu JJ, Loo JS, Bazan GC, Hancock LE, Wuertz S. Oligopolyphenylenevinylene-conjugated oligoelectrolyte membrane insertion molecules selectively disrupt cell envelopes of Gram-positive bacteria. Appl Environ Microbiol. 2015 Mar;81(6):1949-58. doi: 10.1128/AEM.03355-14. Epub 2015 Jan 9. PMID: 25576607; PMCID: PMC4345381.
  15. Johnson DK, Karanicolas J.  Selectivity of small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations.  PLoS Comput Biol: e1004081.
  16. Kuczera K.  Molecular modeling of peptides.  Methods Mol Biol 1268: 15-41.
  17. Lamb AL.  Breaking a pathogen’s iron will: inhibiting siderophore production as an antimicrobial strategy.  Biochim Biophys Acta 1854, 1054-1070.
  18. Lamb AL, Kappock TJ, Silvaggi NR.  You are lost without a map: navigating the sea of protein structures.  Biochim Biophys Acta [Epub ahead of print]
  19. LaFayette S, Houle D, Beaudoin T, Wojewodka G, Radzioch D,  Hoffman L, Burns J, Dandekar A, Smalley N, Chandler JR, Zlosnik J, Speert D, Bernier J, Matouk E, Brochiero E, Rousseau S, Nguyen D. Cystic fibrosis-adapted Pseudomonas aeruginosa quorum sensing lasR mutants cause hyper-inflammatory responses. Science Adv 1: e1500199
  20. Lan L, Appelman C, Smith AR, Yu J, Larsen S, Marquez RT, Wu X, Gao P, Roy A, Anbanandam A, Gowthaman R, Karanicolas J, De Guzman RN, Rogers SA, Aube J, Ji M, Cohen RS, Neufeld KL, Xu L. Natural product (–)-gossypol inhibits colon cancer cell growth by targeting RNA-binding protein Musashi-1. Molecular Oncology 2015 (in press)
  21. Li K, Liu H, Gao W, Chen M, Zeng Y, Liu J, Xu L, Wu D.  Mulberry-like dual-drug complicated nanocarriers assembled with apogossypolone amphiphilic starch micelles and doxorubicin hyaluronic acid nanoparticles for tumor combination and targeted therapy.  Biomaterials 2015; 39(1):131-144.
  22. Liu H, Li K, Xu L, Wu D. Bilayered near-infrared fluorescent nanoparticles based on low molecular weight PEI for tumor-targeted in vivo imaging. Journal of Nanoparticle Research 16: 2784.
  23. Lu J, Zhao W, Liu H, Marquez R, Huang Y, Zhang Y, Li J, Xie W, Venkataramanan R, Xu L, Li S.  An Improved D-α-Tocopherol-Based Nanocarrier for Targeted Delivery of Doxorubicin with Reversal of Multidrug Resistance.  Journal of Controlled Release [Epub ahead of print]
  24. McShan AC, De Guzman RN. The bacterial type III secretion system as a target for developing new antibiotics. Chem Biol Drug Des. 2015 Jan;85(1):30-42. doi: 10.1111/cbdd.12422. PMID: 25521643; PMCID: PMC5261607.
  25. Merkes C, Turkalo TK, Wilder N, Park H, Wenger LW, Lewin SJ, Azuma M.  Ewing sarcoma Ewsa protein regulates chondrogenesis of Meckel’s cartilage through modulation of Sox9 in zebrafish. PLoS ONE: e0116627.
  26. Mostafa HH, van Loben Sels JM, Davido DJ. HSV-1 upregulates p35, alters CDK-5 localization, and stimulates CDK-5 kinase activity during acute infection in neurons. J Virol. 2015 Feb 18. pii: JVI.00106-15.
  27. Newton AH, Danahy DB, Chan MA, Benedict SH.  Timely blockade of ICAM-1.LFA-1 interaction prevents disease onset in a mouse model of emphysema.  Immunotherapy [Epub ahead of print]
  28. Oakley BR, Paolillo V, Zheng Y.  gamma-tubulin complexes in microtubule nucleation and beyond.  Mol Biol Cell 26: 2957-2962.
  29. Paranjape SR, Riley AP, Somoza AD, Oakley CE, Wang CC, Prisinzano TE, Oakley BR, Gamblin TC. Azaphilones Inhibit Tau Aggregation and Dissolve Tau Aggregates in Vitro. ACS Chemical Neuroscience 2015 Apr 15 [Epub ahead of print]
  30. Truong TT, Seyedsayamdost M, Greenberg EP, Chandler JR.  A Burkholderia thailandensis acyl-homoserine lactone-independent LuxR homolog that activates production of the cytotoxin malleilactone.  J. Bacteriol [Eub ahead of print]
  31. Rowland MA, Harrison B, Deeds EJ.  Phosphatase specificity and pathway insulation in signaling networks.  Biophys J. 108(4): 986-96.
  32. Ryu H, Yoshida MM, Sridharan V, Kumagai A, Dunphy WG, Dasso M, Azuma Y.  SUMOylation of the C_terminal domain of DNA topoisomerase IIa regulates the centromeric localization of Claspin.  Cell Cycle [Epub ahead of print]
  33. Shogan BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers R, Hancock LE, Gilbert J, Zaborina O, Alverdy JC.  Collagen Degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak.  Sci Transl Med 7(286):286ra68.
  34. Smith MC, Box AC, Haug JS, Lane WS, Davido DJ.  A Phospho-SIM in the Antiviral Protein PML is Required for Its Recruitment to HSV-1 Genomes.  Cells 3, 1131-1158.
  35. Sridharan V, Park H, Ryu H, Azuma Y.  SUMOylation regulates Polo-like kinase 1-interacting checkpoint helicase (PICH) during mitosis.  J Biol Chem. [Epub ahead of print]
  36. Smalley NE, An D, Parsek M, Chandler JR, Dandekar A. Quorum sensing protects Pseudomonas aeruginosa against cheating by other species in a laboratory co-culture model.  J Bacteriol [EPub ahead of print]
  37. Smith AR, Marquez RT, Tsao W-C, Pathak S, Roy A, Ping J, Wilkerson B, Lan L, Meng W, Neufeld KL, Sun X-F, Xu L. Tumor Suppressive microRNA-137 Negatively Regulates Musashi-1 in Colorectal Cancer. Oncotarget 2015 (in press).
  38. Sundararajan L, Norris ML, Lundquist EA.  SDN-1/Syndecan Acts in Parallel to the Transmembrane Molecule MIG-13 to Promote Anterior Neuroblast Migration.  G3 (Bethesda) [Epub ahead of print].
  39. Tewary SK, Liang L, Lin Z, Lynn A, Cotmore SF, Tattersall P, Zhao H, Tang L.  Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding.  Virology.  [Epub ahead of print]
  40. Truong TT, Seyedsayamdost M, Greenberg EP, Chandler JR. A Burkholderia thailandensis Acyl-Homoserine Lactone-Independent Orphan LuxR Homolog That Activates Production of the Cytotoxin Malleilactone. J Bacteriol. 2015 Nov;197(21):3456-62.  Epub 2015 Aug 17. PMID: 26283771; PMCID: PMC4621068.
  41. Wang B, Chen L, Ni Z, Dai X, Qin L, Wu Y, Li X, Xu L, Lian J, He F.  Hsp90 inhibitor 17-AAG sensitizes Bcl-2 inhibitor (-)-gossypol by suppressing ERK-mediated protective autophagy and Mcl-1 accumulation in hepatocellular carcinoma cells.  Experimental Cell Research, 2014. 328(2):379-387.
  42. Wang B, Li K, Jin M, Qiu R, Liu B, Oakley BR, Xiang X.  The Aspergillus nidulans bimC4 mutation provides an excellent tool for identification of kinesin-14 inhibitors. Fungal Genet. Biol. 82:51-55.
  43. Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J.  Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association. Nat Commun. 6: 6384-95.
  44. Wu X, Lan L, Wilson DM, Marquez RT, Tsao W-C, Gao P, Roy A, Turner B, McDonald P, Tunge JA, Rogers SA, Dixon DA, Aube J, and Xu L. Identification and validation of novel small molecule disruptors of HuR-mRNA interaction. ACS Chem Biol 2015 [Epub ahead of print]
  45. Zeineldin, M. & Neufeld, K.L. “New insights from animal models of colon cancer: Inflammation control as a new facet on the tumor suppressor APC gem” Gastrointestinal Cancer: Targets and Therapy: 2015:5: 39—52
  1. Al-Ani G, Briggs K, Malik SS, Conner M, Azuma Y, Fischer CJ.  Quantitative determination of binding of ISWI to nucleosomes and DNA shows allosteric regulation of DNA binding by nucleotides.  Biochemistry 53, 4334-4345.
  2. Al-Ani G, Malik SS, Eastlund A, Briggs K, Fischer CJ.  ISWI remodels nucleosomes through a random walk.  Biochemistry 53, 4346-57.
  3. Barta ML, Hickey JM, Anbanandam A, Dyer K, Hammel M, Hefty PS.  Atypical response regulator ChxR from Chlamydia trachomatis is structrurally posed for DNA binding.  PLoS One.  2014 Mar 19; 9(3):e91760.
  4. Barta ML, Lovell S, Sinclair AN, Battaile KP, Hefty PS.  Chlamydia trachomatis CT771 (nudH) is an asymmetric Ap4A hydrolase.  Biochemistry [Epub ahead of print].
  5. Barta ML, Thomas K, Yuan H, Lovell S, Battaile KP, Schramm VL, Hefty PS.  Structural and Biochemical Characterization of Chlamydia trachomatis Hypothetical Protein CT263 Supports that Menaquinone Synthesis Occurs through the Futalosine Pathway.  J. Biol. Chem.  [Epub ahead of print]
  6. Basha A, Basha F, Ali SK, Hanson PR, Mitscher LA, Oakley BR.  Recent Progress in the Chemotherapy of Human Fungal Diseases. Emphasis on 1,3-beta-Glucan Synthase and Chitin Synthase Inhibitors. Curr Med Chem 20, 4859-4887.
  7. Chiang Y-M, Wang C C C, Oakley BR. (2014) Analyzing fungal secondary metabolite genes and gene clusters.  In Natural Products: Discourse, Diversity & Design. (Edited by A. Osbourn, R. Goss and G. Carter), John Wiley & Sons, Hoboken, N.J.  pp 175-193.
  8. Chilton AS, Ellis AL, Lamb AL.  Structure of an Aspergillus fumigatus old yellow enzymes (EasA) involved in ergot alkaloid biosynthesis.  Acta Crystallogr F Struct Biol Commun.  70: 1328-32.
  9. Conlin PL, Chandler JR, Kerr B.  Games of life and death: antibiotic resistance and production through the lens of evolutionary game theory.  Curr Opin Micro 21: 35-44.
  10. Frederick RE, Ojha S, Lamb AL, Dubois JL.  How pH modulates the reactivity and selectivity of a siderophore-associated flavin monooxygenase.  Biochemistry.  [Epub ahead of print]
  11. Jain P, Li J, Porubsky P, Neuenswander B, Egan SM, Aube J, Rogers SA.  3-Substituted Biquinolinium Inhibitors of AraC Family Transcriptional Activator VirF from S. flexneri Obtained Through In Situ Chemical Ionization of 3,4-Disubstituted Dihydroquinolines.  Res Avd. [Epub ahead of print]
  12. Jas GS, Middaugh CR, Kuczera K.  Non-exponential kinetics and a complete folding pathway of an α-Helical Heteropeptide: Direct Observation and Comprehensive Molecular Dynamics.  J. Phys. Chem B 118:639-647.
  13. Kemege K, Hickey JM, Barta ML, Wickstrum J, Balwalli N, Lovell S, Battaile KP, Hefty PS.  Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB.  Mol Micrbiol [Epub ahead of print]
  14. King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ.  Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity.  PLoS Genet: e1004322.
  15. Lanfranca MP, Mostafa HH, Davido DJ.  HSV-1 ICP0: an E3 ligase that counteracts host intrinsic and innate immunity.  Cells 3: 438-54.
  16. Li L, Hoa X, Qin J, He F, Smith A, Zhang M, Simeone DM, Qiao XT, Chen ZN, Lawrence TS, Xu L.  Antibody against CD44s inhibits pancreatic tumor initation and postradiation recurrence in mice.  Gastroenterology.  [Epub ahead of print]
  17. Li L, Tang W, Wu X, Karnak D, Meng X, Thompson R, Hao X, Li Y, Qiao XT, Lin J, Fuchs J, Simeone DM, Chen ZN, Lawrence TS, Xu L.  HAb18G/CD147 promotes pSTAT3-mediated pancreatic cancer development via CD44s.  Clin Cancer Res 19, 6703-15.
  18. Liebscher I, Ackley B, Araç D, Ariestanti DM, Aust G, Bae BI, Bista BR, Bridges JP, Duman JG, Engel FB, Giera S, Goffinet AM, Hall RA, Hamann J, Hartmann N, Lin HH, Liu M, Luo R, Mogha A, Monk KR, Peeters MC, Prömel S, Ressl S, Schiöth HB, Sigoillot SM, Song H, Talbot WS, Tall GG, White JP, Wolfrum U, Xu L, Piao X. New functions and signaling mechanisms for the class of adhesion G protein-coupled receptors. Ann N Y Acad Sci. 2014 Dec;1333(1):43-64. Epub 2014 Nov 25. PMID: 25424900; PMCID: PMC4278406.
  19. Liu H, Li K, Lan L, Ma J, Zeng Y, Xu L, Wu D.  Double-layered hyaluronic acid/stearic acid-modified polyethyleneimine nanoparticles encapsulating (−)-gossypol: a nanocarrier for chiral anticancer drugs. Journal of Materials Chemistry B. 2014, 2(32):5238-5248.
  20. Liu T, Sanchez JF, Chiang Y-M, Oakley BR, Wang CCC.  Rational Domain Swaps Reveal Insights about Chain Length Control by Ketosynthase Domains in Fungal Nonreducing Polyketide Synthases. Org Lett 16, 1676-9.
  21. Long AD, Macdonald SJ, King EG.  Dissecting complex traits using the Drosophila Synthetic Population Resource. Trends in Genetics 30: 488–495.
  22. Lothrop AP, Snider GW, Flemer S Jr, Ruggles EL, Davidson RS, Lamb AL, Hondal RJ.  Compensating for the absence of selenocysteine in high-molecular weight thioredoxin reductases: the electrophilic activation hypothesis.  Biochemistry [Epub ahead of print].
  23. Lu J, Zhao W, Huang Y, Liu H, Marquez R, Gibbs RB, Li J, Venkataramanan R, Xu L, Li S, Li S. Targeted Delivery of Doxorubicin by Folic Acid-Decorated Dual Functional Nanocarrier. Mol Pharm [Epub ahead of print].
  24. Marriage TN, EG King, AD Long, SJ Macdonald.  Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation intercross population. Genetics 198: 45–57
  25. Meneely KM, Luo Q, Riley AP, Taylor B, Roy A, Stein RL, Prisinzano TE, Lamb AL.  Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism.  Bioorg Med Chem.  22: 5961-69.
  26. Newton AH, Benedict SH.  Low density lipoprotein promotes human naïve T cell differentiation to Th1 cells.  Hum Immunol [Epub ahead of print]
  27. Ni Z, Wang B, Dai X, Ding W, Yang T, Li X, Lewin S, Xu L, Lian J, He F.  HCC cells with high levels of Bcl-2 are resistant to ABT-737 via activation of the ROS-JNK-autophagy pathway.  Free Radic Biol Med 70, 194-203.
  28. Norris AD, Sundararajan L, Morgan DE, Roberts ZJ, Lundquist EA.  The UNC-6/Netrin receptors UNC-40/DCC and UNC-5 inhibit growth cone filopodial protrusion via UNC-73/Trio, Rac-like GTPases and UNC-33/CRMP.  Development 141: 4395-405.
  29. Osaka I, Hefty PS.  Lipopolysaccharid-binding alkylpolamine DS-96 inhibits Chlamydia trachomatis infection by blocking attachment and entry.  Antimicrob Agents Chemother [Epub ahead of print]
  30. Paranjape, SR, Chiang, YM, Sanchez, JF, Entwistle, R, Wang, CC, Oakley, BR, Gamblin, TC. Inhibition of Tau Aggregation by Three Aspergillus nidulans Secondary Metabolites: 2,ω-Dihydroxyemodin, Asperthecin and Asperbenzaldehyde. Planta Medica 80(1):77-85.
  31. Park H, Turkalo TK, Nelson K, Folmsbee SS, Robb C, Roper B, Azuma M.  Ewing sarcoma EWS protein regulates midzone formation by recruiting Auroroa B kinase to the midzone.  Cell Cycle 13, 2391-2399.
  32. Rankin CA, Galeva NA, Bae K, Ahmad MN, Witte TM, Richter ML.  Isolated RING2 domain of Parkin is sufficient for E2-dependent E3 ligase activity.  Biochemistry 53: 225-34.
  33. Rathinavelan T, Lara-Tejero M, Lefebre M, Chatterjee S, McShan AC, Guo DC, Tang C, Galan JE, De Guzman RN. NMR model of PrgI-SipD interaction and its implications in the needle-tip assembly of the Salmonella type III secretion system.  J Mol Biol.  426: 2958-69.
  34. Rowland MA, Deeds EJ.  Crosstalk and the evolution of specificity in two-component signaling.  Proc Nat Acad Sci USA.  [Epub ahead of print]
  35. Smith MC, Box AC, Haug JS, Lane WS, Davido DJ. A Phospho-SIM in the Antiviral Protein PML is Required for Its Recruitment to HSV-1 Genomes. Cells. 2014 Dec 10;3(4):1131-58. doi: 10.3390/cells3041131. PMID: 25513827; PMCID: PMC4276917.
  36. Stetler DA¸ Davis C, Leavitt K, Schriger I, Benson K, Bhakta S, Wang LC, Oben C, Watters M, Haghnegahdar T and Bortolato M.  Association of low-activity MAOA allelic variants with violent crime in incarcerated offenders.  J Psychiatr Res [Epub ahead of print]
  37. Sundararajan L, Norris ML, Schöneich S, Ackley BD, Lundquist EA. The fat-like cadherin CDH-4 acts cell-non-autonomously in anterior-posterior neuroblast migration. Dev Biol. 2014 Aug 15;392(2):141-52. doi: 10.1016/j.ydbio.2014.06.009. Epub 2014 Jun 19. PMID: 24954154; PMCID: PMC4136450.
  38. Tewary SK, Zhao H, Deng X, Qiu J, Tang L. The human parvovirus B19 non-structural protein 1 N-terminal domain specifically binds to the origin of replication in the viral DNA. Virology. [Epub ahead of print].
  39. Timmons L, Luna H, Martinez J, Moore Z, Nagarajan V, Kemege JM, Asad N.  Systematic comparison of bacterial feeding strains for increased yield of Caenorhabditis elegans males by RNA interference-induced non-disjunction FEBS letters [Epub ahead of print]
  40. Qin J, Yang B, Xu B, Smith A, Xu L, Yuan J, Li L.  Concurrent CD44s and STAT3 expression in human clear cell  renal cellular carcinoma and its impact on survival. International Journal of Clinical and Experimental Pathology 2014, 7(6):3236.
  41. Varahan S, Harms N, Gilmore MS, Tomich JM, Hancock LE.  An ABC Transporter Is Required for Secretion of Peptide Sex Pheromones in Enterococcus faecalis.  MBio. 2014 Sep 23;5(5). pii: e01726-14. doi: 10.1128/mBio.01726-14.
  42. Wang B, Ni Z, Dai X, Qin L, Li X, Xu L, Lian J, and He F. The Bcl-2/xL inhibitor ABT-263 increases the stability of Mcl-1 mRNA and protein in hepatocellular carcinoma cells. Mol Cancer 13: 98.
  43. Wang L, Yang H, Palmbos PL, Ney G, Detzler TA, Coleman D, Leflein J, Davis M, Zhang M, Tang W, Hicks JK, Helchowski CM, Prasad J, Lawrence TS, Xu L, Yu X, Canman CE, Ljungman M, Simeone DM.  ATDC/TRIM29 phosphorylation by ATM/MAPKAP Kinase 2 mediates radioresistance in pancreatic cancer cells.  Cancer Res 74, 1778-88.
  44. Yaegashi J, Oakley BR, Wang CC.  Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans.  J Ind Microbiol Biotechnol [Epub ahead of print].
  45. Xia T, Diprimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weiss DD, Anderson JC, Karanicolas J.  The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.  J Am Chem Soc 135: 18840-9.
  46. Zeineldin M, Jensen D, Paranjape SR, Parelkar NK, Jokar I, Vielhauer GA, Neufeld KL. Human Cancer Xenografts in Outbred Nude Mice Can Be Confounded by Polymorphisms in a Modifier of Tumorigenesis  Genetics. [Epub ahead of print]
  47. Zeineldin M, Miller MA, Sullivan R, Neufeld KL. Nuclear Adenomatous polyposis coli suppresses colitis-associated tumorigenesis in mice  Carcinogenesis [Epub ahead of print]
  48. Zhang P, Huang Y, Hoa L, Marquez R, Lu J, Zhao W, Zhang X, Goa X, Li J, Venkataramanan R, Xu L, Li S.  A PEG-Fmoc conjugate as a nanocarrier for paclitaxel. Biomaterials 2014, 35(25):7146-7156.  
  49. Zhou B, Yang K, Wills E, Tang L, Baines JD.  A Mutation in the DNA Polymerase Accessory Factor of Herpes Simplex Virus 1 Restores Viral DNA Replication in the Presence of Raltegravir.  J Virol. [Epub ahead of print]
  1. Alan JK, Lundquist EA.  Mutationally activated Rho GTPases in cancer.  Small GTPases  [Epub ahead of print].
  2. Alan JK, Struckhoff EC, Lundquist EA.  Multiple cytoskeletal pathways and PI3K signaling mediate CDC-42-induced neuronal protrusion in C. elegans.  Small GTPases [Epub ahead of print].
  3. Anishchenko I, Kundrotas PJ, Tuzikov AV, Vakser IA.  Protein models: The Grand Challenge of protein docking, Proteins [Epub ahead of print]
  4. Asad N, Aw WY, Timmons L.   Natural and Unanticipated Modifiers of RNAi Activity in Caenorhabditiselegans. PLoS One 7(11) e50191 (2012) 
  5. Barta ML, Hickey J, Kemege KE, Lovell S, Battaile KP, Hefty PS.  Structure of CT584 from Chlamydia trachomatis refined to 3.05 Å resolution.  Acta Cryst F69, 1196-1201.
  6. Bender A, Woydziak ZR, Branden , Zhou Z, Ackley BD, Peterson BR.  Novel acid-activated fluorophores reveal a dynamic wave of protons in the intestine of Ceanorhabditis elegans.  ACS Chem Biol  [Epub ahead of print]
  7. Caylor RC, Jin Y, Ackley BD.  The Caenorhabditis elegans voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology.  Neural Dev. 8: 10.
  8. Chatterjee S, Chaudhury S, McShan AC, Kaur K, De Guzman RN.  Structure and biophysics of type III secretion in bacteria.  Biochemistry 52, 2508-17.
  9. Cheng P, Ni Z, Dai X, Wang B, Smith AR, Xu L, Wu D, He F, Lian J.  The novel BH-3 mimetic apogossypolone induces beclin-1- and ROS-mediated autophagy in human hepatocellular cells.  Cell Death and Disease 4, e489.
  10. Chiang YM, Oakley CE, Ahuja M, Entwistle R, Schultz A, Chang SL, Sung CT, Wang CCC, Oakley BR.  An Efficient System for Heterologous Expression of Secondary Metabolite Genes in Aspergillus nidulans.  J. Am. Chem. Soc. 135, 7720-7731.
  11. Cridland JM, Macdonald SJ, Long AD, Thornton KR. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Molecular Biology and Evolution 30: 2311–2327.
  12. Dentler W.  A role for the membrane in regulating chlamydomonas flagellar length.  PLoS One.  8: e53366.
  13. Dotson AL, Novikova L, Stehno-Bittel L, Benedict SH.  Elimination of T cell reactivity to pancreatic  β cells and partial preservation of β cell activity by peptide blockade of LFA-1:ICAM-1 interaction with the NOD mouse model.  Clinical Immunology 148, 149-161.
  14. Gowthaman R, Deeds EJ, Karanicolas J.  The structural properties of non-traditional drug targets present new challenges for virtual screening.  J. Chem. Inf. Model [Epub ahead of print].
  15. Huarcaya Najarro E, Ackley BD.  C. elegans fmi-1/flamingo and Wnt pathway components interact genetically to control the anteroposterior neurite growth of the VD GABAergic neurons.  Dev Biol [Epub ahead of print]
  16. Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. J ChemInf Model. 2012 Dec 20. [Epub ahead of print]
  17. Jo S, Lee HS, Skolnick J, Im W.  Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.  PLoS Comput Biol: e1002946.
  18. Johnson DK, Karanicolas J.  Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface.  PLoS Comput Biol: e1002951.
  19. Khan LA, Zhang H, Abraham N, Sun L, Fleming JT, Buechner M, Hall DH, Gobel V.  Intracellular lumen extension requires ERM-1-dependent apical memebrane expansion and AQP-8-mediated flux.  Nature Cell Biology.  [Epub ahead of print]
  20. Kislukhin G, King EG, Walters KN, Macdonald SJ, and Long AD.  The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans. G3: Genes, Genomes, Genetics 3: 1301–1310.
  21. Koppolu V, Osaka I, Skredenske JM, Kettle B, Hefty PS, Li J,Egan SM.   Small Molecule Inhibitor of Shigella flexneri Master Virulence Regulator, VirF.  Infection and Immunity.  [Epub ahead of print]
  22. Kundrotas PJ, Vakser IA. Protein-protein alternative binding modes do not overlap, Protein Sci. 22:1141-1145.  Highlighted in “In This Issue” section.
  23. Kundrotas PJ, Vakser IA. Global and local structural similarity in protein-protein complexes: Implications for template-based docking, Proteins [Epub ahead of print]
  24. Kundrotas PJ, Vakser IA, Janin J. Structural templates for modeling homodimer. Protein Science. [Epub ahead of print]
  25. Lee KI, Pastor RW, Andersen OS, Im W.  Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.  Chem Phys Lipids [Epub ahead of print]
  26. Lu J, Huang Y, Zhao W, Marquez RT, Meng X, Li J, Gao X, Venkataramanan R, Wang Z, Li S.  PEG-derived embelin as a nanomicellar carrier for delivery of paclitaxel to breast and prostate cancers.  Biomaterials 24, 1591-1600.
  27. Marquez RT, Tsao BW, Faust NF and Xu L. Drug resistance and molecular cancer therapy: Apoptosis vs. Autophagy. In: Justine Rudner, ed., Apoptosis. Chapter. InTech. 2013 (in press).
  28. Meneely KM, Luo Q, Dhar P, Lamb AL.  Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited.  Arch.  Biochem. Biophys.  [Epub ahead of print]
  29. Meneely KM, Luo Q, Lamb AL.  Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities.  Archives of Biochemistry and Biophysics. [Epub ahead of print]
  30. Mostafa HH, Davido DJ.  HSV-1 ICP22 but not US1.5 is Required for Efficient Acute Replication in Mice and VICE Domain Formation.  J Virol [Epub ahead of print]
  31. Mostafa HH, Thompson TW, Davido DJ. N-terminal phosphorylation sites of herpes simplex virus type 1 ICP0 differentially regulate its activities and enhance viral replication. J Virol.2012 Dec 5. [Epub ahead of print]
  32. Novikova L, Smirnova IV, Rawal S, Dotson AL, Benedict SH, Stehno-Bittel L.  Variations in rodent models of type 1 diabetes: islet morphology.  J. Diabetes Res. 2013:965832.
  33. Oakley BR (2013). Aspergillus nidulans. In Brenner’s Encyclopedia of Genetics (Second Edition), Editors-in-Chief: S. Maloy, and K. Hughes, eds. (San Diego: Academic Press), pp. 212-215.
  34. Osaka I, Hefty PS.  A simple resazurin-based microplate assay for measuring Chlamydia infections.  Antimicrob Agents Chemother.  [Epub ahead of print]>
  35. Park S, Im W.  Two dimensional window exchange umbrella sampling for transmembrane helix assembly. J Chem Theory Comput.  9: 13-17.
  36. Perusina Lanfranca M, Mostafa HH, Davido DJ.  Two overlapping regions within the N-terminal half of the HSV-1 E3 ubiquitin ligase ICP0 facilitate the degradation and dissociation of PML and dissociation of Sp100 from ND10.  J Virol [Epub ahead of print]
  37. Rice SA, Davido DJ.  HSV-1 ICP22: hijacking host nuclear functions to enhance viral infection.  Future Microbiol 8, 311-21.
  38. Rowland, M. A., Fontana, W. and Deeds, E. J. Crosstalk and competition in signaling networks. Biophys. J.103:2389-98.  This article is the focus of a “New and Notable” column in Biophysical Journal.
  39. Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Ensemble-based characterization of unbound and bound states on protein energy landscape. Protein Sci. 22: 734-744.
  40. Smith MC, Goddard ET, Perusina Lanfranca M, Davido DJ.  hTERT extends the life of human fibroblasts without compromising type 1 interferon signaling.  PLoS One: e58233.
  41. Sigamani SS, Zhao H, Kamau YN, Baines JD, Tang L.  The structure of the herpes simplex virus DNA-packaging terminase pUL15 nuclease domain suggests an evolutionary lineage among eukaryotic and prokaryotic viruses.  J Virol [Epub ahead of print]
  42. Skredenske JM, Koppolu V, Kolin A, Deng J, Kettle B, Taylor B, Egan SE. Identification of a Small Molecule Inhibitor of Bacterial AraC Family Activators. Journal of Biomolecular Screening.  [Epub ahead of print]
  43. Suderman R, Deeds EJ.  Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of proteins complexes.  PLoS Comput Biol 9(10): e1003278.
  44. Syed LU, Zhang-Swisher L, Huff H, Rochford C, Wang F, Liu J, Wu J, Richter M, Balivada S, Troyer D, Li J.  Luminol-labeled gold nanoparticles for ultrasensitive chemiluminescence-based chemical analysis.  Analyst 138, 5600-5609.
  45. Takusagawa F.  Microsomal prostaglandin E synthase type-2 (mPGES2) is a GSH-dependent heme protein, and dithiothreitol dissociates the bound-heme to produce active PVD2 synthase in vitro.  J Biol Chem [Epub ahead of print]
  46. Tamayo JV, Gujar M, Macdonald SJ, Lundquist EA.  Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans.  BMC Genomics 14: 304.
  47. Tewary SK, Zhao H, Shen W, Qiu J, Tang L.  Structure of the NS1 protein N-terminal origin-recognition/nickase domain from the emerging human bocavirus.  J Virol. [Epub ahead of print]
  48. Vakser IA.  Low-resolution structural modeling of protein interactome.  Curr Opin Struct Biol [Epub ahead of print]
  49. Wang H, Davido DJ, Morrison LA.  HSV-1 strain McKrae is more neuroinvasive than HSV-1 KOS after corneal or vaginal incoluation in mice.  Virus Res.  [Epub ahead of print]
  50. Varahan S, Iyer VS, Moore WT, Hancock LE. Eep confers lysozyme resistance to enterococcus faecalis via the activation of the extracytoplasmic function sigma factor SigV. J Bacteriol. 2013 Jul;195(14):3125-34. doi: 10.1128/JB.00291-13. Epub 2013 May 3. PMID: 23645601; PMCID: PMC3697634.
  51. Wang S, Wang G, Tang G, Wang R, Nikolovska-Coleska Z, Yang D, and Xu L.  Small molecule inhibitors of anti-apoptotic BCL-2 family members and the uses thereof.  United States Patent No. US 8,557,812, issued on Oct. 15, 2013.
  52. Wickstrum J, Sammons LR, Restivo KN, Hefty PS.  Conditional gene expression in Chlamydia trachomatis using the Tet system. PLoS One 8(10): e76743.
  53. Yaegashi J, Praseuth MB, Tyan SW, Sanchez JF, Entwistle R, Chiang YM, Oakley BR, Wang CC.  Molecular genetic characterization of the biosynthesis cluster of a prenylated isoindolinone alkaloid aspernidine A in Asptergillus nidulans.  Org Lett [Epub ahead of print].
  54. Yeh HH, Chang SL, Chiang YM, Bruno KS, Oakley BR, Wu TK, Wang CC.  Engineering fungal nonreducing polyketide synthetase by heterologous expression and domain swapping.  Org Lett 15: 756-759.
  55. Zhao H, Christensen TE, Kamau YN, Tang L.  Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage. Proc Natl Acad Sci USA 110, 8075-80.
  56. Zeineldin M, Neufeld KL.  Understanding the phenotypic variation in rodent models with germline apc mutations.  Cancer Res 73, 2389-99.
  57. Zeineldin M, Neufeld KL.  More than two decades of Apc modeling in rodents.  Biochim Biophys Acta.  [Epub ahead of print]
  1. Ahuja M, Chiang YM, Chang SL, Praseuth MB, Entwistle R, Sanchez JF, Lo HC, Yeh HH, Oakley BR, Wang CC. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22510154
  2. Alan JK, Lundquist EA. Analysis of Rho GTPase function in axon pathfinding using Caenorhabditis elegans. Methods Mol Biol 827:339-58. http://www.ncbi.nlm.nih.gov/pubmed/22144285
  3. Biswas S, Benedict SH, Lynch SG, LeVine SM.  Potential immunological consequences of pharmacological suppression of grastric acid production in patients with multiple sclerosis.BMC Medicine, 10:57. http://www.ncbi.nlm.nih.gov/pubmed/22676575
  4. Cheng X, Im W. NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes. Biophys J 102: L27-9. http://www.ncbi.nlm.nih.gov/pubmed/22500771
  5. Combs, B. and Gamblin, T.C. FTDP-17 Mutations Induce Distinct Effects on Aggregation and Microtubule Interactions. Biochemistry 2012, 51(43): 8597-8607.
  6. Deckert K, Budiardjo SJ, Brunner LC, Lovell S, Karanicolas J. Designing allosteric control into enzymes by chemical rescue of structure.  J. Amer. Chem. Soc. 134: 10055-60. http://www.ncbi.nlm.nih.gov/pubmed/22655749
  7. Deeds EJ, Bachman JA, Fontana W. Optimizing ring assembly reveals the strength of weak interactions. Proc. Natl. Acad. Sci. USA 109(7): 2348-53. http://www.ncbi.nlm.nih.gov/pubmed/22308356
  8. Deeds EJ, Krivine J, Feret J, Danos V, Fontana W. Combinatorial complexity and compositional drift in protein interaction networks. PLoS One. 7(3):e32032 (2012) http://www.ncbi.nlm.nih.gov/pubmed/22412851
  9. Demarco RS, Struckhoff EC, Lundquist EA.  The Rac GTP exchange factor TIAM-1 acts with CDC-42 and the guidance receptor UNC-40/DCC in neuronal protrusion and axon guidance. PLoS Genetics 2012, 8:4, e1002665. http://www.ncbi.nlm.nih.gov/pubmed/22570618
  10. Devore NM and Scott EE. Structures of cyctochrome P450 17A1 with prostate cancer drugs abiraterone and TOK-001. Nature 2012 Jan 22 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22266943
  11. Edgerton-Morgan H, Oakley BR. γ-Tubulin plays a key role in inactivating APC/CCdh1 at the G1-S boundary. J Cell Biol. 2012 Aug 27. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22927465
  12. Entwistle RA, Rizk RS, Cheng DM, Lushington GH, Himes RH, Gupta ML Jr.  Differentiating between models of epothilone binding to microtubules using tubulin mutagenesis, cytotoxicity, and molecular modeling.  ChemMedChem.  2012 Jul 16 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22807375
  13. Estrada DF, Conner M, Joer SC and De Guzman RN. The structure of the hantavirus zinc finger domain is conserved and represents the only natively folded region of the Gn cytoplasmic tail. Front Microbiol 2:251. http://www.ncbi.nlm.nih.gov/pubmed/22203819
  14. Guo C-J, Knox B, Chiang, Y-M, Lo H-C, Sanchez J, Lee K-H, Oakley B, Bruno K, Wang C. Molecular genetic characterization of a cluster in A. terreus for biosynthesis of the meroterpenoid terretonin. Org. Lett. 14:5684-5687.
  15. Jo, S. and Im, W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res. 2012 Oct 26. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/23104379
  16. Karanicolas J. Designing orthogonal signaling pathways: How to fit in with the surroundings. Proc Natl Acad Sci U S A. 2012 Mar 26. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22451928
  17. Kim T, Lee KU, Morris P, Pastor RW, Andersen OS, Im W. Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J 102: 1551-60. http://www.ncbi.nlm.nih.gov/pubmed/22500755
  18. King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ.
  19. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource.Genome Res. 2012 Aug;22(8):1558-66. Epub 2012 Apr 10. http://www.ncbi.nlm.nih.gov/pubmed/22496517
  20. King EG, Macdonald SJ, Long AD. Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 2012, 191: 935-49. http://www.ncbi.nlm.nih.gov/pubmed/22505626
  21. Kirys T, RuvinskyAM, Tuzikov AV, Vakser IA.  Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.Proteins 2012 Apr 27 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22544766
  22. Klionsky DJ1. . .Xu L996. . .et al.  Guidelines for the use and interpretation of assays for monitoring autophagy.  Autophagy 8, 445-544. http://www.landesbioscience.com/journals/3/article/19496/
  23. Kundrotas PJ, Zhu Z, Janin J, Vakser IA.Templates are available to model nearly all complexes of structurally characterized proteins.  Proc. Natl. Acad. Sci. USA 109: 9438-41. http://www.ncbi.nlm.nih.gov/pubmed/22645367
  24. Lee, H.S. and Im, W. Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J Chem Inf Model. 2012 Oct 22;52(10):2784-95. Epub 2012 Sep 28. http://www.ncbi.nlm.nih.gov/pubmed/22978550
  25. Lee HS, Jo S, Lim HS, Im W.  Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.  J Chem Inf Model.  2012 Jul 6.  [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22731511
  26. Lian J, Ni Z, Dai X, Su C, Smith AR and Xu L, and He F. Sorafenib sensitizes (-)-gossypol-induced growth suppression in androgen-independent prostate cancer cells via Mcl-1 inhibition and Bak activation. Molecular Cancer Therapeutics 2011, Dec. in press http://www.ncbi.nlm.nih.gov/pubmed/22188816
  27. Lo HC, Entwistle R, Guo CJ, Ahuja M, Szewczyk E, Hung JH, Chiang YM, Oakley BR. Wang CC. Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids, austinol and dehydroaustinol in Aspergillus nidulans. J Am Chem Soc 2012 Feb 13 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22329759
  28. Macdonald SJ, Mostafa HH, Morrison LA, Davido DJ. Genome Sequence of Herpes Simplex Virus 1 Strain McKrae.J Virol. 2012 Sep;86(17):9540-1. http://www.ncbi.nlm.nih.gov/pubmed/22879612
  29. Macdonald SJ, Mostafa HH, Morrison LA, Davido DJ.Genome Sequence of Herpes Simplex Virus 1 Strain KOS.J Virol. 2012 Jun;86(11):6371-2. http://www.ncbi.nlm.nih.gov/pubmed/22570244
  30. Marquez RT and Xu L. Bcl2:Beclin 1 complex: multiple mechanisms regulating autophagy/apoptosis toggle switch. Am J Cancer Res 2012;2(2). (in press) http://www.ajcr.us/ajcr0000098A.html
  31. Meneely, K.M., and Lamb, A.L. Two structures of a thiazolinyl imine reductase from Yersinia enterocolitica provide insight into catalysis and binding to the nonribosomal peptide synthetase module of HMWP1. Biochemistry. 2012 Oct 23. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/23066849
  32. Najarro EH, Wong L, Zhen M, Carpio EP, Goncharov A, Garriga G, Lundquist EA, Jin Y, Ackley BD. Caenorhabditis elegans Flamingo Cadherin fmi-1 Regulates GABAergic Neuronal Development. J Neurosci. 32(12):4196-211 (2012) http://www.ncbi.nlm.nih.gov/pubmed/22442082
  33. Oakley, C. E., Edgerton-Morgan, H., Oakley, B. R., Tools for Manipulation of Secondary Metabolism Pathways: Rapid Promoter Replacements and Gene Deletions in Aspergillus nidulans. Methods Mol Biol 2012, 944, 143-161.
  34. http://www.ncbi.nlm.nih.gov/pubmed/23065614
  35. O'Bryhim BE, Radel J, Macdonald SJ, Symons RC. The genetic control of avascular area in mouse oxygen-induced retinopathy. Molecular Vision 2012; 18: 377-89. http://www.ncbi.nlm.nih.gov/pubmed/22355249
  36. Olucha J, Meneely KM, Lamb AL. Modification of residue 42 of the active site loop with a lysine-mimetic side chain rescues isochorismate-pyruvate lyase activity in Pseudomonas aeruginosa PchB. Biochemistry. 51: 7525-7532. http://www.ncbi.nlm.nih.gov/pubmed/22970849
  37. Osaka I, Hills JM, Kieweg SL, Shinogle HE, Moore DS, Hefty PS.  An automated image-based method for rapid analysis of Chlamydia infection as a tool for screening antichlamydial agents.Antimicrob Agents Chemother2012 May 21 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22615279
  38. Park S, Kim T, Im W. Transmembrane helix assembly by window exchange umbrella sampling. Phys Rev Lett 108: 108102. http://www.ncbi.nlm.nih.gov/pubmed/22463457
  39. Sanchez JF, Entwistle R, Corcoran D, Oakley BR, Wang CC. Identification and molecular genetic analysis of the cichorine cluster in Aspergillus nidulans. In press: Med Chem Comm Available on line. http://pubs.rsc.org/en/content/articlepdf/2012/md/c2md20055d
  40. Simeone DM, Ljungman M, Xu L, Wang L and He F. Compositions and methods for treating cancer. US Patent No. US 8,088749, issued on Jan. 3, 2012.
  41. Somoza AD, Lee KH, Chiang YM, Oakley BR, Wang CC. Reengineering an azaphilone biosynthesis pathway in Aspergillus nidulins to create lipoxygenase inhibitors. Org. Lett. 2012 Feb 1 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22296232
  42. Soukup, A. A., Y. M. Chiang, J. W. Bok, Y. Reyes-Dominguez, B. R. Oakley, C. C. Wang, J. Strauss, and N. P. Keller. 2012. Overexpression of the Aspergillusnidulans histone 4 acetyltransferaseEsaA increases activation of secondary metabolite production. MolMicrobiol. http://www.ncbi.nlm.nih.gov/pubmed/22882998
  43. Sundararajan L, Lundquist EA.  The Transmembrane Proteins UNC-40/DCC, PTP-3/LAR, and MIG-21 Control Anterior-posterior Neuroblast Migration with Left-right Functional Asymmetry in Caenorhabditis elegans. Genetics 2012 Oct 10. [Epub ahead of print]
  44. Sudharsan R, Azuma Y. The SUMO ligase PIAS1 regulates UV-induced apoptosis by recruiting Daxx to SUMOylated foci. J. Cell Sci. [Epub ahead of print]. http://www.ncbi.nlm.nih.gov/pubmed/22976298
  45. Taheri-Talesh N, Xiong Y, Oakley BR. The functions of myosin II and myosin V homologs in tip growth and septation in Aspergillus nidulans. PLoS One 7, e31218. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031218
  46. Voss K, Combs B, Patterson KR, Binder LI and Gamblin TC. Hsp70 alters tau function and aggregation in an isoform specific manner. Biochemistry 2012 Jan 10 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22236337
  47. Wacker MJ, Tevis O, Hanke J, Howard T, Gilbert W, Orr JA. Characterization of thromboxane A(2) receptor and TRPV1 mRNA expression in cultured sensory neurons. Neurosci Lett. 2012 Mar 7. [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22425716
  48. Yeh H, Chiang Y, Entwistle R, Ahuja M, Lee K, Bruno K, Wu T, Oakley BR, Wang C. Molecular genetic analysis reveals that a nonribosomal peptide synthase-like (NRPS-like) gene in Aspergillus nidulans is responsible for microperfuranone biosynthesis.  Appl. Microbiol. Biotechnol.  2012 May 25 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22627757
  49. Zeineldin, M. and Neufeld, K., Isolation of Epithelial Cells from Mouse Gastrointestinal Tract for Western Blot or RNA analysis. Bio-protocol, invited, peer-reviewed. http://www.bio-protocol.org/wenzhang.aspx?id=292.  Featured protocol under fields of "Molecular Biology" and "Cell Biology" http://www.bio-protocol.org/fllist.aspx?fl1=1&fweek1=1 http://www.bio-protocol.org/fllist.aspx?fl1=4&fweek1=1
  50. Zhao, H., Kamau, Y., Christensen, T. and Tang, L., Structural and functional studies of the bacteriophage Sf6 terminase small subunit reveal a DNA-spooling device facilitated by structural plasticity. J. Mol. Biol. 423, 3, 413-26. http://www.ncbi.nlm.nih.gov/pubmed/22858866
  51. Zhong D, Lefebre M, Kaur K, McDowell MA, Gdowski C, Jo S, Wang Y, Benedict SH, Lea SM, Galan JE, De Guzman RN.  The Salmonella type III secretion system inner rod protein PrgJ is partially folded.  J. Biol. Chem. 2012 May 31 [Epub ahead of print] http://www.ncbi.nlm.nih.gov/pubmed/22654099
  52. PREPARATION OF REGULATORY T CELLS USING ICAM-1 CO-STIMULATION, U.S. Patent Application Serial No. 12/122,377, Benedict, S, Williams K, Dotson, A
  1. Chaguturu R. "Conference report: the Screening Asia Conference 2010: an update." Future Med. Chem. 3: 513
  2. Combs B, Voss KR and Gamblin TC. Pseudohyperphosphorylation has differential effects on polymerization and function of tau isoforms. Biochemistry 2011 Sep 26. [Epub ahead of print]
  3. Dai Y, DeSano J, Tang W, Meng X, Meng Y, Burstein E, Lawrence TS, Xu L. "Natural proteasome inhibitor celastrol suppresses androgen-independent prostate cancer progression by modulating apoptotic protein and NF-kappaB." PloS One. 5(12): e14153.
  4. Dai Y, DeSano J, Yang Q, Tang W, Meng Y, Burstein E, Lawrence TS, Xu L. "Natural IAP inhibitor embelin enhances therapeutic efficacy of ionizing radiation in prostate cancer." Am J Cancer Res 1(2), 128-143.
  5. Deeds EJ, Savage V and Fontana W. Curvature in metabolic scaling: A reply to MacKay. J. Theor. Biol. [Epub ahead of print]
  6. Demarco RS and Lundquist EA "RACK"-ing up the effectors: Receptor for activated C kinase acts downstream of Rac GTPase signaling in growth cone outgrowth. Small GTPases 2:1, 1-4; January/February 2011
  7. DeSano JT, Lawrence, TW and Xu L. Chapter 15, “MicroRNAs: Small but Critical Regulators of Cancer Stem Cells” in: Cancer Stem Cells Theories and Practice, Stanley Shostak, Ed.
  8. Estrada DF, De Guzman RN. “Structural characterization of the crimean-congo hemorrhagic fever virus gn tail provides insight into virus assembly.” J Biol Chem 286: 21678-86.
  9. Giles SS, Soukup AA, Lauer C, Shaaban M, Lin A, Oakley BR, Wang CC, and Keller NP. Cryptic Aspergillus nidulans antimicrobial. Appl Environ Microbiol.
  10. Hickey JM, Lovell S, Battaile KP, Middaugh CR, Hefty PS. "The atypical response regulator ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily. J. Biol. Chem. [Epub ahead of print]
  11. Hofmann FT, Lindemann C, Salia H, Adamitzki P, Karanicolas J, Seebeck FP.  A phosphoarginine containing peptide as an artificial SH2 ligand.ChemCommun.  [Epub ahead of print]
  12. Jo S, Im W. “Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.” Biophys J. 100: 2913-21.
  13. Jo S, Song KC, Desaire H, Mackerell AD Jr, Im W.  Glycan reader: automated sugar identification nd simulation preparation for carbohydrates and glycoproteins.  JComput Chem.[Epub ahead of print]
  14. Karanicolas J, Corn JE, Chen I, Joachimiak, LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR and Baker D. A De Novo Protein Binding Pair By Computational Design and Directed Evolution. Molecular Cell 42:1-11.
  15. Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS. Ab initio structural modeling and experimental validation of Chlamydia trachomatis protein CT296 reveals structural similarity with Fe(II) 2-oxoflutarate dependent enzymes. J. Bacteriol. 2011 Sep 30 [Epub ahead of print]
  16. Kim T, Jo S, Im W. “Solid-State NMR Ensemble Dynamics as a Mediator between Experiment and Simulation.”  Biophys J. 100: 2922-8.
  17. Lamb AL.  Pericyclic reactions catalyzed by chorismate-utilizing enzymes.  Biochemistry.  50: 7476-7483.
  18. Lee KI, Jo S, Egwolf B, Roux B, Pastor RW, Im W.  Web interface for borwnian dynamics simulation of ion transport and its applications to beta-barrel pores.  J. ComputChem 2011 Nov 21 [Epub ahead of print]
  19. Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophys. J. 100: 611–9.
  20. Lian J, Wu X, He F, Karnak D, Tang W, Meng Y, Xiang D, Ji M, Lawrence TS and Xu L. A natural BH3 mimetic induces autophagy in apoptosis-resistant prostate cancer via modulating Bcl-2-Beclin1 interaction at endoplasmic reticulum. Cell Death Differ. 18: 60–71.
  21. Liu S, Vakser IA.  DECK: distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking.  BMC Bioinformatics.12:280.
  22. Liu T, Chiang YM, Somoza AD, Oakley BR, Wang CC.  Engineering an “unnatural” natural product by swapping polyketide synthase domains in Aspergillusnidulans.J Am Chem Soc. 133:13314-6.
  23. Luo Q, Meneely KM and Lamb AL. Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB. J. Am. Chem. Soc. [Epub ahead of print]
  24. Mattingly BC, Buechner M.  The FGD homologue EXC-5 regulates apical trafficking in C. eleganstubules.  Develop Biol[Epub ahead of print]
  25. McNeil CL, Bain CL, Macdonald SJ. Multiple Quantitative Trait Loci Influence the Shape of a Male-Specific Genital Structure in Drosophila melanogaster Genes, Genomes, Genetics 1: 343-351.
  26. Moore CL, Huang MH, RobbennoltSA, Voss K, Combs B, Gamblin TC, Goux WJ.Secondary nucleating sequences affect kinetics and thermodynamics of tau aggregation. Biochemistry. 2011 Nov 15 [Epub ahead of print]
  27. Mostafa HH, Thompson TW, Kushnir AS, Haenchen SD, Bayless AM, Hilliard JG, Link MA, Pitcher LA, Loveday E, Schaffer PA, Davido DJ. Herpes Simplex Virus Type 1 ICP0 Phosphorylation Site Mutants are Attenuated for Viral Replication and Impaired for Explant-Induced Reactivation. J Virol. 2011 Sep 21. [Epub ahead of print]
  28. Norris, AD, and Lundquist, EA. UNC-6/Netrin and its receptors UNC-5 and UNC-40/DCC modulate growth cone protrusion in vivo in C. elegans. Development 2011, 138:4433-4442.
  29. Olucha J, Lamb AL.Mechanistic and structural studies of the N-hydroxylatingflavoproteinmonooxygenases.Bioorg. Chem. [Epub ahead of print]
  30. Olucha J, Meneely KM, Chilton AS, Lamb AL."Two structures of an N-hydroxylating flavoprotein monooxygenase: the ornithine hydroxylase from Pseudomonas aeruginosa." J. Biol. Chem. [Epub ahead of print]
  31. Olucha J, Ouellette AN, Luo Q, Lamb AL."pH dependence of catalysis by Pseudomonas aeruginosa isochorismate-pyruvate lyase: implications for transition state stabilization and the role of lysine 42." Biochemistry.[Epub ahead of print]
  32. Palmer JM, Mallaredy S, Perry DW, Sanchez JF, Thiesen JM, Szewczyk E, Oakley BR, Wang CCC, Keller NP, Mirabito PM. "Telomere position effect is regulated by heterochromatin associated proteins and NkuA in Aspergillus nidulans."  Microbiology 156, 3522-3531.
  33. Parthasarathy S, Altuve A, Terzyan S, Zhang X, Kuczera K, Rivera M, Benson DR. “Accommodating a nonconservative internal mutation by water-mediated hydrogen bonding between β-sheet strands: a comparison of human and rat type B (mitochondrial) cytochrome b(5).” Biochemistry. [Epub ahead of print]
  34. Patterson KR, Ward SM, Combs B, Voss K, Kanaan NM, Morfini G, Brady ST, Gamblin TC, Binder LI.  Heat Shock Protein 70 Prevents both Tau Aggregation and the Inhibitory Effects of Preexisting Tau Aggregates on Fast Axonal Transport.  Biochemistry50, 10300
  35. Rankin CA, Roy A, Zhang Y, Richter M. “Parkin, a top level manager in the cell's sanitation department.” Open Biochem 5:9-26.
  36. Rathinavelan T, Tang C and De Guzman RN. Characterization of the Interaction between the Salmonella Type III Secretion System Tip Protein SipD and the Needle Protein PrgI by Paramagnetic Relaxation Enhancement. J. Biol. Chem. 286: 4922–30.
  37. Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophys. J. 100: 602–10.
  38. Rui H, Kumar R, Im W.  Membrane tension, lipid adaptation, conformational changes and energetics in MscL gating.Biophys J.  101: 671-9.
  39. Sanchez JF, Entwistle R, Hung J-H, Yaegashi J, Jain S, Chiang Y-M, Wang CCC, Oakley BR. Genome-based deletion analysis reveals the prenyl xanthose biosynthesis pathway in Aspergillus nidulas. J. Am. Chem. Soc. 133: 4010-7.
  40. Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D & Eisenberg D. “Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.” Nature. [Epub ahead of print]
  41. Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. "Orientations of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations." J. Phys. Chem. B 115: 6157–65.
  42. Smith MC, Boutell C, Davido DJ. "HSC-1 ICP0: paving the way for viral replication. Future Virol. 6, 421-429.
  43. Smith MC, Bayless AM, Goddard ET, Davido DJ. "CK2 inhibitors increase the sensitivity of HSV-1 to interferon-β." Antiviral Res.[Epub ahead of print]
  44. Spears E, Neufeld KL. "A novel double-negative feedback loop between adenomatous polyposis coli and musashi1 in colon epithelia." J Biol Chem. 2011 Jan 3. [Epub ahead of print]
  45. Szewczyk E, Oakley BR. Microtubule dynamics in mitosis in Aspergillus nidulans.Fungal Genet Biol
  46. Williams KM, Dotson AL, Otto AR, Kohlmeier JE, Benedict SH. Choice of resident costimulatory molecule can influence cell fate in human naïve CD4+ T cell differentiation. Cell Immunol. 2011 Aug 27. [Epub ahead of print]
  47. Wu X, Li M, Tang W, Zheng Y, Lian J, Xu L, and Ji M. Design, synthesis and in vitro antitumor activity evaluation of novel 4-pyrrylamino quinazoline derivatives. Chem Biol Drug Design 2011 Sep 3, [Epub ahead of print]
  48. Xu J, Lan L, Bogard N, Mattione C, and Cohen RS. "Rab11 Is Required for Epithelial Cell Viability, Terminal Differentiation, and Suppression of Tumor-Like Growth in the Drosophila Egg Chamber." PloS One. 6(5): e20180.
  49. Zeineldin M, Cunningham J, McGuinness W, Alltizer P, Cowley B, Blanchat B, Xu W, Pinson D and Neufeld KL. A knock-in mouse model reveals roles for nuclear Apc in cell proliferation, Wnt signal inhibition and tumor suppression. Oncogene. 2011 Sep 26, [Epub ahead of print]
  1. Ashton GH, Morton JP, Myant K, Phesse TJ, Ridgway RA, Marsh V, Wilkins JA, Athineos D, Muncan V, Kemp R, Neufeld K, Clevers H, Brunton V, Winton DJ, Wang X, Sears RC, Clarke AR, Frame MC, Sansom OJ. “Focal adhesion kinase is required for intestinal regeneration and tumorigenesis downstream of Wnt/c-Myc signaling.” Dev Cell 19(2):259-69. 
  2. Chatterjee S, Zhong D, Nordhues BA, Battaile KP, Lovell SW, De Guzman RN. “The crystal structures of the Salmonella type III secretion system tip protein SipD in complex with deoxycholate and chenodeoxycholate.” Protein Sci. 2010 Oct 28. [Epub ahead of print]
  3. Chiang YM, Oakley BR, Keller NP, Wang CC. Unraveling polyketide synthesis in members of the genus Aspergillus, Appl Microbiol Biotechnol. 2010 May; 86(6)
  4. Chiang, Y. M., Szewczyk, E., Davidson, A. D., Entwistle, R., Keller, N. P., Wang, C. C., and Oakley, B. R. Characterization of the Aspergillus nidulans monodictyphenone gene cluster, Applied and Environmental Microbiology 76, 2067-2074
  5. Demarco RS and Lundquist EA. "RACK-1 acts with Rac GTPase signaling and UNC-115/abLIM in Caenorhabditis elegans axon pathfinding and cell migration." PLoS Genetics 6(11):e1001215. 
  6. Dyer JO, Demarco RS, Lundquist EA “Distinct roles of Rac GTPases and the UNC-73/Trio and PIX-1 Rac GTP exchange factors in neuroblast protrusion and migration in C. elegans” Small GTPases 1, 44-61. 
  7. Hegefeld WA, Chen SE, Deleon KY, Kuczera K, Jas GS. “Helix Formation in a Pentapeptide: Experiment and Force-field Dependent Dynamics.” J Phys Chem A. 114(47):12391-402.
  8. Hickey JM, Weldon L, Hefty PS. “The Atypical OmpR/PhoB Response Regulator, ChxR, from Chlamydia trachomatis forms Homodimers in vivo and Binds a Direct Repeat of Nucleotide Sequences.” J Bacteriol. 2010 Nov 5. [Epub ahead of print]
  9. Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. “Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.” J Am Chem Soc. 132: 9857-72.
  10. Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B. 114(42):13342-8. 
  11. Kim T, Im W. “Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane hielix tilt and rotation.” Biophys J 99: 175-83
  12. Kundrotas, P. J., and Vakser, I. A. Accuracy of protein-protein binding sites in high-throughput template-based modeling, PLoS Computational Biology 6, e1000727.
  13. Kundrotas, P. J., Zhu, Z., and Vakser, I. A. GWIDD: Genome-wide protein docking database, Nucleic Acids Research 38, D513-517.
  14. Lan L, Lin S, Zhang S, Cohen RS. “Evidence for a Transport-Trap Mode of Drosophila melanogaster gurken mRNA Localization.” PLoS One 5(11).
  15. Lian J, Karnak D, and Xu L. “The Bcl-2-Beclin 1 interaction in (-)-gossypol-induced autophagy versus apoptosis in prostate cancer cells.” Autophagy 6(8). Epub Oct. 25, 2010.
  16. Nayak, Tania, Edgerton-Morgan, Heather, Horio, Tetsuya, Xiong, Yi, De Souza, Colin P., Osmani, Stephen A. and Oakley, Berl R. “γ-Tubulin regulates the anaphase-promoting complex/cyclosome during interphase.” J. Cell Biol. 190, 317-330
  17. Pan X, Thompson R, Meng X, Wu D, and Xu L. “Tumor-targeted RNA-interference: functional non-viral nanovectors.” Am J Cancer Res 1(1):32-49.
  18. Priyadarshi A, Tang L. “Crystallization and preliminary crystallographic analysis of the type III secretion translocator chaperone SicA from Salmonella enterica.” Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 11):1533-5.
  19. Rathinavelan, T., Zhang, L., Picking, W. L., Weis, D. D., De Guzman, R. N., and Im, W. A repulsive electrostatic mechanism for protein export through the type III secretion apparatus, Biophysical Journal 98, 452-461.
  20. Rui H, Im W. “Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations.” J Comput Chem. [Epub ahead of print] 
  21. Ruvinsky AM and Vakser IA. “Sequence composition and environment effects on residue fluctuations in protein structures.” J Chem Phys 133(15): 155101.
  22. Ryu H, Al-Ani G, Deckert K, Kirkpatrick D, Gygi SP, Dasso M, Azuma Y.“PIASy mediates SUMO-2/3 conjugation of poly(ADP-ribose) polymerase 1 (PARP1) on mitotic chromosomes.”J. Biol. Chem. 285: 14415-23. 
  23. Ryu H, Furuta M, Kirkpatrick D, Gygi SP, Azuma Y. “PIASy-dependent SUMOylation regulates DNA topoisomerase II{alpha} activity.” J Cell Biol. 191(4):783-94. 
  24. Sanchez, J. F., Chiang, Y. M., Szewczyk, E., Davidson, A. D., Ahuja, M., Elizabeth Oakley, C., Woo Bok, J., Keller, N., Oakley, B. R., and Wang, C. C. Molecular genetic analysis of the orsellinic acid/F9775 gene cluster of Aspergillus nidulans, Molecular bioSystems 6, 587-593.
  25. Wang, X., and Ward, R. E. Sec61alpha is required for dorsal closure during Drosophila embryogenesis through its regulation of Dpp signaling, Developmental Dynamics 239, 784-797.
  26. Wang, Y., Coffey, R. J., Osheroff, N., and Neufeld, K. L. Topoisomerase IIalpha binding domains of adenomatous polyposis coli influence cell cycle progression and aneuploidy, PloS one 5, 
  27. Wang Y, Nordhues BA, Zhong D, De Guzman RN. “NMR characterization of the interaction of the Salmonella type III secretion system protein SipD and bile salts.”Biochemistry 18, 42290
  28. Wickstrum, J. R., Skredenske, J. M., Balasubramaniam, V., Jones, K., and Egan, S. M. The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation, Journal of Bacteriology 192, 225-232.
  29. Zhang, L., Huang, M., and Harsay, E. A chemical genetic screen for modulators of exocytic transport identifies inhibitors of a transport mechanism linked to GTR2 function, Eukaryotic Cell 9, 116-126.
  30. Zhang L, Nebane NM, Wennerberg K, Li Y, Neubauer V, Hobrath JV, McKellip S, Rasmussen L, Shindo N, Sosa M, Maddry JA, Ananthan S, Piazza GA, White EL, Harsay E. “A High-Throughput Screen for Chemical Inhibitors of Exocytic Transport in Yeast.”
  31. Zhao H, Sequeira RD, Galeva NA, Tang L. “The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion.” Virology. 2010 Nov 9. [Epub ahead of print]
  32. Zhao, H., Finch, C. J., Sequeira, R. D., Johnson, B. A., Johnson, J. E., Casjens, S. R., and Tang, L. Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine, Proceedings of the National Academy of Sciences of the United States of America 107, 
  33. Zhang, L., Huang, M., and Harsay, E. A chemical genetic screen for modulators of exocytic transport identifies inhibitors of a transport mechanism linked to GTR2 function, Eukaryotic Cell 9, 116-126.