Publications

Selected Publications by SCSB Faculty

Last Updated November 2019

2018

  • Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs. Lu W, Negi SS, Schein CH, Maleki SJ, Hulburt BK, Braun W. Molecular Immunology, 9, 1-8, 2018. doi: 10.1016/j.molimm.2018.03.022.
  • Ehrlichia chaffeensis TRP120 nucleomodulin binds DNA with disordered tandem repeat domain. Klema VJ, Sepuru KM, Füllbrunn N, Farris TR, Dunphy PS, McBride JW, Rajarathnam K, Choi KH. PLoS One. 2018 Apr 11;13(4):e0194891. doi: 10.1371/journal.pone.0194891.
  • Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells. Zhou W, Woodson M, Neupane B, Bai F, Sherman MB, Choi KH, Neelakanta G, Sultana H. PLoS Pathog. 2018 Jan 4;14(1):e1006764. doi: 10.1371/journal.ppat.1006764.
  • Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa. Jeffries CL, Lawrence GG, Golovko G, Kristan M, Orsborne J, Spence K, Hurn E, Bandibabone J, Tantely LM, Raharimalala FN, Keita K, Camara D, Barry Y, Wat'senga F, Manzambi EZ, Afrane YA, Mohammed AR, Abeku TA, Hedge S, Khanipov K, Pimenova M, Fofanov Y, Boyer S, Irish SR, Hughes GL, Walker T. Version 2. Wellcome Open Res. 2018 Nov 27 [revised 2018 Jan 1];3:113. doi: 10.12688/wellcomeopenres.14765.2.
  • Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus Mosquito Vectors. Hegde S, Khanipov K, Albayrak L, Golovko G, Pimenova M, Saldaña MA, Rojas MM, Hornett EA, Motl GC, Fredregill CL, Dennett JA, Debboun M, Fofanov Y, Hughes GL. Front Microbiol. 2018 Sep 10;9:2160. doi: 10.3389/fmicb.2018.02160.
  • S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences. Kalesinskas L, Cudone E, Fofanov Y, Putonti C. Evol Bioinform Online. 2018 Sep 17;14:1176934318797354. doi: 10.1177/1176934318797354. Microbiota dysbiosis and its pathophysiological significance in bowel obstruction. Hegde S, Lin YM, Golovko G, Khanipov K, Cong Y, Savidge T, Fofanov Y, Shi XZ. Sci Rep. 2018 Sep 3;8(1):13044. doi: 10.1038/s41598-018-31033-0.
  • Detection of multi-dimensional co-exclusion patterns in microbial communities. Albayrak L, Khanipov K, Golovko G, Fofanov Y. Bioinformatics. 2018 Nov 1;34(21):3695-3701. doi: 10.1093/bioinformatics/bty414.
  • Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells:interactions of MAPK, MYC and glucocorticoid pathways. Webb MS, Miller AL, Howard TL, Johnson BH, Chumakov S, Fofanov Y, Nguyen-Vu T, Lin CY, Thompson EB. Mol Cell Endocrinol. 2018 Aug 15;471:118-130. doi: 10.1016/j.mce.2018.03.004.
  • Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy. Kautz TF, Guerbois M, Khanipov K, Patterson EI, Langsjoen RM, Yun R, Warmbrod KL, Fofanov Y, Weaver SC, Forrester NL. Virus Evol. 2018 Mar 6;4(1):vey004. doi: 10.1093/ve/vey004.
  • Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity. Patterson EI, Khanipov K, Rojas MM, Kautz TF, Rockx-Brouwer D, Golovko G, Albayrak L, Fofanov Y, Forrester NL. Virus Evol. 2018 Feb 15;4(1):vey001. doi: 10.1093/ve/vey001.
  • GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3. Zhao Y, Chen F, Wu W, Sun M, Bilotta AJ, Yao S, Xiao Y, Huang X, Eaves-Pyles TD, Golovko G, Fofanov Y, D’Souza W, Zhao Q, Liu Z, Cong Y. Mucosal Immunol. 2018 May;11(3):752-762. doi: 10.1038/mi.2017.118.
  • Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Annu Rev Biochem. 2018 Jun 20;87:451-478. doi: 10.1146/annurev-biochem-062917-011942.
  • NMR-based investigations into target DNA search processes of proteins. Iwahara J, Zandarashvili L, Kemme CA, Esadze A. 2018 Methods 148, 57-66. doi: 10.1016/j.ymeth.2018.05.004.
  • Impact of two-bond 15N-15N scalar couplings on 15N transverse relaxation measurements for arginine side chains of proteins. Nguyen D, Iwahara J. J Biomol NMR. 2018 May;71(1):45-51. doi: 10.1007/s10858-018-0189-y.
  • Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition. Dunne M, Denyes JM, Arndt H, Loessner MJ, Leiman PG, Klumpp J. Structure. 2018 Dec 4;26(12):1573-1582.e4. doi: 10.1016/j.str.2018.07.017.
  • Contractile injection systems of bacteriophages and related systems. Taylor NMI, van Raaij MJ, Leiman PG. Mol Microbiol. 2018 Apr;108(1):6-15. doi: 10.1111/mmi.13921.
  • Stretching the arms of the type VI secretion sheath protein. Leiman PG. EMBO Rep. 2018 Feb;19(2):191-193. doi: 10.15252/embr.201745627.
  • Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase. Tafoya S, Liu S, Castillo JP, Atz R, Morais MC, Grimes S, Jardine PJ, Bustamante C. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):7961-7966. doi: 10.1073/pnas.1802736115.
  • Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. J Mol Biol. 2018 Oct 19;430(21):4156-4167. doi: 10.1016/j.jmb.2018.08.013.
  • Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. Drake JA, Pettitt BM. Biophys J. 2018 Jun 19;114(12):2799-2810. doi: 10.1016/j.bpj.2018.04.027.
  • Peptide Solubility Limits: Backbone and Side-Chain Interactions. Sarma R, Wong KY, Lynch GC, Pettitt BM. J Phys Chem B. 2018 Apr 5;122(13):3528-3539. doi: 10.1021/acs.jpcb.7b10734.
  • Dynamics-Derived Insights into Complex Formation between the CXCL8 Monomer and CXCR1 N-Terminal Domain: An NMR Study. Joseph PRB, Spyracopoulos L, Rajarathnam K. Molecules. 2018 Oct 31;23(11). pii: E2825. doi: 10.3390/molecules23112825.
  • Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin. Sepuru KM, Nagarajan B, Desai UR, Rajarathnam K. J Biol Chem. 2018 Nov 16;293(46):17817-17828. doi: 10.1074/jbc.RA118.004866.
  • Lysines and Arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions. Joseph PRB, Sawant KV, Iwahara J, Garofalo RP, Desai UR, Rajarathnam K. Sci Rep. 2018 Aug 16;8(1):12289. doi: 10.1038/s41598-018-30697-y.
  • Interleukin-8 mediates neutrophil-endothelial interactions in pig-to-human xenogeneic models. French BM, Sendil S, Sepuru KM, Ranek J, Burdorf L, Harris D, Redding E, Cheng X, Laird CT, Zhao Y, Cerel B, Rajarathnam K, Pierson RN 3rd, Azimzadeh AM. Xenotransplantation. 2018 Mar;25(2):e12385. doi: 10.1111/xen.12385.
  • Direct detection of lysine side chain NH3+ in protein-heparin complexes using NMR spectroscopy. Sepuru KM, Iwahara J, Rajarathnam K. Analyst. 2018 Feb 7;143(3):635-638. doi: 10.1039/c7an01406f.
  • Glycosaminoglycan Interactions Fine-Tune Chemokine-Mediated Neutrophil Trafficking: Structural Insights and Molecular Mechanisms. Rajarathnam K, Sepuru KM, Joseph PRB, Sawant KV, Brown AJ. J Histochem Cytochem. 2018 Apr;66(4):229-239. doi: 10.1369/0022155417739864.
  • Better Safe than Sorry: A Dual-Function Viral Protein Inhibiting Host Defense. Lechtenberg BC, Routh A. Cell Host Microbe. 2018 Oct 10;24(4):467-469. doi: 10.1016/j.chom.2018.09.012.
  • ClickSeq: Replacing Fragmentation and Enzymatic Ligation with Click-Chemistry to Prevent Sequence Chimeras. Jaworski E, Routh A. Methods Mol Biol. 2018;1712:71-85. doi: 10.1007/978-1-4939-7514-3_6.
  • Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer. Liu J, Misra A, Reddy MVVVS, White MA, Ren G, Rudenko G. J Mol Biol. 430(21):4325-4343 (2018)
  • Targeting vesicle size. Zou J, Shi PY. Nat Mater. 2018 Nov;17(11):955-956. doi: 10.1038/s41563-018-0200-8. No abstract available. Erratum in: Nat Mater. 2018 Dec;17(12):1164.
  • A Single-Dose Live-Attenuated Zika Virus Vaccine with Controlled Infection Rounds that Protects against Vertical Transmission. Xie X, Kum DB, Xia H, Luo H, Shan C, Zou J, Muruato AE, Medeiros DBA, Nunes BTD, Dallmeier K, Rossi SL, Weaver SC, Neyts J, Wang T, Vasconcelos PFC, Shi PY. Cell Host Microbe. 2018 Oct 10;24(4):487-499.e5. doi: 10.1016/j.chom.2018.09.008.
  • A single-dose plasmid-launched live-attenuated Zika vaccine induces protective immunity. Zou J, Xie X, Luo H, Shan C, Muruato AE, Weaver SC, Wang T, Shi PY. EBioMedicine. 2018 Oct;36:92-102. doi: 10.1016/j.ebiom.2018.08.056.
  • Using a Virion Assembly-Defective Dengue Virus as a Vaccine Approach. Shan C, Xie X, Zou J, Züst R, Zhang B, Ambrose R, Mackenzie J, Fink K, Shi PY. J Virol. 2018 Oct 12;92(21). pii: e01002-18. doi: 10.1128/JVI.01002-18.
  • Zika Virus Vaccine: Progress and Challenges. Shan C, Xie X, Shi PY. Cell Host Microbe. 2018 Jul 11;24(1):12-17. doi: 10.1016/j.chom.2018.05.021.
  • An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction. Xia H, Luo H, Shan C, Muruato AE, Nunes BTD, Medeiros DBA, Zou J, Xie X, Giraldo MI, Vasconcelos PFC, Weaver SC, Wang T, Rajsbaum R, Shi PY. Nat Commun. 2018 Jan 29;9(1):414. doi: 10.1038/s41467-017-02816-2.
  • Cellular production of a counterfeit viral protein confers immunity to infection by a related virus. Warner BE, Ballinger MJ, Yerramsetty P, Reed J, Taylor DJ, Smith TJ, Bruenn JA. PeerJ. 2018 Sep 28;6:e5679. doi: 10.7717/peerj.5679.
  • Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Nelson CA, Wilen CB, Dai YN, Orchard RC, Kim AS, Stegeman RA, Hsieh LL, Smith TJ, Virgin HW, Fremont DH. Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):E9201-E9210. doi: 10.1073/pnas.1805797115.
  • Evolution on the Biophysical Fitness Landscape of an RNA Virus. Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI. Mol Biol Evol. 2018 Oct 1;35(10):2390-2400. doi: 10.1093/molbev/msy131.
  • Fungal Secretome Analysis via PepSAVI-MS: Identification of the Bioactive Peptide KP4 from Ustilago maydis. Kirkpatrick CL, Parsley NC, Bartges TE, Cooke ME, Evans WS, Heil LR, Smith TJ, Hicks LM. J Am Soc Mass Spectrom. 2018 May;29(5):859-865. doi: 10.1007/s13361-017-1880-z. Epub 2018 Feb 5. Erratum in: J Am Soc Mass Spectrom. 2018 Sep;29(9):1940.
  • Development of a stretch-induced neurotrauma model for medium-throughput screening in vitro: identification of rifampicin as a neuroprotectant. López-García I, Gero D, Szczesny B, Szoleczky P, Olah G, Módis K, Zhang K, Gao J, Wu P, Sowers LC, DeWitt D, Prough DS, Szabo C. Br J Pharmacol. 2018 Jan;175(2):284-300. doi: 10.1111/bph.13642.
  • TC3A: The Cancer 3’ UTR Atlas. Feng X, Li L, Wagner EJ, Li W. Nucleic Acids Res. 2018 Jan 4;46(D1):D1027-D1030. doi: 10.1093/nar/gkx892.
  • 3’ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su J, Chen K, Masamha CP, Baillat D, Fontes-Garfias CR, Shyu AB, Neilson JR, Wagner EJ, Li W. Nat Genet. 2018 Jun;50(6):783-789. doi: 10.1038/s41588-018-0118-8.
  • Integrator subunit 4 is a ‘Symplekin-like’ scaffold that associates with INTS9/11 to form the Integrator cleavage module. Albrecht TR, Shevtsov SP, Wu Y, Mascibroda LG, Peart NJ, Huang KL, Sawyer IA, Tong L, Dundr M, Wagner EJ. Nucleic Acids Res. 2018 May 4;46(8):4241-4255. doi: 10.1093/nar/gky100.
  • Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCFSlmb degron. Gray KM, Kaifer KA, Baillat D, Wen Y, Bonacci TR, Ebert AD, Raimer AC, Spring AM, Have ST, Glascock JJ, Gupta K, Van Duyne GD, Emanuele MJ, Lamond AI, Wagner EJ, Lorson CL, Matera AG. Mol Biol Cell. 2018 Jan 15;29(2):96-110. doi: 10.1091/mbc.E17-11-0627.
  • The contribution of alternative polyadenylation to the cancer phenotype. Masamha CP, Wagner EJ. Carcinogenesis. 2018 Jan 12;39(1):2-10. doi: 10.1093/carcin/bgx096.
  • Selective and membrane-permeable small molecule inhibitors of nicotinamide N-methyltransferase reverse high fat diet-induced obesity in mice. Neelakantan H, Vance V, Wetzel MD, Wang HL, McHardy SF, Finnerty CC, Hommel JD, Watowich SJ. Biochem Pharmacol. 2018 Jan;147:141-152. doi: 10.1016/j.bcp.2017.11.007.
  • Prediction and prevention of urban arbovirus epidemics: A challenge for the global virology community. Weaver SC. Antiviral Res. 2018 Aug;156:80-84. doi: 10.1016/j.antiviral.2018.06.009.
  • Human and Equine Infection with Alphaviruses and Flaviviruses in Panamá during 2010: A Cross-Sectional Study of Household Contacts during an Encephalitis Outbreak. Carrera JP, Bagamian KH, Travassos da Rosa AP, Wang E, Beltran D, Gundaker ND, Armien B, Arroyo G, Sosa N, Pascale JM, Valderrama A, Tesh RB, Vittor AY, Weaver SC. Am J Trop Med Hyg. 2018 Jun;98(6):1798-1804. doi: 10.4269/ajtmh.17-0679.
  • Bunyavirus Taxonomy: Limitations and Misconceptions Associated with the Current ICTV Criteria Used for Species Demarcation. Blitvich BJ, Beaty BJ, Blair CD, Brault AC, Dobler G, Drebot MA, Haddow AD, Kramer LD, LaBeaud AD, Monath TP, Mossel EC, Plante K, Powers AM, Tesh RB, Turell MJ, Vasilakis N, Weaver SC. Am J Trop Med Hyg. 2018 Jul;99(1):11-16. doi: 10.4269/ajtmh.18-0038.
  • Prevention Practices among United States Pregnant Women Who Travel to Zika Outbreak Areas. Berenson AB, Hirth JM, Guo F, Fuchs EL, Weaver SC. Am J Trop Med Hyg. 2018 Jan;98(1):178-180. doi: 10.4269/ajtmh.17-0595.
  • Zika, Chikungunya, and Other Emerging Vector-Borne Viral Diseases. Weaver SC, Charlier C, Vasilakis N, Lecuit M. Annu Rev Med. 2018 Jan 29;69:395-408. doi: 10.1146/annurev-med-050715-105122.
  • PARP1 depletion improves mitochondrial and heart function in Chagas disease: Effects on POLG dependent mtDNA maintenance. Wen JJ, Yin YW, Garg NJ. PLoS Pathog. 2018 May 31;14(5):e1007065. doi: 10.1371/journal.ppat.1007065.