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Relevant Publications

Alexander Bukreyev – Core B & RP1:

  • Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JSY, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, Merad M, Jin J, Weirauch M, Heinz S, Benner C, van Bakel H, Basler C, García-Sastre A, Bukreyev A, Marazzi I. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science. 2016 May 27;352(6289):aad7993. doi: 10.1126/science.aad7993. Epub 2016 Apr 28. PMID: 27127234; PMCID: PMC5193222. The article was chosen for Icahn School of Medicine at Mount Sinai press releases on 4/28/2016.​

  • Lubaki NM, Younan P, Santos RI, Meyer M, Iampietro M, Koup RA, Bukreyev A. The Ebola Interferon Inhibiting Domains Attenuate and Dysregulate Cell-Mediated Immune Responses. PLoS Pathog. 2016 Dec 8;12(12):e1006031. doi: 10.1371/journal.ppat.1006031. PMID: 27930745; PMCID: PMC5145241. The article was chosen for UTMB press releases on 12/01/2016. ​

  • Younan P, Ramanathan P, Graber J, Gusovsky F, Bukreyev A. The Toll-Like Receptor 4 Antagonist Eritoran Protects Mice from Lethal Filovirus Challenge. mBio. 2017 Apr 25;8(2):e00226-17. doi: 10.1128/mBio.00226-17. PMID: 28442605; PMCID: PMC5405229. ​

  • Iampietro M, Younan P, Nishida A, Dutta M, Lubaki NM, Santos RI, Koup RA, Katze MG, Bukreyev A. Ebola virus glycoprotein directly triggers T lymphocyte death despite of the lack of infection. PLoS Pathog. 2017 May 22;13(5):e1006397. doi: 10.1371/journal.ppat.1006397. PMID: 28542576; PMCID: PMC5456411. The article was chosen for UTMB press releases on 05/24/2017. ​

  • Younan P, Iampietro M, Nishida A, Ramanathan P, Santos RI, Dutta M, Lubaki NM, Koup RA, Katze MG, Bukreyev A. Ebola Virus Binding to Tim-1 on T Lymphocytes Induces a Cytokine Storm. mBio. 2017 Sep 26;8(5):e00845-17. doi: 10.1128/mBio.00845-17. PMID: 28951472; PMCID: PMC5615193. The article was chosen for American Society of Microbiology and UTMB press releases on 09/26/2017.​

  • Younan P, Iampietro M, Bukreyev A. Disabling of lymphocyte immune response by Ebola virus. PLoS Pathog. 2018 Apr 12;14(4):e1006932. doi: 10.1371/journal.ppat.1006932. PMID: 29649305; PMCID: PMC5897007.​

  • Iampietro M, Santos RI, Lubaki NM, Bukreyev A. Ebola Virus Shed Glycoprotein Triggers Differentiation, Infection, and Death of Monocytes Through Toll-Like Receptor 4 Activation. J Infect Dis. 2018 Nov 22;218(suppl_5):S327-S334. doi: 10.1093/infdis/jiy406. PMID: 30085081; PMCID: PMC6249564. ​

  • Younan P, Santos RI, Ramanathan P, Iampietro M, Nishida A, Dutta M, Ammosova T, Meyer M, Katze MG, Popov VL, Nekhai S, Bukreyev A. Ebola virus-mediated T-lymphocyte depletion is the result of an abortive infection. PLoS Pathog. 2019 Oct 24;15(10):e1008068. doi: 10.1371/journal.ppat.1008068. PMID: 31648236; PMCID: PMC6812753. This article was chosen for UTMB Press Release on October 24, 2019. ​

William Russell – Core C:

Proteomics​

  • Tan X, Shi L, Banerjee P, Liu X, Guo HF, Yu J, Bota-Rabassedas N, Rodriguez BL, Gibbons DL, Russell WK, Creighton CJ, Kurie JM. A protumorigenic secretory pathway activated by p53 deficiency in lung adenocarcinoma. J Clin Invest. 2021 Jan 4;131(1):e137186. doi: 10.1172/JCI137186. PMID: 32931483; PMCID: PMC7773359.

  • Huang KL, Jee D, Stein CB, Elrod ND, Henriques T, Mascibroda LG, Baillat D, Russell WK, Adelman K, Wagner EJ. Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination. Mol Cell. 2020 Oct 15;80(2):345-358.e9. doi: 10.1016/j.molcel.2020.08.016. Epub 2020 Sep 22. PMID: 32966759; PMCID: PMC7660970.

  • Newton BW, Russell WK, Russell DH, Ramaiah SK, Jayaraman A. Liver proteome analysis in a rodent model of alcoholic steatosis. J Proteome Res. 2009 Apr;8(4):1663-71. doi: 10.1021/pr800905w. PMID: 19714808; PMCID: PMC2888666.

  • Li L, Huang KL, Gao Y, Cui Y, Wang G, Elrod ND, Li Y, Chen YE, Ji P, Peng F, Russell WK, Wagner EJ, Li W. An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability. Nat Genet. 2021 May 13. doi: 10.1038/s41588-021-00864-5. Epub ahead of print. PMID: 33986536.

  • Monsivais LA, Sheller-Miller S, Russell W, Saade GR, Dixon CL, Urrabaz-Garza R, Menon R. Fetal membrane extracellular vesicle profiling reveals distinct pathways induced by infection and inflammation in vitro. Am J Reprod Immunol. 2020 Sep;84(3):e13282. doi: 10.1111/aji.13282. Epub 2020 Jun 18. PMID: 32506769.

  • Soni K, Jesudhasan P, Cepeda M, Williams B, Hume M, Russell WK, Jayaraman A, Pillai SD. Proteomic analysis to identify the role of LuxS/AI-2 mediated protein expression in Escherichia coli O157:H7. Foodborne Pathog Dis. 2007 Winter;4(4):463-71. doi: 10.1089/fpd.2007.0034. PMID: 18041955.

  • Braunagel SC, Williamson ST, Saksena S, Zhong Z, Russell WK, Russell DH, Summers MD. Trafficking of ODV-E66 is mediated via a sorting motif and other viral proteins: facilitated trafficking to the inner nuclear membrane. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8372-7. doi: 10.1073/pnas.0402727101. Epub 2004 May 18. PMID: 15150405; PMCID: PMC420401.

  • Newton BW, Cologna SM, Moya C, Russell DH, Russell WK, Jayaraman A. Proteomic analysis of 3T3-L1 adipocyte mitochondria during differentiation and enlargement. J Proteome Res. 2011 Oct 7;10(10):4692-702. doi: 10.1021/pr200491h. Epub 2011 Sep 8. PMID: 21815628.

PTM identification​

  • Pandey A, Ding SL, Qin QM, Gupta R, Gomez G, Lin F, Feng X, Fachini da Costa L, Chaki SP, Katepalli M, Case ED, van Schaik EJ, Sidiq T, Khalaf O, Arenas A, Kobayashi KS, Samuel JE, Rivera GM, Alaniz RC, Sze SH, Qian X, Brown WJ, Rice-Ficht A, Russell WK, Ficht TA, de Figueiredo P. Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection. Cell Host Microbe. 2017 May 10;21(5):637-649.e6. doi: 10.1016/j.chom.2017.04.008. PMID: 28494245; PMCID: PMC5538893.

  • Rosas-Acosta G, Russell WK, Deyrieux A, Russell DH, Wilson VG. A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Mol Cell Proteomics. 2005 Jan;4(1):56-72. doi: 10.1074/mcp.M400149-MCP200. Epub 2004 Nov 30. PMID: 15576338; PMCID: PMC3477800.

  • Wadsworth PA, Singh AK, Nguyen N, Dvorak NM, Tapia CM, Russell WK, Stephan C, Laezza F. JAK2 regulates Nav1.6 channel function via FGF14Y158 phosphorylation. Biochim Biophys Acta Mol Cell Res. 2020 Oct;1867(10):118786. doi: 10.1016/j.bbamcr.2020.118786. Epub 2020 Jun 26. PMID: 32599005; PMCID: PMC7984254.

  • Anderson AP, Luo X, Russell W, Yin YW. Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity. Nucleic Acids Res. 2020 Jan 24;48(2):817-829. doi: 10.1093/nar/gkz1018. PMID: 31799610; PMCID: PMC6954441.

  • Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR 3rd, Davis NG. Global analysis of protein palmitoylation in yeast. Cell. 2006 Jun 2;125(5):1003-13. doi: 10.1016/j.cell.2006.03.042. PMID: 16751107; PMCID: PMC2246083.

  • Bailey AO, Panchenko T, Shabanowitz J, Lehman SM, Bai DL, Hunt DF, Black BE, Foltz DR. Identification of the Post-translational Modifications Present in Centromeric Chromatin. Mol Cell Proteomics. 2016 Mar;15(3):918-31. doi: 10.1074/mcp.M115.053710. Epub 2015 Dec 18. PMID: 26685127; PMCID: PMC4813710.

  • Bailey AO, Panchenko T, Sathyan KM, Petkowski JJ, Pai PJ, Bai DL, Russell DH, Macara IG, Shabanowitz J, Hunt DF, Black BE, Foltz DR. Posttranslational modification of CENP-A influences the conformation of centromeric chromatin. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11827-32. doi: 10.1073/pnas.1300325110. Epub 2013 Jul 1. PMID: 23818633; PMCID: PMC3718089.

  • Karakozova M, Kozak M, Wong CC, Bailey AO, Yates JR 3rd, Mogilner A, Zebroski H, Kashina A. Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science. 2006 Jul 14;313(5784):192-6. doi: 10.1126/science.1129344. Epub 2006 Jun 22. PMID: 16794040. ​

With other investigators of P01

  • Su Z, Chang Q, Drelich A, Shelite T, Judy B, Liu Y, Xiao J, Zhou C, He X, Jin Y, Saito T, Tang S, Soong L, Wakamiya M, Fang X, Bukreyev A, Ksiazek T, Russell WK, Gong B. Annexin A2 depletion exacerbates the intracerebral microhemorrhage induced by acute rickettsia and Ebola virus infections. PLoS Negl Trop Dis. 2020 Jul 20;14(7):e0007960. doi: 10.1371/journal.pntd.0007960. PMID: 32687500; PMCID: PMC7392349.

  • Johnson BA, Hage A, Kalveram B, Mears M, Plante JA, Rodriguez SE, Ding Z, Luo X, Bente D, Bradrick SS, Freiberg AN, Popov V, Rajsbaum R, Rossi S, Russell WK, Menachery VD. Peptidoglycan-Associated Cyclic Lipopeptide Disrupts Viral Infectivity. J Virol. 2019 Oct 29;93(22):e01282-19. doi: 10.1128/JVI.01282-19. PMID: 31462558; PMCID: PMC6819921.

Matthew Weirauch – Core D:

  • Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell. 2018 Feb 8;172(4):650-665. doi: 10.1016/j.cell.2018.01.029. Erratum in: Cell. 2018 Oct 4;175(2):598-599. PMID: 29425488.

  • Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nat Genet. 2018 May;50(5):699-707. doi: 10.1038/s41588-018-0102-3. Epub 2018 Apr 16. PMID: 29662164; PMCID: PMC6022759.​

  • Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014 Sep 11;158(6):1431-1443. doi: 10.1016/j.cell.2014.08.009. PMID: 25215497; PMCID: PMC4163041.​

  • Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol. 2015 Aug;33(8):831-8. doi: 10.1038/nbt.3300. Epub 2015 Jul 27. PMID: 26213851.

  • Lu X, Chen X, Forney C, Donmez O, Miller D, Parameswaran S, Hong T, Huang Y, Pujato M, Cazares T, Miraldi ER, Ray JP, de Boer CG, Harley JB, Weirauch MT, Kottyan LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun. 2021 Mar 12;12(1):1611. doi: 10.1038/s41467-021-21854-5. PMID: 33712590; PMCID: PMC7955039. ​

Mariano Garcia-Blanco – RP2:

  • Liao KC, Chuo V, Fagg WS, Modahl CM, Widen S, Garcia-Blanco MA. The RNA binding protein Quaking represses splicing of the Fibronectin EDA exon and downregulates the interferon response. Nucleic Acids Res. 2021 Aug:gkab732. doi: 10.1093/nar/gkab732. Epub ahead of print. PMID: 34428287.

  • Liao KC, Garcia-Blanco MA. Role of Alternative Splicing in Regulating Host Response to Viral Infection. Cells. 2021 Jul;10(7):1720. doi: 10.3390/cells10071720. PMID: 34359890; PMCID: PMC8306335.

  • Schott G, Garcia-Blanco MA. MHC Class III RNA Binding Proteins and Immunity. RNA Biol. 2021 May;18(5):640-646. doi: 10.1080/15476286.2020.1860388. Epub 2020 Dec 20. PMID: 33280511; PMCID: PMC8163431.

  • Campos RK, Wijeratne HRS, Shah P, Garcia-Blanco MA, Bradrick SS. Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins. Nucleic Acids Res. 2020 Sep 25;48(17):9872-9885. doi: 10.1093/nar/gkaa717. PMID: 32890404; PMCID: PMC7515724.

  • Kim B, Arcos S, Rothamel K, Jian J, Rose KL, McDonald WH, Bian Y, Reasoner S, Barrows NJ, Bradrick S, Garcia-Blanco MA, Ascano M. Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP. Mol Cell. 2020 May 21;78(4):624-640.e7. doi: 10.1016/j.molcel.2020.04.013. Epub 2020 May 6. PMID: 32380061; PMCID: PMC7263428.

  • Anderson DE, Pfeffermann K, Kim SY, Sawatsky B, Pearson J, Kovtun M, Corcoran DL, Krebs Y, Sigmundsson K, Jamison SF, Yeo ZZJ, Rennick LJ, Wang LF, Talbot PJ, Duprex WP, Garcia-Blanco MA, von Messling V. Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae. mBio. 2019 May 14;10(3):e00826-19. doi: 10.1128/mBio.00826-19. PMID: 31088929; PMCID: PMC6520455.

  • Fang J, Pietzsch C, Ramanathan P, Santos RI, Ilinykh PA, Garcia-Blanco MA, Bukreyev A, Bradrick SS. Staufen1 Interacts with Multiple Components of the Ebola Virus Ribonucleoprotein and Enhances Viral RNA Synthesis. mBio. 2018 Oct 9;9(5):e01771-18. doi: 10.1128/mBio.01771-18. PMID: 30301857; PMCID: PMC6178623.

  • Galarza-Muñoz G, Briggs FBS, Evsyukova I, Schott-Lerner G, Kennedy EM, Nyanhete T, Wang L, Bergamaschi L, Widen SG, Tomaras GD, Ko DC, Bradrick SS, Barcellos LF, Gregory SG, Garcia-Blanco MA. Human Epistatic Interaction Controls IL7R Splicing and Increases Multiple Sclerosis Risk. Cell. 2017 Mar 23;169(1):72-84.e13. doi: 10.1016/j.cell.2017.03.007. PMID: 28340352; PMCID: PMC5456452.

  • Barrows NJ, Campos RK, Powell ST, Prasanth KR, Schott-Lerner G, Soto-Acosta R, Galarza-Muñoz G, McGrath EL, Urrabaz-Garza R, Gao J, Wu P, Menon R, Saade G, Fernandez-Salas I, Rossi SL, Vasilakis N, Routh A, Bradrick SS, Garcia-Blanco MA. A Screen of FDA-Approved Drugs for Inhibitors of Zika Virus Infection. Cell Host Microbe. 2016 Aug 10;20(2):259-70. doi: 10.1016/j.chom.2016.07.004. Epub 2016 Jul 28. PMID: 27476412; PMCID: PMC4993926.

  • Ward AM, Bidet K, Yinglin A, Ler SG, Hogue K, Blackstock W, Gunaratne J, Garcia-Blanco MA. Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3' UTR structures. RNA Biol. 2011 Nov-Dec;8(6):1173-86. doi: 10.4161/rna.8.6.17836. Epub 2011 Nov 1. PMID: 21957497; PMCID: PMC3256426.

  • Sessions OM, Barrows NJ, Souza-Neto JA, Robinson TJ, Hershey CL, Rodgers MA, Ramirez JL, Dimopoulos G, Yang PL, Pearson JL, Garcia-Blanco MA. Discovery of insect and human dengue virus host factors. Nature. 2009 Apr 23;458(7241):1047-50. doi: 10.1038/nature07967. PMID: 19396146; PMCID: PMC3462662.

Ricardo Rajsbaum – RP3:

  • Cao Z, Xia H, Rajsbaum R, Xia X, Wang H, Shi PY. Ubiquitination of SARS-CoV-2 ORF7a promotes antagonism of interferon response. Cell Mol Immunol. 2021 Mar;18(3):746-748. doi: 10.1038/s41423-020-00603-6. Epub 2021 Jan 20. PMID: 33473190; PMCID: PMC7815971.​

  • ​Giraldo MI, Xia H, Aguilera-Aguirre L, Hage A, van Tol S, Shan C, Xie X, Sturdevant GL, Robertson SJ, McNally KL, Meade-White K, Azar SR, Rossi SL, Maury W, Woodson M, Ramage H, Johnson JR, Krogan NJ, Morais MC, Best SM, Shi PY, Rajsbaum R. Envelope protein ubiquitination drives entry and pathogenesis of Zika virus. Nature. 2020 Sep;585(7825):414-419. doi: 10.1038/s41586-020-2457-8. Epub 2020 Jul 8. PMID: 32641828; PMCID: PMC7501154.​​

  • van Tol S, Atkins C, Bharaj P, Johnson KN, Hage A, Freiberg AN, Rajsbaum R. VAMP8 Contributes to the TRIM6-Mediated Type I Interferon Antiviral Response during West Nile Virus Infection. J Virol. 2020 Jan 6;94(2):e01454-19. doi: 10.1128/JVI.01454-19. PMID: 31694946; PMCID: PMC6955268.​​

  • Bharaj P, Atkins C, Luthra P, Giraldo MI, Dawes BE, Miorin L, Johnson JR, Krogan NJ, Basler CF, Freiberg AN, Rajsbaum R. The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication. J Virol. 2017 Aug 24;91(18):e00833-17. doi: 10.1128/JVI.00833-17. PMID: 28679761; PMCID: PMC5571272.​​

  • Bharaj P, Wang YE, Dawes BE, Yun TE, Park A, Yen B, Basler CF, Freiberg AN, Lee B, Rajsbaum R. The Matrix Protein of Nipah Virus Targets the E3-Ubiquitin Ligase TRIM6 to Inhibit the IKKε Kinase-Mediated Type-I IFN Antiviral Response. PLoS Pathog. 2016 Sep 13;12(9):e1005880. doi: 10.1371/journal.ppat.1005880. PMID: 27622505; PMCID: PMC5021333. ​​

  • Valerdi KM, Hage A, van Tol S, Rajsbaum R, Giraldo MI. The Role of the Host Ubiquitin System in Promoting Replication of Emergent Viruses. Viruses. 2021 Feb 26;13(3):369. doi: 10.3390/v13030369. PMID: 33652634; PMCID: PMC7996891.​​

  • Giraldo MI, Hage A, van Tol S, Rajsbaum R. TRIM Proteins in Host Defense and Viral Pathogenesis. Curr Clin Microbiol Rep. 2020 Aug 8:1-14. doi: 10.1007/s40588-020-00150-8. Epub ahead of print. PMID: 32837832; PMCID: PMC7414267. ​​

  • Hage A, Rajsbaum R. To TRIM or not to TRIM: the balance of host-virus interactions mediated by the ubiquitin system. J Gen Virol. 2019 Dec;100(12):1641-1662. doi: 10.1099/jgv.0.001341. PMID: 31661051; PMCID: PMC7011758.​​

  • Rajsbaum R, Versteeg GA, Schmid S, Maestre AM, Belicha-Villanueva A, Martínez-Romero C, Patel JR, Morrison J, Pisanelli G, Miorin L, Laurent-Rolle M, Moulton HM, Stein DA, Fernandez-Sesma A, tenOever BR, García-Sastre A. Unanchored K48-linked polyubiquitin synthesized by the E3-ubiquitin ligase TRIM6 stimulates the interferon-IKKε kinase-mediated antiviral response. Immunity. 2014 Jun 19;40(6):880-95. doi: 10.1016/j.immuni.2014.04.018. Epub 2014 May 29. PMID: 24882218; PMCID: PMC4114019.​