FluOMICS

Project Publications

Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sanchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, Garcia-Sastre A, Marazzi I.
Influenza virus infection causes global RNAPII termination defects
Nat Struct Mol Biol. 2018;25(9):885-93. Epub 2018/09/05. doi: 10.1038/s41594-018-0124-7. PubMed PMID: 30177761.

Zhang L, Wang J, Munoz-Moreno R, Kim M, Sakthivel R, Mo W, Shao D, Anantharaman A, Garcia-Sastre A, Conrad NK, Fontoura BMA.
Influenza Virus NS1 Protein RNA-Interactome Reveals Intron Targeting
J Virol. 2018. Epub 2018/09/28. doi: 10.1128/JVI.01634-18. PubMed PMID: 30258002; PMCID: PMC6258958.

White KM, Abreu P, Jr., Wang H, De Jesus PD, Manicassamy B, Garcia-Sastre A, Chanda SK, DeVita RJ, Shaw ML.
Broad Spectrum Inhibitor of Influenza A and B Viruses Targeting the Viral Nucleoprotein
ACS Infect Dis. 2018;4(2):146-57. Epub 2017/12/23. doi: 10.1021/acsinfecdis.7b00120. PubMed PMID: 29268608; PMCID: PMC6145453.

Heinz S, Texari L, Hayes MGB, Urbanowski M, Chang MW, Givarkes N, Rialdi A, White KM, Albrecht RA, Pache L, Marazzi I, Garcia-Sastre A, Shaw ML, Benner C.
Transcription Elongation Can Affect Genome 3D Structure
Cell. 2018;174(6):1522-36 e22. Epub 2018/08/28. doi: 10.1016/j.cell.2018.07.047. PubMed PMID: 30146161; PMCID: PMC6130916.

Hancock AS, Stairiker CJ, Boesteanu AC, Monzon-Casanova E, Lukasiak S, Mueller YM, Stubbs AP, Garcia-Sastre A, Turner M, Katsikis PD.
Transcriptome Analysis of Infected and Bystander Type 2 Alveolar Epithelial Cells during Influenza A Virus Infection Reveals In Vivo Wnt Pathway Downregulation
J Virol. 2018;92(21). Epub 2018/08/17. doi: 10.1128/JVI.01325-18. PubMed PMID: 30111569; PMCID: PMC6189488.

Dornfeld D, Dudek AH, Vausselin T, Gunther SC, Hultquist JF, Giese S, Khokhlova-Cubberley D, Chew YC, Pache L, Krogan NJ, Garcia-Sastre A, Schwemmle M, Shaw ML.
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses
Sci Rep. 2018;8(1):2092. Epub 2018/02/03. doi: 10.1038/s41598-018-20458-2. PubMed PMID: 29391557; PMCID: PMC5794779.

Binning JM, Smith AM, Hultquist JF, Craik CS, Caretta Cartozo N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross JD.
Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors
PLoS Pathog. 2018;14(1):e1006830. Epub 2018/01/06. doi: 10.1371/journal.ppat.1006830. PubMed PMID: 29304101; PMCID: PMC5773222.

Beyleveld G, Chin DJ, Moreno Del Olmo E, Carter J, Najera I, Cilloniz C, Shaw ML.
Nucleolar Relocalization of RBM14 by Influenza A Virus NS1 Protein
mSphere. 2018;3(6). Epub 2018/11/16. doi: 10.1128/mSphereDirect.00549-18. PubMed PMID: 30429226; PMCID: PMC6236804.

Schotsaert M, Garcia-Sastre A.
Inactivated influenza virus vaccines: the future of TIV and QIV
Curr Opin Virol. 2017;23:102-6. Epub 2017/05/16. doi: 10.1016/j.coviro.2017.04.005. PubMed PMID: 28505524; PMCID: PMC5502789.

Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, Byun M, Basu U, Garcia-Sastre A, Krogan N, van Bakel H, Marazzi I.
The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.
Cell. 2017;169(4):679-92 e14. Epub 2017/05/06. doi: 10.1016/j.cell.2017.04.021. PubMed PMID: 28475896; PMCID: PMC6217988.

Soonthornvacharin S, Rodriguez-Frandsen A, Zhou Y, Galvez F, Huffmaster NJ, Tripathi S, Balasubramaniam VR, Inoue A, de Castro E, Moulton H, Stein DA, Sanchez-Aparicio MT, De Jesus PD, Nguyen Q, Konig R, Krogan NJ, Garcia-Sastre A, Yoh SM, Chanda SK.
Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation..
Nat Microbiol. 2017;2:17022. doi: 10.1038/nmicrobiol.2017.22. PubMed PMID: 28248290; PMCID: PMC5338947.

Tripathi S, Garcia-Sastre A.
Antiviral innate immunity through the lens of systems biology.
Virus Res. 2016;218:10-7. doi: 10.1016/j.virusres.2015.11.024. PubMed PMID: 26657882; PMCID: PMC4892997.

Schotsaert M, Garcia-Sastre A.
A High-Resolution Look at Influenza Virus Antigenic Drift.
J Infect Dis. 2016;214(7):982. doi: 10.1093/infdis/jiw183. PubMed PMID: 27190189; PMCID: PMC5021226.

Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JS, 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, Garcia-Sastre A, Bukreyev A, Marazzi I.
Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation.
Science. 2016;352(6289):aad7993. doi: 10.1126/science.aad7993. PubMed PMID: 27127234; PMCID: PMC5193222.

Munoz-Moreno R, Cuesta-Geijo MA, Martinez-Romero C, Barrado-Gil L, Galindo I, Garcia-Sastre A, Alonso C.
Antiviral Role of IFITM Proteins in African Swine Fever Virus Infection.
PLoS One. 2016;11(4):e0154366. doi: 10.1371/journal.pone.0154366. PubMed PMID: 27116236; PMCID: PMC4846163.

Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs D, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, Garcia-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LC, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I.
Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection.
Immunity. 2016;44(1):46-58. doi: 10.1016/j.immuni.2015.12.017. PubMed PMID: 26789921; PMCID: PMC4878455.

Yoh SM, Schneider M, Seifried J, Soonthornvacharin S, Akleh RE, Olivieri KC, De Jesus PD, Ruan C, de Castro E, Ruiz PA, Germanaud D, des Portes V, Garcia-Sastre A, Konig R, Chanda SK.
PQBP1 Is a Proximal Sensor of the cGAS-Dependent Innate Response to HIV-1.
Cell. 2015;161(6):1293-305. doi: 10.1016/j.cell.2015.04.050. PubMed PMID: 26046437; PMCID: PMC4503237.

White KM, De Jesus P, Chen Z, Abreu P, Jr., Barile E, Mak PA, Anderson P, Nguyen QT, Inoue A, Stertz S, Koenig R, Pellecchia M, Palese P, Kuhen K, Garcia-Sastre A, Chanda SK, Shaw ML.
A Potent Anti-influenza Compound Blocks Fusion through Stabilization of the Prefusion Conformation of the Hemagglutinin Protein.
ACS Infect Dis. 2015;1(2):98-109. doi: 10.1021/id500022h. PubMed PMID: 25984567; PMCID: PMC4426349.

Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ.
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.
Curr Protoc Bioinformatics. 2015;49:8 19 1-6. doi: 10.1002/0471250953.bi0819s49. PubMed PMID: 25754993; PMCID: PMC4378866.

Tripathi S, Pohl MO, Zhou Y, Rodriguez-Frandsen A, Wang G, Stein DA, Moulton HM, DeJesus P, Che J, Mulder LC, Yanguez E, Andenmatten D, Pache L, Manicassamy B, Albrecht RA, Gonzalez MG, Nguyen Q, Brass A, Elledge S, White M, Shapira S, Hacohen N, Karlas A, Meyer TF, Shales M, Gatorano A, Johnson JR, Jang G, Johnson T, Verschueren E, Sanders D, Krogan N, Shaw M, Konig R, Stertz S, Garcia-Sastre A, Chanda SK.
Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.
Cell Host Microbe. 2015;18(6):723-35. doi: 10.1016/j.chom.2015.11.002. PubMed PMID: 26651948; PMCID: PMC4829074.

Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M.
A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay.
Mol Cell. 2015;57(2):329-40. doi: 10.1016/j.molcel.2014.12.028. PubMed PMID: 25616068; PMCID: PMC4305532.

Miller MS, Rialdi A, Ho JS, Tilove M, Martinez-Gil L, Moshkina NP, Peralta Z, Noel J, Melegari C, Maestre AM, Mitsopoulos P, Madrenas J, Heinz S, Benner C, Young JA, Feagins AR, Basler CF, Fernandez-Sesma A, Becherel OJ, Lavin MF, van Bakel H, Marazzi I.
Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis.
Nat Immunol. 2015;16(5):485-94. doi: 10.1038/ni.3132. PubMed PMID: 25822250; PMCID: PMC4406851.

Cooper DA, Banerjee S, Chakrabarti A, Garcia-Sastre A, Hesselberth JR, Silverman RH, Barton DJ.
RNase L targets distinct sites in influenza A virus RNAs.
J Virol. 2015;89(5):2764-76. doi: 10.1128/JVI.02953-14. PubMed PMID: 25540362; PMCID: PMC4325751.

Ayllon J, Garcia-Sastre A.
The NS1 protein: a multitasking virulence factor.
Curr Top Microbiol Immunol. 2015;386:73-107. doi: 10.1007/82_2014_400. PubMed PMID: 25007846.

Schotsaert M, Garcia-Sastre A.
Influenza vaccines: a moving interdisciplinary field.
Viruses. 2014;6(10):3809-26. doi: 10.3390/v6103809. PubMed PMID: 25302957; PMCID: PMC4213563.

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

Rajsbaum R, Garcia-Sastre A, Versteeg GA.
TRIMmunity: the roles of the TRIM E3-ubiquitin ligase family in innate antiviral immunity.
J Mol Biol. 2014;426(6):1265-84. doi: 10.1016/j.jmb.2013.12.005. PubMed PMID: 24333484; PMCID: PMC3945521.

Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR.
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.
Nat Protoc. 2014;9(11):2539-54. doi: 10.1038/nprot.2014.164. PubMed PMID: 25275790; PMCID: PMC4332878.