Combination attenuation offers strategy for live-attenuated coronavirus vaccines.
Vineet D. Menachery, Lisa Gralinski, Hugh D Mitchell, Kenneth Dinnon III, Sarah R Leist, Boyd Yount, Eileent T McAnarney, Rachel Graham, Katrina M. Waters, Ralph S. Baric.
bioRxiv preprint first posted online Apr. 28, 2018. doi: 10.1101/309591. [publication pending]
MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape.
Vineet D. Menachery, Alexandra Schäfer, Kristin E. Burnum-Johnson, Hugh D. Mitchell, Amie J. Eisfeld, Kevin B. Walters, Carrie D. Nicora, Samuel O. Purvine, Cameron P. Casey, Matthew E. Monroe, Karl K. Weitz, Kelly G. Stratton, Bobbie-Jo M. Webb-Robertson, Lisa E. Gralinski, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Amy C. Sims, Yoshihiro Kawaoka, and Ralph S. Baric.
Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):E1012-E1021. doi: 10.1073/pnas.1706928115.
PMID: 29339515, PMCID: PMC5798318
2017
A Mouse Model of West Nile Virus Infection.
Graham JB, Swarts JL, Lund JM.
Curr Protoc Mouse Biol. 2017 Dec 20;7(4):221-235. doi: 10.1002/cpmo.33.
PMID: 29261232, PMCID: PMC5777180
Extensive Homeostatic T Cell Phenotypic Variation within the Collaborative Cross.
Graham JB, Swarts JL, Mooney M, Choonoo G, Jeng S, Miller DR, Ferris MT, McWeeney S, Lund JM.
Cell Rep. 2017 Nov 21;21(8):2313-2325. doi: 10.1016/j.celrep.2017.10.093.
PMID: 29166619, PMCID: PMC5728448
High-Resolution Maps of Mouse Reference Populations.
Simecek P, Forejt J, Williams RW, Shiroishi T, Takada T, Lu L, Johnson TE, Bennett B, Deschepper CF, Scott-Boyer MP, Pardo-Manuel de Villena F, Churchill GA.
G3 (Bethesda). 2017 Oct 5;7(10):3427-3434. doi: 10.1534/g3.117.300188.
PMID: 28839117, PMCID: PMC5633391
Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross.
Green R, Wilkins C, Thomas S, Sekine A, Hendrick DM, Voss K, Ireton RC, Mooney M, Go JT, Choonoo G, Jeng S, de Villena FP, Ferris MT, McWeeney S, Gale M Jr.
G3 (Bethesda). 2017 Jun 7;7(6):1665-1682. doi: 10.1534/g3.117.041624.
PMID: 28592649, PMCID: PMC5473748
Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice.
Gralinski LE, Menachery VD, Morgan AP, Totura AL, Beall A, Kocher J, Plante J, Harrison-Shostak DC, Schäfer A, Pardo-Manuel de Villena F, Ferris MT, Baric RS.
G3 (Bethesda). 2017 Jun 7;7(6):1653-1663. doi: 10.1534/g3.117.041624.
PMID: 28592648, PMCID: PMC5473747
Structural Variation Shapes the Landscape of Recombination in Mouse.
Morgan AP, Gatti DM, Najarian ML, Keane TM, Galante RJ, Pack AI, Mott R, Churchill GA, de Villena FP.
Genetics. 2017 Jun;206(2):603-619. doi: 10.1534/genetics.116.197988.
PMID: 28592499, PMCID: PMC5499175
Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross.
Shorter JR, Odet F, Aylor DL, Pan W, Kao CY, Fu CP, Morgan AP, Greenstein S, Bell TA, Stevans AM, Feathers RW, Patel S, Cates SE, Shaw GD, Miller DR, Chesler EJ, McMillian L, O'Brien DA, Villena FP.
Genetics. 2017 Jun;206(2):557-572. doi: 10.1534/genetics.116.199596.
PMID: 28592496, PMCID: PMC5499172
Genomes of the Mouse Collaborative Cross.
Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, McMullan RC, Williams LH, Giusti-Rodríguez P, Ferris MT, Sullivan P, Hock P, Miller DR, Bell TA, McMillan L, Churchill GA, de Villena FP.
Genetics. 2017 Jun;206(2):537-556. doi: 10.1534/genetics.116.198838.
PMID: 28592495, PMCID: PMC5499171
Revealing the Innate immune correlates of resistance to West Nile Virus using the collaborative cross mouse model.
Thomas S, Wilkins C, Green R, McMillan AA, Hendrick DM, Voss K, Ireton RC, Gale M Jr.
2016 [publication pending].
2016
RNA-Seq in the Collaborative Cross.
Green R, Wilkins C, Gale M Jr.
System Genetics: Methods and Protocols, Methods in Molecular Biology. 2016 Dec 9;1488:251-263. doi: 10.1007/978-1-4939-6427-7_11.
Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.
Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM, de Villena FP.
G3 (Bethesda). 2016 Dec 7;6(12):4211-4216. doi: 10.1534/g3.116.034751.
PMID: 27765810, PMCID: PMC5144988
Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.
Chesler EJ, Gatti DM, Morgan AP, Strobel M, Trepanier L, Oberbeck D, McWeeney S, Hitzemann R, Ferris M, McMullan R, Clayshultle A, Bell TA, Manuel de Villena FP, Churchill GA.
G3 (Bethesda). 2016 Dec 7;6(12):3893-3902. doi: 10.1534/g3.116.035527.
PMID: 27694113, PMCID: PMC5144960
A mouse model for MERS coronavirus-induced acute respiratory distress syndrome.
Cockrell AS, Yount BL, Scobey T, Jensen K, Douglas M, Beall A, Tang XC, Marasco WA, Heise MT, Baric RS.
Nat Microbiol. 2016 Nov 28;2:16226. doi: 10.1038/nmicrobiol.2016.226.
PMID: 27892925
Neutralization mechanism of a highly potent antibody against Zika virus.
Zhang S, Kostyuchenko VA, Ng TS, Lim XN, Ooi JS, Lambert S, Tan TY, Widman DG, Shi J, Baric RS, Lok SM.
Nat Commun. 2016 Nov 24;7:13679. doi: 10.1038/ncomms13679.
PMID: 27882950, PMCID: PMC5123051
A Mouse Model of Chronic West Nile Virus Disease.
Graham JB, Swarts JL, Wilkins C, Thomas S, Green R, Sekine A, Voss KM, Ireton RC, Mooney M, Choonoo G, Miller DR, Treuting PM, Pardo Manuel de Villena F, Ferris MT, McWeeney S, Gale M Jr, Lund JM.
PLoS Pathog. 2016 Nov 2;12(11):e1005996. doi: 10.1371/journal.ppat.1005996.
PMID: 27806117, PMCID: PMC5091767
Transcriptional profiles of WNV neurovirulence in a genetically diverse Collaborative Cross population.
Green R, Wilkins C, Thomas S, Sekine A, Ireton RC, Ferris MT, Hendrick DM, Voss K, Pardo-Manuel de Villena F, Baric RS, Heise MT, Gale M Jr.
Genom Data. 2016 Oct 14;10:137-140. doi: 10.1016/j.gdata.2016.10.005.
PMID: 27872814, PMCID: PMC5107684
Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model.
Green R, Wilkins C, Thomas S, Sekine A, Ireton RC, Ferris MT, Hendrick DM, Voss K, de Villena FP, Baric R, Heise M, Gale M Jr.
Genom Data. 2016 Oct 14;10:114-117. doi: 10.1016/j.gdata.2016.10.006.
PMID: 27843766, PMCID: PMC5097955
The Evolutionary Fates of a Large Segmental Duplication in Mouse.
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP.
Genetics. 2016 Sep;204(1):267-85. doi: 10.1534/genetics.116.191007.
PMID: 27371833, PMCID: PMC5012392
Dengue Virus Envelope Dimer Epitope Monoclonal Antibodies Isolated from Dengue Patients Are Protective against Zika Virus.
Swanstrom JA, Plante JA, Plante KS, Young EF, McGowan E, Gallichotte EN, Widman DG, Heise MT, de Silva AM, Baric RS.
MBio. 2016 Jul 19;7(4). pii: e01123-16. doi: 10.1128/mBio.01123-16.
PMID: 27435464, PMCID: PMC4958264
Regulation of Retinoic Acid Inducible Gene-I (RIG-I) Activation by the Histone Deacetylase 6.
Liu HM, Jiang F, Loo YM, Hsu S, Hsiang TY, Marcotrigiano J, Gale M Jr.
EBioMedicine. 2016 Jul;9:195-206. doi: 10.1016/j.ebiom.2016.06.015..
PMID: 27372014, PMCID: PMC4972567
Airway Memory CD4(+) T Cells Mediate Protective Immunity against Emerging Respiratory Coronaviruses.
Zhao J, Zhao J, Mangalam AK, Channappanavar R, Fett C, Meyerholz DK, Agnihothram S, Baric RS, David CS, Perlman S.
Immunity. 2016 Jun 21;44(6):1379-91. doi: 10.1016/j.immuni.2016.05.006.
PMID: 27287409, PMCID: PMC4917442
HitWalker2: visual analytics for precision medicine and beyond.
Bottomly D, McWeeney SK, Wilmot B.
Bioinformatics. 2016 Apr 15;32(8):1253-5. doi: 10.1093/bioinformatics/btv739.
PMID: 26708334, PMCID: PMC4824131
2015
The Mouse Universal Genotyping Array: From Substrains to Subspecies.
Morgan AP, Fu CP, Kao CY, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F.
G3 (Bethesda). 2015 Dec 18;6(2):263-79. doi: 10.1534/g3.115.022087.
PMID: 26684931, PMCID: PMC4751547
argyle: An R Package for Analysis of Illumina Genotyping Arrays.
Morgan AP.
G3 (Bethesda). 2015 Dec 18;6(2):281-6. doi: 10.1534/g3.115.023739.
PMID: 26684930, PMCID: PMC4751548
Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross.
Gralinski LE, Ferris MT, Aylor DL, Whitmore AC, Green R, Frieman MB, Deming D, Menachery VD, Miller DR, Buus RJ, Bell TA, Churchill GA, Threadgill DW, Katze MG, McMillan L, Valdar W, Heise MT, Pardo-Manuel de Villena F, Baric RS.
PLoS Genet. 2015 Oct 9;11(10):e1005504. doi: 10.1371/journal.pgen.1005504.
PMID: 26452100, PMCID: PMC4599853
Reply to "Statins may decrease the Fatality Rate of MERS Infection".
Totura AL, Baric RS.
MBio. 2015 Sep 29;6(5):e01303-15. doi: 10.1128/mBio.01303-15.
PMID: 26419878, PMCID: PMC4611038
New Metrics for Evaluating Viral Respiratory Pathogenesis.
Menachery VD, Gralinski LE, Baric RS, Ferris MT.
PLoS One. 2015 Jun 26;10(6):e0131451. doi: 10.1371/journal.pone.0131451.
PMID: 26115403, PMCID: PMC4482571
Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection.
Totura AL, Whitmore A, Agnihothram S, Schäfer A, Katze MG, Heise MT, Baric RS.
MBio. 2015 May 26;6(3):e00638-15. doi: 10.1128/mBio.00638-15.
PMID: 26015500, PMCID: PMC4447251
Genetic diversity in the collaborative cross model recapitulates human West Nile virus disease outcomes.
Graham JB, Thomas S, Swarts J, McMillan AA, Ferris MT, Suthar MS, Treuting PM, Ireton R, Gale M Jr, Lund JM.
MBio. 2015 May 5;6(3):e00493-15. doi: 10.1128/mBio.00493-15.
PMID: 25944860, PMCID: PMC4436067
plethy: management of whole body plethysmography data in R.
Bottomly D, Wilmot B, McWeeney SK.
BMC Bioinformatics. 2015 Apr 29;16:134. doi: 10.1186/s12859-015-0547-7.
PMID: 25924931, PMCID: PMC4434826
Molecular pathology of emerging coronavirus infections.
Gralinski LE, Baric RS.
J Pathol. 2015 Jan;235(2):185-95. doi: 10.1002/path.4454.
PMID: 25270030, PMCID: PMC4267971
2014
Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates.
Selinger C, Tisoncik-Go J, Menachery VD, Agnihothram S, Law GL, Chang J, Kelly SM, Sova P, Baric RS, Katze MG.
BMC Genomics. 2014 Dec 22;15:1161. doi: 10.1186/1471-2164-15-1161..
PMID: 25534508, PMCID: PMC4522970
Coronavirus non-structural protein 16: evasion, attenuation, and possible treatments.
Menachery VD, Debbink K, Baric RS.
Virus Res. 2014 Dec 19;194:191-9. doi: 10.1016/j.virusres.2014.09.009.
PMID: 25278144, PMCID: PMC4260984
Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance.
Rasmussen AL, Okumura A, Ferris MT, Green R, Feldmann F, Kelly SM, Scott DP, Safronetz D, Haddock E, LaCasse R, Thomas MJ, Sova P, Carter VS, Weiss JM, Miller DR, Shaw GD, Korth MJ, Heise MT, Baric RS, de Villena FP, Feldmann H, Katze MG.
Science. 2014 Nov 21;346(6212):987-91. doi: 10.1126/science.1259595.
PMID: 25359852, PMCID: PMC4241145
Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.
Xiong H, Morrison J, Ferris MT, Gralinski LE, Whitmore AC, Green R, Thomas MJ, Tisoncik-Go J, Schroth GP, Pardo-Manuel de Villena F, Baric RS, Heise MT, Peng X, Katze MG.
G3 (Bethesda). 2014 Jun 5;4(8):1429-44. doi: 10.1534/g3.114.011759.
PMID: 24902603, PMCID: PMC4132174
Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses.
Menachery VD, Eisfeld AJ, Schäfer A, Josset L, Sims AC, Proll S, Fan S, Li C, Neumann G, Tilton SC, Chang J, Gralinski LE, Long C, Green R, Williams CM, Weiss J, Matzke MM, Webb-Robertson BJ, Schepmoes AA, Shukla AK, Metz TO, Smith RD, Waters KM, Katze MG, Kawaoka Y, Baric RS.
MBio. 2014 May 20;5(3):e01174-14. doi: 10.1128/mBio.01174-14.
PMID: 24846384, PMCID: PMC4030454
Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2'-o-methyltransferase activity.
Menachery VD, Yount BL Jr, Josset L, Gralinski LE, Scobey T, Agnihothram S, Katze MG, Baric RS.
J Virol. 2014 Apr;88(8):4251-64. doi: 10.1128/JVI.03571-13.
PMID: 24478444, PMCID: PMC3993736
Multi-omic network signatures of disease.
Gibbs DL, Gralinski L, Baric RS, McWeeney SK.
Front Genet. 2014 Jan 7;4:309. doi: 10.3389/fgene.2013.00309.
PMID: 24432028, PMCID: PMC3882664
Quantitative genetics in the study of virus-induced disease.
Ferris MT, Heise MT.
Adv Virus Res. 2014;88:193-225. doi: 10.1016/B978-0-12-800098-4.00004-0.
PMID: 24373313
Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts.
Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR, Thomas MJ, Tisoncik-Go J, Schroth GP, Kawaoka Y, Manuel de Villena FP, Baric RS, Heise MT, Peng X, Katze MG.
RNA Biol. 2014;11(7):875-90. doi: 10.4161/rna.29442.
PMID: 24922324, PMCID: PMC4179962
2013
A decade after SARS: strategies for controlling emerging coronaviruses.
Graham RL, Donaldson EF, Baric RS.
Nat Rev Microbiol. 2013 Dec;11(12):836-48. doi: 10.1038/nrmicro3143.
PMID: 24217413, PMCID: PMC5147543
A systems framework for vaccine design.
Mooney M, McWeeney S, Canderan G, Sékaly RP.
Curr Opin Immunol. 2013 Oct;25(5):551-5. doi: 10.1016/j.coi.2013.09.014.
PMID: 24358511, PMCID: PMC3983719
Crystal structure of the receptor-binding domain from newly emerged Middle East respiratory syndrome coronavirus.
Chen Y, Rajashankar KR, Yang Y, Agnihothram SS, Liu C, Lin YL, Baric RS, Li F.
J Virol. 2013 Oct;87(19):10777-83. doi: 10.1128/JVI.01756-13.
PMID: 23903833, PMCID: PMC3807420
Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus.
Scobey T, Yount BL, Sims AC, Donaldson EF, Agnihothram SS, Menachery VD, Graham RL, Swanstrom J, Bove PF, Kim JD, Grego S, Randell SH, Baric RS.
Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16157-62. doi: 10.1073/pnas.1311542110.
PMID: 24043791, PMCID: PMC3791741