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Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus.

Wilkinson JM, Bao H, Ladinig A, Hong L, Stothard P, Lunney JK, Plastow GS, Harding JC.

BMC Genomics. 2016 May 20;17(1):383. doi: 10.1186/s12864-016-2720-4.


Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes.

Lu D, Akanno EC, Crowley JJ, Schenkel F, Li H, De Pauw M, Moore SS, Wang Z, Li C, Stothard P, Plastow G, Miller SP, Basarab JA.

J Anim Sci. 2016 Apr;94(4):1342-53. doi: 10.2527/jas.2015-0126.


Differences in Whole Blood Gene Expression Associated with Infection Time-Course and Extent of Fetal Mortality in a Reproductive Model of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection.

Wilkinson JM, Ladinig A, Bao H, Kommadath A, Stothard P, Lunney JK, Harding JC, Plastow GS.

PLoS One. 2016 Apr 19;11(4):e0153615. doi: 10.1371/journal.pone.0153615. eCollection 2016.


Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL.

Schroyen M, Eisley C, Koltes JE, Fritz-Waters E, Choi I, Plastow GS, Guan L, Stothard P, Bao H, Kommadath A, Reecy JM, Lunney JK, Rowland RR, Dekkers JC, Tuggle CK.

BMC Genomics. 2016 Mar 8;17(1):196. doi: 10.1186/s12864-016-2547-z.


Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle.

Chen L, Ekine-Dzivenu C, Vinsky M, Basarab J, Aalhus J, Dugan ME, Fitzsimmons C, Stothard P, Li C.

BMC Genet. 2015 Nov 21;16:135. doi: 10.1186/s12863-015-0290-0.


A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project.

Stothard P, Liao X, Arantes AS, De Pauw M, Coros C, Plastow GS, Sargolzaei M, Crowley JJ, Basarab JA, Schenkel F, Moore S, Miller SP.

Gigascience. 2015 Oct 26;4:49. doi: 10.1186/s13742-015-0090-5. eCollection 2015.


Whole genome SNP genotype piecemeal imputation.

Wang Y, Wylie T, Stothard P, Lin G.

BMC Bioinformatics. 2015 Oct 23;16:340. doi: 10.1186/s12859-015-0770-2.


Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers.

Paradis F, Yue S, Grant JR, Stothard P, Basarab JA, Fitzsimmons C.

J Anim Sci. 2015 Jul;93(7):3331-41. doi: 10.2527/jas.2015-8975.


The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity.

Peters DL, Lynch KH, Stothard P, Dennis JJ.

BMC Genomics. 2015 Sep 3;16:664. doi: 10.1186/s12864-015-1848-y.


Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine.

Bao H, Kommadath A, Liang G, Sun X, Arantes AS, Tuggle CK, Bearson SM, Plastow GS, Stothard P, Guan le L.

Sci Rep. 2015 Jul 31;5:12620. doi: 10.1038/srep12620.


Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene.

Dorshorst B, Henegar C, Liao X, Sällman Almén M, Rubin CJ, Ito S, Wakamatsu K, Stothard P, Van Doormaal B, Plastow G, Barsh GS, Andersson L.

PLoS One. 2015 Jun 4;10(6):e0128969. doi: 10.1371/journal.pone.0128969. eCollection 2015.


Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection.

Koltes JE, Fritz-Waters E, Eisley CJ, Choi I, Bao H, Kommadath A, Serão NV, Boddicker NJ, Abrams SM, Schroyen M, Loyd H, Tuggle CK, Plastow GS, Guan L, Stothard P, Lunney JK, Liu P, Carpenter S, Rowland RR, Dekkers JC, Reecy JM.

BMC Genomics. 2015 May 28;16:412. doi: 10.1186/s12864-015-1635-9.


Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis).

Miller JM, Moore SS, Stothard P, Liao X, Coltman DW.

BMC Genomics. 2015 May 20;16:397. doi: 10.1186/s12864-015-1618-x.


Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples.

Choi I, Bao H, Kommadath A, Hosseini A, Sun X, Meng Y, Stothard P, Plastow GS, Tuggle CK, Reecy JM, Fritz-Waters E, Abrams SM, Lunney JK, Guan le L.

BMC Genomics. 2014 Nov 4;15:954. doi: 10.1186/1471-2164-15-954.


Mitochondriome and cholangiocellular carcinoma.

Bahitham W, Liao X, Peng F, Bamforth F, Chan A, Mason A, Stone B, Stothard P, Sergi C.

PLoS One. 2014 Aug 19;9(8):e104694. doi: 10.1371/journal.pone.0104694. eCollection 2014.


Sequence, structural and expression divergence of duplicate genes in the bovine genome.

Liao X, Bao H, Meng Y, Plastow G, Moore S, Stothard P.

PLoS One. 2014 Jul 23;9(7):e102868. doi: 10.1371/journal.pone.0102868. eCollection 2014.


Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.

Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, Liao X, Djari A, Rodriguez SC, Grohs C, Esquerré D, Bouchez O, Rossignol MN, Klopp C, Rocha D, Fritz S, Eggen A, Bowman PJ, Coote D, Chamberlain AJ, Anderson C, VanTassell CP, Hulsegge I, Goddard ME, Guldbrandtsen B, Lund MS, Veerkamp RF, Boichard DA, Fries R, Hayes BJ.

Nat Genet. 2014 Aug;46(8):858-65. doi: 10.1038/ng.3034. Epub 2014 Jul 13.


Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.

Choi JW, Liao X, Stothard P, Chung WH, Jeon HJ, Miller SP, Choi SY, Lee JK, Yang B, Lee KT, Han KJ, Kim HC, Jeong D, Oh JD, Kim N, Kim TH, Lee HK, Lee SJ.

PLoS One. 2014 Jul 3;9(7):e101127. doi: 10.1371/journal.pone.0101127. eCollection 2014.


Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding.

Kommadath A, Bao H, Arantes AS, Plastow GS, Tuggle CK, Bearson SM, Guan le L, Stothard P.

BMC Genomics. 2014 Jun 9;15:452. doi: 10.1186/1471-2164-15-452.


MicroRNA buffering and altered variance of gene expression in response to Salmonella infection.

Bao H, Kommadath A, Plastow GS, Tuggle CK, Guan le L, Stothard P.

PLoS One. 2014 Apr 9;9(4):e94352. doi: 10.1371/journal.pone.0094352. eCollection 2014.

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