Stothard Research Group


The 1000 Bulls Project paper on genes regulating body size has been published in Nature Genetics

Papers and book chapters (see Google Scholar for additional information)

Hailemariam D, Manafiazar G, Basarab J, Stothard P, Miglior F, Plastow G, Wang Z (2020) Comparative analyses of enteric methane emissions, dry matter intake and milk somatic cell count in different residual feed intake categories of dairy cows. Can J Anim Sci.

Mukiibi R, Johnston D, Vinsky M, Fitzsimmons C, Stothard P, Waters SM, Li C (2020) Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes. Sci Rep.

Lam S, Miglior F, Fonseca PAS, Gómez-Redondo I, Zeidan J, Suarez-Vega, A, Schenkel F, Guan L, Waters S, Stothard P, Cánovas A (2020) Identification of functional candidate variants (SNPs and INDELs) and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing. J Dairy Sci.

Butty AM, Chud TCS, Miglior F, Schenkel FS, Kommadath A, Krivushin K, Grant JR, Häfliger IM, Drögemüller C, Cánovas A, Stothard P, Baes CF (2020) High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. Sci Rep 10:8044 doi: 10.1038/s41598-020-64680-3. PubMed

Zhi S, Stothard P, Banting G, Scott C, Huntley K, Ryu K, Otto S, Ashbolt N, Checkley S, Dong T, Ruecker NJ, Neumann NF (2020) Characterization of water treatment-resistant and multidrug-resistant urinary pathogenic Escherichia coli in treated wastewater. Water Res 182:115827 doi: 10.1016/j.watres.2020.115827. PubMed

Hameed A, Lai WA, Shahina M, Stothard P, Young LS, Lin SY, Sridhar KR, Young CC (2020) Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria. FEMS Microbiol Ecol DOI: 10.1093/femsec/fiaa011. PubMed

Wang Y, Zhang F, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C (2020) Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits. BMC Genomics 21:38 DOI: 10.1186/s12864-019-6273-1. PubMed

Zhang F, Wang Y, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C (2020) Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits. BMC Genomics 21:36 DOI: 10.1186/s12864-019-6362-1. PubMed

Hameed A, Shahina M, Lai W, Stothard P, Young L, Lin S, Young CC (2019) Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex. J Glob Antimicrob Resist 20:28-30 doi: 10.1016/j.jgar.2019.11.017. PubMed

Mukiibi R, Vinsky M, Keogh KA, Fitzsimmons C, Stothard P, Waters SM, Li C (2019) Liver transcriptome profiling of beef steers with divergent growth rate, feed intake or metabolic body weight phenotypes. J Anim Sci doi: 10.1093/jas/skz315. PubMed

Butty AM, Sargolzaei M, Miglior F, Stothard P, Schenkel FS, Gredler-Grandl B, Baes CF (2019) Optimizing selection of the reference population for genotype imputation from array to sequence variants. Front Genet doi: 10.3389/fgene.2019.00510. PubMed

Kommadath A, Grant JR, Krivushin K, Butty AM, Baes CF, Carthy TR, Berry DP, Stothard P (2019) A large interactive visual database of copy number variants discovered in taurine cattle. GigaScience doi: 10.1093/gigascience/giz073. PubMed

Jaswal R, Pathak A, Edwards B, Lewis R, Seaman J, Stothard P, Krivushin K, Blom J, Rupp O, Chauhan A (2019) Metagenomics-guided survey, isolation, and characterization of uranium resistant microbiota from the Savannah River site, USA. Genes doi: 10.3390/genes10050325. PubMed

Peters DL, McCutcheon JG, Stothard P, Dennis JJ (2019) Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion. BMC Genomics doi: 10.1186/s12864-019-5674-5. PubMed

Zhi S, Banting G, Stothard P, Ashbolt NJ, Checkley S, Meyer K, Otto S, Neumann N (2019) Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater. Water Res 156:208-222 doi: 10.1016/j.watres.2019.03.024. PubMed

Munyaka PM, Kommadath A, Fouhse J, Wilkinson J, Diether N, Stothard P, Estellé J, Rogel-Gaillard C, Plastow G, Willing BP (2019) Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae. Vaccine 37:1743-1755 doi: 10.1016/j.vaccine.2019.02.016. PubMed

Ju T, Kong JY, Stothard P, Willing BP (2019) Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota. ISME J doi: 10.1038/s41396-019-0364-5. PubMed

Russell T, Cullingham C, Kommadath A, Stothard P, Herbst A, Coltman D (2019) Development of a novel mule deer genomic assembly and species-diagnostic SNP panel for assessing introgression in mule deer, white-tailed deer, and their interspecific hybrids. G3 (Bethesda) doi: 10.1534/g3.118.200838. PubMed

Bolormaa S, Chamberlain AJ, Khansefid M, Stothard P, Swan AA, Mason B, Prowse-Wilkins CP, Duijvesteijn N, Moghaddar N, van der Werf JH, Daetwyler HD, MacLeod IM (2019) Accuracy of imputation to whole-genome sequence in sheep. Genet Sel Evol doi: 10.1186/s12711-018-0443-5. PubMed

Koufariotis L, Hayes BJ, Kelly M, Burns BM, Lyons R, Stothard P, Chamberlain AJ, Moore S (2018) Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled. Sci Rep 8:17761 doi: 10.1038/s41598-018-35698-5. PubMed

Montecillo AD, Raymundo AK, Papa IA, Aquino GMB, Jacildo AJ, Stothard P, Rosana AR (2018) Near-complete genome of Ralstonia solanacearum T523, a phylotype I tomato phytopathogen isolated from the Philippines. Microbiol Resour Announc doi: 10.1128/MRA.01048-18. PubMed

Lin XB, Wang T, Stothard P, Corander J, Wang J, Baines J, Knowles SCL, Baltrūnaitė L, Tasseva G, Schmaltz R, Tollenaar S, Cody LA, Grenier T, Wu W, Ramer-Tait AE, Walter J (2018) The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract. ISME J doi: 10.1038/s41396-018-0211-0. PubMed

Pathak A, Jaswal R, Stothard P, Brooks S, Chauhan A (2018) Draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated sediment. Genome Announc doi: 10.1128/genomeA.00518-18. PubMed

Mukiibi R, Vinsky M, Keogh KA, Fitzsimmons C, Stothard P, Waters SM, Li C (2018) Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle. Sci Rep 8:7303 doi: 10.1038/s41598-018-25605-3. PubMed

Koufariotis LT, Chen YP, Stothard P, Hayes BJ (2018) Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits. BMC Genomics 19:237 doi: 10.1186/s12864-018-4617-x. PubMed

Zhang C, Kemp R, Stothard P, Wang Z, Boddicker N, Krivushin K, Dekkers J, Plastow G (2018) Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants. Genet Sel Evol 50:14 doi: 10.1186/s12711-018-0387-9. PubMed

Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ (2018) Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nat Genet 50:362-367 doi: 10.1038/s41588-018-0056-5. PubMed

Abo-Ismail MK, Lansink N, Akanno E, Karisa B, Crowley JJ, Moore S, Bork E, Stothard P, Basarab JA, Plastow G (2018) Development and validation of a small SNP panel for feed efficiency in beef cattle. J Anim Sci 96:375-397 doi: 10.1093/jas/sky020. PubMed

Chauhan A, Pathak A, Rajneesh J, Edwards III B, Chappell D, Ball C, Garcia-Sillas R, Stothard P, Seaman J (2018) Physiological and comparative genomic analysis of Arthrobacter sp. SRS-W-1-2016 provides insights on niche adaptation for survival in uraniferous soils. Genes doi: 10.3390/genes9010031. PubMed

Hameed A, Shahina M, Hsin-Chieh H, Lai W, Lin S, Stothard P, Young C (2017) Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a Flavobacterium isolated from coastal surface seawater. Mar Genomics https://doi.org/10.1016/j.margen.2017.09.003.

Ye MH, Bao H, Meng Y, Guan LL, Stothard P, Plastow G (2017) Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine-cytokine receptor interaction pathway related to health status. Genome 60:1021-1028. PubMed

Stothard P, Grant JR, Van Domselaar G (2017) Visualizing and comparing circular genomes using the CGView family of tools. Brief Bioinform doi: 10.1007/s40362-017-0041-x. PubMed

Ju T, Shoblak Y, Gao Y, Yang K, Fouhse J, Finlay BB, So YW, Stothard P, Willing BP (2017) Initial gut microbial composition as a key factor driving host response to antibiotic treatment, as exemplified by the presence or absence of commensal Escherichia coli. Appl Environ Microbiol 83:e01107-17. PubMed

Abo-Ismail MK, Brito LF, Miller SP, Sargolzaei M, Grossi DA, Moore SS, Plastow G, Stothard P, Nayeri S, Schenkel FS (2017) Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle. Genet Sel Evol 49:82. PubMed

Kommadath A, Bao H, Choi I, Reecy JM, Koltes JE, Fritz-Waters E, Eisley CJ, Grant JR, Rowland RRR, Tuggle CK, Dekkers JCM, Lunney JK, Guan L, Stothard P, Plastow GS (2017) Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection. Sci Rep 7:46203. PubMed

Peters DL, Stothard P, Dennis JJ (2017) The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP6. PLoS One 12:e0173341. PubMed

Pathak A, Chauhan A, Stothard P, Green S, Maienschein-Cline M, Jaswal R, Seaman J (2017) Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA. Genom Data 12:62-68. PubMed

Nayeri S, Sargolzaei M, Abo-Ismail MK, Miller SP, Schenkel F, Moore SS, Stothard P (2017) Genome-wide association study for lactation persistency, female fertility, longevity and lifetime profit traits in Holstein dairy cattle. J Dairy Sci 100:1246-1258. PubMed

Wang Y, Lin G, Changxi L, Stothard P (2016) Genotype imputation methods and their effects on genomic predictions in cattle. Springer Science Reviews doi:10.1007/s40362-017-0041-x.

Nayeri S, Stothard P (2016) Tissues, metabolic pathways and genes of key importance in lactating dairy cattle. Springer Science Reviews doi:10.1007/s40362-016-0040-3.

Pathak A, Chauhan A, Ewida AYI, Stothard P (2016) Whole genome sequence analysis of an alachlor and endosulfan degrading Micrococcus sp. strain 2385 isolated from Ochlockonee River, Florida. J Genomics 4:42-47. PubMed

Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A (2016) Comparative genomics and metabolomic analysis reveals peculiar characteristics of Rhodococcus opacus strain M213 particularly for naphthalene degradation. PLoS One 11:e0161032. PubMed

Guanxiang L, Malmuthuge N, Bao H, Stothard P, Griebel PJ, Guan LL (2016) Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves. BMC Genomics 17:602. PubMed

Kong RSG, Liang G, Chen Y, Stothard P, Guan LL (2016) Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. BMC Genomics 17:592. PubMed

Chauhan A, Pathak A, Ewida AYI, Griffiths Z, Stothard P (2016) Whole genome sequence analysis of an alachlor and endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida. Genom Data 8:134-138. PubMed

Nayeri S, Sargolzaei M, Abo-Ismail MK, May N, Miller SP, Schenkel F, Moore SS, Stothard P (2016) Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle. BMC Genet 17:75. PubMed

Wilkinson JM, Bao H, Ladinig A, Hong L, Stothard P, Lunney JK, Plastow GS, Harding JCS (2016) Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus. BMC Genomics 17:383. PubMed

Wilkinson JM, Ladinig A, Bao H, Kommadath A, Stothard P, Lunney JK, Harding JCS, Plastow GS (2016) 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. PLoS One 11:e0153615. PubMed

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 (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. BMC Genomics 17:196. PubMed

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 (2016) Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes. J Anim Sci 94:1342-1353. PubMed

Chen L, Ekine-Dzivenu C, Vinsky M, Basarab J, Aalhus J, Dugan MER, Fitzsimmons C, Stothard P, Changxi L (2015) Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle. BMC Genet 16:135. PubMed

Wang Y, Wylie T, Stothard P, Lin G (2015) Whole genome SNP genotype piecemeal imputation. BMC Bioinformatics 16:340. PubMed

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 (2015) A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project. GigaScience 4:49. PubMed

Paradis F, Yue S, Grant JR, Stothard P, Basarab J, Fitzsimmons C (2015) Transcriptomic analysis by RNA-sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers. J Anim Sci 93:3331-3341. PubMed

Peters DL, Lynch KH, Stothard P, Dennis JJ (2015) The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity. BMC Genomics 16:664. PubMed

Bao H, Kommadath A, Liang G, Sun X, Arantes AS, Tuggle CK, Bearson SMD, Plastow GS, Stothard P, Guan LL (2015) Genome-wide whole blood microRNAome and transcriptome analyses revealed miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine. Sci Rep 5:12620. PubMed

Dorshorst B, Henegar C, Liao X, Sallman Almen M, Rubin CJ, Ito S, Wakamatsu K, Stothard P, Van Doormaal B, Plastow G, Barsh GS, Andersson L (2015) Dominant red coat color in Holstein cattle is associated with a missense mutation in the coatomer protein complex, subunit alpha (COPA) gene. PLoS One 10:e0128969. PubMed

Koltes JE, Fritz-Waters E, Eisley CJ, Choi I, Bao H, Kommadath A, Serao 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 (2015) Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection. BMC Genomics 16:412. PubMed

Miller JM, Moore SS, Stothard P, Liao X, Coltman DW (2015) Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 16:397. PubMed

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 LL (2014) Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples. BMC Genomics 15:954. PubMed

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 (2014) Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet 46:858-865. PubMed

Bahitham W, Liao X, Peng F, Bamforth F, Chan A, Mason A, Stone B, Stothard P, Sergi C (2014) Mitochondriome and cholangiocellular carcinoma. PLoS One 9:e104694. PubMed

Liao X, Bao H, Meng Y, Plastow G, Moore SS, Stothard P (2014) Sequence, structural and expression divergence of duplicate genes in the bovine genome. PLoS One 9:e102868. PubMed

Kommadath A, Bao H, Arantes AS, Plastow GS, Tuggle CK, Bearson SMD, Guan le L, Stothard P (2014) Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. BMC Genomics 15:452. PubMed

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 (2014) Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PLoS One 9:e101127. PubMed

Graham M, Van Domselaar G, Stothard P (2014) Prokaryotic genome sequencing and assembly. In: Tastan Bishop O (ed) Bioinformatics and Data Analysis in Microbiology: Caister Academic Press, Norfolk, UK, pp.25-49.

Van Domselaar G, Graham M, Stothard P (2014) Prokaryotic genome annotation. In: Tastan Bishop O (ed) Bioinformatics and Data Analysis in Microbiology: Caister Academic Press, Norfolk, UK, pp.81-111.

Bao H, Kommadath A, Plastow GS, Tuggle CK, Guan le L, Stothard P (2014) microRNA buffering and altered variance of gene expression in response to Salmonella infection. PLoS One 9:e94352. PubMed

Liang Q, Malmuthuge N, McFadden TB, Bao H, Griebel PJ, Stothard P, Guan le L (2014) Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life. PLoS One 9:e92592. PubMed

Zhou C, Dobrinsky J, Tsoi S, Foxcroft GR, Dixon WT, Stothard P, Verstegen J, Dyck MK (2014) Characterization of the altered gene expression profile in early porcine embryos generated from parthenogenesis and somatic cell chromatin transfer. PLoS One 9:e91728. PubMed

Abo-Ismail MK, Vander Voort G, Squires JJ, Swanson KC, Mandell IB, Liao X, Stothard P, Moore S, Plastow G, Miller SP (2014) Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle. BMC Genet 15:14. PubMed

Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, Wang T, Yeung CKL, Chen L, Ma J, Zhang J, Jiang A, Li J, Zhou C, Zhang J, Liu Y, Sun X, Zhao H, Niu Z, Lou P, Xian L, Shen X, Liu S, Zhang S, Zhang M, Zhu L, Shuai S, Bai L, Tang G, Liu H, Jiang Y, Mai M, Xiao J, Wang X, Zhou Q, Wang Z, Stothard P, Xue M, Gao X, Luo Z, Gu Y, Zhu H, Hu X, Zhao Y, Plastow GS, Wang J, Jiang Z, Li K, Li N, Li X, Li R (2013) Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet 45:1431-1438. PubMed

Liao X, Peng F, Forni S, McLaren D, Plastow G, Stothard P (2013) Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome 56:592-598. PubMed

Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, Plastow GS, Guan le L, Stothard P (2013) Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics 14:609. PubMed

Choi JW, Liao X, Park S, Jeon HJ, Chung WH, Stothard P, Park YS, Lee JK, Lee KT, Kim SH, Oh JD, Kim N, Kim TH, Lee HK, Lee SJ (2013) Massively parallel sequencing of Chikso (Korean Brindle cattle) to discover genome-wide SNPs and InDels. Mol Cells 36:203-211. PubMed

Lee KT, Chung WH, Lee SY, Choi JW, Kim J, Lim D, Lee S, Jang GW, Kim B, Choy YH, Liao X, Stothard P, Moore SS, Lee SH, Ahn S, Kim N, Kim TH (2013) Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics 14:519. PubMed

Karisa BK, Thomson J, Wang Z, Stothard P, Moore SS, Plastow GS (2013) Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle. J Anim Sci 91:3502-3513. PubMed

Choi JW, Lee KT, Liao X, Stothard P, An HS, Ahn S, Lee S, Lee SY, Moore SS, Kim TH (2013) Genome-wide copy number variation in Hanwoo, Black Angus and Holstein cattle. Mamm Genome 24:151-163. PubMed

Thomson JM, Bowles V, Choi J, Basu U, Meng Y, Stothard P, Moore SS (2012) The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility. Prion 6:461-469. PubMed

Wang Y, Cai Z, Stothard P, Moore SS, Goebel R, Wang L, Lin G (2012) Fast accurate missing SNP genotype local imputation. BMC Res Notes 5:404. PubMed

Lynch KH, Stothard P, Dennis JJ (2012) Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages. BMC Genomics 13:223. PubMed

Grant JR, Arantes AS, Stothard P (2012) Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics 13:202. PubMed

Canavez FC, Luche DD, Stothard P, Leite KR, Sousa-Canavez JM, Plastow G, Meidanis J, Souza MA, Feijao P, Moore SS, Camara-Lopes LH (2012) Genome sequence and assembly of Bos indicus. J Hered 103:342-348. PubMed

Nalaila SM, Stothard P, Moore SS, Li C, Wang Z (2012) Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method. J Anim Breed Genet 129:107-119. PubMed

Lynch KH, Stothard P, Dennis JJ (2012) Characterization of DC1, a broad host range Bcep22-like podovirus. Appl Environ Microbiol 78:889-891. PubMed

Cruz J, Liu Y, Liang Y, Zhou Y, Wilson M, Dennis JJ, Stothard P, Van Domselaar G, Wishart DS (2012) BacMap: an up-to-date electronic atlas of annotated bacterial genomes. Nucleic Acids Res 40:D599-D604. PubMed

Stothard P, Choi J, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS (2011) Whole genome resequencing of Black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559. PubMed

Nalaila SM, Stothard P, Moore SS, Wang Z, Li C (2011) Whole genome fine mapping of QTL for ultrasound and carcass merit traits in beef cattle. Can J Anim Sci 91:61-73. PubMed

Mujibi FD, Nkrumah JD, Durunna ON, Stothard P, Mah J, Wang Z, Basarab J, Plastow G, Crews DH Jr, Moore SS (2011) Accuracy of genomic breeding values for residual feed intake in crossbred beef cattle. J Anim Sci 89:3353-3361. PubMed

Grant JR, Arantes AS, Liao X, Stothard P (2011) In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 27:2300-2301. PubMed

Marques E, Grant JR, Wang Z, Kolbehdari D, Stothard P, Plastow G, Moore SS (2011) Identification of candidate markers on BTA14 under milk production trait QTL in Holstein. J Anim Breed Genet 128:305-313. PubMed

Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G (2010) Interactive microbial genome visualization with GView. Bioinformatics 26:3125-3126. PubMed

Lynch KH, Stothard P, Dennis JJ (2010) Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex. BMC Genomics 11:599. PubMed

Hernandez-Sanabria E, Guan LL, Goonewardene LA, Li M, Mujibi DF, Stothard P, Moore SS, Leon-Quintero MC (2010) Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits. Appl Environ Microbiol 76:6338-6350. PubMed

Lu YK, Marden J, Han M, Swingley WD, Mastrian SD, Chowdhury SR, Hao J, Helmy T, Kim S, Kurdoglu AA, Matthies HJ, Rollo D, Stothard P, Blankenship RE, Bauer CE, Touchman JW (2010) Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genomics 11:325. PubMed

Berjanskii M, Liang Y, Zhou J, Tang P, Stothard P, Zhou Y, Cruz J, Macdonell C, Lin G, Lu P, Wishart DS (2010) PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res 38:W633-W640. PubMed

Murdoch BM, Clawson ML, Laegreid WW, Stothard P, Settles M, McKay S, Prasad A, Wang Z, Moore SS, Williams JL (2010) A 2cM resolution genome-wide scan of European Holstein cattle affected by classical BSE. BMC Genet 11:20. PubMed

Lynch KH, Seed KD, Stothard P, Dennis JJ (2010) Inactivation of Burkholderia cepacia complex phage KS9 gp41 identifies the phage repressor and generates lytic virions. J Virol 84:1276-1288. PubMed

Stafuzza NB, Abbassi H, Grant JR, Rodrigues-Filho EA, Ianella P, Kadri SM, Amarante MV, Stothard P, Womack JE, Ponce de Leon FA, Amaral ME (2009) Comparative RH maps of the river buffalo and bovine Y-chromosomes. Cytogenet Genome Res 126:132-138. PubMed

Jin W, Grant JR, Stothard P, Moore SS, Guan LL (2009) Characterization of bovine miRNAs by sequencing and bioinformatics analysis. BMC Mol Biol 10:90. PubMed

Kolbehdari D, Wang Z, Grant JR, Murdoch B, Prasad A, Xiu Z, Marques E, Stothard P, Moore SS (2009) A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls. J Anim Breed Genet 126:216-227. PubMed

The Bovine Genome Sequencing and Analysis Consortium (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-528. PubMed

Cai Z, Sabaa H, Wang Y, Goebel R, Wang Z, Xu J, Stothard P, Lin G (2009) Most parsimonious haplotype allele sharing determination. BMC Bioinformatics 10:115. PubMed

Kropinski AM, Borodovsky M, Carver TJ, Cerdeno-Tarraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van Domselaar G, Wishart DS (2009) In silico identification of genes in bacteriophage DNA. In: Clokie MRJ, Kropinski AM (eds) Bacteriophages: Methods and Protocols, Volume 2: Molecular and Applied Aspects: Humana Press, New York, NY, pp.57-89.

Goudie AD, Lynch KH, Seed KD, Stothard P, Shrivastava S, Wishart DS, Dennis JJ (2008) Genome sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex. BMC Genomics 9:615. PubMed

Amaral ME, Grant JR, Riggs PK, Stafuzza NB, Filho EA, Goldammer T, Weikard R, Brunner RM, Kochan KJ, Greco AJ, Jeong J, Cai Z, Lin G, Prasad A, Kumar S, Saradhi GP, Mathew B, Kumar MA, Miziara MN, Mariani P, Caetano AR, Galvao SR, Tantia MS, Vijh RK, Mishra B, Kumar ST, Pelai VA, Santana AM, Fornitano LC, Jones BC, Tonhati H, Moore S, Stothard P, Womack JE (2008) A first generation whole genome RH map of the river buffalo with comparison to domestic cattle. BMC Genomics 9:631. PubMed

Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, Coleman NV (2008) The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol 74:6405-6416. PubMed

Prasad A, Schnabel RD, McKay SD, Murdoch B, Stothard P, Kolbehdari D, Wang Z, Taylor JF, Moore SS (2008) Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle. Anim Genet 39:597-605. PubMed

Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181-W184. PubMed

Grant JR, Stothard P (2008) Bioinformatics tools and methods for plasmid sequence analysis and annotation. In: Lipps G (ed) Plasmids: Current Research and Future Trends: Caister Academic Press, Norfolk, UK, pp.77-110.

Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS (2008) PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res 36:W399-W405. PubMed

Marques E, Schnabel RD, Stothard P, Kolbehdari D, Wang Z, Taylor JF, Moore SS (2008) High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle. BMC Genet 9:45. PubMed

Kolbehdari D, Wang Z, Grant JR, Murdoch B, Prasad A, Xiu Z, Marques E, Stothard P, Moore SS (2008) A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls. J Dairy Sci 91:2844-2856. PubMed

McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, Gill CA, Gao C, Mannen H, Stothard P, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS (2007) Whole genome linkage disequilibrium maps in cattle. BMC Genet 8:74. PubMed

Prasad A, Schiex T, McKay S, Murdoch B, Wang Z, Womack JE, Stothard P, Moore SS (2007) High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly. BMC Genomics 8:310. PubMed

Marques E, de Givry S, Stothard P, Murdoch B, Wang Z, Womack J, Moore SS (2007) A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly. BMC Genomics 8:254. PubMed

Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS (2007) Biospider: a web server for automating metabolome annotations. Pacific Symposium on Biocomputing 12:145-156. PubMed

McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, Gao C, Li C, Matukumalli LK, Stothard P, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS (2007) Construction of whole-genome radiation hybrid and linkage maps for bovine using high-throughput genotyping. Anim Genet 38:120-125. PubMed

Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L (2007) HMDB: the Human Metabolome Database. Nucleic Acids Res 35:D521-D526. PubMed

Stothard P, Wishart DS (2006) Automated bacterial genome analysis and annotation. Curr Opin Microbiol 9:505-510. PubMed

Wishart DS, Knox C, Guo A, Shrivistava S, Hassanali M, Stothard P, Chang Z, Woolsey J (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 34:D668-D672. PubMed

Stothard P, Pilgrim D (2006) Conspecific and interspecific interactions between the Caenorhabditis FEM-2 and FEM-3 sex-determining proteins despite rapid sequence divergence. J Mol Evol 62:281-291. PubMed

Amegbey G, Stothard P, Alexandre I, Adelinda Y, Arrowsmith C, Wishart DS (2005) Solution structure of MTH0776 from Methanobacterium thermoautotrophicum. J Biomol NMR 33:51-56. PubMed

Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 33:W455-W459. PubMed

Vallee M, Gravel C, Palin MF, Reghenas H, Stothard P, Wishart DS, Sirard MA (2005) Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species. Biol Reprod 73:63-71. PubMed

Stothard P, Van Domselaar G, Shrivastava S, Guo A, O'Neill B, Cruz J, Ellison M, Wishart DS (2005) BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res 33:D317-D320. PubMed

Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539. PubMed

Amegbey G, Chang Z, Stothard P, Adelinda Y, Arrowsmith C, Wishart DS (2004) Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum. J Biomol NMR 30:459-460. PubMed

Dong X, Stothard P, Forsythe I, Wishart DS (2004) PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res 32:W660-W664. PubMed

Sundararaj S, Guo A, Habibi Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS (2004) The CyberCell Database (CCDB): a comprehensive, self-updating relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res 32:D293-D295. PubMed

Stothard P, Pilgrim D (2003) Sex-determination gene and pathway evolution in nematodes. BioEssays 25:221-231. PubMed

Stothard P (2003) The Sequence Manipulation Suite. In: Brown SM (ed) Biocomputing: Computer Tools for Biologists: Eaton Publishing, Westborough, MA, pp.175-180. PDF

Stothard P, Hansen D, Pilgrim D (2002) Evolution of the PP2C family in Caenorhabditis: rapid divergence of the sex-determining protein FEM-2. J Mol Evol 54:267-282. PubMed

Stothard P (2001) COMBOSA3D: combining sequence alignments with three-dimensional structures. Bioinformatics 17:198-199. PubMed

Kibenge FS, Kibenge MJ, McKenna PK, Stothard P, Marshall R, Cusack RR, McGeachy S (2001) Antigenic variation among isolates of infectious salmon anaemia virus correlates with genetic variation of the viral haemagglutinin gene. J Gen Virol 82:2869-2879. PubMed

Stothard P (2000) The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102-1104. PubMed

Wishart DS, Stothard P, Van Domselaar GH (2000) PepTool and GeneTool: platform-independent tools for biological sequence analysis. In: Misener S, Krawetz SA (eds) Bioinformatics Methods and Protocols: Humana Press, Totowa, NJ, pp.93-113.