Bolormaa S, MacLeod IM, Khansefid M, Marett LC, Wales WJ, Miglior F, Baes CF, Schenkel FS, Connor EE, Manzanilla-Pech CIV, Stothard P, Herman E, Nieuwhof GJ, Goddard ME, Pryce JE. Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency. Genet Sel Evol. 2022 Sep 6;54(1):60. doi: 10.1186/s12711-022-00749-z. PMID: 36068488.

PubMed

Shadpour S, Chud TCS, Hailemariam D, Plastow G, Oliveira HR, Stothard P, Lassen J, Miglior F, Baes CF, Tulpan D, Schenkel FS. Predicting methane emission in Canadian Holstein dairy cattle using milk mid-infrared reflectance spectroscopy and other commonly available predictors via artificial neural networks. J Dairy Sci. 2022 Oct;105(10):8272-8285. doi: 10.3168/jds.2021-21176. Epub 2022 Aug 31. PMID: 36055858.

PubMed

Shadpour S, Chud TCS, Hailemariam D, Oliveira HR, Plastow G, Stothard P, Lassen J, Baldwin R, Miglior F, Baes CF, Tulpan D, Schenkel FS. Predicting dry matter intake in Canadian Holstein dairy cattle using milk mid-infrared reflectance spectroscopy and other commonly available predictors via artificial neural networks. J Dairy Sci. 2022 Oct;105(10):8257-8271. doi: 10.3168/jds.2021-21297. Epub 2022 Aug 31. PMID: 36055837.

PubMed

Freeman CN, Herman EK, Abi Younes J, Ramsay DE, Erikson N, Stothard P, Links MG, Otto SJG, Waldner C. Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle. BMC Vet Res. 2022 Jun 2;18(1):211. doi: 10.1186/s12917-022-03269-6. PMID: 35655189.

PubMed

Liu R, Hailemariam D, Yang T, Miglior F, Schenkel F, Wang Z, Stothard P, Zhang S, Plastow G. Predicting enteric methane emission in lactating Holsteins based on reference methane data collected by the GreenFeed system. Animal. 2022 Mar;16(3):100469. doi: 10.1016/j.animal.2022.100469. Epub 2022 Feb 18. PMID: 35190321.

PubMed

O'Hara E, Herbst A, Kommadath A, Aiken JM, McKenzie D, Goodarzi N, Skinner P, Stothard P. Neural transcriptomic signature of chronic wasting disease in white-tailed deer. BMC Genomics. 2022 Jan 21;23(1):69. doi: 10.1186/s12864-022-08306-0. PMID: 35062879.

PubMed

Norton KA, Humphreys R, Weatherill C, Duong K, Nguyen VV, Kommadath A, Niri F, Stothard P, McDermid HE. Subfertility in young male mice mutant for chromatin remodeller CECR2. Reproduction. 2022 Jan 21;163(2):69-83. doi: 10.1530/REP-19-0507. PMID: 34904570.

PubMed

Zhou M, Ghoshal B, Stothard P, Guan LL. Distinctive roles between rumen epimural and content bacterial communities on beef cattle feed efficiency: A combined analysis. Curr Res Microb Sci. 2021 Nov 28;2:100085. doi: 10.1016/j.crmicr.2021.100085. PMID: 34934993; PMCID: PMC8654779.

PubMed

Bolormaa S, Swan AA, Stothard P, Khansefid M, Moghaddar N, Duijvesteijn N, van der Werf JHJ, Daetwyler HD, MacLeod IM. A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits. Genet Sel Evol. 2021 Jul 8;53(1):58. doi: 10.1186/s12711-021-00651-0. PMID: 34238208; PMCID: PMC8268212.

PubMed

Manzanilla-Pech CIV, L Vendahl P, Mansan Gordo D, Difford GF, Pryce JE, Schenkel F, Wegmann S, Miglior F, Chud TC, Moate PJ, Williams SRO, Richardson CM, Stothard P, Lassen J. Breeding for reduced methane emission and feed-efficient Holstein cows: An international response. J Dairy Sci. 2021 Aug;104(8):8983-9001. doi: 10.3168/jds.2020-19889. Epub 2021 May 15. PMID: 34001361.

PubMed

Pathak A, Stothard P, Chauhan A. Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column. Microorganisms. 2021 Feb 27;9(3):490. doi: 10.3390/microorganisms9030490. PMID: 33673397; PMCID: PMC7996774.

PubMed

Butty AM, Chud TCS, Cardoso DF, Lopes LSF, Miglior F, Schenkel FS, Cánovas A, Häfliger IM, Drögemüller C, Stothard P, Malchiodi F, Baes CF. Genome-wide association study between copy number variants and hoof health traits in Holstein dairy cattle. J Dairy Sci. 2021 Jul;104(7):8050-8061. doi: 10.3168/jds.2020-19879. Epub 2021 Apr 23. PMID: 33896633.

PubMed

Yang T, Miller M, Forgacs D, Derr J, Stothard P. Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition. Front Genet. 2020 Nov 20;11:585999. doi: 10.3389/fgene.2020.585999. PMID: 33329724; PMCID: PMC7714993.

PubMed

Mukiibi R, Johnston D, Vinsky M, Fitzsimmons C, Stothard P, Waters SM, Li C. Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes. Sci Rep. 2020 Nov 9;10(1):19309. doi: 10.1038/s41598-020-73885-5. PMID: 33168877; PMCID: PMC7653039.

PubMed

Lam S, Miglior F, Fonseca PAS, Gómez-Redondo I, Zeidan J, Suárez-Vega A, Schenkel F, Guan LL, Waters S, Stothard P, Cánovas A. Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing. J Dairy Sci. 2021 Feb;104(2):1928-1950. doi: 10.3168/jds.2020-18241. Epub 2020 Dec 23. PMID: 33358171.

PubMed

Butty AM, Chud TCS, Miglior F, Schenkel FS, Kommadath A, Krivushin K, Grant JR, Häfliger IM, Drögemüller C, Cánovas A, Stothard P, Baes CF. High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. Sci Rep. 2020 May 15;10(1):8044. doi: 10.1038/s41598-020-64680-3. PMID: 32415111; PMCID: PMC7229195.

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. Characterization of water treatment-resistant and multidrug-resistant urinary pathogenic Escherichia coli in treated wastewater. Water Res. 2020 Sep 1;182:115827. doi: 10.1016/j.watres.2020.115827. Epub 2020 Jun 9. PMID: 32580076.

PubMed

Hameed A, Lai WA, Shahina M, Stothard P, Young LS, Lin SY, Sridhar KR, Young CC. Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria. FEMS Microbiol Ecol. 2020 Mar 1;96(3):fiaa011. doi: 10.1093/femsec/fiaa011. PMID: 31960903.

PubMed

Wang Y, Zhang F, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C. 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. 2020 Jan 13;21(1):38. doi: 10.1186/s12864-019-6273-1. PMID: 31931697; PMCID: PMC6958779.

PubMed

Zhang F, Wang Y, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C. 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. 2020 Jan 13;21(1):36. doi: 10.1186/s12864-019-6362-1. PMID: 31931702; PMCID: PMC6956504.

PubMed

Hameed A, Shahina M, Lai WA, Stothard P, Young LS, Lin SY, Young CC. 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. 2020 Mar;20:28-30. doi: 10.1016/j.jgar.2019.11.017. Epub 2019 Dec 3. PMID: 31809939.

PubMed

Mukiibi R, Vinsky M, Keogh K, Fitzsimmons C, Stothard P, Waters SM, Li C. Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes1. J Anim Sci. 2019 Nov 4;97(11):4386-4404. doi: 10.1093/jas/skz315. PMID: 31583405; PMCID: PMC6827404.

PubMed

Butty AM, Sargolzaei M, Miglior F, Stothard P, Schenkel FS, Gredler-Grandl B, Baes CF. Optimizing Selection of the Reference Population for Genotype Imputation From Array to Sequence Variants. Front Genet. 2019 May 31;10:510. doi: 10.3389/fgene.2019.00510. PMID: 31214246; PMCID: PMC6554347.

PubMed

Kommadath A, Grant JR, Krivushin K, Butty AM, Baes CF, Carthy TR, Berry DP, Stothard P. A large interactive visual database of copy number variants discovered in taurine cattle. Gigascience. 2019 Jun 1;8(6):giz073. doi: 10.1093/gigascience/giz073. PMID: 31241156; PMCID: PMC6593363.

PubMed

Jaswal R, Pathak A, Edwards B III, Lewis R III, Seaman JC, Stothard P, Krivushin K, Blom J, Rupp O, Chauhan A. Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes (Basel). 2019 Apr 28;10(5):325. doi: 10.3390/genes10050325. PMID: 31035394; PMCID: PMC6562407.

PubMed

Peters DL, McCutcheon JG, Stothard P, Dennis JJ. Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion. BMC Genomics. 2019 Apr 16;20(1):300. doi: 10.1186/s12864-019-5674-5. PMID: 30991961; PMCID: PMC6469090.

PubMed

Zhi S, Banting G, Stothard P, Ashbolt NJ, Checkley S, Meyer K, Otto S, Neumann NF. Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater. Water Res. 2019 Jun 1;156:208-222. doi: 10.1016/j.watres.2019.03.024. Epub 2019 Mar 21. PMID: 30921537.

PubMed

Munyaka PM, Kommadath A, Fouhse J, Wilkinson J, Diether N, Stothard P, Estellé J, Rogel-Gaillard C, Plastow G, Willing BP. Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae. Vaccine. 2019 Mar 22;37(13):1743-1755. doi: 10.1016/j.vaccine.2019.02.016. Epub 2019 Feb 23. PMID: 30808565.

PubMed

Ju T, Kong JY, Stothard P, Willing BP. Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota. ISME J. 2019 Jun;13(6):1520-1534. doi: 10.1038/s41396-019-0364-5. Epub 2019 Feb 11. PMID: 30742017; PMCID: PMC6776049.

PubMed

Russell T, Cullingham C, Kommadath A, Stothard P, Herbst A, Coltman D. 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). 2019 Mar 7;9(3):911-919. doi: 10.1534/g3.118.200838. PMID: 30670611; PMCID: PMC6404596.

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. Accuracy of imputation to whole-genome sequence in sheep. Genet Sel Evol. 2019 Jan 17;51(1):1. doi: 10.1186/s12711-018-0443-5. PMID: 30654735; PMCID: PMC6337865.

PubMed

Montecillo AD, Raymundo AK, Papa IA, Aquino GMB, Jacildo AJ, Stothard P, Rosana ARR. Near-Complete Genome Sequence of Ralstonia solanacearum T523, a Phylotype I Tomato Phytopathogen Isolated from the Philippines. Microbiol Resour Announc. 2018 Sep 27;7(12):e01048-18. doi: 10.1128/MRA.01048-18. PMID: 30533677; PMCID: PMC6256700.

PubMed

Koufariotis L, Hayes BJ, Kelly M, Burns BM, Lyons R, Stothard P, Chamberlain AJ, Moore S. Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled. Sci Rep. 2018 Dec 10;8(1):17761. doi: 10.1038/s41598-018-35698-5. PMID: 30531891; PMCID: PMC6288114.

PubMed

Lin XB, Wang T, Stothard P, Corander J, Wang J, Baines JF, Knowles SCL, Baltrūnaitė L, Tasseva G, Schmaltz R, Tollenaar S, Cody LA, Grenier T, Wu W, Ramer-Tait AE, Walter J. The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract. ISME J. 2018 Nov;12(11):2770-2784. doi: 10.1038/s41396-018-0211-0. Epub 2018 Jul 16. PMID: 30013162; PMCID: PMC6193996.

PubMed

Pathak A, Jaswal R, Stothard P, Brooks S, Chauhan A. Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment. Genome Announc. 2018 Jun 21;6(25):e00518-18. doi: 10.1128/genomeA.00518-18. PMID: 29930041; PMCID: PMC6013641.

PubMed

Mukiibi R, Vinsky M, Keogh KA, Fitzsimmons C, Stothard P, Waters SM, Li C. Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle. Sci Rep. 2018 May 8;8(1):7303. doi: 10.1038/s41598-018-25605-3. PMID: 29740082; PMCID: PMC5940658.

PubMed

Zhang C, Kemp RA, Stothard P, Wang Z, Boddicker N, Krivushin K, Dekkers J, Plastow G. Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants. Genet Sel Evol. 2018 Apr 6;50(1):14. doi: 10.1186/s12711-018-0387-9. PMID: 29625549; PMCID: PMC5889553.

PubMed

Koufariotis LT, Chen YP, Stothard P, Hayes BJ. Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits. BMC Genomics. 2018 Apr 5;19(1):237. doi: 10.1186/s12864-018-4617-x. PMID: 29618315; PMCID: PMC5885354.

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. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nat Genet. 2018 Mar;50(3):362-367. doi: 10.1038/s41588-018-0056-5. Epub 2018 Feb 19. PMID: 29459679.

PubMed

Abo-Ismail MK, Lansink N, Akanno E, Karisa BK, Crowley JJ, Moore SS, Bork E, Stothard P, Basarab JA, Plastow GS. Development and validation of a small SNP panel for feed efficiency in beef cattle. J Anim Sci. 2018 Mar 6;96(2):375-397. doi: 10.1093/jas/sky020. PMID: 29390120; PMCID: PMC6140863.

PubMed

Chauhan A, Pathak A, Jaswal R, Edwards B III, Chappell D, Ball C, Garcia-Sillas R, Stothard P, Seaman J. Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils. Genes (Basel). 2018 Jan 11;9(1):31. doi: 10.3390/genes9010031. PMID: 29324691; PMCID: PMC5793183.

PubMed

Abo-Ismail MK, Brito LF, Miller SP, Sargolzaei M, Grossi DA, Moore SS, Plastow G, Stothard P, Nayeri S, Schenkel FS. Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle. Genet Sel Evol. 2017 Nov 7;49(1):82. doi: 10.1186/s12711-017-0356-8. PMID: 29115939; PMCID: PMC6389134.

PubMed

Stothard P, Grant JR, Van Domselaar G. Visualizing and comparing circular genomes using the CGView family of tools. Brief Bioinform. 2019 Jul 19;20(4):1576-1582. doi: 10.1093/bib/bbx081. PMID: 28968859; PMCID: PMC6781573.

PubMed

Ye MH, Bao H, Meng Y, Guan LL, Stothard P, Plastow G. Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine-cytokine receptor interaction pathway related to health status. Genome. 2017 Dec;60(12):1021-1028. doi: 10.1139/gen-2017-0074. Epub 2017 Aug 1. PMID: 28763624.

PubMed

Ju T, Shoblak Y, Gao Y, Yang K, Fouhse J, Finlay BB, So YW, Stothard P, Willing BP. 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. 2017 Aug 17;83(17):e01107-17. doi: 10.1128/AEM.01107-17. PMID: 28667114; PMCID: PMC5561281.

PubMed

Kommadath A, Bao H, Choi I, Reecy JM, Koltes JE, Fritz-Waters E, Eisley CJ, Grant JR, Rowland RR, Tuggle CK, Dekkers JC, Lunney JK, Guan LL, Stothard P, Plastow GS. Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection. Sci Rep. 2017 Apr 10;7:46203. doi: 10.1038/srep46203. PMID: 28393889; PMCID: PMC5385538.

PubMed

Pathak A, Chauhan A, Stothard P, Green S, Maienschein-Cline M, Jaswal R, Seaman J. 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. 2017 Feb 27;12:62-68. doi: 10.1016/j.gdata.2017.02.011. PMID: 28373958; PMCID: PMC5367793.

PubMed

Peters DL, Stothard P, Dennis JJ. The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP6. PLoS One. 2017 Mar 14;12(3):e0173341. doi: 10.1371/journal.pone.0173341. PMID: 28291834; PMCID: PMC5349666.

PubMed

Nayeri S, Sargolzaei M, Abo-Ismail MK, Miller S, Schenkel F, Moore SS, Stothard P. Genome-wide association study for lactation persistency, female fertility, longevity, and lifetime profit index traits in Holstein dairy cattle. J Dairy Sci. 2017 Feb;100(2):1246-1258. doi: 10.3168/jds.2016-11770. Epub 2016 Nov 23. PMID: 27889128.

PubMed

Pathak A, Chauhan A, Ewida AY, Stothard P. Whole Genome Sequence Analysis of an Alachlor and Endosulfan Degrading Micrococcus sp. strain 2385 Isolated from Ochlockonee River, Florida. J Genomics. 2016 Sep 8;4:42-7. doi: 10.7150/jgen.16156. PMID: 27672405; PMCID: PMC5033731.

PubMed

Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A. Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation. PLoS One. 2016 Aug 17;11(8):e0161032. doi: 10.1371/journal.pone.0161032. PMID: 27532207; PMCID: PMC4988695.

PubMed

Liang G, Malmuthuge N, Bao H, Stothard P, Griebel PJ, Guan le L. Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves. BMC Genomics. 2016 Aug 11;17(1):602. doi: 10.1186/s12864-016-2957-y. PMID: 27515123; PMCID: PMC4981982.

PubMed

Kong RS, Liang G, Chen Y, Stothard P, Guan le L. Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. BMC Genomics. 2016 Aug 9;17:592. doi: 10.1186/s12864-016-2935-4. PMID: 27506548; PMCID: PMC4979190.

PubMed

Chauhan A, Pathak A, Ewida AY, Griffiths Z, Stothard P. Whole genome sequence analysis of an Alachlor and Endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida. Genom Data. 2016 May 16;8:134-8. doi: 10.1016/j.gdata.2016.05.008. PMID: 27330991; PMCID: PMC4907040.

PubMed

Nayeri S, Sargolzaei M, Abo-Ismail MK, May N, Miller SP, Schenkel F, Moore SS, Stothard P. Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle. BMC Genet. 2016 Jun 10;17(1):75. doi: 10.1186/s12863-016-0386-1. PMID: 27287773; PMCID: PMC4901445.

PubMed

Wang, Y., Lin, G., Li, C., & Stothard, P. (2016). Genotype Imputation Methods and Their Effects on Genomic Predictions in Cattle. Springer Science Reviews, 4(2), 79–98. https://doi.org/10.1007/s40362-017-0041-x

Link

Nayeri, S., & Stothard, P. (2016). Tissues, Metabolic Pathways and Genes of Key Importance in Lactating Dairy Cattle. Springer Science Reviews, 4(2), 49–77. https://doi.org/10.1007/s40362-016-0040-3

Link

Wilkinson JM, Bao H, Ladinig A, Hong L, Stothard P, Lunney JK, Plastow GS, Harding JC. 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. 2016 May 20;17:383. doi: 10.1186/s12864-016-2720-4. PMID: 27207143; PMCID: PMC4875603.

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. Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes. J Anim Sci. 2016 Apr;94(4):1342-53. doi: 10.2527/jas.2015-0126. PMID: 27135994.

PubMed

Wilkinson JM, Ladinig A, Bao H, Kommadath A, Stothard P, Lunney JK, Harding JC, Plastow GS. 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. 2016 Apr 19;11(4):e0153615. doi: 10.1371/journal.pone.0153615. PMID: 27093427; PMCID: PMC4836665.

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. 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. 2016 Mar 8;17:196. doi: 10.1186/s12864-016-2547-z. PMID: 26951612; PMCID: PMC4782518.

PubMed

Chen L, Ekine-Dzivenu C, Vinsky M, Basarab J, Aalhus J, Dugan ME, Fitzsimmons C, Stothard P, Li C. 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. 2015 Nov 21;16:135. doi: 10.1186/s12863-015-0290-0. PMID: 26589139; PMCID: PMC4654876.

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. A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project. Gigascience. 2015 Oct 26;4:49. doi: 10.1186/s13742-015-0090-5. PMID: 26504517; PMCID: PMC4620632.

PubMed

Wang Y, Wylie T, Stothard P, Lin G. Whole genome SNP genotype piecemeal imputation. BMC Bioinformatics. 2015 Oct 23;16:340. doi: 10.1186/s12859-015-0770-2. PMID: 26498158; PMCID: PMC4619096.

PubMed

Paradis F, Yue S, Grant JR, Stothard P, Basarab JA, Fitzsimmons C. Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers. J Anim Sci. 2015 Jul;93(7):3331-41. doi: 10.2527/jas.2015-8975. PMID: 26440002.

PubMed

Peters DL, Lynch KH, Stothard P, Dennis JJ. The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity. BMC Genomics. 2015 Sep 3;16(1):664. doi: 10.1186/s12864-015-1848-y. PMID: 26335566; PMCID: PMC4559383.

PubMed

Bao H, Kommadath A, Liang G, Sun X, Arantes AS, Tuggle CK, Bearson SM, Plastow GS, Stothard P, Guan le L. Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine. Sci Rep. 2015 Jul 31;5:12620. doi: 10.1038/srep12620. PMID: 26227241; PMCID: PMC4521145.

PubMed

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. Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA) Gene. PLoS One. 2015 Jun 4;10(6):e0128969. doi: 10.1371/journal.pone.0128969. PMID: 26042826; PMCID: PMC4456281.

PubMed

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. Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection. BMC Genomics. 2015 May 28;16(1):412. doi: 10.1186/s12864-015-1635-9. PMID: 26016888; PMCID: PMC4446061.

PubMed

Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics. 2015 May 20;16(1):397. doi: 10.1186/s12864-015-1618-x. PMID: 25990117; PMCID: PMC4438629.

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 le L. Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples. BMC Genomics. 2014 Nov 4;15(1):954. doi: 10.1186/1471-2164-15-954. PMID: 25374277; PMCID: PMC4230834.

PubMed

Bahitham W, Liao X, Peng F, Bamforth F, Chan A, Mason A, Stone B, Stothard P, Sergi C. Mitochondriome and cholangiocellular carcinoma. PLoS One. 2014 Aug 19;9(8):e104694. doi: 10.1371/journal.pone.0104694. PMID: 25137133; PMCID: PMC4138114.

PubMed

Liao X, Bao H, Meng Y, Plastow G, Moore S, Stothard P. Sequence, structural and expression divergence of duplicate genes in the bovine genome. PLoS One. 2014 Jul 23;9(7):e102868. doi: 10.1371/journal.pone.0102868. PMID: 25054921; PMCID: PMC4108385.

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. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014 Aug;46(8):858-65. doi: 10.1038/ng.3034. Epub 2014 Jul 13. PMID: 25017103.

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. Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PLoS One. 2014 Jul 3;9(7):e101127. doi: 10.1371/journal.pone.0101127. PMID: 24992012; PMCID: PMC4081042.

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.

Link

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.

Link

Kommadath A, Bao H, Arantes AS, Plastow GS, Tuggle CK, Bearson SM, Guan le L, Stothard P. Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. BMC Genomics. 2014 Jun 9;15(1):452. doi: 10.1186/1471-2164-15-452. PMID: 24912583; PMCID: PMC4070558.

PubMed

Bao H, Kommadath A, Plastow GS, Tuggle CK, Guan le L, Stothard P. MicroRNA buffering and altered variance of gene expression in response to Salmonella infection. PLoS One. 2014 Apr 9;9(4):e94352. doi: 10.1371/journal.pone.0094352. PMID: 24718561; PMCID: PMC3981782.

PubMed

Liang G, Malmuthuge N, McFadden TB, Bao H, Griebel PJ, Stothard P, Guan le L. Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life. PLoS One. 2014 Mar 28;9(3):e92592. doi: 10.1371/journal.pone.0092592. PMID: 24682221; PMCID: PMC3969364.

PubMed

Zhou C, Dobrinsky J, Tsoi S, Foxcroft GR, Dixon WT, Stothard P, Verstegen J, Dyck MK. Characterization of the altered gene expression profile in early porcine embryos generated from parthenogenesis and somatic cell chromatin transfer. PLoS One. 2014 Mar 14;9(3):e91728. doi: 10.1371/journal.pone.0091728. PMID: 24633136; PMCID: PMC3954727.

PubMed

Abo-Ismail MK, Vander Voort G, Squires JJ, Swanson KC, Mandell IB, Liao X, Stothard P, Moore S, Plastow G, Miller SP. Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle. BMC Genet. 2014 Jan 30;15:14. doi: 10.1186/1471-2156-15-14. PMID: 24476087; PMCID: PMC3927660.

PubMed

Liao X, Peng F, Forni S, McLaren D, Plastow G, Stothard P. Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome. 2013 Oct;56(10):592-8. doi: 10.1139/gen-2013-0082. Epub 2013 Aug 2. PMID: 24237340.

PubMed

Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, Wang T, Yeung CK, 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. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet. 2013 Dec;45(12):1431-8. doi: 10.1038/ng.2811. Epub 2013 Oct 27. PMID: 24162736.

PubMed

Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, Plastow GS, Guan LL, Stothard P. Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics. 2013 Sep 10;14:609. doi: 10.1186/1471-2164-14-609. PMID: 24020371; PMCID: PMC3847189.

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. Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels. Mol Cells. 2013 Sep;36(3):203-11. doi: 10.1007/s10059-013-2347-0. Epub 2013 Aug 1. PMID: 23912596; PMCID: PMC3887973.

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. Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics. 2013 Jul 30;14:519. doi: 10.1186/1471-2164-14-519. PMID: 23899338; PMCID: PMC3750754.

PubMed

Karisa BK, Thomson J, Wang Z, Stothard P, Moore SS, Plastow GS. Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle. J Anim Sci. 2013 Aug;91(8):3502-13. doi: 10.2527/jas.2012-6170. Epub 2013 Jun 4. PMID: 23736061.

PubMed

Choi JW, Lee KT, Liao X, Stothard P, An HS, Ahn S, Lee S, Lee SY, Moore SS, Kim TH. Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle. Mamm Genome. 2013 Apr;24(3-4):151-63. doi: 10.1007/s00335-013-9449-z. Epub 2013 Mar 30. PMID: 23543395.

PubMed

Thomson JM, Bowles V, Choi JW, Basu U, Meng Y, Stothard P, Moore S. The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility. Prion. 2012 Nov-Dec;6(5):461-9. doi: 10.4161/pri.21866. Epub 2012 Aug 23. PMID: 22918267; PMCID: PMC3510855.

PubMed

Wang Y, Cai Z, Stothard P, Moore S, Goebel R, Wang L, Lin G. Fast accurate missing SNP genotype local imputation. BMC Res Notes. 2012 Aug 3;5:404. doi: 10.1186/1756-0500-5-404. PMID: 22863359; PMCID: PMC3499149.

PubMed

Lynch KH, Stothard P, Dennis JJ. Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages. BMC Genomics. 2012 Jun 7;13:223. doi: 10.1186/1471-2164-13-223. PMID: 22676492; PMCID: PMC3483164.

PubMed

Grant JR, Arantes AS, Stothard P. Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics. 2012 May 23;13:202. doi: 10.1186/1471-2164-13-202. PMID: 22621371; PMCID: PMC3469350.

PubMed

Nalaila SM, Stothard P, Moore SS, Li C, Wang Z. Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method. J Anim Breed Genet. 2012 Apr;129(2):107-19. doi: 10.1111/j.1439-0388.2011.00954.x. Epub 2011 Sep 8. PMID: 22394233.

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. Genome sequence and assembly of Bos indicus. J Hered. 2012 May-Jun;103(3):342-8. doi: 10.1093/jhered/esr153. Epub 2012 Feb 7. PMID: 22315242.

PubMed

Lynch KH, Stothard P, Dennis JJ. Characterization of DC1, a broad-host-range Bcep22-like podovirus. Appl Environ Microbiol. 2012 Feb;78(3):889-91. doi: 10.1128/AEM.07097-11. Epub 2011 Dec 2. PMID: 22139000; PMCID: PMC3264122.

PubMed

Cruz J, Liu Y, Liang Y, Zhou Y, Wilson M, Dennis JJ, Stothard P, Van Domselaar G, Wishart DS. BacMap: an up-to-date electronic atlas of annotated bacterial genomes. Nucleic Acids Res. 2012 Jan;40(Database issue):D599-604. doi: 10.1093/nar/gkr1105. Epub 2011 Dec 1. PMID: 22135301; PMCID: PMC3245156.

PubMed

Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics. 2011 Nov 15;12:559. doi: 10.1186/1471-2164-12-559. PMID: 22085807; PMCID: PMC3229636.

PubMed

Marques E, Grant JR, Wang Z, Kolbehdari D, Stothard P, Plastow G, Moore SS. Identification of candidate markers on bovine chromosome 14 (BTA14) under milk production trait quantitative trait loci in Holstein. J Anim Breed Genet. 2011 Aug;128(4):305-13. doi: 10.1111/j.1439-0388.2010.00910.x. Epub 2011 Apr 13. PMID: 21749477.

PubMed

Grant JR, Arantes AS, Liao X, Stothard P. In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics. 2011 Aug 15;27(16):2300-1. doi: 10.1093/bioinformatics/btr372. Epub 2011 Jun 22. PMID: 21697123; PMCID: PMC3150039.

PubMed

Mujibi FD, Nkrumah JD, Durunna ON, Stothard P, Mah J, Wang Z, Basarab J, Plastow G, Crews DH Jr, Moore SS. Accuracy of genomic breeding values for residual feed intake in crossbred beef cattle. J Anim Sci. 2011 Nov;89(11):3353-61. doi: 10.2527/jas.2010-3361. Epub 2011 Jun 3. PMID: 21642493.

PubMed

Lynch KH, Stothard P, Dennis JJ. Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex. BMC Genomics. 2010 Oct 25;11:599. doi: 10.1186/1471-2164-11-599. PMID: 20973964; PMCID: PMC3091744.

PubMed

Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G. Interactive microbial genome visualization with GView. Bioinformatics. 2010 Dec 15;26(24):3125-6. doi: 10.1093/bioinformatics/btq588. Epub 2010 Oct 17. PMID: 20956244; PMCID: PMC2995121.

PubMed

Hernandez-Sanabria E, Guan LL, Goonewardene LA, Li M, Mujibi DF, Stothard P, Moore SS, Leon-Quintero MC. Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits. Appl Environ Microbiol. 2010 Oct;76(19):6338-50. doi: 10.1128/AEM.01052-10. Epub 2010 Aug 13. PMID: 20709849; PMCID: PMC2950479.

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. Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genomics. 2010 May 25;11:325. doi: 10.1186/1471-2164-11-325. PMID: 20500872; PMCID: PMC2890560.

PubMed

Berjanskii M, Liang Y, Zhou J, Tang P, Stothard P, Zhou Y, Cruz J, MacDonell C, Lin G, Lu P, Wishart DS. PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W633-40. doi: 10.1093/nar/gkq375. Epub 2010 May 11. PMID: 20460469; PMCID: PMC2896095.

PubMed

Murdoch BM, Clawson ML, Laegreid WW, Stothard P, Settles M, McKay S, Prasad A, Wang Z, Moore SS, Williams JL. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE. BMC Genet. 2010 Mar 29;11:20. doi: 10.1186/1471-2156-11-20. PMID: 20350325; PMCID: PMC2853485.

PubMed

Stafuzza NB, Abbassi H, Grant JR, Rodrigues-Filho EA, Ianella P, Kadri SM, Amarante MV, Stohard P, Womack JE, de León FA, Amaral ME. Comparative RH maps of the river buffalo and bovine Y chromosomes. Cytogenet Genome Res. 2009;126(1-2):132-8. doi: 10.1159/000245912. Epub 2009 Dec 9. PMID: 20016162.

PubMed

Lynch KH, Seed KD, Stothard P, Dennis JJ. Inactivation of Burkholderia cepacia complex phage KS9 gp41 identifies the phage repressor and generates lytic virions. J Virol. 2010 Feb;84(3):1276-88. doi: 10.1128/JVI.01843-09. Epub 2009 Nov 25. PMID: 19939932; PMCID: PMC2812329.

PubMed

Jin W, Grant JR, Stothard P, Moore SS, Guan LL. Characterization of bovine miRNAs by sequencing and bioinformatics analysis. BMC Mol Biol. 2009 Sep 16;10:90. doi: 10.1186/1471-2199-10-90. PMID: 19758457; PMCID: PMC2761914.

PubMed

Kolbehdari D, Wang Z, Grant JR, Murdoch B, Prasad A, Xiu Z, Marques E, Stothard P, Moore SS. A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls. J Anim Breed Genet. 2009 Jun;126(3):216-27. doi: 10.1111/j.1439-0388.2008.00793.x. PMID: 19646150.

PubMed

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8. doi: 10.1126/science.1169588. PMID: 19390049; PMCID: PMC2943200.

PubMed

Cai Z, Sabaa H, Wang Y, Goebel R, Wang Z, Xu J, Stothard P, Lin G. Most parsimonious haplotype allele sharing determination. BMC Bioinformatics. 2009 Apr 21;10:115. doi: 10.1186/1471-2105-10-115. PMID: 19379528; PMCID: PMC2691739.

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.

Link

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, Galvão 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. A first generation whole genome RH map of the river buffalo with comparison to domestic cattle. BMC Genomics. 2008 Dec 24;9:631. doi: 10.1186/1471-2164-9-631. PMID: 19108729; PMCID: PMC2625372.

PubMed

Goudie AD, Lynch KH, Seed KD, Stothard P, Shrivastava S, Wishart DS, Dennis JJ. Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex. BMC Genomics. 2008 Dec 18;9:615. doi: 10.1186/1471-2164-9-615. PMID: 19094239; PMCID: PMC2628397.

PubMed

Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, Coleman NV. 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. 2008 Oct;74(20):6405-16. doi: 10.1128/AEM.00197-08. Epub 2008 Aug 22. PMID: 18723656; PMCID: PMC2570305.

PubMed

Prasad A, Schnabel RD, McKay SD, Murdoch B, Stothard P, Kolbehdari D, Wang Z, Taylor JF, Moore SS. Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle. Anim Genet. 2008 Dec;39(6):597-605. doi: 10.1111/j.1365-2052.2008.01772.x. Epub 2008 Aug 18. PMID: 18717667; PMCID: PMC2659388.

PubMed

Marques E, Schnabel RD, Stothard P, Kolbehdari D, Wang Z, Taylor JF, Moore SS. High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle. BMC Genet. 2008 Jul 8;9:45. doi: 10.1186/1471-2156-9-45. PMID: 18611270; PMCID: PMC2478670.

PubMed

Kolbehdari D, Wang Z, Grant JR, Murdoch B, Prasad A, Xiu Z, Marques E, Stothard P, Moore SS. A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls. J Dairy Sci. 2008 Jul;91(7):2844-56. doi: 10.3168/jds.2007-0585. PMID: 18565942.

PubMed

Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS. PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. doi: 10.1093/nar/gkn296. Epub 2008 May 16. PMID: 18487273; PMCID: PMC2447794.

PubMed

Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W181-4. doi: 10.1093/nar/gkn179. Epub 2008 Apr 14. PMID: 18411202; PMCID: PMC2447734.

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.

Link

Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS. BioSpider: a web server for automating metabolome annotations. Pac Symp Biocomput. 2007:145-56. PMID: 17990488.

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. Whole genome linkage disequilibrium maps in cattle. BMC Genet. 2007 Oct 25;8:74. doi: 10.1186/1471-2156-8-74. PMID: 17961247; PMCID: PMC2174945.

PubMed

Prasad A, Schiex T, McKay S, Murdoch B, Wang Z, Womack JE, Stothard P, Moore SS. High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly. BMC Genomics. 2007 Sep 4;8:310. doi: 10.1186/1471-2164-8-310. PMID: 17784962; PMCID: PMC2064936.

PubMed

Marques E, de Givry S, Stothard P, Murdoch B, Wang Z, Womack J, Moore SS. A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly. BMC Genomics. 2007 Jul 26;8:254. doi: 10.1186/1471-2164-8-254. PMID: 17655763; PMCID: PMC1959194.

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. Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet. 2007 Apr;38(2):120-5. doi: 10.1111/j.1365-2052.2006.01564.x. Epub 2007 Feb 15. PMID: 17302794; PMCID: PMC2063635.

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. HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. doi: 10.1093/nar/gkl923. PMID: 17202168; PMCID: PMC1899095.

PubMed

Stothard P, Wishart DS. Automated bacterial genome analysis and annotation. Curr Opin Microbiol. 2006 Oct;9(5):505-10. doi: 10.1016/j.mib.2006.08.002. Epub 2006 Aug 22. PMID: 16931121.

PubMed

Stothard P, Pilgrim D. Conspecific and interspecific interactions between the FEM-2 and the FEM-3 sex-determining proteins despite rapid sequence divergence. J Mol Evol. 2006 Mar;62(3):281-91. doi: 10.1007/s00239-005-0084-5. Epub 2006 Feb 13. PMID: 16477523.

PubMed

Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72. doi: 10.1093/nar/gkj067. PMID: 16381955; PMCID: PMC1347430.

PubMed

Amegbey G, Stothard P, Kuznetsova E, Yee A, Arrowsmith CH, Wishart DS. Solution Structure of MTH0776 from Methanobacterium thermoautotrophicum. J Biomol NMR. 2005 Sep;33(1):51-6. doi: 10.1007/s10858-005-1275-5. PMID: 16222557.

PubMed

Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9. doi: 10.1093/nar/gki593. PMID: 15980511; PMCID: PMC1160269.

PubMed

Vallée M, Gravel C, Palin MF, Reghenas H, Stothard P, Wishart DS, Sirard MA. Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species. Biol Reprod. 2005 Jul;73(1):63-71. doi: 10.1095/biolreprod.104.037069. Epub 2005 Mar 2. PMID: 15744023.

PubMed

Amegbey G, Chang Z, Stothard P, Yee A, Arrowsmith C, Wishart DS. Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum. J Biomol NMR. 2004 Dec;30(4):459-60. doi: 10.1007/s10858-004-4341-5. PMID: 15630567.

PubMed

Stothard P, Van Domselaar G, Shrivastava S, Guo A, O'Neill B, Cruz J, Ellison M, Wishart DS. BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D317-20. doi: 10.1093/nar/gki075. PMID: 15608206; PMCID: PMC540029.

PubMed

Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics. 2005 Feb 15;21(4):537-9. doi: 10.1093/bioinformatics/bti054. Epub 2004 Oct 12. PMID: 15479716.

PubMed

Dong X, Stothard P, Forsythe IJ, Wishart DS. PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W660-4. doi: 10.1093/nar/gkh410. PMID: 15215471; PMCID: PMC441548.

PubMed

Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D293-5. doi: 10.1093/nar/gkh108. PMID: 14681416; PMCID: PMC308842.

PubMed

Stothard P, Pilgrim D. Sex-determination gene and pathway evolution in nematodes. Bioessays. 2003 Mar;25(3):221-31. doi: 10.1002/bies.10239. PMID: 12596226.

PubMed

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

Link

Stothard P, Hansen D, Pilgrim D. Evolution of the PP2C family in Caenorhabditis: rapid divergence of the sex-determining protein FEM-2. J Mol Evol. 2002 Feb;54(2):267-82. doi: 10.1007/s0023901-0008-y. PMID: 11821919.

PubMed

Kibenge FSB, Kibenge MJT, McKenna PK, Stothard P, Marshall R, Cusack RR, McGeachy S. Antigenic variation among isolates of infectious salmon anaemia virus correlates with genetic variation of the viral haemagglutinin gene. J Gen Virol. 2001 Dec;82(Pt 12):2869-2879. doi: 10.1099/0022-1317-82-12-2869. PMID: 11714961.

PubMed

Stothard PM. COMBOSA3D: combining sequence alignments with three-dimensional structures. Bioinformatics. 2001 Feb;17(2):198-9. doi: 10.1093/bioinformatics/17.2.198. PMID: 11238080.

PubMed

Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 2000 Jun;28(6):1102, 1104. doi: 10.2144/00286ir01. PMID: 10868275.

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.

Link