Papers
Cruz J, Liu Y, Liang Y, Zhou Y, Wilson M, Dennis JJ, Stothard P, Van Domselaar G, Wishart DS (2011) BacMap: an up-to-date electronic atlas of annotated bacterial genomes. Nucleic Acids Res.
Lynch KH, Stothard P, Dennis JJ (2011) Characterization of DC1, a broad host range Bcep22-like podovirus. Appl Environ Microbiol.
Nalaila SM, Stothard P, Moore SS, Li C, Wang Z (2011) Whole genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method. J Anim Breed Genet.
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.
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.
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.
Grant JR, Arantes AS, Xiaoping L, Stothard P (2011) In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 27:2300-2301.
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.
Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G (2010) Interactive microbial genome visualization with GView. Bioinformatics 26:3125-3126.
Lynch KH, Stothard P, Dennis JJ (2010) Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex. BMC Genomics 11:599.
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 19:6338-6350.
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.
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.
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 Genetics 11:20.
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.
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.
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.
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.
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.
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.
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. Methods Mol Biol 502:557-589.
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.
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.
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.
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. Animal Genetics 39:597-605.
Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181-W184.
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.
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 Genetics 9:45.
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.
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 Genetics 8:74.
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.
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.
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.
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. Animal Genetics 38:120-125.
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.
Stothard P, Wishart DS (2006) Automated bacterial genome analysis and annotation. Curr Opin Microbiol 9:505-510.
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.
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.
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.
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.
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.
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.
Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.
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.
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.
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.
Stothard P, Pilgrim D (2003) Sex-determination gene and pathway evolution in nematodes. BioEssays 25:221-231.
Stothard P (2003) The Sequence Manipulation Suite. In: Brown SM (ed) Biocomputing: computer tools for biologists: Eaton Publishing, Westborough, MA, pp.175-180.
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.
Stothard P (2001) COMBOSA3D: combining sequence alignments with three-dimensional structures. Bioinformatics 17:198-199.
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.
Stothard P (2000) The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102-1104.
Wishart DS, Stothard P, Van Domselaar GH (2000) PepTool and GeneTool: platform-independent tools for biological sequence analysis. Methods Mol Biol 132:93-113.