Profile
Paul Stothard’s group analyzes and interprets huge sequence, genotype, and gene expression datasets relative to livestock breeding and bacterial genome analysis. These efforts have contributed to three publications in Nature Genetics (DOI:10.1038/s41588-018-0056-5, DOI:10.1038/ng.3034, DOI:10.1038/ng.2811) and have helped to identify causative variants affecting a variety of traits, from coat colour (DOI:10.1371/journal.pone.0128969) to disease resilience (DOI:10.1186/s12864-015-1635-9). His group also developed a popular collection of microbial genome analysis software tools (DOI:10.1093/bioinformatics/bti054, DOI:10.1186/1471-2164-13-202, DOI:10.1093/nar/gki075, DOI:10.1093/nar/gki593) that he continues to update and use in several collaborations to investigate bacterial genome function and evolution (e.g. DOI:10.1038/s41396-019-0364-5, DOI:10.1038/s41396-018-0211-0). He has led or co-led large-scale projects, including two Genome Canada-funded Large-Scale Applied Research Projects. He has authored 94 peer-reviewed articles, is an associate editor of BMC Genomics, and was a member of the board of The Bioinformatics Organization (2005-2014). He has trained 6 postdocs and 5 research associates. His students and staff have gone on to work in industry (The Maschhoffs, IBM, Geneseeq Technology, Electronic Arts), academia (China, US, Canada), and government (Agriculture and Agri-Food Canada).
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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 University of Alberta Publication 2020-03-01 Asif Hameed, Mariyam Shahina, Wei-An Lai,
Paul Stothard , Li-Sen Young, Shih-Yao Lin, Chiu-Chung Young
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 University of Alberta Publication 2020-01-01 Feng Zhang, Yining Wang, Robert Mukiibi, Liuhong Chen, Michael Vinsky, Graham Plastow, John Basarab,
Paul Stothard , Changxi Li
Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes1 University of Alberta Publication 2019-10-01 Robert Mukiibi, Michael Vinsky, Kate Keogh, Carolyn Fitzsimmons,
Paul Stothard , Siné ad M Waters, Changxi Li
Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota University of Alberta Publication 2019-02-01 A large interactive visual database of copy number variants discovered in taurine cattle University of Alberta Publication 2019-06-01 Arun Kommadath, Jason R Grant, Kirill Krivushin, Adrien M Butty, Christine F Baes, Tara R Carthy, Donagh P Berry,
Paul Stothard Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater University of Alberta Publication 2019-06-01 Shuai Zhi, Graham Banting,
Paul Stothard , Nicholas J. Ashbolt, Sylvia Checkley, Kelsey Meyer, Simon Otto, Norman F. Neumann
Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA University of Alberta Publication 2019-04-01 Jaswal, Pathak, III, III, Seaman,
Paul Stothard , Krivushin, Blom, Rupp, Chauhan
Novel Stenotrophomonas maltophilia temperate phage DLP 4 is capable of lysogenic conversion University of Alberta Publication 2019-04-01 Danielle L. Peters, Jaclyn G. McCutcheon,
Paul Stothard , Jonathan J. Dennis
Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae University of Alberta Publication 2019-03-01 Peris M. Munyaka, Arun Kommadath, Janelle Fouhse, Jamie Wilkinson, Natalie Diether,
Paul Stothard , Jordi Estellé, Claire Rogel-Gaillard, Graham Plastow, Benjamin P. Willing
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 University of Alberta Publication 2019-01-01 Ty Russell, Catherine Cullingham, Arun Kommadath,
Paul Stothard , Allen Herbst, David Coltman
Accuracy of imputation to whole-genome sequence in sheep University of Alberta Publication 2019-01-01 Sunduimijid Bolormaa, Amanda J. Chamberlain, Majid Khansefid,
Paul Stothard , Andrew A. Swan, Brett Mason, Claire P. Prowse-Wilkins, Naomi Duijvesteijn, Nasir Moghaddar, Julius H. van der Werf, Hans D. Daetwyler, Iona M. MacLeod
Optimizing Selection of the Reference Population for Genotype Imputation From Array to Sequence Variants University of Alberta Publication 2019-05-01 Adrien M. Butty, Mehdi Sargolzaei, Filippo Miglior,
Paul Stothard , Flavio S. Schenkel, Birgit Gredler-Grandl, Christine F. Baes
Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle University of Alberta Publication 2018-05-01 Robert Mukiibi, Michael Vinsky, Kate A. Keogh, Carolyn Fitzsimmons,
Paul Stothard , Siné ad M. Waters, Changxi Li
The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract University of Alberta Publication 2018-07-01 Xiaoxi B. Lin, Tuo Wang,
Paul Stothard , Jukka Corander, Jun Wang, John F. Baines, Sarah C. L. Knowles, Laima Baltr\=u nait\.e, Guergana Tasseva, Robert Schmaltz, Stephanie Tollenaar, Liz A. Cody, Theodore Grenier, Wei Wu, Amanda E. Ramer-Tait, Jens Walter
Near-Complete Genome Sequence of Ralstonia solanacearum T523, a Phylotype I Tomato Phytopathogen Isolated from the Philippines University of Alberta Publication 2018-09-01 Andrew D. Montecillo, Asuncion K. Raymundo, Irene A. Papa, Genevieve Mae B. Aquino, Arian J. Jacildo,
Paul Stothard , Albert Remus R. Rosana
Draft Genome Sequence ofPseudomonassp . Strain B1, Isolated from a Contaminated Sediment University of Alberta Publication 2018-06-01 Ashish Pathak, Rajneesh Jaswal,
Paul Stothard , Scott Brooks, Ashvini Chauhan
Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants University of Alberta Publication 2018-04-01 Chunyan Zhang, Robert Alan Kemp,
Paul Stothard , Zhiquan Wang, Nicholas Boddicker, Kirill Krivushin, Jack Dekkers, Graham Plastow
Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits University of Alberta Publication 2018-04-01 Lambros T. Koufariotis, Yi-Ping Phoebe Chen,
Paul Stothard , Ben J. Hayes
Visualizing and comparing circular genomes using the CGView family of tools University of Alberta Publication 2017-07-01 Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals University of Alberta Publication 2018-02-01 Aniek C. Bouwman, Hans D. Daetwyler, Amanda J. Chamberlain, Carla Hurtado Ponce, Mehdi Sargolzaei, Flavio S. Schenkel, Goutam Sahana, Armelle Govignon-Gion, Simon Boitard, Marlies Dolezal, Hubert Pausch, Rasmus F. Brø ndum, Phil J. Bowman, Bo Thomsen, Bernt Guldbrandtsen, Mogens S. Lund, Bertrand Servin, Dorian J. Garrick, James Reecy, Johanna Vilkki, Alessandro Bagnato, Min Wang, Jesse L. Hoff, Robert D. Schnabel, Jeremy F. Taylor, Anna A. E. Vinkhuyzen, Frank Panitz, Christian Bendixen, Lars-Erik Holm, Birgit Gredler, Chris Hozé, Mekki Boussaha, Marie-Pierre Sanchez, Dominique Rocha, Aurelien Capitan, Thierry Tribout, Anne Barbat, Pascal Croiseau, Cord Drögemüller, Vidhya Jagannathan, Christy Vander Jagt, John J. Crowley, Anna Bieber, Deirdre C. Purfield, Donagh P. Berry, Reiner Emmerling, Kay-Uwe Götz, Mirjam Frischknecht, Ingolf Russ, Johann Sölkner, Curtis P. Van Tassell, Ruedi Fries,
Paul Stothard , Roel F. Veerkamp, Didier Boichard, Mike E. Goddard, Ben J. Hayes
Complete genome sequence of Siansivirga zeaxanthinifaciens CC -SAMT-1T, a flavobacterium isolated from coastal surface seawater University of Alberta Publication 2018-02-01 Asif Hameed, Mariyam Shahina, Hsin-Chieh Huang, Wei-An Lai, Shih-Yao Lin,
Paul Stothard , Chiu-Chung Young
Development and validation of a small SNP panel for feed efficiency in beef cattle1 University of Alberta Publication 2018-01-01 M K Abo-Ismail, N Lansink, E Akanno, B K Karisa, J J Crowley, S S Moore, E Bork,
Paul Stothard , J A Basarab, G S Plastow
Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS -W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils University of Alberta Publication 2018-01-01 Ashvini Chauhan, Ashish Pathak, Rajneesh Jaswal, Bobby Edwards III, Demario Chappell, Christopher Ball, Reyna Garcia-Sillas,
Paul Stothard , John Seaman
Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle University of Alberta Publication 2017-11-01 Mohammed K. Abo-Ismail, Luiz F. Brito, Stephen P. Miller, Mehdi Sargolzaei, Daniela A. Grossi, Steve S. Moore, Graham Plastow,
Paul Stothard , Shadi Nayeri, Flavio S. Schenkel
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 University of Alberta Publication 2017-06-01 Tingting Ju, Yasmeen Shoblak, Yanhua Gao, Kaiyuan Yang, Janelle Fouhse, B. Brett Finlay, Yee Wing So,
Paul Stothard , Benjamin P. Willing
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 University of Alberta Publication 2017-06-01 Ashish Pathak, Ashvini Chauhan,
Paul Stothard , Stefan Green, Mark Maienschein-Cline, Rajneesh Jaswal, John Seaman
Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection University of Alberta Publication 2017-04-01 Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Elyn Fritz-Waters, Chris J. Eisley, Jason R. Grant, Robert R. R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan,
Paul Stothard , Graham S. Plastow
The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP 6 University of Alberta Publication 2017-03-01 Genome-wide association study for lactation persistency, female fertility, longevity, and lifetime profit index traits in Holstein dairy cattle University of Alberta Publication 2017-02-01 S. Nayeri, M. Sargolzaei, M.K. Abo-Ismail, S. Miller, F. Schenkel, S.S. Moore,
Paul Stothard Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine\textendash cytokine receptor interaction pathway related to health status University of Alberta Publication 2017-12-01 Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves University of Alberta Publication 2016-08-01 Guanxiang Liang, Nilusha Malmuthuge, Hua Bao,
Paul Stothard , Philip J. Griebel, Le Luo Guan
Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake University of Alberta Publication 2016-08-01 Rebecca S. G. Kong, Guanxiang Liang, Yanhong Chen,
Paul Stothard , Le Luo Guan
Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation University of Alberta Publication 2016-08-01 Ashish Pathak, Ashvini Chauhan, Jochen Blom, Karl J. Indest, Carina M. Jung,
Paul Stothard , Gopal Bera, Stefan J. Green, Andrew Ogram
Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle University of Alberta Publication 2016-06-01 Shadi Nayeri, Mehdi Sargolzaei, Mohammed K. Abo-Ismail, Natalie May, Stephen P. Miller, Flavio Schenkel, Stephen S. Moore,
Paul Stothard Whole genome sequence analysis of an Alachlor and Endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida University of Alberta Publication 2016-06-01 Ashvini Chauhan, Ashish Pathak, Ayman Y.I. Ewida, Zabrenna Griffiths,
Paul Stothard Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus University of Alberta Publication 2016-05-01 Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong,
Paul Stothard , Joan K. Lunney, Graham S. Plastow, John C. S. Harding
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 University of Alberta Publication 2016-04-01 Jamie M. Wilkinson, Andrea Ladinig, Hua Bao, Arun Kommadath,
Paul Stothard , Joan K. Lunney, John C. S. Harding, Graham S. Plastow
Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes1 University of Alberta Publication 2016-04-01 D. Lu, E. C. Akanno, J. J. Crowley, F. Schenkel, H. Li, M. De Pauw, S. S. Moore, Z. Wang, C. Li,
Paul Stothard , G. Plastow, S. P. Miller, J. A. Basarab
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 University of Alberta Publication 2016-03-01 Martine Schroyen, Christopher Eisley, James E. Koltes, Eric Fritz-Waters, Igseo Choi, Graham S. Plastow, Leluo Guan,
Paul Stothard , Hua Bao, Arun Kommadath, James M. Reecy, Joan K. Lunney, Robert R. R. Rowland, Jack C. M. Dekkers, Christopher K. Tuggle
Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection University of Alberta Publication 2015-05-01 James E. Koltes, Eric Fritz-Waters, Chris J. Eisley, Igseo Choi, Hua Bao, Arun Kommadath, Nick V. L. Serã o, Nicholas J. Boddicker, Sam M. Abrams, Martine Schroyen, Hyelee Loyd, Chris K. Tuggle, Graham S. Plastow, Leluo Guan,
Paul Stothard , Joan K. Lunney, Peng Liu, Susan Carpenter, Robert R. R. Rowland, Jack C. M. Dekkers, James M. Reecy
Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle University of Alberta Publication 2015-11-01 Liuhong Chen, Chinyere Ekine-Dzivenu, Michael Vinsky, John Basarab, Jennifer Aalhus, Mike E. R. Dugan, Carolyn Fitzsimmons,
Paul Stothard , Changxi Li
Whole genome SNP genotype piecemeal imputation University of Alberta Publication 2015-10-01 The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity University of Alberta Publication 2015-09-01 Danielle L. Peters, Karlene H. Lynch,
Paul Stothard , Jonathan J. Dennis
Genome-wide whole blood microRNAome and transcriptome analyses reveal miRNA-mRNA regulated host response to foodborne pathogen Salmonella infection in swine University of Alberta Publication 2015-07-01 Hua Bao, Arun Kommadath, Guanxiang Liang, Xu Sun, Adriano S. Arantes, Christopher K. Tuggle, Shawn M.D. Bearson, Graham S. Plastow,
Paul Stothard , Le Luo Guan
Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers1 University of Alberta Publication 2015-07-01 F. Paradis, S. Yue, J. R. Grant,
Paul Stothard , J. A. Basarab, C. Fitzsimmons
Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA ) Gene University of Alberta Publication 2015-06-01 Ben Dorshorst, Corneliu Henegar, Xiaoping Liao, Markus Sällman Almé n, Carl-Johan Rubin, Shosuke Ito, Kazumasa Wakamatsu,
Paul Stothard , Brian Van Doormaal, Graham Plastow, Gregory S. Barsh, Leif Andersson
Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis) University of Alberta Publication 2015-05-01 Joshua M Miller, Stephen S Moore,
Paul Stothard , Xiaoping Liao, David W Coltman
A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project University of Alberta Publication 2015-10-01 Paul Stothard , Xiaoping Liao, Adriano S. Arantes, Mary De Pauw, Colin Coros, Graham S. Plastow, Mehdi Sargolzaei, John J. Crowley, John A. Basarab, Flavio Schenkel, Stephen Moore, Stephen P. Miller
Increasing gene discovery and coverage using RNA -seq of globin RNA reduced porcine blood samples University of Alberta Publication 2014-01-01 Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xu Sun, Yan Meng,
Paul Stothard , Graham S Plastow, Christopher K Tuggle, James M Reecy, Eric Fritz-Waters, Samuel M Abrams, Joan K Lunney, Le Guan
Mitochondriome and Cholangiocellular Carcinoma University of Alberta Publication 2014-08-01 Wesam Bahitham, Xiaoping Liao, Fred Peng, Fiona Bamforth, Alicia Chan, Andrew Mason, Bradley Stone,
Paul Stothard , Consolato Sergi
Sequence, Structural and Expression Divergence of Duplicate Genes in the Bovine Genome University of Alberta Publication 2014-07-01 Xiaoping Liao, Hua Bao, Yan Meng, Graham Plastow, Stephen Moore,
Paul Stothard Whole-Genome Analyses of Korean Native and Holstein Cattle Breeds by Massively Parallel Sequencing University of Alberta Publication 2014-07-01 Jung-Woo Choi, Xiaoping Liao,
Paul Stothard , Won-Hyong Chung, Heoyn-Jeong Jeon, Stephen P. Miller, So-Young Choi, Jeong-Koo Lee, Bokyoung Yang, Kyung-Tai Lee, Kwang-Jin Han, Hyeong-Cheol Kim, Dongkee Jeong, Jae-Don Oh, Namshin Kim, Tae-Hun Kim, Hak-Kyo Lee, Sung-Jin Lee
Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding University of Alberta Publication 2014-01-01 Arun Kommadath, Hua Bao, Adriano S Arantes, Graham S Plastow, Christopher K Tuggle, Shawn MD Bearson, Le Guan,
Paul Stothard MicroRNA Buffering and Altered Variance of Gene Expression in Response to Salmonella Infection University of Alberta Publication 2014-04-01 Hua Bao, Arun Kommadath, Graham S. Plastow, Christopher K. Tuggle, Le Luo Guan,
Paul Stothard Potential Regulatory Role of MicroRNAs in the Development of Bovine Gastrointestinal Tract during Early Life University of Alberta Publication 2014-03-01 Guanxiang Liang, Nilusha Malmuthuge, Thomas B. McFadden, Hua Bao, Philip J. Griebel,
Paul Stothard , Le Luo Guan
Characterization of the Altered Gene Expression Profile in Early Porcine Embryos Generated from Parthenogenesis and Somatic Cell Chromatin Transfer University of Alberta Publication 2014-03-01 Chi Zhou, John Dobrinsky, Stephen Tsoi, George R. Foxcroft, Walter T. Dixon,
Paul Stothard , John Verstegen, Michael K. Dyck
Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle University of Alberta Publication 2014-01-01 Mohammed K Abo-Ismail, Gordon Vander Voort, James J Squires, Kendall C Swanson, Ira B Mandell, Xiaoping Liao,
Paul Stothard , Stephen Moore, Graham Plastow, Stephen P Miller
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle University of Alberta Publication 2014-07-01 Hans D Daetwyler, Auré lien Capitan, Hubert Pausch,
Paul Stothard , Rianne van Binsbergen, Rasmus F Brøndum, Xiaoping Liao, Anis Djari, Sabrina C Rodriguez, Cécile Grohs, Diane Esquerré, Olivier Bouchez, Marie-Noëlle Rossignol, Christophe Klopp, Dominique Rocha, Sébastien Fritz, André Eggen, Phil J Bowman, David Coote, Amanda J Chamberlain, Charlotte Anderson, Curt P VanTassell, Ina Hulsegge, Mike E Goddard, Bernt Guldbrandtsen, Mogens S Lund, Roel F Veerkamp, Didier A Boichard, Ruedi Fries, Ben J Hayes
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars University of Alberta Publication 2013-10-01 Mingzhou Li, Shilin Tian, Long Jin, Guangyu Zhou, Ying Li, Yuan Zhang, Tao Wang, Carol K L Yeung, Lei Chen, Jideng Ma, Jinbo Zhang, Anan Jiang, Ji Li, Chaowei Zhou, Jie Zhang, Yingkai Liu, Xiaoqing Sun, Hongwei Zhao, Zexiong Niu, Pinger Lou, Lingjin Xian, Xiaoyong Shen, Shaoqing Liu, Shunhua Zhang, Mingwang Zhang, Li Zhu, Surong Shuai, Lin Bai, Guoqing Tang, Haifeng Liu, Yanzhi Jiang, Miaomiao Mai, Jian Xiao, Xun Wang, Qi Zhou, Zhiquan Wang,
Paul Stothard , Ming Xue, Xiaolian Gao, Zonggang Luo, Yiren Gu, Hongmei Zhu, Xiaoxiang Hu, Yaofeng Zhao, Graham S Plastow, Jinyong Wang, Zhi Jiang, Kui Li, Ning Li, Xuewei Li, Ruiqiang Li
Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection University of Alberta Publication 2013-10-01 Xiaoping Liao, Fred Peng, Selma Forni, David McLaren, Graham Plastow,
Paul Stothard Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species University of Alberta Publication 2013-01-01 Hua Bao, Arun Kommadath, Xu Sun, Yan Meng, Adriano S Arantes, Graham S Plastow, Le Guan,
Paul Stothard Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle1 University of Alberta Publication 2013-08-01 B. K. Karisa, J. Thomson, Z. Wang,
Paul Stothard , S. S. Moore, G. S. Plastow
Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity University of Alberta Publication 2013-01-01 Kyung-Tai Lee, Won-Hyong Chung, Sung-Yeoun Lee, Jung-Woo Choi, Jiwoong Kim, Dajeong Lim, Seunghwan Lee, Gul-Won Jang, Bumsoo Kim, Yun Choy, Xiaoping Liao,
Paul Stothard , Stephen S Moore, Sang-Heon Lee, Sungmin Ahn, Namshin Kim, Tae-Hun Kim
Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle University of Alberta Publication 2013-03-01 Jung-Woo Choi, Kyung-Tai Lee, Xiaoping Liao,
Paul Stothard , Hyeon-Seung An, Sungmin Ahn, Seunghwan Lee, Sung-Yeoun Lee, Stephen S. Moore, Tae-Hun Kim
Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels University of Alberta Publication 2013-08-01 Jung-Woo Choi, Xiaoping Liao, Sairom Park, Heoyn-Jeong Jeon, Won-Hyong Chung,
Paul Stothard , Yeon-Soo Park, Jeong-Koo Lee, Kyung-Tai Lee, Sang-Hwan Kim, Jae-Don Oh, Namshin Kim, Tae-Hun Kim, Hak-Kyo Lee, Sung-Jin Lee
The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility University of Alberta Publication 2012-11-01 Jennifer M. Thomson, Victoria Bowles, Jung-Woo Choi, Urmila Basu, Yan Meng,
Paul Stothard , Stephen Moore
Fast accurate missing SNP genotype local imputation University of Alberta Publication 2012-01-01 Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages University of Alberta Publication 2012-01-01 Comparing thousands of circular genomes using the CGView Comparison Tool University of Alberta Publication 2012-01-01 Genome Sequence and Assembly of Bos indicus University of Alberta Publication 2012-02-01 F. C. Canavez, D. D. Luche,
Paul Stothard , K. R. M. Leite, J. M. Sousa-Canavez, G. Plastow, J. Meidanis, M. A. Souza, P. Feijao, S. S. Moore, L. H. Camara-Lopes
Whole-genome QTL scan for ultrasound and carcass merit traits in beef cattle using Bayesian shrinkage method University of Alberta Publication 2011-09-01 Characterization of DC 1, a Broad-Host-Range Bcep22-Like Podovirus University of Alberta Publication 2011-12-01 BacMap : an up-to-date electronic atlas of annotated bacterial genomes University of Alberta Publication 2011-12-01 J. Cruz, Y. Liu, Y. Liang, Y. Zhou, M. Wilson, J. J. Dennis,
Paul Stothard , G. Van Domselaar, D. S. Wishart
Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery University of Alberta Publication 2011-11-01 Paul Stothard , Jung-Woo Choi, Urmila Basu, Jennifer M Sumner-Thomson, Yan Meng, Xiaoping Liao, Stephen S Moore
Accuracy of genomic breeding values for residual feed intake in crossbred beef cattle1 University of Alberta Publication 2011-11-01 F. D. N. Mujibi, J. D. Nkrumah, O. N. Durunna,
Paul Stothard , J. Mah, Z. Wang, J. Basarab, G. Plastow, D. H. Crews, S. S. Moore
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP University of Alberta Publication 2011-06-01 Identification of candidate markers on bovine chromosome 14 (BTA 14) under milk production trait quantitative trait loci in Holstein University of Alberta Publication 2011-04-01 E. Marques, J.R. Grant, Z. Wang, D. Kolbehdari,
Paul Stothard , G. Plastow, S.S. Moore
Whole genome fine mapping of quantitative trait loci for ultrasound and carcass merit traits in beef cattle University of Alberta Publication 2011-03-01 Sungael Nalaila,
Paul Stothard , Stephen Moore, Zhiquan Wang, Changxi Li
Interactive microbial genome visualization with GView University of Alberta Publication 2010-10-01 Aaron Petkau, Matthew Stuart-Edwards,
Paul Stothard , Gary Van Domselaar
Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex University of Alberta Publication 2010-01-01 Correlation of Particular Bacterial PCR -Denaturing Gradient Gel Electrophoresis Patterns with Bovine Ruminal Fermentation Parameters and Feed Efficiency Traits University of Alberta Publication 2010-08-01 E. Hernandez-Sanabria, L. L. Guan, L. A. Goonewardene, M. Li, D. F. Mujibi,
Paul Stothard , S. S. Moore, M. C. Leon-Quintero
Metabolic flexibility revealed in the genome of the cyst-forming $\upalpha$-1 proteobacterium Rhodospirillum centenum University of Alberta Publication 2010-01-01 Yih-Kuang Lu, Jeremiah Marden, Mira Han, Wesley D Swingley, Stephen D Mastrian, Sugata Chowdhury, Jicheng Hao, Tamer Helmy, Sun Kim, Ahmet A Kurdoglu, Heather J Matthies, David Rollo,
Paul Stothard , Robert E Blankenship, Carl E Bauer, Jeffrey W Touchman
PROSESS : a protein structure evaluation suite and server University of Alberta Publication 2010-05-01 M. Berjanskii, Y. Liang, J. Zhou, P. Tang,
Paul Stothard , Y. Zhou, J. Cruz, C. MacDonell, G. Lin, P. Lu, D. S. Wishart
A 2cM genome-wide scan of European Holstein cattle affected by classical BSE University of Alberta Publication 2010-01-01 Brenda M Murdoch, Michael L Clawson, William W Laegreid,
Paul Stothard , Matthew Settles, Stephanie McKay, Aparna Prasad, Zhiquan Wang, Stephen S Moore, John L Williams
Inactivation of Burkholderia cepacia Complex Phage KS 9 gp41 Identifies the Phage Repressor and Generates Lytic Virions University of Alberta Publication 2009-11-01 Characterization of bovine miRNAs by sequencing and bioinformatics analysis University of Alberta Publication 2009-01-01 Weiwu Jin, Jason R Grant,
Paul Stothard , Stephen S Moore, Le Guan
A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls University of Alberta Publication 2009-06-01 D. Kolbehdari, Z. Wang, J.R. Grant, B. Murdoch, A. Prasad, Z. Xiu, E. Marques,
Paul Stothard , S.S. Moore
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution University of Alberta Publication 2009-04-01 And C. G. Elsik, R. L. Tellam, K. C. Worley, R. A. Gibbs, D. M. Muzny, G. M. Weinstock, D. L. Adelson, E. E. Eichler, L. Elnitski, R. Guigo, D. L. Hamernik, S. M. Kappes, H. A. Lewin, D. J. Lynn, F. W. Nicholas, A. Reymond, M. Rijnkels, L. C. Skow, E. M. Zdobnov, L. Schook, J. Womack, T. Alioto, S. E. Antonarakis, A. Astashyn, C. E. Chapple, H.-C. Chen, J. Chrast, F. Camara, O. Ermolaeva, C. N. Henrichsen, W. Hlavina, Y. Kapustin, B. Kiryutin, P. Kitts, F. Kokocinski, M. Landrum, D. Maglott, K. Pruitt, V. Sapojnikov, S. M. Searle, V. Solovyev, A. Souvorov, C. Ucla, C. Wyss, J. M. Anzola, D. Gerlach, E. Elhaik, D. Graur, J. T. Reese, R. C. Edgar, J. C. McEwan, G. M. Payne, J. M. Raison, T. Junier, E. V. Kriventseva, E. Eyras, M. Plass, R. Donthu, D. M. Larkin, J. Reecy, M. Q. Yang, L. Chen, Z. Cheng, C. G. Chitko-McKown, G. E. Liu, L. K. Matukumalli, J. Song, B. Zhu, D. G. Bradley, F. S.L. Brinkman, L. P.L. Lau, M. D. Whiteside, A. Walker, T. T. Wheeler, T. Casey, J. B. German, D. G. Lemay, N. J. Maqbool, A. J. Molenaar, S. Seo,
Paul Stothard , C. L. Baldwin, R. Baxter, C. L. Brinkmeyer-Langford, W. C. Brown, C. P. Childers, T. Connelley, S. A. Ellis, K. Fritz, E. J. Glass, C. T.A. Herzig, A. Iivanainen, K. K. Lahmers, A. K. Bennett, C. M. Dickens, J. G.R. Gilbert, D. E. Hagen, H. Salih, J. Aerts, A. R. Caetano, B. Dalrymple, J. F. Garcia, C. A. Gill, S. G. Hiendleder, E. Memili, D. Spurlock, J. L. Williams, L. Alexander, M. J. Brownstein, L. Guan, R. A. Holt, S. J.M. Jones, M. A. Marra, R. Moore, S. S. Moore, A. Roberts, M. Taniguchi, R. C. Waterman, J. Chacko, M. M. Chandrabose, A. Cree, M. D. Dao, H. H. Dinh, R. A. Gabisi, S. Hines, J. Hume, S. N. Jhangiani, V. Joshi, C. L. Kovar, L. R. Lewis, Y.-s. Liu, J. Lopez, M. B. Morgan, N. B. Nguyen, G. O. Okwuonu, S. J. Ruiz, J. Santibanez, R. A. Wright, C. Buhay, Y. Ding, S. Dugan-Rocha, J. Herdandez, M. Holder, A. Sabo, A. Egan, J. Goodell, K. Wilczek-Boney, G. R. Fowler, M. E. Hitchens, R. J. Lozado, C. Moen, D. Steffen, J. T. Warren, J. Zhang, R. Chiu, J. E. Schein, K. J. Durbin, P. Havlak, H. Jiang, Y. Liu, X. Qin, Y. Ren, Y. Shen, H. Song, S. N. Bell, C. Davis, A. J. Johnson, S. Lee, L. V. Nazareth, B. M. Patel, L.-L. Pu, S. Vattathil, R. L. Williams, S. Curry, C. Hamilton, E. Sodergren, D. A. Wheeler, W. Barris, G. L. Bennett, A. Eggen, R. D. Green, G. P. Harhay, M. Hobbs, O. Jann, J. W. Keele, M. P. Kent, S. Lien, S. D. McKay, S. McWilliam, A. Ratnakumar, R. D. Schnabel, T. Smith, W. M. Snelling, T. S. Sonstegard, R. T. Stone, Y. Sugimoto, A. Takasuga, J. F. Taylor, C. P. Van Tassell, M. D. MacNeil, A. R.R. Abatepaulo, C. A. Abbey, V. Ahola, I. G. Almeida, A. F. Amadio, E. Anatriello, S. M. Bahadue, F. H. Biase, C. R. Boldt, J. A. Carroll, W. A. Carvalho, E. P. Cervelatti, E. Chacko, J. E. Chapin, Y. Cheng, J. Choi, A. J. Colley, T. A. de Campos, M. De Donato, I. K.F. d. M. Santos, C. J.F. de Oliveira, H. Deobald, E. Devinoy, K. E. Donohue, P. Dovc, A. Eberlein, C. J. Fitzsimmons, A. M. Franzin, G. R. Garcia, S. Genini, C. J. Gladney, J. R. Grant, M. L. Greaser, J. A. Green, D. L. Hadsell, H. A. Hakimov, R. Halgren, J. L. Harrow, E. A. Hart, N. Hastings, M. Hernandez, Z.-L. Hu, A. Ingham, T. Iso-Touru, C. Jamis, K. Jensen, D. Kapetis, T. Kerr, S. S. Khalil, H. Khatib, D. Kolbehdari, C. G. Kumar, D. Kumar, R. Leach, J. C-M Lee, C. Li, K. M. Logan, R. Malinverni, E. Marques, W. F. Martin, N. F. Martins, S. R. Maruyama, R. Mazza, K. L. McLean, J. F. Medrano, B. T. Moreno, D. D. More, C. T. Muntean, H. P. Nandakumar, M. F.G. Nogueira, I. Olsaker, S. D. Pant, F. Panzitta, R. C.P. Pastor, M. A. Poli, N. Poslusny, S. Rachagani, S. Ranganathan, A. Razpet, P. K. Riggs, G. Rincon, N. Rodriguez-Osorio, S. L. Rodriguez-Zas, N. E. Romero, A. Rosenwald, L. Sando, S. M. Schmutz, L. Shen, L. Sherman, B. R. Southey, Y. S. Lutzow, J. V. Sweedler, I. Tammen, B. P. V.L. Telugu, J. M. Urbanski, Y. T. Utsunomiya, C. P. Verschoor, A. J. Waardenberg, Z. Wang, R. Ward, R. Weikard, T. H. Welsh, S. N. White, L. G. Wilming, K. R. Wunderlich, J. Yang, F.-Q. Zhao
Most parsimonious haplotype allele sharing determination University of Alberta Publication 2009-01-01 A first generation whole genome RH map of the river buffalo with comparison to domestic cattle University of Alberta Publication 2008-01-01 M Elisabete J Amaral, Jason R Grant, Penny K Riggs, Nedenia B Stafuzza, Edson Filho, Tom Goldammer, Rosemarie Weikard, Ronald M Brunner, Kelli J Kochan, Anthony J Greco, Jooha Jeong, Zhipeng Cai, Guohui Lin, Aparna Prasad, Satish Kumar, G Pardha Saradhi, Boby Mathew, M Aravind Kumar, Melissa N Miziara, Paola Mariani, Alexandre R Caetano, Stephan R Galvã o, Madhu S Tantia, Ramesh K Vijh, Bina Mishra, ST Bharani Kumar, Vanderlei A Pelai, Andre M Santana, Larissa C Fornitano, Brittany C Jones, Humberto Tonhati, Stephen Moore,
Paul Stothard , James E Womack
Genomic sequence and activity of KS 10, a transposable phage of the Burkholderia cepacia complex University of Alberta Publication 2008-01-01 Amanda D Goudie, Karlene H Lynch, Kimberley D Seed,
Paul Stothard , Savita Shrivastava, David S Wishart, Jonathan J Dennis
High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle University of Alberta Publication 2008-01-01 Elisa Marques, Robert D Schnabel,
Paul Stothard , Davood Kolbehdari, Zhiquan Wang, Jeremy F Taylor, Stephen S Moore
The CGView Server: a comparative genomics tool for circular genomes University of Alberta Publication 2008-05-01 PolySearch : a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites University of Alberta Publication 2008-05-01 The Genome of Polaromonas sp. Strain JS 666: Insights into the Evolution of a Hydrocarbon- and Xenobiotic-Degrading Bacterium, and Features of Relevance to Biotechnology University of Alberta Publication 2008-08-01 T. E. Mattes, A. K. Alexander, P. M. Richardson, A. C. Munk, C. S. Han,
Paul Stothard , N. V. Coleman
Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle University of Alberta Publication 2008-12-01 A. Prasad, R. D. Schnabel, S. D. McKay, B. Murdoch,
Paul Stothard , D. Kolbehdari, Z. Wang, J. F. Taylor, S. S. Moore
A Whole-Genome Scan to Map Quantitative Trait Loci for Conformation and Functional Traits in Canadian Holstein Bulls University of Alberta Publication 2008-07-01 D. Kolbehdari, Z. Wang, J.R. Grant, B. Murdoch, A. Prasad, Z. Xiu, E. Marques,
Paul Stothard , S.S. Moore
Whole genome linkage disequilibrium maps in cattle University of Alberta Publication 2007-01-01 Stephanie D McKay, Robert D Schnabel, Brenda M Murdoch, Lakshmi K Matukumalli, Jan Aerts, Wouter Coppieters, Denny Crews, Emmanuel Neto, Clare A Gill, Chuan Gao, Hideyuki Mannen,
Paul Stothard , Zhiquan Wang, Curt P Van Tassell, John L Williams, Jeremy F Taylor, Stephen S Moore
High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly University of Alberta Publication 2007-01-01 Aparna Prasad, Thomas Schiex, Stephanie McKay, Brenda Murdoch, Zhiquan Wang, James E Womack,
Paul Stothard , Stephen S Moore
A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly University of Alberta Publication 2007-01-01 Elisa Marques, Simon de Givry,
Paul Stothard , Brenda Murdoch, Zhiquan Wang, James Womack, Stephen S Moore
Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping University of Alberta Publication 2007-02-01 S. D. McKay, R. D. Schnabel, B. M. Murdoch, J. Aerts, C. A. Gill, C. Gao, C. Li, L. K. Matukumalli,
Paul Stothard , Z. Wang, C. P. Van Tassell, J. L. Williams, J. F. Taylor, S. S. Moore
HMDB : the Human Metabolome Database University of Alberta Publication 2007-01-01 D. S. Wishart, D. Tzur, C. Knox, R. Eisner, A. C. Guo, N. Young, D. Cheng, K. Jewell, D. Arndt, S. Sawhney, C. Fung, L. Nikolai, M. Lewis, M.-A. Coutouly, I. Forsythe, P. Tang, S. Shrivastava, K. Jeroncic,
Paul Stothard , G. Amegbey, D. Block, David. D. Hau, J. Wagner, J. Miniaci, M. Clements, M. Gebremedhin, N. Guo,
Yifan Zhang , G. E. Duggan, G. D. MacInnis, A. M. Weljie, R. Dowlatabadi, F. Bamforth, D. Clive,
Russell Greiner , L. Li, T. Marrie, B. D. Sykes, H. J. Vogel, L. Querengesser
Automated bacterial genome analysis and annotation University of Alberta Publication 2006-10-01 Conspecific and Interspecific Interactions Between the FEM -2 and the FEM-3 Sex-Determining Proteins Despite Rapid Sequence Divergence University of Alberta Publication 2006-02-01 Solution Structure of MTH 0776 from Methanobacterium Thermoautotrophicum University of Alberta Publication 2005-09-01 Godwin Amegbey,
Paul Stothard , Ekaterina Kuznetsova, Adelinda Yee, Cheryl H. Arrowsmith, David S. Wishart
Identification of Novel and Known Oocyte-Specific Genes Using Complementary DNA Subtraction and Microarray Analysis in Three Different Species1 University of Alberta Publication 2005-07-01 Maud Valle\' e, Catherine Gravel, Marie-France Palin, He\'le\`ne Reghenas,
Paul Stothard , David S. Wishart, Marc-Andre\' Sirard
BASys : a web server for automated bacterial genome annotation University of Alberta Publication 2005-07-01 Circular genome visualization and exploration using CGView University of Alberta Publication 2004-10-01 BacMap : an interactive picture atlas of annotated bacterial genomes University of Alberta Publication 2004-12-01 Letter to the Editor: Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum University of Alberta Publication 2004-12-01 Godwin Amegbey, Zhan Chang,
Paul Stothard , Adelinda Yee, Cheryl Arrowsmith, David S. Wishart
PlasMapper : a web server for drawing and auto-annotating plasmid maps University of Alberta Publication 2004-07-01 Sex-determination gene and pathway evolution in nematodes University of Alberta Publication 2003-02-01 Evolution of the PP 2C Family in Caenorhabditis: Rapid Divergence of the Sex-Determining Protein FEM-2 University of Alberta Publication 2002-02-01 COMBOSA 3D: combining sequence alignments with three-dimensional structures University of Alberta Publication 2001-02-01 Antigenic variation among isolates of infectious salmon anaemia virus correlates with genetic variation of the viral haemagglutinin gene University of Alberta Publication 2001-12-01 Frederick S. B. Kibenge, Rebecca Marshall, Patricia K. McKenna,
Paul Stothard , Sandi McGeachy, Molly J. T. Kibenge, R. Roland Cusack
