Works by Stothard, Paul

Results: 113

Solution Structure of MTH0776 from Methanobacterium Thermoautotrophicum.

Published in:

Journal of Biomolecular NMR, 2005, v. 33, n. 1, p. 51, doi. 10.1007/s10858-005-1275-5

By:

Amegbey, Godwin;
Stothard, Paul;
Kuznetsova, Ekaterina;
Yee, Adelinda;
Arrowsmith, Cheryl H.;
Wishart, David S.

Publication type:

Article

Letter to the Editor: Complete1H,13C and15N NMR assignments of MTH0776 fromMethanobacterium thermoautotrophicum.

Published in:

Journal of Biomolecular NMR, 2004, v. 30, n. 4, p. 459, doi. 10.1007/s10858-004-4341-5

By:

Amegbey, Godwin;
Chang, Zhan;
Stothard, Paul;
Yee, Adelinda;
Arrowsmith, Cheryl;
Wishart, David S.

Publication type:

Article

Accuracy of imputation to whole-genome sequence in sheep.

Published in:

Genetics Selection Evolution, 2019, v. 51, n. 1, p. 1, doi. 10.1186/s12711-018-0443-5

By:

Bolormaa, Sunduimijid;
Chamberlain, Amanda J.;
Khansefid, Majid;
Stothard, Paul;
Swan, Andrew A.;
Mason, Brett;
Prowse-Wilkins, Claire P.;
Duijvesteijn, Naomi;
Moghaddar, Nasir;
van der Werf, Julius H.;
Daetwyler, Hans D.;
MacLeod, Iona M.

Publication type:

Article

Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants.

Published in:

Genetics Selection Evolution, 2018, v. 50, n. 1, p. 1, doi. 10.1186/s12711-018-0387-9

By:

Zhang, Chunyan;
Kemp, Robert Alan;
Stothard, Paul;
Wang, Zhiquan;
Boddicker, Nicholas;
Krivushin, Kirill;
Dekkers, Jack;
Plastow, Graham

Publication type:

Article

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle.

Published in:

Genetics Selection Evolution, 2017, v. 49, p. 1, doi. 10.1186/s12711-017-0356-8

By:

Abo-Ismail, Mohammed K.;
Brito, Luiz F.;
Miller, Stephen P.;
Sargolzaei, Mehdi;
Grossi, Daniela A.;
Moore, Steve S.;
Plastow, Graham;
Stothard, Paul;
Nayeri, Shadi;
Schenkel, Flavio S.

Publication type:

Article

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP.

Published in:

Bioinformatics, 2011, v. 27, n. 16, p. 2300, doi. 10.1093/bioinformatics/btr372

By:

Grant, Jason R.;
Arantes, Adriano S.;
Liao, Xiaoping;
Stothard, Paul

Publication type:

Article

Interactive microbial genome visualization with GView.

Published in:

Bioinformatics, 2010, v. 26, n. 24, p. 3125, doi. 10.1093/bioinformatics/btq588

By:

Petkau, Aaron;
Stuart-Edwards, Matthew;
Stothard, Paul;
Van Domselaar, Gary

Publication type:

Article

Differential survival of potentially pathogenic, septicemia- and meningitis-causing E. coli across the wastewater treatment train.

Published in:

NPJ Clean Water, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s41545-022-00177-y

By:

Yu, Daniel;
Ryu, Kanghee;
Otto, Simon J. G.;
Stothard, Paul;
Banting, Graham;
Ruecker, Norma;
Neumann, Norman F.;
Zhi, Shuai

Publication type:

Article

Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column.

Published in:

Microorganisms, 2021, v. 9, n. 3, p. 490, doi. 10.3390/microorganisms9030490

By:

Pathak, Ashish;
Stothard, Paul;
Chauhan, Ashvini;
Weimer, Bart C.

Publication type:

Article

Tryptic oncopeptide secreted from the gut bacterium Cronobacter malonaticus PO3 promotes colorectal cancer.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-94666-y

By:

Shastry, Rajesh Padumane;
Hameed, Asif;
Banerjee, Shukla;
Prabhu, Ashwini;
Bajire, Sukesh Kumar;
Pavan, Sonnenahalli Rudramurthy;
Dhanyashree, Honagodu Ravichandra;
Kotimoole, Chinmaya Narayana;
Stothard, Paul;
Surya, Suprith;
Keshava Prasad, Thottethodi Subrahmanya;
Shetty, Rohan;
Shen, Fo-Ting;
Bhandary, Yashodhar Prabhakar

Publication type:

Article

Tryptic oncopeptide secreted from the gut bacterium Cronobacter malonaticus PO3 promotes colorectal cancer.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-94666-y

By:

Shastry, Rajesh Padumane;
Hameed, Asif;
Banerjee, Shukla;
Prabhu, Ashwini;
Bajire, Sukesh Kumar;
Pavan, Sonnenahalli Rudramurthy;
Dhanyashree, Honagodu Ravichandra;
Kotimoole, Chinmaya Narayana;
Stothard, Paul;
Surya, Suprith;
Keshava Prasad, Thottethodi Subrahmanya;
Shetty, Rohan;
Shen, Fo-Ting;
Bhandary, Yashodhar Prabhakar

Publication type:

Article

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

Published in:

Scientific Reports, 2015, p. 12620, doi. 10.1038/srep12620

By:

Bao, Hua;
Kommadath, Arun;
Liang, Guanxiang;
Sun, Xu;
Arantes, Adriano S.;
Tuggle, Christopher K.;
Bearson, Shawn M.D.;
Plastow, Graham S.;
Stothard, Paul;
Guan, Le Luo

Publication type:

Article

Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.585999

By:

Yang, Tianfu;
Miller, Michelle;
Forgacs, David;
Derr, James;
Stothard, Paul

Publication type:

Article

BacMap: an up-to-date electronic atlas of annotated bacterial genomes.

Published in:

Nucleic Acids Research, 2012, p. D599, doi. 10.1093/nar/gkr1105

By:

Cruz, Joseph;
Liu, Yifeng;
Liang, Yongjie;
Zhou, You;
Wilson, Michael;
Dennis, Jonathan J.;
Stothard, Paul;
Van Domselaar, Gary;
Wishart, David S.

Publication type:

Article

PROSESS: a protein structure evaluation suite and server.

Published in:

Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W633, doi. 10.1093/nar/gkq375

By:

Berjanskii, Mark;
Liang, Yongjie;
Zhou, Jianjun;
Tang, Peter;
Stothard, Paul;
Zhou, You;
Cruz, Joseph;
MacDonell, Cam;
Lin, Guohui;
Lu, Paul;
Wishart, David S.

Publication type:

Article

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.

Published in:

Nucleic Acids Research, 2008, v. 36, n. suppl_2, p. W399, doi. 10.1093/nar/gkn296

By:

Cheng, Dean;
Knox, Craig;
Young, Nelson;
Stothard, Paul;
Damaraju, Sambasivarao;
Wishart, David S.

Publication type:

Article

The CGView Server: a comparative genomics tool for circular genomes.

Published in:

Nucleic Acids Research, 2008, v. 36, n. suppl_2, p. W181, doi. 10.1093/nar/gkn179

By:

Grant, Jason R.;
Stothard, Paul

Publication type:

Article

HMDB: the Human Metabolome Database.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d521, doi. 10.1093/nar/gkl923

By:

Wishart, David S.;
Tzur, Dan;
Knox, Craig;
Eisner, Roman;
Guo, An Chi;
Young, Nelson;
Cheng, Dean;
Jewell, Kevin;
Arndt, David;
Sawhney, Summit;
Fung, Chris;
Nikolai, Lisa;
Lewis, Mike;
Coutouly, Marie-Aude;
Forsythe, Ian;
Tang, Peter;
Shrivastava, Savita;
Jeroncic, Kevin;
Stothard, Paul;
Amegbey, Godwin

Publication type:

Article

DrugBank: a comprehensive resource for in silico drug discovery and exploration.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d668, doi. 10.1093/nar/gkj067

By:

Wishart, David S.;
Knox, Craig;
Guo, An Chi;
Shrivastava, Savita;
Hassanali, Murtaza;
Stothard, Paul;
Chang, Zhan;
Woolsey, Jennifer

Publication type:

Article

BASys: a web server for automated bacterial genome annotation.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w455, doi. 10.1093/nar/gki593

By:

Van Domselaar, Gary H.;
Stothard, Paul;
Shrivastava, Savita;
Cruz, Joseph A.;
Guo, AnChi;
Dong, Xiaoli;
Lu, Paul;
Szafron, Duane;
Greiner, Russ;
Wishart, David S.

Publication type:

Article

BacMap: an interactive picture atlas of annotated bacterial genomes.

Published in:

Nucleic Acids Research, 2005, v. 33, n. suppl 1, p. d317

By:

Stothard, Paul;
Van Domselaar, Gary;
Shrivastava, Savita;
Guo, Anchi;
O'Neill, Brian;
Cruz, Joseph;
Ellison, Michael;
Wishart, David S.

Publication type:

Article

PlasMapper: a web server for drawing and auto-annotating plasmid maps.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w660, doi. 10.1093/nar/gkh410

By:

Dong, Xiaoli;
Stothard, Paul;
Forsythe, Ian J.;
Wishart, David S.

Publication type:

Article

The CyberCell Database (CCDB): a comprehensive, self‐updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d293

By:

Sundararaj, Shan;
Guo, Anchi;
Habibi‐Nazhad, Bahram;
Rouani, Melania;
Stothard, Paul;
Ellison, Michael;
Wishart, David S.

Publication type:

Article

Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection1.

Published in:

Genome, 2013, v. 56, n. 10, p. 592, doi. 10.1139/gen-2013-0082

By:

Liao, Xiaoping;
Peng, Fred;
Forni, Selma;
McLaren, David;
Plastow, Graham;
Stothard, Paul;
Scherer, Steve

Publication type:

Article

Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle.

Published in:

Mammalian Genome, 2013, v. 24, n. 3/4, p. 151, doi. 10.1007/s00335-013-9449-z

By:

Choi, Jung-Woo;
Lee, Kyung-Tai;
Liao, Xiaoping;
Stothard, Paul;
An, Hyeon-Seung;
Ahn, Sungmin;
Lee, Seunghwan;
Lee, Sung-Yeoun;
Moore, Stephen;
Kim, Tae-Hun

Publication type:

Article

Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection.

Published in:

Scientific Reports, 2017, p. 46203, doi. 10.1038/srep46203

By:

Kommadath, Arun;
Bao, Hua;
Choi, Igseo;
Reecy, James M.;
Koltes, James E.;
Fritz-Waters, Elyn;
Eisley, Chris J.;
Grant, Jason R.;
Rowland, Robert R. R.;
Tuggle, Christopher K.;
Dekkers, Jack C. M.;
Lunney, Joan K.;
Guan, Le Luo;
Stothard, Paul;
Plastow, Graham S.

Publication type:

Article

The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility.

Published in:

Prion, 2012, v. 6, n. 5, p. 461, doi. 10.4161/pri.21866

By:

Thomson, Jennifer M.;
Bowles, Victoria;
Choi, Jung-Woo;
Basu, Urmila;
Meng, Yan;
Stothard, Paul;
Moore, Stephen

Publication type:

Article

Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2019, v. 13, n. 6, p. 1520, doi. 10.1038/s41396-019-0364-5

By:

Ju, Tingting;
Kong, Ji Yoon;
Stothard, Paul;
Willing, Benjamin P.

Publication type:

Article

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2018, v. 12, n. 11, p. 2770, doi. 10.1038/s41396-018-0211-0

By:

Lin, Xiaoxi B.;
Wang, Tuo;
Stothard, Paul;
Corander, Jukka;
Wang, Jun;
Baines, John F.;
Knowles, Sarah C. L.;
Baltrūnaitė, Laima;
Tasseva, Guergana;
Schmaltz, Robert;
Tollenaar, Stephanie;
Cody, Liz A.;
Grenier, Theodore;
Wu, Wei;
Ramer-Tait, Amanda E.;
Walter, Jens

Publication type:

Article

Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits.

Published in:

BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4617-x

By:

Koufariotis, Lambros T.;
Chen, Yi-Ping Phoebe;
Stothard, Paul;
Hayes, Ben J.

Publication type:

Article

Whole genome SNP genotype piecemeal imputation.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 340, doi. 10.1186/s12859-015-0770-2

By:

Yining Wang;
Wylie, Tim;
Stothard, Paul;
Guohui Lin

Publication type:

Article

Most parsimonious haplotype allele sharing determination.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-115

By:

Zhipeng Cai;
Sabaa, Hadi;
Yining Wang;
Goebel, Randy;
Zhiquan Wang;
Jiaofen Xu;
Stothard, Paul;
Guohui Lin

Publication type:

Article

Circular genome visualization and exploration using CGView.

Published in:

Bioinformatics, 2005, v. 21, n. 4, p. 537, doi. 10.1093/bioinformatics/bti054

By:

Stothard, Paul;
Wishart, David S.

Publication type:

Article

Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility.

Published in:

Applied Microbiology (2673-8007), 2024, v. 4, n. 1, p. 376, doi. 10.3390/applmicrobiol4010026

By:

Kommu, Navya;
Stothard, Paul;
Chukwujindu, Christian;
Pathak, Ashish;
Chauhan, Ashvini

Publication type:

Article

large interactive visual database of copy number variants discovered in taurine cattle.

Published in:

GigaScience, 2019, v. 8, n. 6, p. 1, doi. 10.1093/gigascience/giz073

By:

Kommadath, Arun;
Grant, Jason R;
Krivushin, Kirill;
Butty, Adrien M;
Baes, Christine F;
Carthy, Tara R;
Berry, Donagh P;
Stothard, Paul

Publication type:

Article

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

Published in:

GigaScience, 2015, v. 4, p. 1, doi. 10.1186/s13742-015-0090-5

By:

Stothard, Paul;
Xiaoping Liao;
Arantes, Adriano S.;
De Pauw, Mary;
Coros, Colin;
Plastow, Graham S.;
Sargolzaei, Mehdi;
Crowley, John J.;
Basarab, John A.;
Schenkel, Flavio;
Moore, Stephen;
Miller, Stephen P.

Publication type:

Article

Optimizing Selection of the Reference Population for Genotype Imputation From Array to Sequence Variants.

Published in:

Frontiers in Genetics, 2019, p. N.PAG, doi. 10.3389/fgene.2019.00510

By:

Butty, Adrien M.;
Sargolzaei, Mehdi;
Miglior, Filippo;
Stothard, Paul;
Schenkel, Flavio S.;
Gredler-Grandl, Birgit;
Baes, Christine F.

Publication type:

Article

Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA.

Published in:

Genes, 2019, v. 10, n. 5, p. 325, doi. 10.3390/genes10050325

By:

Jaswal, Rajneesh;
Pathak, Ashish;
Edwards III, Bobby;
Lewis III, Robert;
Seaman, John C.;
Stothard, Paul;
Krivushin, Kirill;
Blom, Jochen;
Rupp, Oliver;
Chauhan, Ashvini

Publication type:

Article

Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils.

Published in:

Genes, 2018, v. 9, n. 1, p. 31, doi. 10.3390/genes9010031

By:

Chauhan, Ashvini;
Pathak, Ashish;
Jaswal, Rajneesh;
Edwards, Bobby;
Chappell, Demario;
Ball, Christopher;
Garcia-Sillas, Reyna;
Stothard, Paul;
Seaman, John

Publication type:

Article

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

Published in:

Nature Genetics, 2014, v. 46, n. 8, p. 858, doi. 10.1038/ng.3034

By:

Daetwyler, Hans D;
Capitan, Aurélien;
Pausch, Hubert;
Stothard, Paul;
van Binsbergen, Rianne;
Brøndum, Rasmus F;
Liao, Xiaoping;
Djari, Anis;
Rodriguez, Sabrina C;
Grohs, Cécile;
Esquerré, Diane;
Bouchez, Olivier;
Rossignol, Marie-Noëlle;
Klopp, Christophe;
Rocha, Dominique;
Fritz, Sébastien;
Eggen, André;
Bowman, Phil J;
Coote, David;
Chamberlain, Amanda J

Publication type:

Article

Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-5674-5

By:

Peters, Danielle L.;
McCutcheon, Jaclyn G.;
Stothard, Paul;
Dennis, Jonathan J.

Publication type:

Article

A novel Kayvirus species phage RuSa1 removes biofilm and lyses multiple clinical strains of methicillin resistant Staphylococcus aureus.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-92032-6

By:

Suchithra, Kokkarambath Vannadil;
Hameed, Asif;
Rekha, Punchappady Devasya;
Stothard, Paul;
Arun, Ananthapadmanabha Bhagwath

Publication type:

Article

A novel Kayvirus species phage RuSa1 removes biofilm and lyses multiple clinical strains of methicillin resistant Staphylococcus aureus.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-92032-6

By:

Suchithra, Kokkarambath Vannadil;
Hameed, Asif;
Rekha, Punchappady Devasya;
Stothard, Paul;
Arun, Ananthapadmanabha Bhagwath

Publication type:

Article

Circulating serum metabolites as biomarkers and predictors of residual feed intake in lactating dairy cows.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-85610-1

By:

Hailemariam, Dagnachew;
Manafiazar, Ghader;
Baes, Christine;
Schenkel, Flavio;
Miglior, Filippo;
Stothard, Paul;
Plastow, Graham

Publication type:

Article

Ketone body oxidation and susceptibility to ethyl acetoacetate in a novel hemolytic multidrug-resistant strain Leptospira interrogans KeTo originated from sewage water.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-76546-z

By:

Sonam, Amin;
Hameed, Asif;
Rekha, Punchappady Devasya;
Stothard, Paul;
Tellis, Rouchelle Charmaine;
Arun, Ananthapadmanabha Bhagwath

Publication type:

Article

Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle.

Published in:

Frontiers in Microbiology, 2024, p. 01, doi. 10.3389/fmicb.2024.1386319

By:

Herman, Emily K.;
Lacoste, Stacey R.;
Freeman, Claire N.;
Otto, Simon J. G.;
McCarthy, E. Luke;
Links, Matthew G.;
Stothard, Paul;
Waldner, Cheryl L.

Publication type:

Article

PHASTEST: faster than PHASTER, better than PHAST.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W443, doi. 10.1093/nar/gkad382

By:

Wishart, David S;
Han, Scott;
Saha, Sukanta;
Oler, Eponine;
Peters, Harrison;
Grant, Jason R;
Stothard, Paul;
Gautam, Vasuk

Publication type:

Article

Proksee: in-depth characterization and visualization of bacterial genomes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W484, doi. 10.1093/nar/gkad326

By:

Grant, Jason R;
Enns, Eric;
Marinier, Eric;
Mandal, Arnab;
Herman, Emily K;
Chen, Chih-yu;
Graham, Morag;
Van Domselaar, Gary;
Stothard, Paul

Publication type:

Article

PlasMapper 3.0—a web server for generating, editing, annotating and visualizing publication quality plasmid maps.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W459, doi. 10.1093/nar/gkad276

By:

Wishart, David S;
Ren, Leah;
Leong-Sit, Jacques;
Saha, Sukanta;
Grant, Jason R;
Stothard, Paul;
Singh, Upasana;
Kropielnicki, Abby;
Oler, Eponine;
Peters, Harrison;
Gautam, Vasuk

Publication type:

Article

Fast accurate missing SNP genotype local imputation.

Published in:

BMC Research Notes, 2012, v. 5, n. 1, p. 404, doi. 10.1186/1756-0500-5-404

By:

Yining Wang;
Zhipeng Cai;
Stothard, Paul;
Moore, Steve;
Goebel, Randy;
Lusheng Wang;
Guohui Lin

Publication type:

Article