Works by Watson, Mick

Results: 60

poRe GUIs for parallel and real-time processing of MinION sequence data.

Published in:

Bioinformatics, 2017, v. 33, n. 14, p. 2207, doi. 10.1093/bioinformatics/btx136

By:

Stewart, Robert D.;
Watson, Mick

Publication type:

Article

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 140, doi. 10.1093/bioinformatics/btu601

By:

Corpas, Manuel;
Jimenez, Rafael C.;
Bongcam-Rudloff, Erik;
Budd, Aidan;
Brazas, Michelle D.;
Fernandes, Pedro L.;
Gaeta, Bruno;
van Gelder, Celia;
Korpelainen, Eija;
Lewitter, Fran;
McGrath, Annette;
MacLean, Daniel;
Palagi, Patricia M.;
Rother, Kristian;
Taylor, Jan;
Via, Allegra;
Watson, Mick;
Schneider, Maria Victoria;
Attwood, Teresa K.

Publication type:

Article

poRe: an R package for the visualization and analysis of nanopore sequencing data.

Published in:

Bioinformatics, 2015, v. 31, n. 1, p. 114, doi. 10.1093/bioinformatics/btu590

By:

Watson, Mick;
Thomson, Marian;
Risse, Judith;
Talbot, Richard;
Santoyo-Lopez, Javier;
Gharbi, Karim;
Blaxter, Mark

Publication type:

Article

viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.

Published in:

Bioinformatics, 2013, v. 29, n. 15, p. 1902, doi. 10.1093/bioinformatics/btt297

By:

Watson, Mick;
Schnettler, Esther;
Kohl, Alain

Publication type:

Article

Bovine host genome acts on rumen microbiome function linked to methane emissions.

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03293-0

By:

Martínez-Álvaro, Marina;
Auffret, Marc D.;
Duthie, Carol-Anne;
Dewhurst, Richard J.;
Cleveland, Matthew A.;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Author Correction: Assembly of hundreds of novel bacterial genomes from the chicken caecum.

Published in:

2021

By:

Glendinning, Laura;
Stewart, Robert D.;
Pallen, Mark J.;
Watson, Kellie A.;
Watson, Mick

Publication type:

Correction Notice

From FAANG to fork: application of highly annotated genomes to improve farmed animal production.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s13059-020-02197-8

By:

Clark, Emily L.;
Archibald, Alan L.;
Daetwyler, Hans D.;
Groenen, Martien A. M.;
Harrison, Peter W.;
Houston, Ross D.;
Kühn, Christa;
Lien, Sigbjørn;
Macqueen, Daniel J.;
Reecy, James M.;
Robledo, Diego;
Watson, Mick;
Tuggle, Christopher K.;
Giuffra, Elisabetta

Publication type:

Article

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s13059-020-02144-7

By:

Wilkinson, Toby;
Korir, Daniel;
Ogugo, Moses;
Stewart, Robert D.;
Watson, Mick;
Paxton, Edith;
Goopy, John;
Robert, Christelle

Publication type:

Article

Assembly of hundreds of novel bacterial genomes from the chicken caecum.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-1947-1

By:

Glendinning, Laura;
Stewart, Robert D.;
Pallen, Mark J.;
Watson, Kellie A.;
Watson, Mick

Publication type:

Article

Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae).

Published in:

Zoological Journal of the Linnean Society, 2014, v. 170, n. 1, p. 222, doi. 10.1111/zoj12084

By:

Cappellini, Enrico;
Gentry, Anthea;
Palkopoulou, Eleftheria;
Ishida, Yasuko;
Cram, David;
Roos, Anna-Marie;
Watson, Mick;
Johansson, Ulf S.;
Fernholm, Bo;
Agnelli, Paolo;
Barbagli, Fausto;
Littlewood, D. Tim J.;
Kelstrup, Christian D.;
Olsen, Jesper V.;
Lister, Adrian M.;
Roca, Alfred L.;
Dalén, Love;
Gilbert, M. Thomas P.

Publication type:

Article

High throughput analysis of MHC class I and class II diversity of Zambian indigenous cattle populations.

Published in:

HLA: Immune Response Genetics, 2023, v. 101, n. 5, p. 458, doi. 10.1111/tan.14976

By:

Silwamba, Isaac;
Vasoya, Deepali;
Simuunza, Martin;
Tzelos, Thomas;
Nalubamba, King S.;
Simulundu, Edgar;
Vrettou, Christina;
Mainda, Geoffrey;
Watson, Mick;
Muma, John Bwalya;
Connelley, Timothy

Publication type:

Article

The Antiviral RNAi Response in Vector and Non-vector Cells against Orthobunyaviruses.

Published in:

PLoS Neglected Tropical Diseases, 2017, v. 11, n. 1, p. 1, doi. 10.1371/journal.pntd.0005272

By:

Dietrich, Isabelle;
Shi, Xiaohong;
McFarlane, Melanie;
Blomström, Anne-Lie;
Skelton, Jessica K.;
Kohl, Alain;
Elliott, Richard M.;
Schnettler, Esther;
Watson, Mick

Publication type:

Article

Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods.

Published in:

PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0106491

By:

Snelling, Timothy J.;
Genç, Buğra;
McKain, Nest;
Watson, Mick;
Waters, Sinéad M.;
Creevey, Christopher J.;
Wallace, R. John

Publication type:

Article

Global Gene Expression Profiling of Myeloid Immune Cell Subsets in Response to In Vitro Challenge with Porcine Circovirus 2b.

Published in:

PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0091081

By:

Mavrommatis, Bettina;
Offord, Victoria;
Patterson, Robert;
Watson, Mick;
Kanellos, Theo;
Steinbach, Falko;
Grierson, Sylvia;
Werling, Dirk

Publication type:

Article

A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data.

Published in:

Frontiers in Genetics, 2017, v. 8, p. 1, doi. 10.3389/fgene.2017.00023

By:

Roumpeka, Despoina D.;
Wallace, R. John;
Escalettes, Frank;
Fotheringham, Ian;
Watson, Mick

Publication type:

Article

Keywords: missassembly, copy number variable regions, structural variation, draft assemblies, false positives.

Published in:

Frontiers in Genetics, 2015, v. 6, p. 1, doi. 10.3389/fgene.2015.00338

By:

Warr, Amanda;
Robert, Christelle;
Hume, David;
Archibald, Alan L.;
Deeb, Nader;
Watson, Mick;
Facioni Guimaraes, Simone Eliza;
Groenen, Martien

Publication type:

Article

A lesson from the ice bucket challenge: using social networks to publicize science.

Published in:

2014

By:

Koohy, Hashem;
Koohy, Behrad;
Watson, Mick

Publication type:

Opinion

Quality assessment and control of high-throughput sequencing data.

Published in:

Frontiers in Genetics, 2014, v. 5, p. 1, doi. 10.3389/fgene.2014.00235

By:

Watson, Mick

Publication type:

Article

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

Published in:

PLoS Genetics, 2016, v. 12, n. 2, p. 1, doi. 10.1371/journal.pgen.1005846

By:

Roehe, Rainer;
Dewhurst, Richard J.;
Duthie, Carol-Anne;
Rooke, John A.;
McKain, Nest;
Ross, Dave W.;
Hyslop, Jimmy J.;
Waterhouse, Anthony;
Freeman, Tom C.;
Watson, Mick;
Wallace, R. John

Publication type:

Article

Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.01229

By:

Auffret, Marc D.;
Stewart, Robert D.;
Dewhurst, Richard J.;
Duthie, Carol-Anne;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.00659

By:

Martínez-Álvaro, Marina;
Auffret, Marc D.;
Stewart, Robert D.;
Dewhurst, Richard J.;
Duthie, Carol-Anne;
Rooke, John A.;
Wallace, R. John;
Shih, Barbara;
Freeman, Tom C.;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Characterisation of the British honey bee metagenome.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07426-0

By:

Regan, Tim;
Barnett, Mark W.;
Laetsch, Dominik R.;
Bush, Stephen J.;
Wragg, David;
Budge, Giles E.;
Highet, Fiona;
Dainat, Benjamin;
de Miranda, Joachim R.;
Watson, Mick;
Blaxter, Mark;
Freeman, Tom C.

Publication type:

Article

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03317-6

By:

Stewart, Robert D.;
Auffret, Marc D.;
Warr, Amanda;
Wiser, Andrew H.;
Press, Maximilian O.;
Langford, Kyle W.;
Liachko, Ivan;
Snelling, Timothy J.;
Dewhurst, Richard J.;
Walker, Alan W.;
Roehe, Rainer;
Watson, Mick

Publication type:

Article

Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing.

Published in:

Immunogenetics, 2016, v. 68, n. 10, p. 765, doi. 10.1007/s00251-016-0945-7

By:

Vasoya, Deepali;
Law, Andy;
Motta, Paolo;
Yu, Mingyan;
Muwonge, Adrian;
Cook, Elizabeth;
Li, Xiaoying;
Bryson, Karen;
MacCallam, Amanda;
Sitt, Tatjana;
Toye, Philip;
Bronsvoort, Barend;
Watson, Mick;
Morrison, W.;
Connelley, Timothy

Publication type:

Article

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome.

Published in:

Animal Microbiome, 2022, v. 4, n. 1, p. 1, doi. 10.1186/s42523-022-00207-7

By:

Smith, Rebecca H.;
Glendinning, Laura;
Walker, Alan W.;
Watson, Mick

Publication type:

Article

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.

Published in:

PeerJ, 2021, p. 1, doi. 10.7717/peerj.10941

By:

Gilroy, Rachel;
Ravi, Anuradha;
Getino, Maria;
Pursley, Isabella;
Horton, Daniel L.;
Alikhan, Nabil-Fareed;
Baker, Dave;
Gharbi, Karim;
Hall, Neil;
Watson, Mick;
Adriaenssens, Evelien M.;
Foster-Nyarko, Ebenezer;
Jarju, Sheikh;
Secka, Arss;
Antonio, Martin;
Oren, Aharon;
Chaudhuri, Roy R.;
La Ragione, Roberto;
Hildebrand, Falk;
Pallen, Mark J.

Publication type:

Article

The automatic annotation of bacterial genomes.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1093/bib/bbs007

By:

Richardson, Emily J.;
Watson, Mick

Publication type:

Article

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-81668-9

By:

Glendinning, Laura;
Genç, Buğra;
Wallace, R. John;
Watson, Mick

Publication type:

Article

Single-cell RNA-seq reveals CD16<sup>-</sup> monocytes as key regulators of human monocyte transcriptional response to Toxoplasma.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-78250-0

By:

Patir, Anirudh;
Gossner, Anton;
Ramachandran, Prakash;
Alves, Joana;
Freeman, Tom C.;
Henderson, Neil C.;
Watson, Mick;
Hassan, Musa A.

Publication type:

Article

Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2111-2

By:

Robert, Christelle;
Kapetanovic, Ronan;
Beraldi, Dario;
Watson, Mick;
Archibald, Alan L.;
Hume, David A.

Publication type:

Article

The rumen microbial metagenome associated with high methane production in cattle.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2032-0

By:

Wallace, R. John;
Rooke, John A.;
McKain, Nest;
Duthie, Carol-Anne;
Hyslop, Jimmy J.;
Ross, David W.;
Waterhouse, Anthony;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 550, doi. 10.1186/1471-2164-15-550

By:

Robert, Christelle;
Fuentes-Utrilla, Pablo;
Troup, Karen;
Loecherbach, Julia;
Turner, Frances;
Talbot, Richard;
Archibald, Alan L;
Mileham, Alan;
Deeb, Nader;
Hume, David A;
Watson, Mick

Publication type:

Article

Correction: Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions.

Published in:

2022

By:

Martínez-Álvaro, Marina;
Mattock, Jennifer;
Auffret, Marc;
Weng, Ziqing;
Duthie, Carol-Anne;
Dewhurst, Richard J.;
Cleveland, Matthew A.;
Watson, Mick;
Roehe, Rainer

Publication type:

Correction Notice

Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions.

Published in:

Microbiome, 2022, v. 10, n. 1, p. 1, doi. 10.1186/s40168-022-01352-6

By:

Martínez-Álvaro, Marina;
Mattock, Jennifer;
Auffret, Marc;
Weng, Ziqing;
Duthie, Carol-Anne;
Dewhurst, Richard J.;
Cleveland, Matthew A.;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1760-x

By:

Bickhart, Derek M.;
Watson, Mick;
Koren, Sergey;
Panke-Buisse, Kevin;
Cersosimo, Laura M.;
Press, Maximilian O.;
Van Tassell, Curtis P.;
Van Kessel, Jo Ann S.;
Haley, Bradd J.;
Kim, Seon Woo;
Heiner, Cheryl;
Suen, Garret;
Bakshy, Kiranmayee;
Liachko, Ivan;
Sullivan, Shawn T.;
Myer, Phillip R.;
Ghurye, Jay;
Pop, Mihai;
Weimer, Paul J.;
Phillippy, Adam M.

Publication type:

Article

Livestock 2.0 – genome editing for fitter, healthier, and more productive farmed animals.

Published in:

Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1583-1

By:

Tait-Burkard, Christine;
Doeschl-Wilson, Andrea;
McGrew, Mike J.;
Archibald, Alan L.;
Sang, Helen M.;
Houston, Ross D.;
Whitelaw, C. Bruce;
Watson, Mick

Publication type:

Article

Successful test launch for nanopore sequencing.

Published in:

Nature Methods, 2015, v. 12, n. 4, p. 303, doi. 10.1038/nmeth.3327

By:

Loman, Nicholas J;
Watson, Mick

Publication type:

Article

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

Published in:

PLoS Genetics, 2017, v. 13, n. 9, p. 1, doi. 10.1371/journal.pgen.1006997

By:

Clark, Emily L.;
Bush, Stephen J.;
McCulloch, Mary E. B.;
Farquhar, Iseabail L.;
Young, Rachel;
Lefevre, Lucas;
Pridans, Clare;
Tsang, Hiu;
Wu, Chunlei;
Afrasiabi, Cyrus;
Watson, Mick;
Whitelaw, C. Bruce;
Freeman, Tom C.;
Summers, Kim M.;
Archibald, Alan L.;
Hume, David A.

Publication type:

Article

Visualization and analysis of RNA-Seq assembly graphs.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 14, p. 7262, doi. 10.1093/nar/gkz599

By:

Nazarie, Fahmi W;
Shih, Barbara;
Angus, Tim;
Barnett, Mark W;
Chen, Sz-Hau;
Summers, Kim M;
Klein, Karsten;
Faulkner, Geoffrey J;
Saini, Harpreet K;
Watson, Mick;
Dongen, Stijn van;
Enright, Anton J;
Freeman, Tom C

Publication type:

Article

Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations.

Published in:

Genome Biology & Evolution, 2021, v. 13, n. 3, p. 1, doi. 10.1093/gbe/evab014

By:

Wiener, Pamela;
Robert, Christelle;
Ahbara, Abulgasim;
Salavati, Mazdak;
Abebe, Ayele;
Kebede, Adebabay;
Wragg, David;
Friedrich, Juliane;
Vasoya, Deepali;
Hume, David A;
Djikeng, Appolinaire;
Watson, Mick;
Prendergast, James G D;
Hanotte, Olivier;
Mwacharo, Joram M;
Clark, Emily L

Publication type:

Article

Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis.

Published in:

Parasites & Vectors, 2015, v. 8, n. 1, p. 1, doi. 10.1186/s13071-015-1210-x

By:

Weisheit, Sabine;
Villar, Margarita;
Tykalová, Hana;
Popara, Marina;
Loecherbach, Julia;
Watson, Mick;
Růžek, Daniel;
Grubhoffer, Libor;
de la Fuente, José;
Fazakerley, John K.;
Bell-Sakyi, Lesley

Publication type:

Article

The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.

Published in:

Microbiome, 2017, v. 5, p. 1, doi. 10.1186/s40168-017-0378-z

By:

Auffret, Marc D.;
Dewhurst, Richard J.;
Duthie, Carol-Anne;
Rooke, John A.;
Wallace, R. John;
Freeman, Tom C.;
Stewart, Robert;
Watson, Mick;
Roehe, Rainer

Publication type:

Article

Errors in RNA-Seq quantification affect genes of relevance to human disease.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0734-x

By:

Robert, Christelle;
Watson, Mick

Publication type:

Article

When will ‘open science’ become simply ‘science’?

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 101, doi. 10.1186/s13059-015-0669-2

By:

Watson, Mick

Publication type:

Article

Illuminating the future of DNA sequencing.

Published in:

Genome Biology, 2014, v. 15, n. 2, p. 108, doi. 10.1186/gb4165

By:

Watson, Mick

Publication type:

Article

KOunt: a reproducible KEGG orthologue abundance workflow.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad483

By:

Mattock, Jennifer;
Martínez-Álvaro, Marina;
Cleveland, Matthew A;
Roehe, Rainer;
Watson, Mick

Publication type:

Article

nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad150

By:

Guizard, Sébastien;
Miedzinska, Katarzyna;
Smith, Jacqueline;
Smith, Jonathan;
Kuo, Richard I;
Davey, Megan;
Archibald, Alan;
Watson, Mick

Publication type:

Article

MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs).

Published in:

Bioinformatics, 2019, v. 35, n. 12, p. 2150, doi. 10.1093/bioinformatics/bty905

By:

Stewart, Robert D;
Auffret, Marc D;
Snelling, Timothy J;
Roehe, Rainer;
Watson, Mick

Publication type:

Article

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

Published in:

GigaScience, 2017, v. 6, n. 3, p. 1, doi. 10.1093/gigascience/gix007

By:

Brown, Bonnie L.;
Watson, Mick;
Minot, Samuel S.;
Rivera, Maria C.;
Franklin, Rima B.

Publication type:

Article

Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle.

Published in:

Frontiers in Genetics, 2019, p. 1, doi. 10.3389/fgene.2019.00701

By:

Lima, Joana;
Auffret, Marc D.;
Stewart, Robert D.;
Dewhurst, Richard J.;
Duthie, Carol-Anne;
Snelling, Timothy J.;
Walker, Alan W.;
Freeman, Tom C.;
Watson, Mick;
Roehe, Rainer

Publication type:

Article