Works by Rutherford, Kim

Results: 29

A framework for community curation of interspecies interactions literature.

Published in:

eLife, 2023, p. 1, doi. 10.7554/eLife.84658

By:

Cuzick, Alayne;
Seager, James;
Wood, Valerie;
Urban, Martin;
Rutherford, Kim;
Hammond-Kosack, Kim E.

Publication type:

Article

Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species.

Published in:

Ecology & Evolution (20457758), 2018, v. 8, n. 17, p. 8736, doi. 10.1002/ece3.4411

By:

Dussex, Nicolas;
Taylor, Helen R.;
Stovall, Willam R.;
Rutherford, Kim;
Dodds, Ken G.;
Clarke, Shannon M.;
Gemmell, Neil J.

Publication type:

Article

PomBase: a comprehensive online resource for fission yeast.

Published in:

Nucleic Acids Research, 2012, p. D695, doi. 10.1093/nar/gkr853

By:

Wood, Valerie;
Harris, Midori A.;
McDowall, Mark D.;
Rutherford, Kim;
Vaughan, Brendan W.;
Staines, Daniel M.;
Aslett, Martin;
Lock, Antonia;
Bähler, Jürg;
Kersey, Paul J.;
Oliver, Stephen G.

Publication type:

Article

modMine: flexible access to modENCODE data.

Published in:

Nucleic Acids Research, 2012, p. D1082, doi. 10.1093/nar/gkr921

By:

Contrino, Sergio;
Smith, Richard N.;
Butano, Daniela;
Carr, Adrian;
Hu, Fengyuan;
Lyne, Rachel;
Rutherford, Kim;
Kalderimis, Alex;
Sullivan, Julie;
Carbon, Seth;
Kephart, Ellen T.;
Lloyd, Paul;
Stinson, E. O.;
Washington, Nicole L.;
Perry, Marc D.;
Ruzanov, Peter;
Zha, Zheng;
Lewis, Suzanna E.;
Stein, Lincoln D.;
Micklem, Gos

Publication type:

Article

GeneDB: a resource for prokaryotic and eukaryotic organisms.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 1, p. d339

By:

Hertz‐Fowler, Christiane;
Peacock, Chris S.;
Wood, Valerie;
Aslett, Martin;
Kerhornou, Arnaud;
Mooney, Paul;
Tivey, Adrian;
Berriman, Matthew;
Hall, Neil;
Rutherford, Kim;
Parkhill, Julian;
Ivens, Alasdair C.;
Rajandream, Marie‐Adele;
Barrell, Bart

Publication type:

Article

Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal to his5.

Published in:

Yeast, 2000, v. 16, n. 15, p. 1405, doi. 10.1002/1097-0061(200011)16:15<1405::AID-YEA625>3.0.CO;2-H

By:

Xiang, Zheng;
Moore, Karen;
Wood, Valerie;
Rajandream, Maire-Adèle;
Barrell, Barclay G.;
Skelton, Jason;
Churcher, Carol M.;
Lyne, Michael H.;
Devlin, Karen;
Gwilliam, Rhian;
Rutherford, Kim M.;
Aves, Stephen J.

Publication type:

Article

ACT: the Artemis comparison tool.

Published in:

Bioinformatics, 2005, v. 21, n. 16, p. 3422, doi. 10.1093/bioinformatics/bti553

By:

Tim J. Carver;
Kim M. Rutherford;
Matthew Berriman;
Marie-Adele Rajandream;
Barclay G. Barrell;
Julian Parkhill

Publication type:

Article

Artemis: sequence visualization and annotation.

Published in:

Bioinformatics, 2000, v. 16, n. 10, p. 944, doi. 10.1093/bioinformatics/16.10.944

By:

Rutherford, Kim;
Parkhill, Julian;
Crook, James;
Horsnell, Terry;
Rice, Peter;
Rajandream, Marie-Adèle;
Barrell, Bart

Publication type:

Article

A genome‐wide investigation of adaptive signatures in protein‐coding genes related to tool behaviour in New Caledonian and Hawaiian crows.

Published in:

Molecular Ecology, 2021, v. 30, n. 4, p. 973, doi. 10.1111/mec.15775

By:

Dussex, Nicolas;
Kutschera, Verena E.;
Wiberg, R. Axel W.;
Parker, Darren J.;
Hunt, Gavin R.;
Gray, Russell D.;
Rutherford, Kim;
Abe, Hideaki;
Fleischer, Robert C.;
Ritchie, Michael G.;
Rutz, Christian;
Wolf, Jochen B. W.;
Gemmell, Neil J.

Publication type:

Article

Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish.

Published in:

Biology of Sex Differences, 2015, v. 6, p. 1, doi. 10.1186/s13293-015-0044-8

By:

Hui Liu;
Lamm, Melissa S.;
Rutherford, Kim;
Black, Michael A.;
Godwin, John R.;
Gemmell, Neil J.

Publication type:

Article

Viewing and annotating sequence data with Artemis.

Published in:

Briefings in Bioinformatics, 2003, v. 4, n. 2, p. 124, doi. 10.1093/bib/4.2.124

By:

Berriman, Matt;
Rutherford, Kim

Publication type:

Article

Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 1, p. 225, doi. 10.1093/molbev/msx293

By:

Todd, Erica V;
Liu, Hui;
Lamm, Melissa S;
Thomas, Jodi T;
Rutherford, Kim;
Thompson, Kelly C;
Godwin, John R;
Gemmell, Neil J

Publication type:

Article

Canto: an online tool for community literature curation.

Published in:

2014

By:

Rutherford, Kim M.;
Harris, Midori A.;
Lock, Antonia;
Oliver, Stephen G.;
Wood, Valerie

Publication type:

Product Review

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Published in:

Bioinformatics, 2012, v. 28, n. 23, p. 3163, doi. 10.1093/bioinformatics/bts577

By:

Smith, Richard N.;
Aleksic, Jelena;
Butano, Daniela;
Carr, Adrian;
Contrino, Sergio;
Hu, Fengyuan;
Lyne, Mike;
Lyne, Rachel;
Kalderimis, Alex;
Rutherford, Kim;
Stepan, Radek;
Sullivan, Julie;
Wakeling, Matthew;
Watkins, Xavier;
Micklem, Gos

Publication type:

Article

Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2435-6

By:

Zondag, Lisa E.;
Rutherford, Kim;
Gemmell, Neil J.;
Wilson, Megan J.

Publication type:

Article

Genetic sex assignment in wild populations using genotyping‐by‐sequencing data: A statistical threshold approach.

Published in:

Molecular Ecology Resources, 2018, v. 18, n. 2, p. 179, doi. 10.1111/1755-0998.12767

By:

Stovall, William R.;
Taylor, Helen R.;
Black, Michael;
Grosser, Stefanie;
Rutherford, Kim;
Gemmell, Neil J.

Publication type:

Article

Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4197-1

By:

Chen Wu;
Jordan, Melissa D.;
Newcomb, Richard D.;
Gemmell, Neil J.;
Bank, Sarah;
Meusemann, Karen;
Dearden, Peter K.;
Duncan, Elizabeth J.;
Grosser, Sefanie;
Rutherford, Kim;
Gardner, Paul P.;
Crowhurst, Ross N.;
Steinwender, Bernd;
Tooman, Leah K.;
Stevens, Mark I.;
Buckley, Thomas R.

Publication type:

Article

DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses.

Published in:

PeerJ, 2020, p. 1, doi. 10.7717/peerj.9420

By:

Ferreira, Sara;
Ashby, Rachael;
Jeunen, Gert-Jan;
Rutherford, Kim;
Collins, Catherine;
Todd, Erica V.;
Gemmell, Neil J.

Publication type:

Article

PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions.

Published in:

Nucleic Acids Research, 2022, v. 50, n. D1, p. D837, doi. 10.1093/nar/gkab1037

By:

Urban, Martin;
Cuzick, Alayne;
Seager, James;
Wood, Valerie;
Rutherford, Kim;
Venkatesh, Shilpa Yagwakote;
Sahu, Jashobanta;
Iyer, S Vijaylakshmi;
Khamari, Lokanath;
De Silva, Nishadi;
Martinez, Manuel Carbajo;
Pedro, Helder;
Yates, Andrew D;
Hammond-Kosack, Kim E

Publication type:

Article

PHI-base: the pathogen–host interactions database.

Published in:

Nucleic Acids Research, 2020, v. 48, n. D1, p. D613, doi. 10.1093/nar/gkz904

By:

Urban, Martin;
Cuzick, Alayne;
Seager, James;
Wood, Valerie;
Rutherford, Kim;
Venkatesh, Shilpa Yagwakote;
De Silva, Nishadi;
Martinez, Manuel Carbajo;
Pedro, Helder;
Yates, Andy D;
Hassani-Pak, Keywan;
Hammond-Kosack, Kim E

Publication type:

Article

PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D821, doi. 10.1093/nar/gky961

By:

Lock, Antonia;
Rutherford, Kim;
Harris, Midori A;
Hayles, Jacqueline;
Oliver, Stephen G;
Bähler, Jürg;
Wood, Valerie

Publication type:

Article

PHI-base: a new interface and further additions for the multi-species pathogen--host interactions database.

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D604, doi. 10.1093/nar/gkw1089

By:

Urban, Martin;
Cuzick, Alayne;
Rutherford, Kim;
Irvine, Alistair;
Pedro, Helder;
Pant, Rashmi;
Sadanadan, Vidyendra;
Khamari, Lokanath;
Billal, Santoshkumar;
Mohanty, Sagar;
Hammond-Kosack, Kim E.

Publication type:

Article

PomBase 2015: updates to the fission yeast database.

Published in:

Nucleic Acids Research, 2015, v. 43, n. D1, p. D656, doi. 10.1093/nar/gku1040

By:

McDowall, Mark D.;
Harris, Midori A.;
Lock, Antonia;
Rutherford, Kim;
Staines, Daniel M.;
Bähler, Jürg;
Kersey, Paul J.;
Oliver, Stephen G.;
Wood, Valerie

Publication type:

Article

Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications.

Published in:

Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baaa028

By:

Lock, Antonia;
Harris, Midori A;
Rutherford, Kim;
Hayles, Jacqueline;
Wood, Valerie

Publication type:

Article

PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability.

Published in:

Genetics, 2024, v. 227, n. 1, p. 1, doi. 10.1093/genetics/iyae007

By:

Rutherford, Kim M;
Lera-Ramírez, Manuel;
Wood, Valerie

Publication type:

Article

Revised fission yeast gene and allele nomenclature guidelines for machine readability.

Published in:

Genetics, 2023, v. 225, n. 3, p. 1, doi. 10.1093/genetics/iyad143

By:

Lera-Ramírez, Manuel;
Bähler, Jürg;
Mata, Juan;
Rutherford, Kim;
Hoffman, Charles S.;
Lambert, Sarah;
Oliferenko, Snezhana;
Martin, Sophie G.;
Gould, Kathleen L.;
Li-Lin Du;
Sabatinos, Sarah A.;
Forsburg, Susan L.;
Nielsen, Olaf;
Nurse, Paul;
Wood, Valerie

Publication type:

Article

JaponicusDB: rapid deployment of a model organism database for an emerging model species.

Published in:

Genetics, 2022, v. 220, n. 4, p. 1, doi. 10.1093/genetics/iyab223

By:

Rutherford, Kim M.;
Harris, Midori A.;
Oliferenko, Snezhana;
Wood, Valerie

Publication type:

Article

Fission stories: using PomBase to understand Schizosaccharomyces pombe biology.

Published in:

Genetics, 2022, v. 220, n. 4, p. 1, doi. 10.1093/genetics/iyab222

By:

Harris, Midori A.;
Rutherford, Kim M.;
Hayles, Jacqueline;
Lock, Antonia;
Bähler, Jürg;
Oliver, Stephen G.;
Mata, Juan;
Wood, Valerie

Publication type:

Article

Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3915-z

By:

Ling Jie Lee, Stephanie;
Horsfield, Julia A.;
Black, Michael A.;
Rutherford, Kim;
Fisher, Amanda;
Gemmell, Neil J.

Publication type:

Article