Kim Rutherford

Software Development and Bioinformatics

Information

Profile

I am a software developer and bioinformatician. For the last 19 years I have been helping biologists to capture, analyse and interpret genomic data.

Skills and Experience

Work experience

June 2010 – Present

Programmer S. pombe genome database (PomBase)
Department of Biochemistry, University of Cambridge

Tasks
web and database programming
system administration for curation.pombase.org
Major projects
Canto - a community curation tool
PomBase v2
Sept 2012 – Dec 2016

Scientific Officer (part time) Gemmell lab
Department of Anatomy, University of Otago

Tasks
bioinformatics support for the group
genome and transcriptome assembly and analysis
mentoring / training of group members in bioinformatics
tuatara genome project
Feb 2009 – June 2010

Computer Associate Baulcombe Group
Department of Plant Sciences, University of Cambridge

Tasks
bioinformatics support
creation of a short read analysis pipeline
Sept 2007 – Feb 2009

Programmer modENCODE Data Coordination Center
Cambridge Systems Biology Centre

Tasks
helped create the data warehouse for the modENCODE project:
modMine
Feb 2004 – Sept 2007

Programmer FlyMine/InterMine group
Department of Genetics, University of Cambridge

Tasks
Java programming for the InterMine project
Sept 1998 – Feb 2004

Principal Computer Programmer Pathogen Sequencing Unit
The Sanger Institute

Tasks
programming and bioinformatics support
Major projects
Artemis - a genome analysis and annotation tool
ACT - a genome comparison viewer

Publications

Scopus profile Google Scholar ORCID Europe PMC
Feb 2000
The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.
J. Parkhill et al.
Nature. 2000 Feb 10;403(6770):665-8.
Mar 2000
Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.
J. Parkhill et al.
Nature. 2000 Mar 30;404(6777):502-6.
Oct 2000
Artemis: sequence visualisation and annotation.
K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M-A. Rajandream and B. Barrell
Bioinformatics. 2000 Oct;16(10):944-5.
Feb 2001
Massive gene decay in the leprosy bacillus.
S. Cole et al.
Nature. 2001 Feb 22;409(6823):1007-11.
June 2001
A Re-annotation of the Saccharomyces cerevisiae Genome.
V. Wood, K. M. Rutherford, A. Ivens, M-A Rajandream and B. Barrell
Comp Funct Genomics. 2001 June; 2(3): 143–154.
Oct 2001
Genome sequence of Yersinia pestis, the causative agent of plague.
J. Parkhill et al.
Nature. 2001 Oct 4;413(6855):523-7.
Oct 2001
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
J. Parkhill et al.
Nature. 2001 Oct 25;413(6858):848-52.
Feb 2002
The genome sequence of Schizosaccharomyces pombe.
V. Wood et al.
Nature. 2002 Feb 21;415(6874):871-80.
May 2002
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
S. Bentley et al.
Nature. 2002 May 9;417(6885):141-7.
Oct 2002
Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13.
N. Hall et al.
Nature. 2002 Oct 3;419(6906):527-31.
Oct 2002
Genome sequence of the human malaria parasite Plasmodium falciparum.
J. Malcolm et al.
Nature. 2002 Oct 3;419(6906):498-511.
June 2003
Viewing and annotating sequence data with Artemis.
M. Berriman and K. Rutherford
Brief Bioinform. 2003 Jun;4(2):124-32.
Aug 2003
The DNA sequence of chromosome I of an African trypanosome: Gene content, chromosome organisation, recombination and polymorphism
N. Hall et al.
Nucl. Acids Res. (2003) 31 (16): 4864-4873.
Nov 2003
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
A. Cerdeño‐Tárraga et al.
Nucleic Acids Res. 2003 Nov 15;31(22):6516-23.
Jan 2004
GeneDB: a resource for prokaryotic and eukaryotic organisms.
Hertz-Fowler C et al.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D339-43.
June 2004
Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance.
M. Holden et al.
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9786-91a
Sep 2004
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.
M. Holden et al.
Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14240-5.
Jan 2005
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses
N. Hall
Science 07 Jan 2005: Vol. 307, Issue 5706, pp. 82-86
June 2005
A Human-Curated Annotation of the Candida albicans Genome
Braun et al.
PLoS Genet. 2005 Jul;1(1):36-57. Epub 2005 Jun 17
Aug 2005
ACT: the Artemis comparison tool.
T. Carver, K. Rutherford, M. Berriman, M-A. Rajandream, B.. Barrell and J. Parkhill
Bioinformatics. 2005 Aug 15;21(16):3422-3
Sep 2005
WebACT - An online companion for the Artemis Comparison Tool
J. Abbott, D. Aanensen, K. Rutherford, S. Butcher and B. Spratt
Bioinformatics. 2005 Sep 15;21(18):3665-6. Epub 2005 Aug 2
July 2007
FlyMine: an integrated database for Drosophila and Anopheles genomics.
R. Lyne et al.
Genome Biol. 2007;8(7):R129.
Dec 2010
Integrative Analysis of the C. elegans Genome by the modENCODE Project.
The modENCODE Consortium
Science. 2010 Dec 24;330(6012):1775-87.
Dec 2010
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE.
The modENCODE Consortium
Science. 2010 Dec 24;330(6012):1787-97.
Nov 2011
The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium. Nucleic Acids Res. 2012 Jan;40(Database issue):D559-64. Epub 2011 Nov 18.
Jan 2012
PomBase: a comprehensive online resource for fission yeast.
V. Wood, M.A. Harris, M.D. McDowall, K. Rutherford, B.W. Vaughan, D.M. Staines, M. Aslett, A. Lock, J. Bähler, P.J. Kersey, S.G. Oliver
Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9.
Jan 2012
modMine: flexible access to modENCODE data.
S. Contrino, R.N. Smith, D. Butano, A. Carr, F. Hu, R. Lyne, K. Rutherford, A. Kalderimis, J. Sullivan, S. Carbon, E.T. Kephart, P. Lloyd, E.O. Stinson, N.L. Washington, M.D. Perry, P. Ruzanov, Z. Zha, S.E. Lewis, L.D. Stein, G. Micklem
Nucleic Acids Res. 2012 Jan;40(Database issue):D1082-8.
Sep 2012
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
R.N. Smith, J. Aleksic, D. Butano, A. Carr, S. Contrino, F. Hu, M. Lyne, R. Lyne, A. Kalderimis, K. Rutherford, R. Stepan, J. Sullivan, M. Wakeling, X. Watkins, G. Micklem
Bioinformatics. (2012) 28 (23):3163-3165.
Jan 2013
Gene ontology annotations and resources.
Gene Ontology Consortium
Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050
Feb 2014
Canto: An online tool for community literature curation
K. Rutherford, M. A. Harris, A. Lock, S. G. Oliver and V. Wood
Bioinformatics (2014) doi: 10.1093/bioinformatics/btu103
June 2014
Improving functional annotation for industrial microbes: A case study with Pichia pastoris
D. Dikicioglu, V. Wood, K. Rutherford, M. McDowall, S. Oliver
Trends in Biotechnology (2014) 10.1016/j.tibtech.2014.05.003
Oct 2014
PomBase 2015: updates to the fission yeast database
M. McDowall, M. Harris, A. Lock, K. Rutherford, D. Staines, J. Bähler, P. Kersey, S. Oliver and V. Wood
Nucl. Acids Res. (2014) doi: 10.1093/nar/gku1040
Dec 2014
Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia
D. E. Janes et al.
Biol Lett. 2014 Dec; 10(12): 20140809.
Jan 2015
Gene Ontology Consortium: going forward
The Gene Ontology Consortium
Nucl. Acids Res. (28 January 2015) 43 (D1): D1049-D1056.
Nov 2015
Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish
H. Liu, M. Lamm, K. Rutherford, M. Black, J. Godwin and N. Gemmell
Biology of Sex Differences (2015) 6:26
Feb 2016
Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis
L. Zondag, K. Rutherford, N. Gemmell and M. Wilson
BMC Genomics (2016) 17:114 DOI 10.1186/s12864-016-2435-6
Nov 2016
The Gene Ontology Consortium; Expansion of the Gene Ontology knowledgebase and resources.
The Gene Ontology Consortium
Nucleic Acids Res 2017; 45 (D1): D331-D338. doi: 10.1093/nar/gkw1108
Jan 2017
PHI-base: A new interface and further additions for the multi-species pathogen-host interactions database.
Urban, M., Alayne Cuzick, A., Rutherford, K., Irvine, A., Pedro, H., Pant, R., Sadanadan, V., Khamari, L., Billal, S., Mohanty S., and. Hammond-Kosack, K.E.
Nucleic Acids Research (2017) doi: 10.1093/nar/gkw1089
July 2017
Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development
S.L.J. Lee, J.A. Horsfield, M.A. Black, K. Rutherford, A. Fisher, N.J. Gemmell
BMC Genomics (2017) 18:557 doi: 10.1186/s12864-017-3915-z
July 2017
Male-female relatedness at specific SNP-linkage groups influences cryptic female choice in Chinook salmon (Oncorhynchus tshawytscha)
C. Gessner, S.L. Johnson, P. Fisher, S. Clarke, K. Rutherford, J. Symonds, N.J. Gemmell
Proc. R. Soc. B 2017 284 20170853; DOI: 10.1098/rspb.2017.0853.