Kim Rutherford

Software Development and Bioinformatics

Information

Profile

I am a software developer and bioinformatician. For the last 20 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
Major projects
Canto - a community curation tool
PomBase v2
JaponicusDB
Secondments
FlyBase - 3 months customising Canto for drosophila phenotypes
PHI-base - 6 months adapting Canto for pathogen-host interaction phenotype curation
Sept 2012 – Dec 2016

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

Tasks
bioinformatics support
genome and transcriptome assembly and analysis
bioinformatics mentoring and training
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
Oct 2001 – 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
Apr 1999 – Oct 2001
Senior Computer Programmer Pathogen Sequencing Unit
The Sanger Institute
Sept 1998 – Apr 1999
Computer Programmer Pathogen Sequencing Unit
The Sanger Institute

Publications

● Google Scholar ● ORCID ● Europe PMC ● ResearcherID ● Scopus profile

Nov 2021
JaponicusDB: Rapid deployment of a model organism database for an emerging model species
K. Rutherford, M. Harris, S. Oliferenko, V. Wood
Genetics (accepted, in press)
Preprint: DOI: 10.1101/2021.09.23.461587
Nov 2021
Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology
M. Harris, K. Rutherford, J. Hayles, A. Lock, J. Bähler, S. Oliver, J. Mata, V. Wood
Preprint: DOI: 10.1101/2021.09.07.459264
Nov 2021
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
M. Urban et al.
NAR DOI: 10.1093/nar/gkab1037
Feb 2021
A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows
N. Dussex et al.
Molecular Ecology. DOI: 10.1111/mec.15775
Jan 2021
The Gene Ontology resource: enriching a GOld mine
The Gene Ontology Consortium
Nucleic Acids Research. DOI: 10.1093/nar/gkaa1113
Nov 2020
Dense sampling of bird diversity increases power of comparative genomics
S. Feng et al.
Nature. DOI: 10.1038/s41586-020-2873-9
Sep 2020
Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns
V. Wood at al.
Open Biology. DOI: 10.1098/rsob.200149
Aug 2020
The tuatara genome reveals ancient features of amniote evolution
N. Gemmell, K. Rutherford, et al.
Nature. DOI: 10.1038/s41586-020-2561-9
July 2020
DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses
S. Ferreira, R. Ashby, G-J. Jeunen, K. Rutherford, C. Collins, E.V. Todd, N.J. Gemmell
PeerJ. DOI: 10.7717/peerj.9420
Apr 2020
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications
A. Lock, M. Harris, K. Rutherford, J. Hayles, V. Wood
Database. DOI: 10.1093/database/baaa028
Jan 2020
PHI-base: the pathogen–host interactions database
M. Urban, A. Cuzick, J. Seager, V. Wood, K. Rutherford, S. Yagwakote Venkatesh, N. De Silva, M. Carbajo Martinez, H. Pedro, A.D. Yates, K. Hassani-Pak, K.E. Hammond-Kosack
Nucleic Acids Research. DOI: 10.1093/nar/gkz904
Mar 2019
Molecular structure of sauropsid β-keratins from tuatara (Sphenodon punctatus)
D. Parry, R. Fraser, L. Alibardi, K. Rutherford, N. Gemmell
Journal of Structural Biology. DOI: 10.1016/j.jsb.2019.04.008
Jan 2019
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information
A. Lock, K. Rutherford, M.A. Harris, J Hayles, S.G. Oliver, J. Bähler, V. Wood
Nucleic Acids Research. DOI: 10.1093/nar/gky961
Dec 2018
Stress, novel sex genes and epigenetic reprogramming orchestrate socially-controlled sex change
E.V. Todd, O. Ortega-Recalde, H. Liu, M.S. Lamm, K.M. Rutherford, H. Cross, M.A. Black, O. Kardailsky, J.A. Graves, T.A. Hore, J.R. Godwin, N.J. Gemmell
Science Advances. DOI: 10.1126/sciadv.aaw7006
Nov 2018
Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?
V. Wood, A. Lock, M. Harris, K. Rutherford, J. Bahler, S Oliver
Open Biology. DOI: 10.1098/rsob.180241
Oct 2018
RNAcentral: a hub of information for non-coding RNA sequences
The RNAcentral Constortium
Nucleic Acids Research. DOI: 10.1093/nar/gky1034
Oct 2018
The Gene Ontology Resource: 20 years and still GOing strong
The Gene Ontology Consortium
Nucleic Acids Research. DOI: 10.1093/nar/gky1055
Aug 2018
Evolutionary history of the podoplanin gene
J. Renart, D. San Mauro, A. Agorreta, K. Rutherford, N. J. Gemmell, M Quintanill
Gene Reports. DOI: 10.1016/j.genrep.2018.08.005
Aug 2018
Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species
N. Dussex, H.R. Taylor, W.R. Stovall, K. Rutherford, K.G. Dodds, S.M. Clarke, N.J. Gemmell
Ecology and Evolution. DOI: 10.1002/ece3.4411
Apr 2018
Adipose Transcriptome Analysis Provides Novel Insights into Molecular Regulation of Prolonged Fasting in Northern Elephant Seal Pups
B. Martinez, J. Khudyakov, K. Rutherford, D. Crocker, N. Gemmell, R. Ortiz
Physiological Genomics. DOI: 10.1152/physiolgenomics.00002.2018
Apr 2018
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution
S. Blanchoud, K. Rutherford, L. Zondag, N. Gemmell, M Wilson
Scientific Reports. DOI: 10.1038/s41598-018-23749-w.
Feb 2018
Genetic sex assignment in wild populations using GBS data: a statistical threshold approach
W. Stovall, H.R. Taylor, M. Black, S. Grosser, K. Rutherford, N.J. Gemmell
Molecular Ecology Resources. DOI: 10.1111/1755-0998.12767
Dec 2017
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution
C. Wu, M.D. Jordan, R.D. Newcomb, N.J. Gemmell, S. Bank, K. Meusemann, P.K. Dearden, E.J. Duncan, S. Grosser, K. Rutherford, P.P. Gardner, R.N. Crowhurst, B. Steinwender, L.K. Tooman, M.I. Stevens, T.R. Buckley
BMC Genomics. DOI: 10.1186/s12864-017-4197-1.
Dec 2017
Identification of sex differences in zebrafish (Danio rerio) brains during early sexual differentiation and masculinisation using 17α-methyltestoterone
S.L.J. Lee, J.A. Horsfield, M.A. Black, K.M. Rutherford, N.J. Gemmell
Biology of Reproduction. DOI: 10.1093/biolre/iox175
Nov 2017
Female mimicry by sneaker males has a transcriptomic signature in both the brain and gonad in a sex changing fish
E.V. Todd, H. Liu, M.S. Lamm, J.T. Thomas, K. Rutherford, K.C. Thompson, J.R. Godwin, N.J. Gemmell
Molecular Biology and Evolution. DOI: 10.1093/molbev/msx293
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. DOI: 10.1098/rspb.2017.0853.
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. DOI: 10.1186/s12864-017-3915-z
June 2017
PomBase – the scientific resource for fission yeast
V. Wood, A. Lock, K. Rutherford, M.A. Harris
Methods in Molecular Biology. DOI: 10.17863/CAM.12124
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. DOI: 10.1093/nar/gkw1089
Nov 2016
The Gene Ontology Consortium; Expansion of the Gene Ontology knowledgebase and resources.
The Gene Ontology Consortium
Nucleic Acids Research. DOI: 10.1093/nar/gkw1108
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. DOI: 10.1186/s12864-016-2435-6
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. DOI: 10.1186/s13293-015-0044-8
Jan 2015
Gene Ontology Consortium: going forward
The Gene Ontology Consortium
Nucleic Acids Research. DOI: 10.1093/nar/gku1179
Dec 2014
Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia
D. E. Janes et al.
Biology Letters. DOI: 10.1098/rsbl.2014.0809
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
Nucleic Acids Research. DOI: 10.1093/nar/gku1040
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. DOI: 10.1016/j.tibtech.2014.05.003
Feb 2014
Canto: An online tool for community literature curation
K. Rutherford, M. A. Harris, A. Lock, S. G. Oliver and V. Wood
Bioinformatics. DOI: 10.1093/bioinformatics/btu103
Jan 2013
Gene ontology annotations and resources.
Gene Ontology Consortium
Nucleic Acids Research. DOI: 10.1093/nar/gks1050
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. DOI: 10.1093/bioinformatics/bts577
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 Research. DOI: 10.1093/nar/gkr921
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 Research. DOI: 10.1093/nar/gkr853
Nov 2011
The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic Acids Research. DOI: 10.1093/nar/gkr1028
Dec 2010
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE.
The modENCODE Consortium
Science. DOI: 10.1126/science.1198374
Dec 2010
Integrative Analysis of the C. elegans Genome by the modENCODE Project.
The modENCODE Consortium
Science. DOI: 10.1126/science.1196914
July 2007
FlyMine: an integrated database for Drosophila and Anopheles genomics.
R. Lyne et al.
Genome Biology. DOI: 10.1186/gb-2007-8-7-r129
Sep 2005
WebACT - An online companion for the Artemis Comparison Tool
J. Abbott, D. Aanensen, K. Rutherford, S. Butcher and B. Spratt
Bioinformatics. DOI: 10.1093/bioinformatics/bti601
Aug 2005
ACT: the Artemis comparison tool.
T. Carver, K. Rutherford, M. Berriman, M-A. Rajandream, B.. Barrell and J. Parkhill
Bioinformatics. DOI: 10.1093/bioinformatics/bti553
June 2005
A Human-Curated Annotation of the Candida albicans Genome
B.R. Braun et al.
PLoS Genetics. DOI: 10.1371/journal.pgen.0010001
Jan 2005
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses
N. Hall et al.
Science. DOI: 10.1126/science.1103717
Sep 2004
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.
M. Holden et al.
Proc Natl Acad Sci. DOI: 10.1073/pnas.0403302101
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. DOI: 10.1073/pnas.0402521101
Jan 2004
GeneDB: a resource for prokaryotic and eukaryotic organisms.
Hertz-Fowler C et al.
Nucleic Acids Research. DOI: 10.1093/nar/gkh007
Nov 2003
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
A. Cerdeño‐Tárraga et al.
Nucleic Acids Research. DOI: 10.1093/nar/gkg874
Aug 2003
The DNA sequence of chromosome I of an African trypanosome: Gene content, chromosome organisation, recombination and polymorphism
N. Hall et al.
Nucleic Acids Research. DOI: 10.1093/nar/gkg674
June 2003
Viewing and annotating sequence data with Artemis.
M. Berriman and K. Rutherford
Briefing in Bioinformatics. DOI: 10.1093/bib/4.2.124
Oct 2002
Genome sequence of the human malaria parasite Plasmodium falciparum.
J. Malcolm et al.
Nature. DOI: 10.1038/nature01097
Oct 2002
Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13.
N. Hall et al.
Nature. DOI: 10.1038/nature01095
May 2002
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
S. Bentley et al.
Nature. DOI: 10.1038/417141a
Feb 2002
The genome sequence of Schizosaccharomyces pombe.
V. Wood et al.
Nature. DOI: 10.1038/nature724
Oct 2001
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
J. Parkhill et al.
Nature. DOI: 10.1038/35101607
Oct 2001
Genome sequence of Yersinia pestis, the causative agent of plague.
J. Parkhill et al.
Nature. DOI: 10.1038/35097083
June 2001
A Re-annotation of the Saccharomyces cerevisiae Genome.
V. Wood, K. M. Rutherford, A. Ivens, M-A Rajandream and B. Barrell
Comparative and Functional Genomics. DOI: 10.1002/cfg.86
Feb 2001
Massive gene decay in the leprosy bacillus.
S. Cole et al.
Nature. DOI: 10.1038/35059006
Oct 2000
Artemis: sequence visualisation and annotation.
K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M-A. Rajandream and B. Barrell
Bioinformatics. DOI: 10.1093/bioinformatics/16.10.944
Sep 2000
Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere‐distal to his5.
Z. Xiang et al.
Yeast. PMID:11054821
Mar 2000
Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.
J. Parkhill et al.
Nature. DOI: 10.1038/35006655
Feb 2000
The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.
J. Parkhill et al.
Nature. DOI: 10.1038/35001088

Book Chapters

Apr 2018
PomBase: The Scientific Resource for Fission Yeast
“Eukaryotic Genomic Databases : Methods and Protocols”
A Lock, K Rutherford, M.A. Harris, V. Wood
Methods in Molecular Biology. DOI: 10.1007/978-1-4939-7737-6_4