Paul Kersey

Paul Kersey

Team Leader - Kersey team: Non-vertebrate genomics

Dr Kersey’s team handles genome-scale data from non-vertebrate species, mainly utilising the Ensembl software platform. The team maintains the Ensembl Genomes resource, which operates as a series of collaborations with community-focused groups in individual domains. Major collaborative efforts include VectorBase (for invertebrate vectors of human pathogens), WormBase (for nematode), PomBase (for fission yeast), PhytoPath (for plant pathogens) and Microme (for bacterial pathways). Paul received his PhD from the University of Edinburgh in 1995 and has been at EMBL since 1999, working on a variety of resources for completely sequenced genomes (and their corresponding proteins) including UniProt, GOA, Integr8, and IPI, prior to the launch of Ensembl Genomes in 2009.

PhD University of Edinburgh 1992. Postdoctoral work at University of Edinburgh and MRC Human Genetics Unit, Edinburgh. At EMBL-EBI since 1999.

ORCID iD: 0000-0002-7054-800X

Tel:+44 (0)1223 494 601 / Fax:

Kersey team

The Non-vertebrate Genomics team, led by Dr Paul Kersey, develops Ensembl Genomes and related resources. Ensembl Genomes provides portals for bacteria, protists, fungi, plants and invertebrate metazoa, offering access to genome-scale data through a set of programmatic and interactive interfaces, exploiting developments originating in the vertebrate-focused Ensembl project.

Our major areas of interest include broad-range comparative genomics and the visualisation and interpretation of genomic variation, which is being increasingly studied in species throughout the taxonomy. Even small communities with little informatics infrastructure can now perform highly complex and data generative experiments that were once the sole domain of large, internationally coordinated sequencing projects. Through collaborating with EMBL-EBI and re-using our established toolset, such small communities can store, analyse and disseminate data more cheaply and powerfully than if they develop their own tools.

Collaborations

We collaborate closely with VectorBase, a resource focused on the annotation of invertebrate vectors; WormBase, a resource for nematode biology; and PomBase, focused on the fission yeast Schizosaccharomyces pombe. Plant science collaborations include Gramene in the US and several European groups in the transPLANT project. We developed PhytoPath, a new portal for plant pathogen data, and are involved in the development of Microme, a resource for bacterial metabolic pathways.

Publications

2016

WormBase 2016: expanding to enable helminth genomic research.
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C, Harris TW, Kishore R, Lee R, Lomax J, Li Y, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Schindelman G, Stanley E, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW.
Nucleic acids research Volume 44 (2016) p.D774-80

PhytoPath: an integrative resource for plant pathogen genomics.
Pedro H, Maheswari U, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ.
Nucleic acids research Volume 44 (2016) p.D688-93

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.
Bolser D, Staines DM, Pritchard E, Kersey P.
Methods in molecular biology (Clifton, N.J.) Volume 1374 (2016) p.115-140

Gramene 2016: comparative plant genomics and pathway resources.
Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.
Nucleic acids research Volume 44 (2016) p.D1133-40

Ensembl Genomes 2016: more genomes, more complexity.
Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM.
Nucleic acids research Volume 44 (2016) p.D574-80

2015

PomBase 2015: updates to the fission yeast database.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V.
Nucleic acids research Volume 43 (2015) p.D656-61

Gene Ontology Consortium: going forward.
Gene Ontology Consortium.
Nucleic acids research Volume 43 (2015) p.D1049-56

RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium.
Nucleic acids research Volume 43 (2015) p.D123-9

Towards recommendations for metadata and data handling in plant phenotyping.
Krajewski P, Chen D, Ćwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.
Journal of experimental botany Volume 66 (2015) p.5417-5427

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.
Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D.
Nucleic acids research Volume 43 (2015) p.D707-13

Increased brain activation during working memory processing after pediatric mild traumatic brain injury (mTBI).
Westfall DR, West JD, Bailey JN, Arnold TW, Kersey PA, Saykin AJ, McDonald BC.
Journal of pediatric rehabilitation medicine Volume 8 (2015) p.297-308

Triticeae resources in Ensembl Plants.
Bolser DM, Kerhornou A, Walts B, Kersey P.
Plant & cell physiology Volume 56 (2015) p.e3

2014

Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
Nayduch D, Cohnstaedt LW, Saski C, Lawson D, Kersey P, Fife M, Carpenter S.
Virus research Volume 182 (2014) p.43-49

Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.
Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I.
Medical mycology Volume 52 (2014) p.472-481

Gramene 2013: comparative plant genomics resources.
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
Nucleic acids research Volume 42 (2014) p.D1193-9

WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic acids research Volume 42 (2014) p.D789-93

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P.
PloS one Volume 9 (2014) p.e96855

Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM.
Nucleic acids research Volume 42 (2014) p.D546-52

2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.
GigaScience Volume 2 (2013) p.10

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic acids research Volume 41 (2013) p.D530-5

2012

Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N.
Nature Volume 491 (2012) p.705-710

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium.
Nature Volume 487 (2012) p.94-98

WormBase 2012: more genomes, more data, new website.
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic acids research Volume 40 (2012) p.D735-41

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D, VectorBase Consortium.
Nucleic acids research Volume 40 (2012) p.D729-34

PomBase: a comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG.
Nucleic acids research Volume 40 (2012) p.D695-9

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Nucleic acids research Volume 40 (2012) p.D91-7

WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW.
Worm Volume 1 (2012) p.15-21

WormBase: Annotating many nematode genomes
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg P.
Worm Volume 1 (2012) p.15-21

The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic acids research Volume 40 (2012) p.D559-64

2011

Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P.
Database : the journal of biological databases and curation Volume 2011 (2011) p.bar030

Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D.
Nucleic acids research Volume 39 (2011) p.D1085-94

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.
Genome research Volume 21 (2011) p.2224-2241

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.
Nature Volume 477 (2011) p.419-423

RNAcentral: A vision for an international database of RNA sequences.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNA (New York, N.Y.) Volume 17 (2011) p.1941-1946

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2156-2158

2010

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome biology Volume 11 (2010) p.402

Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A.
Nucleic acids research Volume 38 (2010) p.D563-9

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium.
The Plant cell Volume 22 (2010) p.2530-2536

2009

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic acids research Volume 37 (2009) p.D169-74

2008

In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Molecular biotechnology Volume 38 (2008) p.165-177

Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Combinatorial chemistry & high throughput screening Volume 11 (2008) p.653-660

2007

The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 406 (2007) p.1-21

2006

Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R.
Omics : a journal of integrative biology Volume 10 (2006) p.114-118

Databases and resources for in silico proteome analysis.
Pruess M, Kersey P, Kulikova T, Apweiler R.
Methods of biochemical analysis Volume 49 (2006) p.397-414

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nature cell biology Volume 8 (2006) p.1183-1189

2005

The Integr8 project--a resource for genomic and proteomic data.
Pruess M, Kersey P, Apweiler R.
In silico biology Volume 5 (2005) p.179-185

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.
Nucleic acids research Volume 33 (2005) p.D297-302

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G.
Nucleic acids research Volume 33 (2005) p.D141-6

2004

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.
Nature biotechnology Volume 22 (2004) p.177-183

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
PLoS biology Volume 2 (2004) p.e162

The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R.
Proteomics Volume 4 (2004) p.1985-1988

2003

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Nucleic acids research Volume 31 (2003) p.414-417

Integr8: enhanced inter-operability of European molecular biology databases.
Kersey PJ, Morris L, Hermjakob H, Apweiler R.
Methods of information in medicine Volume 42 (2003) p.154-160

Automated annotation of microbial proteomes in SWISS-PROT.
Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A.
Computational biology and chemistry Volume 27 (2003) p.49-58

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.
Genome research Volume 13 (2003) p.662-672

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Orchard S, Kersey P, Hermjakob H, Apweiler R.
Comparative and functional genomics Volume 4 (2003) p.16-19

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R.
Comparative and functional genomics Volume 4 (2003) p.203-206

MCB-mediated regulation of cell cycle-specific cdc22+ transcription in fission yeast.
Maqbool Z, Kersey PJ, Fantes PA, McInerny CJ.
Molecular genetics and genomics : MGG Volume 269 (2003) p.765-775

2002

Interactive InterPro-based comparisons of proteins in whole genomes.
Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.
Bioinformatics (Oxford, England) Volume 18 (2002) p.374-375

Applications of InterPro in protein annotation and genome analysis.
Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Briefings in bioinformatics Volume 3 (2002) p.285-295

2001

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E.
Nucleic acids research Volume 29 (2001) p.44-48

2000

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Kersey P, Hermjakob H, Apweiler R.
Bioinformatics (Oxford, England) Volume 16 (2000) p.1048-1049

1996

Cell cycle, DNA damage and heat shock regulate suc22+ expression in fission yeast.
Harris P, Kersey PJ, McInerny CJ, Fantes PA.
Molecular & general genetics : MGG Volume 252 (1996) p.284-291

1995

Positive and negative roles for cdc10 in cell cycle gene expression.
McInerny CJ, Kersey PJ, Creanor J, Fantes PA.
Nucleic acids research Volume 23 (1995) p.4761-4768

0

Biological Databases: Infrastructure, Content and Integration
Williams AL, Kersey PJ, Pruess M, Apweiler R.
Volume (0) p.11–28

Integr8: Navigating Genome Reviews and the Proteome Analysis Database
Kersey P, Kulikova T, Pruess M.
Volume (0) p.201-217

Sequence clustering as a method of protein functional annotation
Petryszak R, Kersey P.
Volume (0) p.11-23

Computational Methods and Bioinformatic Tools
Cullen P, Lorkowski S, Hennig S, Poustka A, Panopoulou G, Lehrach H, Korsching E, Pickeral O, Herwig R, Kel A, Tchekmenev D, Wingender E, Streicher J, Müller GB, Kawashima T, Makabe KW, Dubchak I, Ji H, Okubo K, Kawamoto S, Fricke E, Karas D, Haubrock M, Land S, Rotert S, Chen X, Pontius J, Eveno E, Auffray C, Decraene C, Chelala C, Piétu G, Devignes M-D, Mariage-Samson R, Imbeaud S, Bortoli S, Amit A, Ringwald M, de Veer MJ, Williams BRG, Walker EM, Davies JA, Grunau C, Baldock R, Davidson DR, Stoeckert CJ Jr., Pizarro A, Manduchi E, Grant GR, Crabtree J, Liu J, Le PV, McWeeney SK, Welle S, Ball CA, Botstein D, Binkley G, Sherlock GJ, Cherry JM, Dolinski K, Issel-Tarver L, Schroeder M, Dwight SS, Wenig S, Matese JC, Jin H, Gollub J, Hebert J, Kaloper M, Brown PO, Hernandez-Boussard T, Kumar A, Cheung K, Marenco L, Snyder M, Tosches N, Bertone P, Miller P, Masiar P, Liu Y, Pesole G, Marc P, Biswas M, Kersey P, Apweiler R, Hoogland C.
Volume (0) p.769–904