Publications by authors named "Paul Kersey"

72Publications

Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens.

Front Microbiol 2019 7;10:2477. Epub 2019 Nov 7.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.3389/fmicb.2019.02477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854995PMC
November 2019

Plant genome sequences: past, present, future.

Curr Opin Plant Biol 2019 04 19;48:1-8. Epub 2018 Dec 19.

Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13695266183009
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http://dx.doi.org/10.1016/j.pbi.2018.11.001DOI Listing
April 2019

Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.

Methods Mol Biol 2018 ;1757:471-491

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-4939-7737-6_15DOI Listing
January 2019

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data.

Methods Mol Biol 2017 ;1533:1-31

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1007/978-1-4939-6658-5_1DOI Listing
January 2018

WormBase ParaSite - a comprehensive resource for helminth genomics.

Mol Biochem Parasitol 2017 07 27;215:2-10. Epub 2016 Nov 27.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1016/j.molbiopara.2016.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5486357PMC
July 2017

First Draft Genome Sequence of a UK Strain (UK99) of Fusarium culmorum.

Genome Announc 2016 Sep 15;4(5). Epub 2016 Sep 15.

Rothamsted Research, Harpenden, Hertfordshire, United Kingdom

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http://dx.doi.org/10.1128/genomeA.00771-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026426PMC
September 2016

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

Methods Mol Biol 2016 ;1374:115-40

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1007/978-1-4939-3167-5_6DOI Listing
May 2016

PhytoPath: an integrative resource for plant pathogen genomics.

Nucleic Acids Res 2016 Jan 17;44(D1):D688-93. Epub 2015 Oct 17.

The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK

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http://dx.doi.org/10.1093/nar/gkv1052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702788PMC
January 2016

Towards recommendations for metadata and data handling in plant phenotyping.

J Exp Bot 2015 Sep 4;66(18):5417-27. Epub 2015 Jun 4.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466 Stadt Seeland, Germany.

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http://dx.doi.org/10.1093/jxb/erv271DOI Listing
September 2015

Triticeae resources in Ensembl Plants.

Plant Cell Physiol 2015 Jan 27;56(1):e3. Epub 2014 Nov 27.

Ensembl Genomes, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

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http://dx.doi.org/10.1093/pcp/pcu183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301745PMC
January 2015

PomBase 2015: updates to the fission yeast database.

Nucleic Acids Res 2015 Jan 31;43(Database issue):D656-61. Epub 2014 Oct 31.

Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, Cambridgeshire CB2 1GA, UK

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http://dx.doi.org/10.1093/nar/gku1040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383888PMC
January 2015

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.

PLoS One 2014 12;9(5):e96855. Epub 2014 May 12.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096855PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018402PMC
January 2015

Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.

Virus Res 2014 Mar 17;182:43-9. Epub 2013 Dec 17.

Vector-borne Viral Disease Programme, The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK.

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http://dx.doi.org/10.1016/j.virusres.2013.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979112PMC
March 2014

Gramene 2013: comparative plant genomics resources.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D1193-9. Epub 2013 Nov 11.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkt1110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964986PMC
January 2014

WormBase 2014: new views of curated biology.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D789-93. Epub 2013 Nov 4.

Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, Genome Sequencing Center, Washington University, School of Medicine, St Louis, MO 63108, USA, Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Genetics Campus, Washington University School of Medicine, St. Louis, MO 63110, USA, Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/nar/gkt1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965043PMC
January 2014

Ensembl Genomes 2013: scaling up access to genome-wide data.

Nucleic Acids Res 2014 Jan 25;42(Database issue):D546-52. Epub 2013 Oct 25.

The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK, Wellcome Trust Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK, Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA and USDA-ARS, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1093/nar/gkt979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965094PMC
January 2014

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

WormBase: Annotating many nematode genomes.

Worm 2012 Jan;1(1):15-21

European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge UK.

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http://dx.doi.org/10.4161/worm.19574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670165PMC
January 2012

PomBase: a comprehensive online resource for fission yeast.

Nucleic Acids Res 2012 Jan 28;40(Database issue):D695-9. Epub 2011 Oct 28.

Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1093/nar/gkr853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245111PMC
January 2012

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

Database (Oxford) 2011 23;2011:bar030. Epub 2011 Jul 23.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1093/database/bar030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170168PMC
November 2011

Building a biological space based on protein sequence similarities and biological ontologies.

Comb Chem High Throughput Screen 2008 Sep;11(8):653-60

EMBL Outstation The European Bioinfomatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.2174/138620708785739925DOI Listing
September 2008

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.

Comp Funct Genomics 2003 ;4(1):16-9

EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/cfg.232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447389PMC
June 2010

The EMBL Nucleotide Sequence and Genome Reviews Databases.

Methods Mol Biol 2007 ;406:1-21

EMBL-Outstation The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://link.springer.com/content/pdf/10.1007/978-1-59745-535
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http://dx.doi.org/10.1007/978-1-59745-535-0_1DOI Listing
January 2009

In silico characterization of proteins: UniProt, InterPro and Integr8.

Mol Biotechnol 2008 Feb 4;38(2):165-77. Epub 2007 Oct 4.

EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1007/s12033-007-9003-xDOI Listing
February 2008

Linking publication, gene and protein data.

Nat Cell Biol 2006 Nov;8(11):1183-9

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1038/ncb1495DOI Listing
November 2006

Databases and resources for in silico proteome analysis.

Methods Biochem Anal 2006 ;49:397-414

European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.

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September 2006

Genome Reviews: standardizing content and representation of information about complete genomes.

OMICS 2006 ;10(2):114-8

EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://www.liebertpub.com/doi/10.1089/omi.2006.10.114
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http://dx.doi.org/10.1089/omi.2006.10.114DOI Listing
November 2007

The Integr8 project--a resource for genomic and proteomic data.

In Silico Biol 2005 ;5(2):179-85

EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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October 2005

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.

Nucleic Acids Res 2005 Jan;33(Database issue):D141-6

Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, via Celoria 26, 20133 Milano, Italy.

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http://dx.doi.org/10.1093/nar/gki021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539975PMC
January 2005

The International Protein Index: an integrated database for proteomics experiments.

Proteomics 2004 Jul;4(7):1985-8

EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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http://dx.doi.org/10.1002/pmic.200300721DOI Listing
July 2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Authors:
Tadashi Imanishi Takeshi Itoh Yutaka Suzuki Claire O'Donovan Satoshi Fukuchi Kanako O Koyanagi Roberto A Barrero Takuro Tamura Yumi Yamaguchi-Kabata Motohiko Tanino Kei Yura Satoru Miyazaki Kazuho Ikeo Keiichi Homma Arek Kasprzyk Tetsuo Nishikawa Mika Hirakawa Jean Thierry-Mieg Danielle Thierry-Mieg Jennifer Ashurst Libin Jia Mitsuteru Nakao Michael A Thomas Nicola Mulder Youla Karavidopoulou Lihua Jin Sangsoo Kim Tomohiro Yasuda Boris Lenhard Eric Eveno Yoshiyuki Suzuki Chisato Yamasaki Jun-ichi Takeda Craig Gough Phillip Hilton Yasuyuki Fujii Hiroaki Sakai Susumu Tanaka Clara Amid Matthew Bellgard Maria de Fatima Bonaldo Hidemasa Bono Susan K Bromberg Anthony J Brookes Elspeth Bruford Piero Carninci Claude Chelala Christine Couillault Sandro J de Souza Marie-Anne Debily Marie-Dominique Devignes Inna Dubchak Toshinori Endo Anne Estreicher Eduardo Eyras Kaoru Fukami-Kobayashi Gopal R Gopinath Esther Graudens Yoonsoo Hahn Michael Han Ze-Guang Han Kousuke Hanada Hideki Hanaoka Erimi Harada Katsuyuki Hashimoto Ursula Hinz Momoki Hirai Teruyoshi Hishiki Ian Hopkinson Sandrine Imbeaud Hidetoshi Inoko Alexander Kanapin Yayoi Kaneko Takeya Kasukawa Janet Kelso Paul Kersey Reiko Kikuno Kouichi Kimura Bernhard Korn Vladimir Kuryshev Izabela Makalowska Takashi Makino Shuhei Mano Regine Mariage-Samson Jun Mashima Hideo Matsuda Hans-Werner Mewes Shinsei Minoshima Keiichi Nagai Hideki Nagasaki Naoki Nagata Rajni Nigam Osamu Ogasawara Osamu Ohara Masafumi Ohtsubo Norihiro Okada Toshihisa Okido Satoshi Oota Motonori Ota Toshio Ota Tetsuji Otsuki Dominique Piatier-Tonneau Annemarie Poustka Shuang-Xi Ren Naruya Saitou Katsunaga Sakai Shigetaka Sakamoto Ryuichi Sakate Ingo Schupp Florence Servant Stephen Sherry Rie Shiba Nobuyoshi Shimizu Mary Shimoyama Andrew J Simpson Bento Soares Charles Steward Makiko Suwa Mami Suzuki Aiko Takahashi Gen Tamiya Hiroshi Tanaka Todd Taylor Joseph D Terwilliger Per Unneberg Vamsi Veeramachaneni Shinya Watanabe Laurens Wilming Norikazu Yasuda Hyang-Sook Yoo Marvin Stodolsky Wojciech Makalowski Mitiko Go Kenta Nakai Toshihisa Takagi Minoru Kanehisa Yoshiyuki Sakaki John Quackenbush Yasushi Okazaki Yoshihide Hayashizaki Winston Hide Ranajit Chakraborty Ken Nishikawa Hideaki Sugawara Yoshio Tateno Zhu Chen Michio Oishi Peter Tonellato Rolf Apweiler Kousaku Okubo Lukas Wagner Stefan Wiemann Robert L Strausberg Takao Isogai Charles Auffray Nobuo Nomura Takashi Gojobori Sumio Sugano

PLoS Biol 2004 Jun 20;2(6):e162. Epub 2004 Apr 20.

Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pbio.0020162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393292PMC
June 2004

Automated annotation of microbial proteomes in SWISS-PROT.

Comput Biol Chem 2003 Feb;27(1):49-58

SWISS-PROT Group, Swiss Institute of Bioinformatics, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1016/s1476-9271(02)00094-4DOI Listing
February 2003

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Genome Res 2003 Apr 12;13(4):662-72. Epub 2003 Mar 12.

EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1101/gr.461403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430163PMC
April 2003

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.

Nucleic Acids Res 2003 Jan;31(1):414-7

EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165552PMC
http://dx.doi.org/10.1093/nar/gkg105DOI Listing
January 2003