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Ewan Birney
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Research Profile (preview)
Occupations
Activities & Behaviors
Concepts & Ideas
Genes & Molecular Sequences
Procedures
Chemicals & Drugs
Phenomena
Living Beings
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Network (preview)
11
Durbin, Richard
9
Flicek, Paul
7
Clamp, Michele
7
Hubbard, Tim
5
Ettwiller, Laurence
5
Bateman, Alex
4
Apweiler, Rolf
4
Eddy, Sean
4
D'Eustachio, Peter
4
Sonnhammer, Erik
4
Vastrik, Imre
4
Schmidt, Esther
3
Hermjakob, Henning
3
Mulder, Nicola
3
Kahlem, Pascal
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All Publications
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2009: Kahlem Pascal; Clegg Andrew; Reisinger Florian; Xenarios Ioannis; Hermjakob Henning; Orengo Christine; Birney Ewan
ENFIN--A European network for integrative systems biology.
Comptes rendus biologies 2009;332(11):1050-8.
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2009: Flicek Paul; Birney Ewan
Sense from sequence reads: methods for alignment and assembly.
Nature methods 2009;6(11 Suppl):S6-S12.
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2009: Megy K; Hammond M; Lawson D; Bruggner R V; Birney E; Collins F H
Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2009;9(3):308-13.
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2009: Paten Benedict; Herrero Javier; Beal Kathryn; Birney Ewan
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Bioinformatics (Oxford, England) 2009;25(3):295-301.
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2009: Vilella Albert J; Severin Jessica; Ureta-Vidal Abel; Heng Li; Durbin Richard; Birney Ewan
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Genome research 2009;19(2):327-35.
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2009: Durinck Steffen; Spellman Paul T; Birney Ewan; Huber Wolfgang
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Nature protocols 2009;4(8):1184-91.
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2008: Paten Benedict; Herrero Javier; Fitzgerald Stephen; Beal Kathryn; Flicek Paul; Holmes Ian; Birney Ewan
Genome-wide nucleotide-level mammalian ancestor reconstruction.
Genome research 2008;18(11):1829-43.
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2008: Paten Benedict; Herrero Javier; Beal Kathryn; Fitzgerald Stephen; Birney Ewan
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Genome research 2008;18(11):1814-28.
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2008: Rakyan Vardhman K; Down Thomas A; Thorne Natalie P; Flicek Paul; Kulesha Eugene; Gräf Stefan; Tomazou Eleni M; Bäckdahl Liselotte; Johnson Nathan; Herberth Marlis; Howe Kevin L; Jackson David K; Miretti Marcos M; Fiegler Heike; Marioni John C; Birney Ewan; Hubbard Tim J P; Carter Nigel P; Tavaré Simon; Beck Stephan
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Genome research 2008;18(9):1518-29.
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2008: O'Reilly Paul F; Birney Ewan; Balding David J
Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
Genome research 2008;18(8):1304-13.
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2008: Down Thomas A; Rakyan Vardhman K; Turner Daniel J; Flicek Paul; Li Heng; Kulesha Eugene; Gräf Stefan; Johnson Nathan; Herrero Javier; Tomazou Eleni M; Thorne Natalie P; Bäckdahl Liselotte; Herberth Marlis; Howe Kevin L; Jackson David K; Miretti Marcos M; Marioni John C; Birney Ewan; Hubbard Tim J P; Durbin Richard; Tavaré Simon; Beck Stephan
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Nature biotechnology 2008;26(7):779-85.
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2008: Tsesmetzis Nicolas; Couchman Matthew; Higgins Janet; Smith Alison; Doonan John H; Seifert Georg J; Schmidt Esther E; Vastrik Imre; Birney Ewan; Wu Guanming; D'Eustachio Peter; Stein Lincoln D; Morris Richard J; Bevan Michael W; Walsh Sean V
Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
The Plant cell 2008;20(6):1426-36.
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2008: Twigger Simon N; Pruitt Kim D; Fernández-Suárez Xosé M; Karolchik Donna; Worley Kim C; Maglott Donna R; Brown Garth; Weinstock George; Gibbs Richard A; Kent Jim; Birney Ewan; Jacob Howard J
What everybody should know about the rat genome and its online resources.
Nature genetics 2008;40(5):523-7.
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2008: Zerbino Daniel R; Birney Ewan
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome research 2008;18(5):821-9.
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2008: Birney Ewan
Levers and fulcrums: progress in cis-regulatory motif models.
Nature methods 2008;5(4):297-8.
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2008: Margulies Elliott H; Birney Ewan
Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Nature reviews. Genetics 2008;9(4):303-13.
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2008: Bruford Elspeth A; Lush Michael J; Wright Mathew W; Sneddon Tam P; Povey Sue; Birney Ewan
The HGNC Database in 2008: a resource for the human genome.
Nucleic acids research 2008;36(Database issue):D445-8.
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2008: Fernández-Suárez Xosé M; Birney Ewan
Advanced genomic data mining.
PLoS computational biology 2008;4(9):e1000121.
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2007: Kahlem Pascal; Birney Ewan
ENFIN a network to enhance integrative systems biology.
Annals of the New York Academy of Sciences 2007;1115():23-31.
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2007: Birney Ewan
Evolutionary genomics: come fly with us.
Nature 2007;450(7167):184-5.
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2007: Birney Ewan
Double Dutch for duplications.
Nature genetics 2007;39(11):1303-4.
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2007: Spudich Giulietta; Fernández-Suárez Xosé M; Birney Ewan
Genome browsing with Ensembl: a practical overview.
Briefings in functional genomics & proteomics 2007;6(3):202-19.
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2007: Del Bene Filippo; Ettwiller Laurence; Skowronska-Krawczyk Dorota; Baier Herwig; Matter Jean-Marc; Birney Ewan; Wittbrodt Joachim
In vivo validation of a computationally predicted conserved Ath5 target gene set.
PLoS genetics 2007;3(9):1661-71.
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2007: Gräf Stefan; Nielsen Fiona G G; Kurtz Stefan; Huynen Martijn A; Birney Ewan; Stunnenberg Henk; Flicek Paul
Optimized design and assessment of whole genome tiling arrays.
Bioinformatics (Oxford, England) 2007;23(13):i195-204.
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2007: Scherer Stephen W; Lee Charles; Birney Ewan; Altshuler David M; Eichler Evan E; Carter Nigel P; Hurles Matthew E; Feuk Lars
Challenges and standards in integrating surveys of structural variation.
Nature genetics 2007;39(7 Suppl):S7-15.
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2007: Ettwiller Laurence; Paten Benedict; Ramialison Mirana; Birney Ewan; Wittbrodt Joachim
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.
Nature methods 2007;4(7):563-5.
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2007: Koch Christoph M; Andrews Robert M; Flicek Paul; Dillon Shane C; Karaöz Ulas; Clelland Gayle K; Wilcox Sarah; Beare David M; Fowler Joanna C; Couttet Phillippe; James Keith D; Lefebvre Gregory C; Bruce Alexander W; Dovey Oliver M; Ellis Peter D; Dhami Pawandeep; Langford Cordelia F; Weng Zhiping; Birney Ewan; Carter Nigel P; Vetrie David; Dunham Ian
The landscape of histone modifications across 1% of the human genome in five human cell lines.
Genome research 2007;17(6):691-707.
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2007: Mirabeau Olivier; Perlas Emerald; Severini Cinzia; Audero Enrica; Gascuel Olivier; Possenti Roberta; Birney Ewan; Rosenthal Nadia; Gross Cornelius
Identification of novel peptide hormones in the human proteome by hidden Markov model screening.
Genome research 2007;17(3):320-7.
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2007: Hoffman Michael M; Birney Ewan
Estimating the neutral rate of nucleotide substitution using introns.
Molecular biology and evolution 2007;24(2):522-31.
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2007: Lawson Daniel; Arensburger Peter; Atkinson Peter; Besansky Nora J; Bruggner Robert V; Butler Ryan; Campbell Kathryn S; Christophides George K; Christley Scott; Dialynas Emmanuel; Emmert David; Hammond Martin; Hill Catherine A; Kennedy Ryan C; Lobo Neil F; MacCallum M Robert; Madey Greg; Megy Karine; Redmond Seth; Russo Susan; Severson David W; Stinson Eric O; Topalis Pantelis; Zdobnov Evgeny M; Birney Ewan; Gelbart William M; Kafatos Fotis C; Louis Christos; Collins Frank H
VectorBase: a home for invertebrate vectors of human pathogens.
Nucleic acids research 2007;35(Database issue):D503-5.
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2007: Vastrik Imre; D'Eustachio Peter; Schmidt Esther; Gopinath Gopal; Croft David; de Bono Bernard; Gillespie Marc; Jassal Bijay; Lewis Suzanna; Matthews Lisa; Wu Guanming; Birney Ewan; Stein Lincoln
Reactome: a knowledge base of biologic pathways and processes.
Genome biology 2007;8(3):R39.
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2007: Sharakhova Maria V; Hammond Martin P; Lobo Neil F; Krzywinski Jaroslaw; Unger Maria F; Hillenmeyer Maureen E; Bruggner Robert V; Birney Ewan; Collins Frank H
Update of the Anopheles gambiae PEST genome assembly.
Genome biology 2007;8(1):R5.
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2006: Cunningham Fiona; Rios Daniel; Griffiths Mark; Smith James; Ning Zemin; Cox Tony; Flicek Paul; Marin-Garcin Pablo; Herrero Javier; Rogers Jane; van der Weyden Louise; Bradley Allan; Birney Ewan; Adams David J
TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Nature genetics 2006;38(8):853.
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2006: Meynert Alison; Birney Ewan
Picking pyknons out of the human genome.
Cell 2006;125(5):836-8.
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2006: Guigó Roderic; Flicek Paul; Abril Josep F; Reymond Alexandre; Lagarde Julien; Denoeud France; Antonarakis Stylianos; Ashburner Michael; Bajic Vladimir B; Birney Ewan; Castelo Robert; Eyras Eduardo; Ucla Catherine; Gingeras Thomas R; Harrow Jennifer; Hubbard Tim; Lewis Suzanna E; Reese Martin G
EGASP: the human ENCODE Genome Annotation Assessment Project.
Genome biology 2006;7 Suppl 1():S2.1-31.
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2006: Kahlem Pascal; Birney Ewan
Dry work in a wet world: computation in systems biology.
Molecular systems biology 2006;2():40.
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2005: Birney Ewan; Ciliberto Andrea; Colding-Jørgensen Morten; Goldbeter Albert; Hohmann Stefan; Kuiper Martin; Lehrach Hans; Miczka Gisela; Mosekilde Erik; Westerhoff Hans; Wolkenhauer Olaf
Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004.
Systems biology 2005;152(2):55-60.
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2005: Cox Charles; Bignell Graham; Greenman Chris; Stabenau Arne; Warren William; Stephens Philip; Davies Helen; Watt Stephen; Teague Jon; Edkins Sara; Birney Ewan; Easton Douglas F; Wooster Richard; Futreal P Andrew; Stratton Michael R
A survey of homozygous deletions in human cancer genomes.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(12):4542-7.
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2005: Joshi-Tope G; Gillespie M; Vastrik I; D'Eustachio P; Schmidt E; de Bono B; Jassal B; Gopinath G R; Wu G R; Matthews L; Lewis S; Birney E; Stein L
Reactome: a knowledgebase of biological pathways.
Nucleic acids research 2005;33(Database issue):D428-32.
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2005: Hubbard Simon J; Grafham Darren V; Beattie Kevin J; Overton Ian M; McLaren Stuart R; Croning Michael D R; Boardman Paul E; Bonfield James K; Burnside Joan; Davies Robert M; Farrell Elizabeth R; Francis Matthew D; Griffiths-Jones Sam; Humphray Sean J; Hyland Christopher; Scott Carol E; Tang Haizhou; Taylor Ruth G; Tickle Cheryll; Brown William R A; Birney Ewan; Rogers Jane; Wilson Stuart A
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Genome research 2005;15(1):174-83.
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2005: Ettwiller Laurence; Paten Benedict; Souren Marcel; Loosli Felix; Wittbrodt Jochen; Birney Ewan
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates.
Genome biology 2005;6(12):R104.
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2005: Eyras Eduardo; Reymond Alexandre; Castelo Robert; Bye Jacqueline M; Camara Francisco; Flicek Paul; Huckle Elizabeth J; Parra Genis; Shteynberg David D; Wyss Carine; Rogers Jane; Antonarakis Stylianos E; Birney Ewan; Guigo Roderic; Brent Michael R
Gene finding in the chicken genome.
BMC bioinformatics 2005;6():131.
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2005: Slater Guy St C; Birney Ewan
Automated generation of heuristics for biological sequence comparison.
BMC bioinformatics 2005;6():31.
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2004: Kersey Paul J; Duarte Jorge; Williams Allyson; Karavidopoulou Youla; Birney Ewan; Apweiler Rolf
The International Protein Index: an integrated database for proteomics experiments.
Proteomics 2004;4(7):1985-8.
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2004: Hammond Martin P; Birney Ewan
Genome information resources - developments at Ensembl.
Trends in genetics : TIG 2004;20(6):268-72.
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2004: Birney Ewan; Clamp Michele; Durbin Richard
GeneWise and Genomewise.
Genome research 2004;14(5):988-95.
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2004: Montgomery Stephen B; Astakhova Tamara; Bilenky Mikhail; Birney Ewan; Fu Tony; Hassel Maik; Melsopp Craig; Rak Marcin; Robertson A Gordon; Sleumer Monica; Siddiqui Asim S; Jones Steven J M
Sockeye: a 3D environment for comparative genomics.
Genome research 2004;14(5):956-62.
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2004: Stabenau Arne; McVicker Graham; Melsopp Craig; Proctor Glenn; Clamp Michele; Birney Ewan
The Ensembl core software libraries.
Genome research 2004;14(5):929-33.
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2004: Dermitzakis Emmanouil T; Kirkness Ewen; Schwarz Scott; Birney Ewan; Reymond Alexandre; Antonarakis Stylianos E
Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.
Genome research 2004;14(5):852-9.
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2004: Birney Ewan; Clamp Michele
Biological database design and implementation.
Briefings in bioinformatics 2004;5(1):31-8.
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2004: Zimdahl Heike; Nyakatura Gerald; Brandt Petra; Schulz Herbert; Hummel Oliver; Fartmann Berthold; Brett David; Droege Marcus; Monti Jan; Lee Young-Ae; Sun Yinyan; Zhao Shaying; Winter Eitan E; Ponting Chris P; Chen Yuan; Kasprzyk Arek; Birney Ewan; Ganten Detlev; Hubner Norbert
A SNP map of the rat genome generated from cDNA sequences.
Science (New York, N.Y.) 2004;303(5659):807.
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2004: Mongin Emmanuel; Louis Christos; Holt Robert A; Birney Ewan; Collins Frank H
The Anopheles gambiae genome: an update.
Trends in parasitology 2004;20(2):49-52.
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2004: Kasprzyk Arek; Keefe Damian; Smedley Damian; London Darin; Spooner William; Melsopp Craig; Hammond Martin; Rocca-Serra Philippe; Cox Tony; Birney Ewan
EnsMart: a generic system for fast and flexible access to biological data.
Genome research 2004;14(1):160-9.
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2003: Ettwiller Laurence M; Rung Johan; Birney Ewan
Discovering novel cis-regulatory motifs using functional networks.
Genome research 2003;13(5):883-95.
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2003: Salzberg Steven; Birney Ewan; Eddy Sean; White Owen
Unrestricted free access works and must continue.
Nature 2003;422(6934):801.
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2003: Ureta-Vidal Abel; Ettwiller Laurence; Birney Ewan
Comparative genomics: genome-wide analysis in metazoan eukaryotes.
Nature reviews. Genetics 2003;4(4):251-62.
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2003: Brooksbank Catherine; Camon Evelyn; Harris Midori A; Magrane Michele; Martin Maria Jesus; Mulder Nicola; O'Donovan Claire; Parkinson Helen; Tuli Mary Ann; Apweiler Rolf; Birney Ewan; Brazma Alvis; Henrick Kim; Lopez Rodrigo; Stoesser Guenter; Stoehr Peter; Cameron Graham
The European Bioinformatics Institute's data resources.
Nucleic acids research 2003;31(1):43-50.
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2003: Joshi-Tope G; Vastrik I; Gopinath G R; Matthews L; Schmidt E; Gillespie M; D'Eustachio P; Jassal B; Lewis S; Wu G; Birney E; Stein L
The Genome Knowledgebase: a resource for biologists and bioinformaticists.
Cold Spring Harbor symposia on quantitative biology 2003;68():237-43.
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2003: Birney E;
Ensembl: a genome infrastructure.
Cold Spring Harbor symposia on quantitative biology 2003;68():213-5.
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2002: Stajich Jason E; Block David; Boulez Kris; Brenner Steven E; Chervitz Stephen A; Dagdigian Chris; Fuellen Georg; Gilbert James G R; Korf Ian; Lapp Hilmar; Lehväslaiho Heikki; Matsalla Chad; Mungall Chris J; Osborne Brian I; Pocock Matthew R; Schattner Peter; Senger Martin; Stein Lincoln D; Stupka Elia; Wilkinson Mark D; Birney Ewan
The Bioperl toolkit: Perl modules for the life sciences.
Genome research 2002;12(10):1611-8.
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2002: Rust Alistair G; Mongin Emmanuel; Birney Ewan
Genome annotation techniques: new approaches and challenges.
Drug discovery today 2002;7(11 Suppl):S70-6.
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2002: Bateman Alex; Birney Ewan; Cerruti Lorenzo; Durbin Richard; Etwiller Laurence; Eddy Sean R; Griffiths-Jones Sam; Howe Kevin L; Marshall Mhairi; Sonnhammer Erik L L
The Pfam protein families database.
Nucleic acids research 2002;30(1):276-80.
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2002: Lewis S E; Searle S M J; Harris N; Gibson M; Lyer V; Richter J; Wiel C; Bayraktaroglir L; Birney E; Crosby M A; Kaminker J S; Matthews B B; Prochnik S E; Smithy C D; Tupy J L; Rubin G M; Misra S; Mungall C J; Clamp M E
Apollo: a sequence annotation editor.
Genome biology 2002;3(12):RESEARCH0082.
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2002: Birney Ewan; Clamp Michele; Hubbard Tim
Databases and tools for browsing genomes.
Annual review of genomics and human genetics 2002;3():293-310.
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2001: Futreal P A; Kasprzyk A; Birney E; Mullikin J C; Wooster R; Stratton M R
Cancer and genomics.
Nature 2001;409(6822):850-2.
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2001: Birney E; Bateman A; Clamp M E; Hubbard T J
Mining the draft human genome.
Nature 2001;409(6822):827-8.
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2001: Apweiler R; Attwood T K; Bairoch A; Bateman A; Birney E; Biswas M; Bucher P; Cerutti L; Corpet F; Croning M D; Durbin R; Falquet L; Fleischmann W; Gouzy J; Hermjakob H; Hulo N; Jonassen I; Kahn D; Kanapin A; Karavidopoulou Y; Lopez R; Marx B; Mulder N J; Oinn T M; Pagni M; Servant F; Sigrist C J; Zdobnov E M
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic acids research 2001;29(1):37-40.
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2000: Apweiler R; Attwood T K; Bairoch A; Bateman A; Birney E; Biswas M; Bucher P; Cerutti L; Corpet F; Croning M D; Durbin R; Falquet L; Fleischmann W; Gouzy J; Hermjakob H; Hulo N; Jonassen I; Kahn D; Kanapin A; Karavidopoulou Y; Lopez R; Marx B; Mulder N J; Oinn T M; Pagni M; Servant F; Sigrist C J; Zdobnov E M;
InterPro--an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics (Oxford, England) 2000;16(12):1145-50.
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2000: Birney E; Durbin R
Using GeneWise in the Drosophila annotation experiment.
Genome research 2000;10(4):547-8.
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2000: Cuff J A; Birney E; Clamp M E; Barton G J
ProtEST: protein multiple sequence alignments from expressed sequence tags.
Bioinformatics (Oxford, England) 2000;16(2):111-6.
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2000: Hubbard T; Birney E
Open annotation offers a democratic solution to genome sequencing.
Nature 2000;403(6772):825.
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2000: Bateman A; Birney E; Durbin R; Eddy S R; Howe K L; Sonnhammer E L
The Pfam protein families database.
Nucleic acids research 2000;28(1):263-6.
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1999: Jareborg N; Birney E; Durbin R
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.
Genome research 1999;9(9):815-24.
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1999: Bateman A; Birney E; Durbin R; Eddy S R; Finn R D; Sonnhammer E L
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Nucleic acids research 1999;27(1):260-2.
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1998: Sonnhammer E L; Eddy S R; Birney E; Bateman A; Durbin R
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Nucleic acids research 1998;26(1):320-2.
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1998: Pocock M R; Hubbard T; Birney E
SPEM: a parser for EMBL style flat file database entries.
Bioinformatics (Oxford, England) 1998;14(9):823-4.
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1997: Birney E; Durbin R
Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():56-64.
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