Submitted

Apollo, an annotation editor
Searle, SMJ, Harris N., Gibson M., Iyer V., Richter J., Wiel C., Bayraktaroglu L., Birney E., Crosby L., and others
(Submitted), doi:
EGASP: The human ENCODE GENOME ANNOTATION ASSESSMENT PROJECT
Bajic, B., Birney E., Castelo R., Eyras E., and Gingeras T. R.
(Submitted),
International Chicken Genome Sequencing Consortium et al.(2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Hillier, LW, Miller W., Birney E., and Warren W.
Nature. Volume 432, (Submitted), p.695–716
Long Distance and Global Transcription Networks Characterize ENCODE Regions
Guigó, R., Denoeud F., Reymond A., Kapranov P., Rozowsky J., Zheng D., Castelo R., Frankish A., Harrow J., Ghosh S., et al.
(Submitted),
Modeling Competition of Transcription Factors for DNA Binding Sites Improves Binding Site Predictions
Hestand, M. S., Hoffman M. M., Birney E., van Ommen G. J. B., den Dunnen J. T., and AC’t Hoen P.
In Silico and Wet Lab Approaches to Study Transcriptional Regulation. (Submitted), p.45

2013

Ensembl 2013
Flicek, P., AHMED I., Amode M. R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fairley S., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D48–D55
Factorbook. org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
Wang, J., Zhuang J., Iyer S., Lin X. Y., Greven M. C., Kim B. H., Moore J., Pierce B. G., Dong X., Virgil D., et al.
Nucleic Acids Research. Volume 41, Number D1, (2013), p.D171–D176

2012

The making of ENCODE: Lessons for big-data projects
Birney, E.
Nature. Volume 489, Number 7414, (2012), p.49–51
Modeling gene expression using chromatin features in various cellular contexts
Dong, X., Greven M. C., Kundaje A., Djebali S., Brown J. B., Cheng C., Gingeras T. R., Gerstein M., Guigó R., Birney E., et al.
Genome biology. Volume 13, Number 9, (2012), p.R53
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
Lee, B. K., Bhinge A. A., Battenhouse A., McDaniell R. M., Liu Z., Song L., Ni Y., Birney E., Lieb J. D., Furey TS, et al.
Genome research. Volume 22, Number 1, (2012), p.9–24
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
Cheng, C., Alexander R., Min R., Leng J., Yip K. Y., Rozowsky J., Yan K. K., Dong X., Djebali S., Ruan Y., et al.
Genome research. Volume 22, Number 9, (2012), p.1658–1667
Major submissions tool developments at the European nucleotide archive
Amid, C., Birney E., Bower L., Cerdeño-Tárraga A., Cheng Y., Cleland I., Faruque N., Gibson R., Goodgame N., Hunter C., et al.
Nucleic acids research. Volume 40, Number D1, (2012), p.D43–D47
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
Yip, K. Y., Cheng C., Bhardwaj N., Brown J. B., Leng J., Kundaje A., Rozowsky J., Birney E., Bickel P., Snyder M., et al.
Genome biology. Volume 13, Number 9, (2012), p.R48
Ensembl 2012
Flicek, P., Amode M. R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fairley S., Fitzgerald S., et al.
Nucleic acids research. Volume 40, Number D1, (2012), p.D84–D90
Analysis of variation at transcription factor binding sites in Drosophila and humans
Spivakov, M., Akhtar J., Kheradpour P., Beal K., Girardot C., Koscielny G., Herrero J., Kellis M., Furlong E. E. M., and Birney E.
Genome biology. Volume 13, Number 9, (2012), p.R49
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Wang, J., Zhuang J., Iyer S., Lin X. Y., Whitfield T. W., Greven M. C., Pierce B. G., Dong X., Kundaje A., Cheng Y., et al.
Genome research. Volume 22, Number 9, (2012), p.1798–1812
Integrative annotation of chromatin elements from ENCODE data
Hoffman, M. M., Ernst J., Wilder S. P., Kundaje A., Harris R. S., Libbrecht M., Giardine B., Bilmes J. A., Birney E., Hardison R. C., et al.
Genome Res. (2012),
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species
Kersey, P. J., Staines D. M., Lawson D., Kulesha E., Derwent P., Humphrey J. C., Hughes D. S. T., Keenan S., Kerhornou A., Koscielny G., et al.
Nucleic acids research. Volume 40, Number D1, (2012), p.D91–D97
Paralogous annotation of disease-causing variants in long QT syndrome genes
Ware, J. S., Walsh R., Cunningham F., Birney E., and Cook S. A.
Human Mutation. (2012),
The genomic basis of adaptive evolution in threespine sticklebacks
Jones, F. C., Grabherr M. G., Chan Y. F., Russell P., Mauceli E., Johnson J., Swofford R., Pirun M., Zody M. C., White S., et al.
Nature. Volume 484, Number 7392, (2012), p.55–61
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium, The, Dunham I., Birney E., Lajoie B. R., Sanyal A., Dong X., Greven M., Lin X., Wang J., Whitfield T. W., et al.
(2012),
The future of DNA sequence archiving
Cochrane, G., Cook C. E., and Birney E.
GigaScience. Volume 1, Number 1, (2012), p.2
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
Schulz, M. H., Zerbino D. R., Vingron M., and Birney E.
Bioinformatics. Volume 28, Number 8, (2012), p.1086–1092
A transcription factor collective defines cardiac cell fate and reflects lineage history
Junion, G., Spivakov M., Girardot C., Braun M., Gustafson E. H., Birney E., and Furlong E. E. M.
Cell. Volume 148, Number 3, (2012), p.473–486

2011

Chromatin and heritability: how epigenetic studies can complement genetic approaches
Birney, E.
Trends in Genetics. Volume 27, Number 5, (2011), p.172–176
The European nucleotide archive
Leinonen, R., Akhtar R., Birney E., Bower L., Cerdeno-Tárraga A., Cheng Y., Cleland I., Faruque N., Goodgame N., Gibson R., et al.
Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D28–D31
A high-resolution map of human evolutionary constraint using 29 mammals
Lindblad-Toh, K., Garber M., Zuk O., Lin M. F., Parker B. J., Washietl S., Kheradpour P., Ernst J., Jordan G., Mauceli E., et al.
Nature. Volume 478, Number 7370, (2011), p.476–482
Mouse genomic variation and its effect on phenotypes and gene regulation
Keane, T. M., Goodstadt L., Danecek P., White M. A., Wong K., Yalcin B., Heger A., Agam A., Slater G., Goodson M., et al.
Nature. Volume 477, Number 7364, (2011), p.289–294
Efficient storage of high throughput DNA sequencing data using reference-based compression
Fritz, M. H. Y., Leinonen R., Cochrane G., and Birney E.
Genome research. Volume 21, Number 5, (2011), p.734–740
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
Song, L., Zhang Z., Grasfeder L. L., Boyle A. P., Giresi P. G., Lee B. K., Sheffield N. C., Gräf S., Huss M., Keefe D., et al.
Genome research. Volume 21, Number 10, (2011), p.1757–1767
Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology
Kahlem, P., DiCara A., Durot M., Hancock J. M., Klipp E., Schächter V., Segal E., Xenarios I., Birney E., and Mendoza L.
(2011),
A user's guide to the encyclopedia of DNA elements (ENCODE)
Consortium, ENCODE Project, and others
PLoS Biol. Volume 9, Number 4, (2011), p.e1001046
Reactome: a database of reactions, pathways and biological processes
Croft, D., O’Kelly G., Wu G., Haw R., Gillespie M., Matthews L., Caudy M., Garapati P., Gopinath G., Jassal B., et al.
Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D691
Ensembl 2011
Flicek, P., Amode M. R., Barrell D., Beal K., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., et al.
Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D800
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
Boyle, A. P., Song L., Lee B. K., London D., Keefe D., Birney E., Iyer V. R., Crawford G. E., and Furey TS
Genome research. Volume 21, Number 3, (2011), p.456–464

2010

Allele-specific and heritable chromatin signatures in humans
Birney, E., Lieb J. D., Furey TS, Crawford G. E., and Iyer V. R.
Human molecular genetics. Volume 19, Number R2, (2010), p.R204–R209
The consequence of natural selection on genetic variation in the mouse
Reuveni, E., Birney E., and Gross C. T.
Genomics. Volume 95, Number 4, (2010), p.196–202
A new strategy for genome assembly using short sequence reads and reduced representation libraries
Young, A. L., Abaan H. O., Zerbino D., Mullikin J. C., Birney E., and Margulies E. H.
Genome research. Volume 20, Number 2, (2010), p.249–256
A database and API for variation, dense genotyping and resequencing data
Rios, D., McLaren W. M., Chen Y., Birney E., Stabenau A., Flicek P., and Cunningham F.
BMC bioinformatics. Volume 11, Number 1, (2010), p.238
Genomic information infrastructure after the deluge
Parkhill, J., Birney E., Kersey P., and others
Genome Biol. Volume 11, (2010), p.402 doi:
EMMA—mouse mutant resources for the international scientific community
Wilkinson, P., Sengerova J., Matteoni R., Chen C. K., Soulat G., Ureta-Vidal A., Fessele S., Hagn M., Massimi M., Pickford K., et al.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D570–D576
Improvements to services at the European Nucleotide Archive
Leinonen, R., Akhtar R., Birney E., Bonfield J., Bower L., Corbett M., Cheng Y., Demiralp F., Faruque N., Goodgame N., et al.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D39–D45
Heritable individual-specific and allele-specific chromatin signatures in humans
McDaniell, R., Lee B. K., Song L., Liu Z., Boyle A. P., Erdos M. R., Scott L. J., Morken M. A., Kucera K. S., Battenhouse A., et al.
Science. Volume 328, Number 5975, (2010), p.235
Ensembl’s 10th year
Flicek, P., Aken BL, Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Coates G., Fairley S., et al.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D557–D562
A draft sequence of the Neandertal genome
Green, R. E., Krause J., Briggs A. W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M. H. Y., et al.
science. Volume 328, Number 5979, (2010), p.710
The BioPAX community standard for pathway data sharing
Demir, E., Cary M. P., Paley S., Fukuda K., Lemer C., Vastrik I., Wu G., D'Eustachio P., Schaefer C., Luciano J., et al.
Nature biotechnology. Volume 28, Number 9, (2010), p.935–942
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
Atanur, S. S., Birol İ., Guryev V., Hirst M., Hummel O., Morrissey C., Behmoaras J., Fernandez-Suarez X. M., Johnson M. D., McLaren W. M., et al.
Genome research. Volume 20, Number 6, (2010), p.791–803
Ensembl Genomes: extending Ensembl across the taxonomic space
Kersey, P. J., Lawson D., Birney E., Derwent PS, Haimel M., Herrero J., Keenan S., Kerhornou A., Koscielny G., Kähäri A., et al.
Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D563–D569 doi:
Ensembl variation resources
Chen, Y., Cunningham F., Rios D., McLaren W. M., Smith J., Pritchard B., Spudich G. M., Brent S., Kulesha E., Marin-Garcia P., et al.
BMC genomics. Volume 11, Number 1, (2010), p.293
An international bioinformatics infrastructure to underpin the Arabidopsis community
Bastow, R., Beynon J., Estelle M., Friesner J., Grotewold E., Lavagi I., Lindsey K., Meyers B., Provart N., Benfey P., et al.
(2010),
A small cell lung cancer genome reports complex tobacco exposure signatures
Pleasance, E. D., Stephens P. J., O'Meara S., McBride D. J., Meynert A., Jones D., Lin M. L., Beare D., Lau K. W., Greenman C., et al.
Nature. Volume 463, Number 7278, (2010), p.184
Assemblies: the good, the bad, the ugly
Birney, E.
Nature Methods. Volume 8, Number 1, (2010), p.59–60
An effective model for natural selection in promoters
Hoffman, M. M., and Birney E.
Genome research. Volume 20, Number 5, (2010), p.685–692
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
Smedley, D., Schofield P., Chen C. K., Aidinis V., Ainali C., Bard J., Balling R., Birney E., Blake A., Bongcam-Rudloff E., et al.
Database: the journal of biological databases and curation. Volume 2010, (2010),
Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria
Gnad, F., Forner F., Zielinska D. F., Birney E., Gunawardena J., and Mann M.
Molecular & Cellular Proteomics. Volume 9, Number 12, (2010), p.2642–2653
The systematic annotation of the three main GPCR families in Reactome
Jassal, B., Jupe S., Caudy M., Birney E., Stein L., Hermjakob H., and D’Eustachio P.
Database: the journal of biological databases and curation. Volume 2010, (2010),

2009

ENFIN–A European network for integrative systems biology.
Kahlem, P., Clegg A., Reisinger F., Xenarios I., Hermjakob H., Orengo C., Birney E., and others
Comptes rendus biologies. Volume 332, Number 11, (2009), p.1050
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
Durinck, S., Spellman P. T., Birney E., and Huber W.
Nature protocols. Volume 4, Number 8, (2009), p.1184–1191
MAPU 2.0: high-accuracy proteomes mapped to genomes
Gnad, F., Oroshi M., Birney E., and Mann M.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D902–D906
Benefits and Best Practices of Rapid Pre-Publication Data Release
Birney, E., Hudson T. J., Green E. D., Gunter C., Eddy S., Rogers J., Harris J. R., Ehrlich S. D., Apweiler R., Austin C. P., et al.
Nature. Volume 461, Number 7261, (2009), p.168
VectorBase: a data resource for invertebrate vector genomics
Lawson, D., Arensburger P., Atkinson P., Besansky N. J., Bruggner R. V., Butler R., Campbell K. S., Christophides G. K., Christley S., Dialynas E., et al.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D583–D587
Reactome knowledgebase of human biological pathways and processes
Matthews, L., Gopinath G., Gillespie M., Caudy M., Croft D., de Bono B., Garapati P., Hemish J., Hermjakob H., Jassal B., et al.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D619–D622
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
Vilella, A. J., Severin J., Ureta-Vidal A., Heng L., Durbin R., and Birney E.
Genome research. Volume 19, Number 2, (2009), p.327–335
Ensembl 2009
Hubbard, T. J. P., Aken BL, Ayling S., Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Clarke L., et al.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D690–D697
Petabyte-scale innovations at the European Nucleotide Archive
Cochrane, G., Akhtar R., Bonfield J., Bower L., Demiralp F., Faruque N., Gibson R., Hoad G., Hubbard T., Hunter C., et al.
Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D19–D25
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
Paten, B., Herrero J., Beal K., and Birney E.
Bioinformatics. Volume 25, Number 3, (2009), p.295
Sense from sequence reads: methods for alignment and assembly
Flicek, P., and Birney E.
Nature Methods. Volume 6, (2009), p.S6–S12
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
Pruitt, K. D., Harrow J., Harte R. A., Wallin C., Diekhans M., Maglott D. R., Searle S., Farrell C. M., Loveland J. E., Ruef B. J., et al.
Genome research. Volume 19, Number 7, (2009), p.1316–1323
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
Zerbino, D. R., McEwen G. K., Margulies E. H., and Birney E.
PloS one. Volume 4, Number 12, (2009), p.e8407
A small-cell lung cancer genome with complex signatures of tobacco exposure
Pleasance, E. D., Stephens P. J., O’Meara S., McBride D. J., Meynert A., Jones D., Lin M. L., Beare D., Lau K. W., Greenman C., et al.
Nature. Volume 463, Number 7278, (2009), p.184–190
Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase
Megy, K., Hammond M., Lawson D., Bruggner R. V., Birney E., and Collins F. H.
Infection, Genetics and Evolution. Volume 9, Number 3, (2009), p.308–313

2008

What everybody should know about the rat genome and its online resources
Twigger, S. N., Pruitt K. D., Fernandez-Suarez X. M., Karolchik D., Worley K. C., Maglott D. R., Brown G., Weinstock G., Gibbs R. A., Kent J., et al.
Nature genetics. Volume 40, Number 5, (2008), p.523–527
Integrating biological data–the distributed annotation system
Jenkinson, A., Albrecht M., Birney E., Blankenburg H., Down T., Finn R., Hermjakob H., Hubbard T., Jimenez R., Jones P., et al.
BMC bioinformatics. Volume 9, Number Suppl 8, (2008), p.S3
The HGNC Database in 2008: a resource for the human genome
Bruford, E. A., Lush M. J., Wright M. W., Sneddon T. P., Povey S., and Birney E.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D445–D448
SNP and haplotype mapping for genetic analysis in the rat
Saar, K., Beck A., Bihoreau M. T., Birney E., Brocklebank D., Chen Y., Cuppen E., Demonchy S., Dopazo J., Flicek P., et al.
Nature genetics. Volume 40, Number 5, (2008), p.560–566
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
Rakyan, V. K., Down T. A., Thorne N. P., Flicek P., Kulesha E., Gräf S., Tomazou E. M., Bäckdahl L., Johnson N., Herberth M., et al.
Genome research. Volume 18, Number 9, (2008), p.1518–1529
Confounding between recombination and selection, and the Ped/Pop method for detecting selection
O’Reilly, P. F., Birney E., and Balding D. J.
Genome research. Volume 18, Number 8, (2008), p.1304–1313
Arabidopsis reactome: a foundation knowledgebase for plant systems biology
Tsesmetzis, N., Couchman M., Higgins J., Smith A., Doonan J. H., Seifert G. J., Schmidt E. E., Vastrik I., Birney E., Wu G., et al.
The Plant Cell Online. Volume 20, Number 6, (2008), p.1426–1436
Genome analysis of the platypus reveals unique signatures of evolution
Warren, W. C., Hillier L. D. W., Graves J. A. M., Birney E., Ponting C. P., Grützner F., Belov K., Miller W., Clarke L., Chinwalla A. T., et al.
Nature. Volume 453, Number 7192, (2008), p.175–183
Advanced genomic data mining
Fernández-Suárez, X. M., and Birney E.
PLoS computational biology. Volume 4, Number 9, (2008), p.e1000121
Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
Margulies, E. H., and Birney E.
Nature Reviews Genetics. Volume 9, Number 4, (2008), p.303–313
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
Cochrane, G., Akhtar R., Aldebert P., Althorpe N., Baldwin A., Bates K., Bhattacharyya S., Bonfield J., Bower L., Browne P., et al.
Nucleic Acids Research. Volume 36, Number suppl 1, (2008), p.D5–D12
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Down, T. A., Rakyan V. K., Turner D. J., Flicek P., Li H., Kulesha E., Gräf S., Johnson N., Herrero J., Tomazou E. M., et al.
Nature biotechnology. Volume 26, Number 7, (2008), p.779–785
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
Zerbino, D. R., and Birney E.
Genome research. Volume 18, Number 5, (2008), p.821–829
Levers and fulcrums: progress in cis-regulatory motif models
Birney, E., and others
Nature methods. Volume 5, Number 4, (2008), p.297–298
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs
Paten, B., Herrero J., Beal K., Fitzgerald S., and Birney E.
Genome research. Volume 18, Number 11, (2008), p.1814–1828
Genome-wide nucleotide-level mammalian ancestor reconstruction
Paten, B., Herrero J., Fitzgerald S., Beal K., Flicek P., Holmes I., and Birney E.
Genome research. Volume 18, Number 11, (2008), p.1829–1843
An integrated resource for genome-wide identification and analysis
Rakyan, V. K., Down T. A., Thorne N. P., Flicek P., Kulesha E., Graf S., Tomazou E. M., Backdahl L., Johnson N., Herberth M., et al.
(2008),
ENFIN-An Integrative Structure for Systems Biology
Reisinger, F., Corpas M., Hancock J., Hermjakob H., Birney E., and Kahlem P.
Data Integration in the Life Sciences. (2008), p.132–143
Ensembl 2008
Flicek, P., Aken BL, Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., et al.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D707–D714

2007

Evolutionary and biomedical insights from the rhesus macaque genome
Gibbs, R. A., Rogers J., Katze M. G., Bumgarner R., Weinstock G. M., Mardis E. R., Remington K. A., Strausberg R. L., Venter J. C., Wilson R. K., et al.
science. Volume 316, Number 5822, (2007), p.222
Optimising oligonucleotide array design for ChIP-on-chip
Nielsen, F., Graef S., Zhang X., Kurtz S., Denissov S., Green R., Birney E., Flicek P., Huynen M., and Stunnenberg H.
BMC Bioinformatics. Volume 8, (2007), p.1–1
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
Ettwiller, L., Paten B., Ramialison M., Birney E., and Wittbrodt J.
Nature methods. Volume 4, Number 7, (2007), p.563–565
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, E. H., Cooper G. M., Asimenos G., Thomas D. J., Dewey C. N., Siepel A., Birney E., Keefe D., Schwartz A. S., Hou M., et al.
Genome research. Volume 17, Number 6, (2007), p.760–774
Reactome: An integrated expert model of human molecular processes and access toolkit
de Bono, B., Vastrik I., D'Eustachio P., Schmidt E., Gopinath G., Croft D., Gillespie M., Jassal B., Lewis S., Matthews L., et al.
J. Integr. Bioinformatics. Volume 4, (2007), p.84
Update of the Anopheles gambiae PEST genome assembly
Sharakhova, M. V., Hammond M. P., Lobo N. F., Krzywinski J., Unger M. F., Hillenmeyer M. E., Bruggner R. V., Birney E., and Collins F. H.
Genome biology. Volume 8, Number 1, (2007), p.R5
Genome browsing with Ensembl: a practical overview
Spudich, G., Fernández-Suárez X. M., and Birney E.
Briefings in functional genomics & proteomics. Volume 6, Number 3, (2007), p.202–219
Reactome: a knowledge base of biologic pathways and processes
Vastrik, I., D'Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., de Bono B., Gillespie M., Jassal B., Lewis S., et al.
Genome biology. Volume 8, Number 3, (2007), p.R39
Ensembl 2007
Hubbard, T. J. P., Aken BL, Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D610–D617
Optimized design and assessment of whole genome tiling arrays
Gräf, S., Nielsen F. G. G., Kurtz S., Huynen M. A., Birney E., Stunnenberg H., and Flicek P.
Bioinformatics. Volume 23, Number 13, (2007), p.i195–i204
Genome sequence of Aedes aegypti, a major arbovirus vector
Nene, V., Wortman J. R., Lawson D., Haas B., Kodira C., Tu Z. J., Loftus B., Xi Z., Megy K., Grabherr M., et al.
Science. Volume 316, Number 5832, (2007), p.1718
In vivo validation of a computationally predicted conserved Ath5 target gene set
Del Bene, F., Ettwiller L., Skowronska-Krawczyk D., Baier H., Matter J. M., Birney E., and Wittbrodt J.
PLoS genetics. Volume 3, Number 9, (2007), p.e159
Identification of novel peptide hormones in the human proteome by hidden Markov model screening
Mirabeau, O., Perlas E., Severini C., Audero E., Gascuel O., Possenti R., Birney E., Rosenthal N., and Gross C.
Genome research. Volume 17, Number 3, (2007), p.320–327
VectorBase: a home for invertebrate vectors of human pathogens
Lawson, D., Arensburger P., Atkinson P., Besansky N. J., Bruggner R. V., Butler R., Campbell K. S., Christophides G. K., Christley S., Dialynas E., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D503–D505
Challenges and standards in integrating surveys of structural variation
Scherer, S. W., Lee C., Birney E., Altshuler D. M., Eichler E. E., Carter N. P., Hurles M. E., and Feuk L.
Nature genetics. Volume 39, (2007), p.S7–S15
Reactome–a knowledgebase of human biological pathways
D'Eustachio, P., Croft D., de Bono B., Gopinath G., Gillespie M., Jassal B., Matthews L., Schmidt E., Vastrik I., Wu G., et al.
(2007),
Estimating the neutral rate of nucleotide substitution using introns
Hoffman, M. M., and Birney E.
Molecular biology and evolution. Volume 24, Number 2, (2007), p.522–531
Evolutionary genomics: come fly with us
Birney, E.
Nature. Volume 450, Number 7167, (2007), p.184–185
ENFIN—a Network to Enhance Integrative Systems Biology
Kahlem, P., and Birney E.
Annals of the New York Academy of Sciences. Volume 1115, Number 1, (2007), p.23–31
The implications of alternative splicing in the ENCODE protein complement
Tress, M. L., Martelli P. L., Frankish A., Reeves G. A., Wesselink J. J., Yeats C., Albrecht M., Hegyi H., Giorgetti A., Raimondo D., et al.
Proceedings of the National Academy of Sciences. Volume 104, Number 13, (2007), p.5495
Double Dutch for duplications
Birney, E.
Nature genetics. Volume 39, Number 11, (2007), p.1303–1304
The landscape of histone modifications across 1% of the human genome in five human cell lines
Koch, C. M., Andrews R. M., Flicek P., Dillon S. C., Karaöz U., Clelland G. K., Wilcox S., Beare D. M., Fowler J. C., Couttet P., et al.
Genome research. Volume 17, Number 6, (2007), p.691–707
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium, The, Birney E., Stamatoyannopoulos J. A., Dutta A., Guigó R., Gingeras T. R., Margulies E. H., Weng Z., Snyder M., Dermitzakis E. T., et al.
Nature. Volume 447, Number 7146, (2007), p.799–816

2006

In: In Silico Genomics and Proteomics ISBN 1-59454-995-8 Editors: N. Mulder and R. Apweiler, pp. 109-123{\copyright} 2006 Nova Science Publishers, Inc.
Fernandez, X. M., Searle S., and Birney E.
In silico genomics and proteomics: functional annotation of genomes and proteins. (2006), p.109
Reactome–a knowledgebase of biological pathways
Schmidt, E., Birney E., Croft D., de Bono B., D’Eustachio P., Gillespie M., Gopinath G., Jassal B., Lewis S., Matthews L., et al.
On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops. (2006), p.710–719
TranscriptSNPView: a genome-wide catalog of mouse coding variation
Cunningham, F., Rios D., Griffiths M., Smith J., Ning Z., Cox T., Flicek P., Marin-Garcin P., Herrero J., Rogers J., et al.
Nature genetics. Volume 38, Number 8, (2006), p.853
EGASP: the human ENCODE genome annotation assessment project
Guigó, R., Flicek P., Abril J. F., Reymond A., Lagarde J., Denoeud F., Antonarakis S., Ashburner M., Bajic V. B., Birney E., et al.
Genome Biol. Volume 7, Number Suppl 1, (2006), p.S2
The Distributed Annotation System for integration of biological data
Prlić, A., Birney E., Cox T., Down T., Finn R., Gräf S., Jackson D., Kähäri A., Kulesha E., Pettett R., et al.
Data Integration in the Life Sciences. (2006), p.195–203
Picking pyknons out of the human genome
Meynert, A., and Birney E.
Cell. Volume 125, Number 5, (2006), p.836–838
Ensembl 2006
Birney, E., Andrews D., Caccamo M., Chen Y., Clarke L., Coates G., Cox T., Cunningham F., Curwen V., Cutts T., et al.
Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D556–D561
Dry work in a wet world: computation in systems biology
Kahlem, P., and Birney E.
Molecular systems biology. Volume 2, Number 1, (2006),
EGASP: the human ENCODE Genome Annotation Assessment Project
Guigó Serra, R., Flicek P., Abril Ferrando J. F., Reymond A., Lagarde J., Denoeud F., Antonarakis S. E., Ashburner M., Bajic V. B., Birney E., et al.
Genome Biology, 2006, vol. 7, Suppl. 1: S2. (2006),

2005

Protein sequence analysis and domain identification
Ponting, C. P., and Birney E.
The Proteomics Protocols Handbook. (2005), p.527–541
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
Ettwiller, L., Paten B., Souren M., Loosli F., Wittbrodt J., and Birney E.
Genome biology. Volume 6, Number 12, (2005), p.R104
Automated generation of heuristics for biological sequence comparison
Slater, G., and Birney E.
Bmc Bioinformatics. Volume 6, Number 1, (2005), p.31
Reactome: a knowledgebase of biological pathways
Joshi-Tope, G., Gillespie M., Vastrik I., D'Eustachio P., Schmidt E., de Bono B., Jassal B., Gopinath GR, Wu GR, Matthews L., et al.
Nucleic acids research. Volume 33, Number suppl 1, (2005), p.D428–D432
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
Hubbard, S. J., Grafham D. V., Beattie K. J., Overton I. M., McLaren S. R., Croning M. D. R., Boardman P. E., Bonfield J. K., Burnside J., Davies R. M., et al.
Genome research. Volume 15, Number 1, (2005), p.174–183
Gene finding in the chicken genome
Eyras, E., Reymond A., Castelo R., Bye J., Camara F., Flicek P., Huckle E., Parra G., Shteynberg D., Wyss C., et al.
BMC bioinformatics. Volume 6, Number 1, (2005), p.131
Gene finding in the chicken genome
Eyras Jiménez, E., Reymond A., Castelo R., Bye J. M., Cámara F., Flicek P., Huckle E. J., Parra Farré G., Shteynberg D. D., Wyss C., et al.
(2005),
A survey of homozygous deletions in human cancer genomes
Cox, C., Bignell G., Greenman C., Stabenau A., Warren W., Stephens P., Davies H., Watt S., Teague J., Edkins S., et al.
Proceedings of the National Academy of Sciences of the United States of America. Volume 102, Number 12, (2005), p.4542
Ensembl 2005
Hubbard, T., Andrews D., Caccamo M., Cameron G., Chen Y., Clamp M., Clarke L., Coates G., Cox T., Cunningham F., et al.
Nucleic acids research. Volume 33, Number suppl 1, (2005), p.D447–D453

2004

Genome information resources-developments at Ensembl
Hammond, M. P., and Birney E.
TRENDS in Genetics. Volume 20, Number 6, (2004), p.268–272
A SNP map of the rat genome generated from cDNA sequences
Zimdahl, H., Nyakatura G., Brandt P., Schulz H., Hummel O., Fartmann B., Brett D., Droege M., Monti J., Lee Y., et al.
Science. Volume 303, Number 5659, (2004), p.807
Biological database design and implementation
Birney, E., and Clamp M.
Briefings in bioinformatics. Volume 5, Number 1, (2004), p.31–38
Sockeye: a 3D environment for comparative genomics
Montgomery, S. B., Astakhova T., Bilenky M., Birney E., Fu T., Hassel M., Melsopp C., Rak M., Robertson A. G., Sleumer M., et al.
Genome research. Volume 14, Number 5, (2004), p.956–962
GeneWise and genomewise
Birney, E., Clamp M., and Durbin R.
Genome research. Volume 14, Number 5, (2004), p.988–995
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
Dermitzakis, E. T., Kirkness E., Schwarz S., Birney E., Reymond A., and Antonarakis S. E.
Genome research. Volume 14, Number 5, (2004), p.852–859
The Ensembl core software libraries
Stabenau, A., McVicker G., Melsopp C., Proctor G., Clamp M., and Birney E.
Genome research. Volume 14, Number 5, (2004), p.929–933
The International Protein Index: an integrated database for proteomics experiments
Kersey, P. J., Duarte J., Williams A., Karavidopoulou Y., Birney E., and Apweiler R.
Proteomics. Volume 4, Number 7, (2004), p.1985–1988 doi:
An overview of Ensembl
Birney, E., Andrews T. D., Bevan P., Caccamo M., Chen Y., Clarke L., Coates G., Cuff J., Curwen V., Cutts T., et al.
Genome research. Volume 14, Number 5, (2004), p.925–928
Ensembl 2004
Birney, E., Andrews D., Bevan P., Caccamo M., Cameron G., Chen Y., Clarke L., Coates G., Cox T., Cuff J., et al.
Nucleic acids research. Volume 32, Number suppl 1, (2004), p.D468–D470
EnsMart: a generic system for fast and flexible access to biological data
Kasprzyk, A., Keefe D., Smedley D., London D., Spooner W., Melsopp C., Hammond M., Rocca-Serra P., Cox T., and Birney E.
Genome Research. Volume 14, Number 1, (2004), p.160–169
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Hillier, L. D. W., Miller W., Birney E., Warren W., Hardison R. C., Ponting C. P., Bork P., Burt D. W., Groenen M. A. M., Delany M. E., et al.
Nature. Volume 432, Number 7018, (2004), p.695–716
The Anopheles gambiae genome: an update
Mongin, E., Louis C., Holt R. A., Birney E., and Collins F. H.
Trends in parasitology. Volume 20, Number 2, (2004), p.49–52

2003

Discovering novel cis-regulatory motifs using functional networks
Ettwiller, L. M., Rung J., and Birney E.
Genome research. Volume 13, Number 5, (2003), p.883–895
Ensembl: a genome infrastructure
Birney, E., and others
Cold Spring Harbor symposia on quantitative biology. Volume 68, (2003), p.213–216
Unrestricted free access works and must continue
Salzberg, S., Birney E., Eddy S., and White O.
Nature. Volume 422, Number 6934, (2003), p.801–801
The European Bioinformatics Institute's data resources
Brooksbank, C., Camon E., Harris M. A., Magrane M., Martin M. J., Mulder N., O'Donovan C., Parkinson H., Tuli M. A., Apweiler R., et al.
Nucleic acids research. Volume 31, Number 1, (2003), p.43–50 doi:
Comparative genomics: genome-wide analysis in metazoan eukaryotes
Ureta-Vidal, A., Ettwiller L., Birney E., and others
Nature Reviews Genetics. Volume 4, Number 4, (2003), p.251–262
The Genome Knowledgebase: a resource for biologists and bioinformaticists
Joshi-Tope, G., Vastrik I., Gopinath GR, Matthews L., Schmidt E., Gillespie M., D'Eustachio P., Jassal B., Lewis S., Wu G., et al.
Cold Spring Harbor symposia on quantitative biology. Volume 68, (2003), p.237–244
Ensembl 2002: accommodating comparative genomics
Clamp, M., Andrews D., Barker D., Bevan P., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., et al.
Nucleic Acids Research. Volume 31, Number 1, (2003), p.38–42

2002

Initial sequencing and comparative analysis of the mouse genome
Chinwalla, A. T., Cook L. L., Delehaunty K. D., Fewell G. A., Fulton L. A., Fulton R. S., Graves T. A., Hillier L. D. W., Mardis E. R., McPherson J. D., et al.
Nature. Volume 420, Number 6915, (2002), p.520–562
Apollo: a sequence annotation editor
Lewis, SE, Searle SM, Harris N., Gibson M., Lyer V., Richter J., Wiel C., Bayraktaroglir L., Birney E., Crosby MA, et al.
Genome Biol. Volume 3, Number 12, (2002), p.1–14
Immunity-related genes and gene families in Anopheles gambiae
Christophides, G. K., Zdobnov E., Barillas-Mury C., Birney E., Blandin S., Blass C., Brey P. T., Collins F. H., Danielli A., Dimopoulos G., et al.
Science. Volume 298, Number 5591, (2002), p.159
Genome annotation techniques: new approaches and challenges
Rust, A. G., Mongin E., and Birney E.
Drug discovery today. Volume 7, Number 11, (2002), p.S70–S76
A physical map of the mouse genome
Gregory, S. G., Sekhon M., Schein J., Zhao S., Osoegawa K., Scott C. E., Evans R. S., Burridge P. W., Cox T. V., Fox C. A., et al.
Nature. Volume 418, Number 6899, (2002), p.743–750
The Ensembl genome database project
Hubbard, T., Barker D., Birney E., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., Down T., et al.
Nucleic acids research. Volume 30, Number 1, (2002), p.38–41
The Bioperl toolkit: Perl modules for the life sciences
Stajich, J. E., Block D., Boulez K., Brenner S. E., Chervitz S. A., Dagdigian C., Fuellen G., Gilbert J. G. R., Korf I., Lapp H., et al.
Genome research. Volume 12, Number 10, (2002), p.1611–1618
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Okazaki, Y., Furuno M., Kasukawa T., Adachi J., Bono H., Kondo S., Nikaido I., Osato N., Saito R., Suzuki H., et al.
Nature. Volume 420, Number 6915, (2002), p.563–573
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
Zdobnov, E. M., von Mering C., Letunic I., Torrents D., Suyama M., Copley R. R., Christophides G. K., Thomasova D., Holt R. A., Subramanian G. M., et al.
Science. Volume 298, Number 5591, (2002), p.149
Databases and tools for browsing genomes
Birney, E., Clamp M., and Hubbard T.
Annual review of genomics and human genetics. Volume 3, Number 1, (2002), p.293–310
The genome sequence of the malaria mosquito Anopheles gambiae
Holt, R. A., Subramanian G. M., Halpern A., Sutton G. G., Charlab R., Nusskern D. R., Wincker P., Clark A. G., Ribeiro J. M. C., Wides R., et al.
Science. Volume 298, Number 5591, (2002), p.129

2001

Progress in sequencing the mouse genome
Lindblad-Toh, K., Lander E. S., McPherson J. D., Waterston R. H., Rodgers J., and Birney E.
genesis. Volume 31, Number 4, (2001), p.137–141
Integration of cytogenetic landmarks into the draft sequence of the human genome
Cheung, VG, Nowak N., Jang W., Kirsch IR, Zhao S., Chen X. N., Furey TS, Kim U. J., Kuo W. L., Olivier M., et al.
Nature. Volume 409, Number 6822, (2001), p.953–958
Cancer and genomics
Futreal, P. A., Kasprzyk A., Birney E., Mullikin J. C., Wooster R., and Stratton M. R.
Nature. Volume 409, Number 6822, (2001), p.850–852
Hidden Markov models in biological sequence analysis
Birney, E.
IBM Journal of Research and Development. Volume 45, Number 3.4, (2001), p.449–454

2000

The Bioperl project: motivation and usage
Stajich, J., and Birney E.
ACM SIGBIO Newsletter. Volume 20, Number 2, (2000), p.13–14
Searching Databases to Find Protein Domain Organization-V.-Profile Methods
Bateman, A., and Birney E.
Advances in Protein Chemistry. Volume 54, (2000), p.149–154
Identification of domains from protein sequences
Ponting, C. P., and Birney E.
METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-. Volume 143, (2000), p.53–70
Open annotation offers a democratic solution to genome sequencing
Hubbard, T., Birney E., and others
Nature. Volume 403, Number 6772, (2000), p.825
Hidden Markov models for database similarity searches
Birney, E.
Bioinformatics: Sequence, Structure and Databanks: A Practical Approach. (2000), p.77
Using GeneWise in the Drosophila annotation experiment
Birney, E., and Durbin R.
Genome Research. Volume 10, Number 4, (2000), p.547–548
Comparative genomics of the eukaryotes
Rubin, G. M., Yandell M. D., Wortman J. R., Gabor G. L., Nelson C. R., Hariharan I. K., Fortini M. E., Li P. W., Apweiler R., Fleischmann W., et al.
Science. Volume 287, Number 5461, (2000), p.2204
Sequence alignment in bioinformatics
Birney, E.
(2000),
ProtEST: protein multiple sequence alignments from expressed sequence tags
Cuff, J. A., Birney E., Clamp M. E., and Barton G. J.
Bioinformatics. Volume 16, Number 2, (2000), p.111–116

1999

Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
Jareborg, N., Birney E., and Durbin R.
Genome Research. Volume 9, Number 9, (1999), p.815–824

1998

SPEM: a parser for EMBL style flat file database entries.
Pocock, M. R., Hubbard T., and Birney E.
Bioinformatics. Volume 14, Number 9, (1998), p.823–824

1997

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison
Birney, E., Durbin R., and others
Proc. Int. Conf. Intell. Syst. Mol. Biol. Volume 5, (1997), p.56–64

1996

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames
Birney, E., Thompson J. D., and Gibson T. J.
Nucleic acids research. Volume 24, Number 14, (1996), p.2730

1994

PH domain: the first anniversary
Gibson, T. J., Hyvonen M., Musacchio A., Saraste M., and Birney E.
Trends in biochemical sciences. Volume 19, Number 9, (1994), p.349–353

1993

A putative homology of U2AF65 in S. cerevisiae
Birney, E., Kumar S., and Krainer A. R.
Nucleic Acids Research. Volume 21, Number 5, (1993), p.1333–1333
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors
Birney, E., Kumar S., and Krainer A. R.
Nucleic acids research. Volume 21, Number 25, (1993), p.5803

1992

A putative homolog of U2AF65 in S. cerevisiae.
Birney, E., Kumar S., and Krainer A. R.
Nucleic acids research. Volume 20, Number 17, (1992), p.4663