E Birney

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Ensembl 2005
    T Hubbard
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 33:D447-53. 2005
  2. pmc The future of DNA sequence archiving
    Guy Cochrane
    EMBL Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
    Gigascience 1:2. 2012
  3. pmc Analysis of variation at transcription factor binding sites in Drosophila and humans
    Mikhail Spivakov
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    Genome Biol 13:R49. 2012
  4. pmc Modeling gene expression using chromatin features in various cellular contexts
    Xianjun Dong
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Genome Biol 13:R53. 2012
  5. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
  6. pmc Locus Reference Genomic sequences: an improved basis for describing human DNA variants
    Raymond Dalgleish
    Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
    Genome Med 2:24. 2010
  7. pmc The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
    Laurence Ettwiller
    EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    Genome Biol 6:R104. 2005
  8. pmc Reactome: a knowledge base of biologic pathways and processes
    Imre Vastrik
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genome Biol 8:R39. 2007
  9. pmc Update of the Anopheles gambiae PEST genome assembly
    Maria V Sharakhova
    Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556 0369, USA
    Genome Biol 8:R5. 2007
  10. pmc Ensembl variation resources
    Yuan Chen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:293. 2010

Research Grants

  1. The Nomenclature of Human Genes
    Ewan Birney; Fiscal Year: 2007

Detail Information

Publications108 found, 100 shown here

  1. pmc Ensembl 2005
    T Hubbard
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 33:D447-53. 2005
    ..The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution...
  2. pmc The future of DNA sequence archiving
    Guy Cochrane
    EMBL Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
    Gigascience 1:2. 2012
    ..Here, we propose a graded system in which the ease of reproduction of a sequencing-based experiment and the relative availability of a sample for resequencing define the level of lossy compression applied to stored data...
  3. pmc Analysis of variation at transcription factor binding sites in Drosophila and humans
    Mikhail Spivakov
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    Genome Biol 13:R49. 2012
    ....
  4. pmc Modeling gene expression using chromatin features in various cellular contexts
    Xianjun Dong
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Genome Biol 13:R53. 2012
    ..ENCODE also generated the genome-wide mapping of eleven histone marks, one histone variant, and DNase I hypersensitivity sites in seven cell lines...
  5. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
    ..While this large amount of data creates a valuable resource, it is nonetheless overwhelmingly complex and simultaneously incomplete since it covers only a small fraction of all human transcription factors...
  6. pmc Locus Reference Genomic sequences: an improved basis for describing human DNA variants
    Raymond Dalgleish
    Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
    Genome Med 2:24. 2010
    ..Further information can be found on the LRG web site: http://www.lrg-sequence.org...
  7. pmc The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
    Laurence Ettwiller
    EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    Genome Biol 6:R104. 2005
    ..We then used deeper comparative analysis across vertebrates to identify the active instances of these motifs. We have shown experimentally in Medaka fish that a subset of these predictions is involved in transcription...
  8. pmc Reactome: a knowledge base of biologic pathways and processes
    Imre Vastrik
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genome Biol 8:R39. 2007
    ..Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets...
  9. pmc Update of the Anopheles gambiae PEST genome assembly
    Maria V Sharakhova
    Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556 0369, USA
    Genome Biol 8:R5. 2007
    ....
  10. pmc Ensembl variation resources
    Yuan Chen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:293. 2010
    ..Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics...
  11. pmc Gene finding in the chicken genome
    Eduardo Eyras
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 6:131. 2005
    ..We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method...
  12. pmc A database and API for variation, dense genotyping and resequencing data
    Daniel Rios
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 11:238. 2010
    ..The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources...
  13. pmc Automated generation of heuristics for biological sequence comparison
    Guy St C Slater
    The Ensembl Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:31. 2005
    ....
  14. pmc Integrating biological data--the Distributed Annotation System
    Andrew M Jenkinson
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
    ..DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics...
  15. pmc GeneWise and Genomewise
    Ewan Birney
    The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:988-95. 2004
    ..The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence...
  16. pmc An overview of Ensembl
    Ewan Birney
    EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:925-8. 2004
    ....
  17. ncbi request reprint Biological database design and implementation
    Ewan Birney
    EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Brief Bioinform 5:31-8. 2004
    ..Our experience has led us to emphasise simplicity and conservative technology choices when building these databases. This is a short paper of advice that we hope is useful to people designing their own biological database...
  18. pmc Allele-specific and heritable chromatin signatures in humans
    Ewan Birney
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Hum Mol Genet 19:R204-9. 2010
    ..A detailed understanding of the relationship between normal genetic variation and chromatin variation can shed light on how polymorphisms in non-coding regions in the human genome might underlie phenotypic variation and disease...
  19. pmc Using GeneWise in the Drosophila annotation experiment
    E Birney
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 10:547-8. 2000
    ..Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights...
  20. doi request reprint Chromatin and heritability: how epigenetic studies can complement genetic approaches
    Ewan Birney
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Trends Genet 27:172-6. 2011
    ..In particular, I see more benefit to epigenetic studies being performed in the context of genetic studies, rather than as separate investigations...
  21. pmc Mining the draft human genome
    E Birney
    The European Bioinformatics Institute, Hinxton, Cambridge, UK
    Nature 409:827-8. 2001
    ..We need to appreciate both the scale of the challenge of vertebrate genome analysis and the limitations of current gene prediction methods and understanding...
  22. ncbi request reprint Databases and tools for browsing genomes
    Ewan Birney
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
    Annu Rev Genomics Hum Genet 3:293-310. 2002
    ..This article reviews the database systems and tools for analysis that have so far been developed to address this...
  23. pmc Ensembl 2006
    E Birney
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 34:D556-61. 2006
    ....
  24. pmc Ensembl 2004
    E Birney
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 32:D468-70. 2004
    ..With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data...
  25. pmc Ensembl 2002: accommodating comparative genomics
    M Clamp
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 31:38-42. 2003
    ..With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation...
  26. pmc Ensembl 2008
    P Flicek
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:D707-14. 2008
    ..We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure...
  27. pmc Ensembl 2007
    T J P Hubbard
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 35:D610-7. 2007
    ....
  28. pmc Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
    A Bateman
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 27:260-2. 1999
    ..1 are that we now use the more advanced version 2 of the HMMER software, which is more sensitive and provides expectation values for matches, and that it now includes proteins from both SP-TrEMBL and SWISS-PROT...
  29. pmc The Ensembl genome database project
    T Hubbard
    The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 30:38-41. 2002
    ..The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops...
  30. pmc Ensembl 2009
    T J P Hubbard
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 37:D690-7. 2009
    ..ensemblgenomes.org/)...
  31. ncbi request reprint Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison
    E Birney
    Sanger Centre, Cambridge, UK
    Proc Int Conf Intell Syst Mol Biol 5:56-64. 1997
    ....
  32. pmc Ensembl Genomes: extending Ensembl across the taxonomic space
    P J Kersey
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D563-9. 2010
    ..Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site...
  33. pmc EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010
    ..g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org...
  34. pmc The Pfam protein families database
    A Bateman
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 28:263-6. 2000
    ..These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package...
  35. ncbi request reprint Genome information resources - developments at Ensembl
    Martin P Hammond
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Trends Genet 20:268-72. 2004
    ..Users can now display their own data in the context of other annotation. In addition, a fast and flexible data retrieval system, EnsMart, has been developed...
  36. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
    ..New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource...
  37. ncbi request reprint Ensembl: a genome infrastructure
    E Birney
    EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Cold Spring Harb Symp Quant Biol 68:213-5. 2003
  38. pmc The HGNC Database in 2008: a resource for the human genome
    Elspeth A Bruford
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Nucleic Acids Res 36:D445-8. 2008
    ..genenames.org, with direct links to the searchable HGNC database and other related database resources, such as the HCOP orthology search tool and manually curated gene family webpages...
  39. ncbi request reprint SPEM: a parser for EMBL style flat file database entries
    M R Pocock
    Informatics, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 14:823-4. 1998
    ..We present a set of Perl modules for the flexible and robust parsing and editing of EMBL/SWISS-PROT databases...
  40. pmc The InterPro database, an integrated documentation resource for protein families, domains and functional sites
    R Apweiler
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 29:37-40. 2001
    ..The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk...
  41. pmc VectorBase: a home for invertebrate vectors of human pathogens
    Daniel Lawson
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 35:D503-5. 2007
    ....
  42. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  43. ncbi request reprint Sense from sequence reads: methods for alignment and assembly
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:S6-S12. 2009
    ..We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools...
  44. pmc Advanced genomic data mining
    Xose M Fernandez-Suarez
    European Bioinformatics Institute, Ensembl Group, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 4:e1000121. 2008
  45. ncbi request reprint The International Protein Index: an integrated database for proteomics experiments
    Paul J Kersey
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Proteomics 4:1985-8. 2004
    ..IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases...
  46. pmc VectorBase: a data resource for invertebrate vector genomics
    Daniel Lawson
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D583-7. 2009
    ..We have continued to develop both the software infrastructure and tools for interrogating the stored data...
  47. pmc Improvements to services at the European Nucleotide Archive
    Rasko Leinonen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D39-45. 2010
    ..In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services...
  48. doi request reprint ENFIN--A European network for integrative systems biology
    Pascal Kahlem
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    C R Biol 332:1050-8. 2009
    ..The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet...
  49. pmc Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
    Daniel R Zerbino
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    PLoS ONE 4:e8407. 2009
    ..Despite the short length of their reads, micro-read sequencing technologies have shown their usefulness for de novo sequencing. However, especially in eukaryotic genomes, complex repeat patterns are an obstacle to large assemblies...
  50. pmc Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
    Database (Oxford) 2010:baq014. 2010
    ..We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf...
  51. pmc The European Nucleotide Archive
    Rasko Leinonen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D28-31. 2011
    ....
  52. pmc EnsMart: a generic system for fast and flexible access to biological data
    Arek Kasprzyk
    European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 1SH, UK
    Genome Res 14:160-9. 2004
    ..Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets...
  53. pmc Ensembl 2011
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D800-6. 2011
    ..Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types...
  54. pmc The European Bioinformatics Institute's data resources
    Catherine Brooksbank
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:43-50. 2003
    ..The EBI's databases and tools are all available on our website at www.ebi.ac.uk...
  55. pmc Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
    Guy Cochrane
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 36:D5-12. 2008
    ..Priorities are discussed in terms of how reliably information can be captured, the long-term benefits of its capture and the ease with which it can be captured...
  56. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    ..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
  57. pmc Petabyte-scale innovations at the European Nucleotide Archive
    Guy Cochrane
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D19-25. 2009
    ....
  58. pmc Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase
    K Megy
    EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Infect Genet Evol 9:308-13. 2009
    ..We present VectorBase, a genomic resource centre that is both involved in the annotation of vector genomes and act as a portal for access to the genomic information (http://www.vectorbase.org)...
  59. ncbi request reprint Cancer and genomics
    P A Futreal
    Cancer Genome Project, Sanger Centre, Cambridge, UK
    Nature 409:850-2. 2001
    ..Our experiment underscores the limited amount and variable quality of DNA sequence from cancer cells that is currently available...
  60. pmc Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
    N Jareborg
    The Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 9:815-24. 1999
    ..This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies. [This paper contains supplementary data that can be found at http://www.genome.org [corrected]]...
  61. ncbi request reprint ENFIN a network to enhance integrative systems biology
    Pascal Kahlem
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Ann N Y Acad Sci 1115:23-31. 2007
    ..We will give an overview of the projects tackled within ENFIN and discuss the challenges associated with integration for systems biology...
  62. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
    ..All data are made available in a number of formats and will be kept up to date with the Ensembl project...
  63. ncbi request reprint A physical map of the mouse genome
    Simon G Gregory
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 418:743-50. 2002
    ..The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy...
  64. ncbi request reprint Comparative genomics: genome-wide analysis in metazoan eukaryotes
    Abel Ureta-Vidal
    EnsEMBL Project, Room A2 06, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Rev Genet 4:251-62. 2003
    ..Each of these areas improves the methods of deciphering long genomic sequences and uncovering what lies hidden in them...
  65. pmc The Ensembl core software libraries
    Arne Stabenau
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genome Res 14:929-33. 2004
    ..The architecture of the core software libraries, the schema, and the factors influencing their design are described. All code and data are freely available...
  66. ncbi request reprint Optimized design and assessment of whole genome tiling arrays
    Stefan Graf
    EMBL European Bioinformatics Institute, Hinxton, Cambridge, UK
    Bioinformatics 23:i195-204. 2007
    ..We have identified a number of design parameters to be optimized including uniqueness of the probe sequences within the whole genome, melting temperature and self-hybridization potential...
  67. ncbi request reprint Picking pyknons out of the human genome
    Alison Meynert
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
    Cell 125:836-8. 2006
    ..Although it is unclear how pyknons might have arisen, it is possible that they may be involved in a new form of gene regulation...
  68. pmc An effective model for natural selection in promoters
    Michael M Hoffman
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
    Genome Res 20:685-92. 2010
    ..The results show the first clear correlations between such a model and evolutionary processes...
  69. pmc The systematic annotation of the three main GPCR families in Reactome
    Bijay Jassal
    European Bioinformatics Institute, Hinxton, Cambridge CB101SD, UK
    Database (Oxford) 2010:baq018. 2010
    ..Database URL: http://www.reactome.org...
  70. ncbi request reprint Genome browsing with Ensembl: a practical overview
    Giulietta Spudich
    EMBL Outstation EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB101SD, UK
    Brief Funct Genomic Proteomic 6:202-19. 2007
    ..Genes and annotation are accessible through the Ensembl browser (http://www.ensembl.org), and through direct queries of its databases using the Perl API (Application Programme Interface), MySQL or BioMart...
  71. pmc A survey of homozygous deletions in human cancer genomes
    Charles Cox
    Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Proc Natl Acad Sci U S A 102:4542-7. 2005
    ..They may also reflect a tendency to reduce the adverse effects of homozygous deletions by minimizing the number of genes removed...
  72. ncbi request reprint Estimating the neutral rate of nucleotide substitution using introns
    Michael M Hoffman
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England
    Mol Biol Evol 24:522-31. 2007
    ..Although the intron method may be more useful for shorter evolutionary distances, it is less useful at longer distances due to the poor alignment of less-conserved positions...
  73. pmc The landscape of histone modifications across 1% of the human genome in five human cell lines
    Christoph M Koch
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SA, United Kingdom
    Genome Res 17:691-707. 2007
    ..These results provide an overview of the functional relationship among histone modifications and gene expression in human cells...
  74. pmc Patterns of somatic mutation in human cancer genomes
    Christopher Greenman
    Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 446:153-8. 2007
    ..Systematic sequencing of cancer genomes therefore reveals the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated...
  75. pmc Discovering novel cis-regulatory motifs using functional networks
    Laurence M Ettwiller
    European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genome Res 13:883-95. 2003
    ....
  76. ncbi request reprint Unrestricted free access works and must continue
    Steven Salzberg
    Nature 422:801. 2003
  77. ncbi request reprint Immunity-related genes and gene families in Anopheles gambiae
    George K Christophides
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 298:159-65. 2002
    ..Representative expression profiles confirm that sequence diversification is accompanied by specific responses to different immune challenges. Alternative RNA splicing may also contribute to expansion of the immune repertoire...
  78. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  79. pmc TranscriptSNPView: a genome-wide catalog of mouse coding variation
    Fiona Cunningham
    Nat Genet 38:853. 2006
  80. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  81. pmc Dry work in a wet world: computation in systems biology
    Pascal Kahlem
    Mol Syst Biol 2:40. 2006
  82. ncbi request reprint The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
  83. pmc Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
    Simon J Hubbard
    Faculty of Life Sciences, The University of Manchester, Manchester, M60 1QD, United Kingdom
    Genome Res 15:174-83. 2005
    ....
  84. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  85. pmc 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
    Emmanouil T Dermitzakis
    Division of Medical Genetics, University of Geneva Medical School, CH 1211 Geneva, Switzerland
    Genome Res 14:852-9. 2004
    ..We propose models for a global role of CNGs in genome function and regulation, through long-distance cis or trans chromosomal interactions...
  86. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  87. ncbi request reprint A SNP map of the rat genome generated from cDNA sequences
    Heike Zimdahl
    Max Delbrück Center for Molecular Medicine MDC, Robert Rossle Str 10, 13092 Berlin Buch, Germany
    Science 303:807. 2004
  88. pmc Sockeye: a 3D environment for comparative genomics
    Stephen B Montgomery
    Canada s Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 14:956-62. 2004
    ..By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization...
  89. pmc Identification of novel peptide hormones in the human proteome by hidden Markov model screening
    Olivier Mirabeau
    Mouse Biology Unit, EMBL, 00016 Monterotondo, Italy
    Genome Res 17:320-7. 2007
    ..Peptide hormones and their receptors are important diagnostic and therapeutic targets, and our results suggest that spexin and augurin are novel peptide hormones likely to be involved in physiological homeostasis...
  90. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....
  91. doi request reprint Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Elliott H Margulies
    Genome Technology Branch, Genome Informatics Section, National Human Genome Research Institute, National Institutes of Health, 5625 Fishers Lane, Room 5N 01N, MSC9400, Bethesda, Maryland 20892, USA
    Nat Rev Genet 9:303-13. 2008
    ..Approaches to determining the biological significance of constrained sequence are also explored...
  92. pmc Challenges and standards in integrating surveys of structural variation
    Stephen W Scherer
    The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, Room 14 701, Ontario M5G 1L7, Canada
    Nat Genet 39:S7-15. 2007
    ..From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research...
  93. doi request reprint Levers and fulcrums: progress in cis-regulatory motif models
    Ewan Birney
    Nat Methods 5:297-8. 2008
  94. pmc What everybody should know about the rat genome and its online resources
    Simon N Twigger
    Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
    Nat Genet 40:523-7. 2008
    ....
  95. ncbi request reprint Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    Evgeny M Zdobnov
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 298:149-59. 2002
    ....
  96. pmc An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Vardhman K Rakyan
    Institute of Cell and Molecular Science, Barts and The London, London E1 2AT, United Kingdom
    Genome Res 18:1518-29. 2008
    ....
  97. pmc A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    Thomas A Down
    Wellcome Trust Cancer Research UK Gurdon Institute, and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nat Biotechnol 26:779-85. 2008
    ....
  98. ncbi request reprint Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    Laurence Ettwiller
    Developmental Biology Unit, EMBL Heidelberg, Heidelberg, Germany
    Nat Methods 4:563-5. 2007
    ..Newly discovered motifs and their features (identity, conservation, position in sequence) are displayed on a web interface...
  99. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  100. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...

Research Grants3

  1. The Nomenclature of Human Genes
    Ewan Birney; Fiscal Year: 2007
    ....