R Durbin

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi The DNA sequence and analysis of human chromosome 13
    A Dunham
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nature 428:522-8. 2004
  4. ncbi 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
  5. ncbi [X]uniqMAP: unique gene sequence regions in the human and mouse genomes
    Jose L Jimenez
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Genomics 7:249. 2006
  6. ncbi A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database
    Jose L Jimenez
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 8:R90. 2007
  7. ncbi Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
    Ian Sudbery
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
    Genome Biol 10:R112. 2009
  8. ncbi Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase
    Alan M Moses
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
    Genome Biol 8:R23. 2007
  9. ncbi The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
  10. ncbi Enhanced protein domain discovery using taxonomy
    Lachlan Coin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 5:56. 2004

Detail Information

Publications30

  1. ncbi 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
    ....
  2. ncbi 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...
  3. ncbi The DNA sequence and analysis of human chromosome 13
    A Dunham
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nature 428:522-8. 2004
    ..Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb...
  4. ncbi 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
    ....
  5. ncbi [X]uniqMAP: unique gene sequence regions in the human and mouse genomes
    Jose L Jimenez
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Genomics 7:249. 2006
    ..The design of specific oligos involves the determination of unique DNA regions in the gene/transcripts of interest from the targeted organism. This process is tedious, time consuming and it does not scale up for high-throughput studies...
  6. ncbi A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database
    Jose L Jimenez
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 8:R90. 2007
    ..Detailed analysis of this structural dataset reveals that phosphorylation sites are found in a heterogeneous range of structural and sequence contexts. mtcPTM is available on the web http://www.mitocheck.org/cgi-bin/mtcPTM/search...
  7. ncbi Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
    Ian Sudbery
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
    Genome Biol 10:R112. 2009
    ....
  8. ncbi Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase
    Alan M Moses
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
    Genome Biol 8:R23. 2007
    ..Our data suggest that regulatory modules may exist in protein sequence as clusters of short sequence motifs...
  9. ncbi The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
    ....
  10. ncbi Enhanced protein domain discovery using taxonomy
    Lachlan Coin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 5:56. 2004
    ..This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids...
  11. ncbi A map of human genome variation from population-scale sequencing
    Richard M Durbin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Nature 467:1061-73. 2010
    ..These methods and public data will support the next phase of human genetic research...
  12. ncbi Dynamic programming alignment accuracy
    I Holmes
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, England
    J Comput Biol 5:493-504. 1998
    ....
  13. ncbi 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...
  14. ncbi 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
    ....
  15. ncbi 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...
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi The DNA sequence and comparative analysis of human chromosome 10
    P Deloukas
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nature 429:375-81. 2004
    ..Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence...
  20. ncbi 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/)...
  21. ncbi Alfresco--a workbench for comparative genomic sequence analysis
    N Jareborg
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
    Genome Res 10:1148-57. 2000
    ..As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of the UTY locus is presented...
  22. ncbi The DNA sequence and biological annotation of human chromosome 1
    S G Gregory
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nature 441:315-21. 2006
    ....
  23. ncbi 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...
  24. ncbi Improved techniques for the identification of pseudogenes
    L Coin
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Bioinformatics 20:i94-100. 2004
    ..The latter methods have been used to find sets of genes enriched for pseudogenes, but are not specific enough to accurately separate pseudogenes from expressed genes...
  25. ncbi The DNA sequence and analysis of human chromosome 6
    A J Mungall
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 425:805-11. 2003
    ..Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome...
  26. ncbi 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...
  27. ncbi A computational scan for U12-dependent introns in the human genome sequence
    A Levine
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 29:4006-13. 2001
    ..This new larger reference set of U12-dependent introns will serve as a resource for future studies of both the properties and evolution of the U12 spliceosome...
  28. ncbi 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...
  29. ncbi DNA sequence and analysis of human chromosome 9
    S J Humphray
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 429:369-74. 2004
    ..We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection...
  30. ncbi 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]]...