Michele Clamp

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi request reprint The Jalview Java alignment editor
    Michele Clamp
    The Wellcome Trust Sanger Institute, Hinxton, UK
    Bioinformatics 20:426-7. 2004
  2. pmc ESTGenes: alternative splicing from ESTs in Ensembl
    Eduardo Eyras
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 14:976-87. 2004
  3. pmc The otter annotation system
    Stephen M J Searle
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:963-70. 2004
  4. 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
  5. 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
  6. ncbi request reprint The DNA sequence of human chromosome 22
    I Dunham
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 402:489-95. 1999
  7. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 20
    P Deloukas
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 414:865-71. 2001
  8. pmc The Ensembl automatic gene annotation system
    Val Curwen
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:942-50. 2004
  9. pmc The Ensembl analysis pipeline
    Simon C Potter
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Genome Res 14:934-41. 2004
  10. 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

Detail Information

Publications23

  1. ncbi request reprint The Jalview Java alignment editor
    Michele Clamp
    The Wellcome Trust Sanger Institute, Hinxton, UK
    Bioinformatics 20:426-7. 2004
    ..The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments...
  2. pmc ESTGenes: alternative splicing from ESTs in Ensembl
    Eduardo Eyras
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 14:976-87. 2004
    ..ensembl.org as ESTgenes for the mosquito, Caenorhabditis briggsae, C. elegans, zebrafish, human, mouse, and rat genomes. Here we also report on the results of this method applied to the human and mouse genomes...
  3. pmc The otter annotation system
    Stephen M J Searle
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:963-70. 2004
    ..The Human and Vertebrate Annotation (HAVANA) group annotators at the Sanger center are using this to annotate human chromosomes 1 and 20...
  4. 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...
  5. 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...
  6. ncbi request reprint The DNA sequence of human chromosome 22
    I Dunham
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 402:489-95. 1999
    ..4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome...
  7. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 20
    P Deloukas
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 414:865-71. 2001
    ....
  8. pmc The Ensembl automatic gene annotation system
    Val Curwen
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:942-50. 2004
    ..gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org...
  9. pmc The Ensembl analysis pipeline
    Simon C Potter
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Genome Res 14:934-41. 2004
    ..Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis...
  10. 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...
  11. 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...
  12. 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
    ....
  13. 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...
  14. 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...
  15. 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...
  16. pmc An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:4795-800. 2005
    ....
  17. 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...
  18. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  19. 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...
  20. 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
    ....
  21. 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
    ....
  22. pmc Biopipe: a flexible framework for protocol-based bioinformatics analysis
    Shawn Hoon
    Institute of Molecular and Cell Biology, National University of Singapore, Singapore 117609
    Genome Res 13:1904-15. 2003
    ..This will enable researchers to discuss and interpret the data better as the once implicit assumptions are now explicitly defined within the Biopipe framework...
  23. pmc Distinguishing protein-coding and noncoding genes in the human genome
    Michele Clamp
    Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:19428-33. 2007
    ..It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes...