Research Topics
| Michele ClampSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Detail Information
Publications
The Jalview Java alignment editorMichele 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...
ESTGenes: alternative splicing from ESTs in EnsemblEduardo 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...- The otter annotation systemStephen 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... - Biological database design and implementationEwan 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... - GeneWise and GenomewiseEwan 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... - The DNA sequence of human chromosome 22I 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... - The DNA sequence and comparative analysis of human chromosome 20P Deloukas
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Nature 414:865-71. 2001.... - The Ensembl automatic gene annotation systemVal 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... - The Ensembl analysis pipelineSimon 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... - The Ensembl core software librariesArne 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... - The Ensembl genome database projectT 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... - An overview of EnsemblEwan Birney
EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Genome Res 14:925-8. 2004.... - Ensembl 2004E 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... - Ensembl 2002: accommodating comparative genomicsM 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... - The genome sequence of the malaria mosquito Anopheles gambiaeRobert 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... - An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencingElliott 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.... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott 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... - Databases and tools for browsing genomesEwan 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... - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard 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 <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - Initial sequencing and comparative analysis of the mouse genomeRobert 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.... - Biopipe: a flexible framework for protocol-based bioinformatics analysisShawn 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... - Distinguishing protein-coding and noncoding genes in the human genomeMichele 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...