Thomas M Keane

Summary

Affiliation: National University of Ireland
Country: Ireland

Publications

  1. pmc Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    Thomas M Keane
    Department of Biology, National University of Ireland, Maynooth, Co Kildare, Ireland
    BMC Evol Biol 6:29. 2006
  2. pmc MultiPhyl: a high-throughput phylogenomics webserver using distributed computing
    Thomas M Keane
    Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Hinxton, UK
    Nucleic Acids Res 35:W33-7. 2007
  3. pmc High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
    Petr Danecek
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
    Genome Biol 13:26. 2012
  4. pmc RetroSeq: transposable element discovery from next-generation sequencing data
    Thomas M Keane
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Bioinformatics 29:389-90. 2013
  5. pmc Mouse genomic variation and its effect on phenotypes and gene regulation
    Thomas M Keane
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    Nature 477:289-94. 2011
  6. pmc Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly
    Kim Wong
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 11:R128. 2010
  7. pmc 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
  8. pmc New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq
    Thomas D Otto
    Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Microbiol 76:12-24. 2010
  9. pmc ABACAS: algorithm-based automatic contiguation of assembled sequences
    Samuel Assefa
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Bioinformatics 25:1968-9. 2009
  10. pmc Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes
    Charles A Steward
    The Wellcome Trust Sanger Institute, Hinxton, UK
    Genomics 95:105-10. 2010

Detail Information

Publications11

  1. pmc Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    Thomas M Keane
    Department of Biology, National University of Ireland, Maynooth, Co Kildare, Ireland
    BMC Evol Biol 6:29. 2006
    ..These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner...
  2. pmc MultiPhyl: a high-throughput phylogenomics webserver using distributed computing
    Thomas M Keane
    Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Hinxton, UK
    Nucleic Acids Res 35:W33-7. 2007
    ..A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php...
  3. pmc High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
    Petr Danecek
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
    Genome Biol 13:26. 2012
    ..Recently the Mouse Genomes Project generated genome sequences for 17 laboratory mouse strains and rich catalogues of variants. We also generated RNA-seq data from whole brain RNA from 15 of the sequenced strains...
  4. pmc RetroSeq: transposable element discovery from next-generation sequencing data
    Thomas M Keane
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Bioinformatics 29:389-90. 2013
    ..We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls...
  5. pmc Mouse genomic variation and its effect on phenotypes and gene regulation
    Thomas M Keane
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    Nature 477:289-94. 2011
    ..These sequences provide a starting point for a new era in the functional analysis of a key model organism...
  6. pmc Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly
    Kim Wong
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 11:R128. 2010
    ..We applied SVMerge to the analysis of a HapMap trio, demonstrating enhanced structural variant detection, breakpoint refinement, and a lower false discovery rate. SVMerge can be downloaded from http://svmerge.sourceforge.net...
  7. pmc 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...
  8. pmc New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq
    Thomas D Otto
    Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Microbiol 76:12-24. 2010
    ..These data reveal new features of the P. falciparum transcriptional landscape and significantly advance our understanding of the parasite's red blood cell-stage transcriptome...
  9. pmc ABACAS: algorithm-based automatic contiguation of assembled sequences
    Samuel Assefa
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Bioinformatics 25:1968-9. 2009
    ..The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated...
  10. pmc Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes
    Charles A Steward
    The Wellcome Trust Sanger Institute, Hinxton, UK
    Genomics 95:105-10. 2010
    ..These BAC libraries represent a powerful resource for functional studies, such as gene targeting in NOD embryonic stem (ES) cell lines, and for sequencing and mapping experiments...
  11. pmc Next-generation sequencing of vertebrate experimental organisms
    Daniel J Turner
    Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Mamm Genome 20:327-38. 2009
    ..We also describe how next-generation sequencing may be applied in the context of vertebrate model organism genetics...