Thomas Down

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc What can we learn from noncoding regions of similarity between genomes?
    Thomas A Down
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 5:131. 2004
  2. pmc Computational detection and location of transcription start sites in mammalian genomic DNA
    Thomas A Down
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 12:458-61. 2002
  3. pmc NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
    Thomas A Down
    Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
    Nucleic Acids Res 33:1445-53. 2005
  4. pmc Multi-genome biology
    Thomas A Down
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 7:305. 2006
  5. pmc A machine learning strategy to identify candidate binding sites in human protein-coding sequence
    Thomas Down
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 7:419. 2006
  6. pmc Large-scale discovery of promoter motifs in Drosophila melanogaster
    Thomas A Down
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 3:e7. 2007
  7. pmc iMotifs: an integrated sequence motif visualization and analysis environment
    Matias Piipari
    Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
    Bioinformatics 26:843-4. 2010
  8. pmc Metamotifs--a generative model for building families of nucleotide position weight matrices
    Matias Piipari
    Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
    BMC Bioinformatics 11:348. 2010
  9. pmc NestedMICA as an ab initio protein motif discovery tool
    Mutlu Doğruel
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    BMC Bioinformatics 9:19. 2008
  10. pmc Integrating sequence and structural biology with DAS
    Andreas Prlic
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:333. 2007

Detail Information

Publications18

  1. pmc What can we learn from noncoding regions of similarity between genomes?
    Thomas A Down
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Bioinformatics 5:131. 2004
    ..It seems reasonable to assume that these conserved regions are more likely to contain functional elements than less-conserved portions of the genome...
  2. pmc Computational detection and location of transcription start sites in mammalian genomic DNA
    Thomas A Down
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 12:458-61. 2002
    ....
  3. pmc NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
    Thomas A Down
    Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA, UK
    Nucleic Acids Res 33:1445-53. 2005
    ..When tested on a real set of regulatory sequences, NestedMICA produced motifs which were good predictors for all five abundant classes of annotated binding sites...
  4. pmc Multi-genome biology
    Thomas A Down
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 7:305. 2006
    ..A report on the Genome Informatics meeting held at Cold Spring Harbor Laboratory, Cold Spring Harbor, USA, 28 October-1 November 2005...
  5. pmc A machine learning strategy to identify candidate binding sites in human protein-coding sequence
    Thomas Down
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    BMC Bioinformatics 7:419. 2006
    ..It would be useful to identify further candidate sequences, however identifying them computationally is hard since exon sequences are also constrained by their functional role in coding for proteins...
  6. pmc Large-scale discovery of promoter motifs in Drosophila melanogaster
    Thomas A Down
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 3:e7. 2007
    ..We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes...
  7. pmc iMotifs: an integrated sequence motif visualization and analysis environment
    Matias Piipari
    Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
    Bioinformatics 26:843-4. 2010
    ..The application includes a bundled and graphically integrated version of the NestedMICA motif inference suite that has no outside dependencies. Problems associated with local deployment of software are therefore avoided...
  8. pmc Metamotifs--a generative model for building families of nucleotide position weight matrices
    Matias Piipari
    Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
    BMC Bioinformatics 11:348. 2010
    ....
  9. pmc NestedMICA as an ab initio protein motif discovery tool
    Mutlu Doğruel
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    BMC Bioinformatics 9:19. 2008
    ..NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length...
  10. pmc Integrating sequence and structural biology with DAS
    Andreas Prlic
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:333. 2007
    ..The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence...
  11. pmc Adding some SPICE to DAS
    Andreas Prlic
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
    Bioinformatics 21:ii40-1. 2005
    ..We have extended the protocol to be applicable to macromolecular structures. Here we present SPICE, a new DAS client that can be used to visualize protein sequence and structure annotations...
  12. pmc Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells
    Amanda L Evans
    Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 7:e33346. 2012
    ..Work in the frog and the zebrafish has identified some direct genomic targets of Brachyury, but little is known about Brachyury targets in the mouse...
  13. 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...
  14. pmc Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
    Alexander W Bruce
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 19:994-1005. 2009
    ..These relationships have never been reported in mammalian systems for any transcription factor...
  15. pmc Smicl is required for phosphorylation of RNA polymerase II and affects 3'-end processing of RNA at the midblastula transition in Xenopus
    Clara Collart
    Wellcome Trust CR UK Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, UK
    Development 136:3451-61. 2009
    ..Our work links the onset of zygotic gene expression in the Xenopus embryo with the translocation of Smicl from cytoplasm to nucleus, the phosphorylation of Rpb1 and the 3'-end processing of newly transcribed mRNAs...
  16. 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
    ....
  17. 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
    ....
  18. pmc DNA methylation profiling of human chromosomes 6, 20 and 22
    Florian Eckhardt
    Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany
    Nat Genet 38:1378-85. 2006
    ..Our data suggest DNA methylation to be ontogenetically more stable than previously thought...