Research Topics
| Thomas DownSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Detail Information
Publications
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...- Computational detection and location of transcription start sites in mammalian genomic DNAThomas A Down
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
Genome Res 12:458-61. 2002.... - NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequenceThomas 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... - Multi-genome biologyThomas 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... - A machine learning strategy to identify candidate binding sites in human protein-coding sequenceThomas 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... - Large-scale discovery of promoter motifs in Drosophila melanogasterThomas 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... - iMotifs: an integrated sequence motif visualization and analysis environmentMatias Piipari
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
Bioinformatics 26:843-4. 2010..0 licensed library libxms for the Perl, Ruby, R and Objective-C programming languages for input and output of XMS formatted annotated sequence motif set files. CONTACT: matias.piipari@gmail.com; imotifs@googlegroups.com... - Metamotifs--a generative model for building families of nucleotide position weight matricesMatias Piipari
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
BMC Bioinformatics 11:348. 2010.... - NestedMICA as an ab initio protein motif discovery toolMutlu 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... - Adding some SPICE to DASAndreas Prlic
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
Bioinformatics 21:ii40-1. 2005..Here we present SPICE, a new DAS client that can be used to visualize protein sequence and structure annotations. AVAILABILITY: http://www.efamily.org.uk/software/dasclients/spice/.. - Integrating sequence and structural biology with DASAndreas 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... - Integrating biological data--the Distributed Annotation SystemAndrew 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... - Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence levelAlexander 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... - Smicl is required for phosphorylation of RNA polymerase II and affects 3'-end processing of RNA at the midblastula transition in XenopusClara 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... - 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.... - A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysisThomas 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.... - DNA methylation profiling of human chromosomes 6, 20 and 22Florian Eckhardt
Epigenomics AG, , 10178 Berlin, Germany
Nat Genet 38:1378-85. 2006..Our data suggest DNA methylation to be ontogenetically more stable than previously thought...