Works by Down, Thomas A.

Results: 33

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 5, p. 1445, doi. 10.1093/nar/gki282

By:

Down, Thomas A.;
Hubbard, Tim J. P.

Publication type:

Article

Inactive or moderately active human promoters are enriched for inter-individual epialleles.

Published in:

Genome Biology, 2013, v. 14, n. 5, p. 1, doi. 10.1186/gb-2013-14-5-r43

By:

Gemma, Carolina;
Ramagopalan, Sreeram V.;
Down, Thomas A.;
Beyan, Huriya;
Hawa, Mohammed I.;
Holland, Michelle L.;
Hurd, Paul J.;
Giovannoni, Gavin;
Leslie, R. David;
Ebers, George C.;
Rakyan, Vardhman K.

Publication type:

Article

The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells.

Published in:

EMBO Journal, 2013, v. 32, n. 13, p. 1941, doi. 10.1038/emboj.2013.118

By:

Puszyk, William;
Down, Thomas;
Grimwade, David;
Chomienne, Christine;
Oakey, Rebecca J;
Solomon, Ellen;
Guidez, Fabien

Publication type:

Article

Assessing Computational Methods of Cis-Regulatory Module Prediction.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pcbi.1001020

By:

Jing Su;
Teichmann, Sarah A.;
Down, Thomas A.

Publication type:

Article

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 1, p. 95, doi. 10.1371/journal.pcbi.0030007

By:

Down, Thomas A.;
Bergman, Casey M.;
Jing Su;
Hubbard, Tim J. P.

Publication type:

Article

Differential chromatin marking of introns and expressed exons by H3K36me3.

Published in:

Nature Genetics, 2009, v. 41, n. 3, p. 376, doi. 10.1038/ng.322

By:

Kolasinska-Zwierz, Paulina;
Down, Thomas;
Latorre, Isabel;
Tao Liu;
Liu, X. Shirley;
Ahringer, Julie

Publication type:

Article

DNA methylation profiling of human chromosomes 6, 20 and 22.

Published in:

Nature Genetics, 2006, v. 38, n. 12, p. 1378, doi. 10.1038/ng1909

By:

Eckhardt, Florian;
Lewin, Joern;
Cortese, Rene;
Rakyan, Vardhman K.;
Attwood, John;
Burger, Matthias;
Burton, John;
Cox, Tony V.;
Davies, Rob;
Down, Thomas A.;
Haefliger, Carolina;
Horton, Roger;
Howe, Kevin;
Jackson, David K.;
Kunde, Jan;
Koenig, Christoph;
Liddle, Jennifer;
Niblett, David;
Otto, Thomas;
Pettett, Roger

Publication type:

Article

A census of human cancer genes.

Published in:

Nature Reviews Cancer, 2004, v. 4, n. 3, p. 177, doi. 10.1038/nrc1299

By:

Futreal, P. Andrew;
Coin, Lachlan;
Marshall, Mhairi;
Down, Thomas;
Hubbard, Timothy;
Wooster, Richard;
Rahman, Nazneen;
Stratton, Michael R.

Publication type:

Article

The landscape of RNA polymerase II transcription initiation in C. elegans reveals a novel enhancer architecture.

Published in:

2013

By:

Chen, Ron;
Down, Thomas;
Ahringer, Julie

Publication type:

Conference Paper/Materials

Dalliance: interactive genome viewing on the web.

Published in:

Bioinformatics, 2011, v. 27, n. 6, p. 889, doi. 10.1093/bioinformatics/btr020

By:

Down, Thomas A.;
Piipari, Matias;
Hubbard, Tim J. P.

Publication type:

Article

iMotifs: an integrated sequence motif visualization and analysis environment.

Published in:

Bioinformatics, 2010, v. 26, n. 6, p. 843, doi. 10.1093/bioinformatics/btq026

By:

Piipari, Matias;
Down, Thomas A.;
Saini, Harpreet;
Enright, Anton;
Hubbard, Tim J. P.

Publication type:

Article

Adding Some SPICE to DAS.

Published in:

Bioinformatics, 2005, v. 21, p. ii40, doi. 10.1093/bioinformatics/bti1106

By:

Prlić, Andreas;
Down, Thomas A.;
Hubbard, Tim J. P.

Publication type:

Article

Dasty and UniProt DAS: a perfect pair for protein feature visualization.

Published in:

Bioinformatics, 2005, v. 21, n. 14, p. 3198, doi. 10.1093/bioinformatics/bti506

By:

Philip Jones;
Nisha Vinod;
Thomas Down;
Andre Hackmann;
Andreas Kahari;
Ernst Kretschmann;
Antony Quinn;
Daniela Wieser;
Henning Hermjakob;
Rolf Apweiler

Publication type:

Article

ddbRNA: detection of conserved secondary structures in multiple alignments.

Published in:

Bioinformatics, 2003, v. 19, n. 13, p. 1606, doi. 10.1093/bioinformatics/btg229

By:

Diego di Bernardo;
Thomas Down;
Tim Hubbard

Publication type:

Article

Epigenome-wide association studies for common human diseases.

Published in:

Nature Reviews Genetics, 2011, v. 12, n. 8, p. 529, doi. 10.1038/nrg3000

By:

Rakyan, Vardhman K.;
Down, Thomas A.;
Balding, David J.;
Beck, Stephan

Publication type:

Article

Metamotifs -- a generative model for buildingfamilies of nucleotide position weight matrices.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 348, doi. 10.1186/1471-2105-11-348

By:

Piipari, ,2Matias;
Down, Thomas A.;
Hubbard, Tim J. P.

Publication type:

Article

Integrating biological data -- the Distributed Annotation System.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S8-S3

By:

Jenkinson, Andrew M.;
Albrecht, Mario;
Birney, Ewan;
Blankenburg, Hagen;
Down, Thomas;
Finn, Robert D.;
Hermjakob, Henning;
Hubbard, Tim J. P.;
Jimenez, Rafael C.;
Jones, Philip;
Kähäri, Andreas;
Kulesha, Eugene;
Macías, José R.;
Reeves, Gabrielle A.;
Prlić, Andreas

Publication type:

Article

NestedMICA as an ab initio protein motif discovery tool.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-19

By:

Doğruel, Mutlu;
Down, Thomas A.;
Hubbard, Tim J. P.

Publication type:

Article

Integrating sequence and structural biology with DAS.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 333, doi. 10.1186/1471-2105-8-333

By:

Prlić, Andreas;
Down, Thomas A;
Kulesha, Eugene;
Finn, Robert D;
Kähäri, Andreas;
Hubbard, Tim JP

Publication type:

Article

An interactive genome browser of association results from the UK10K cohorts project.

Published in:

Bioinformatics, 2015, v. 31, n. 24, p. 4029, doi. 10.1093/bioinformatics/btv491

By:

Geihs, Matthias;
Ying Yan;
Walter, Klaudia;
Jie Huang;
Memari, Yasin;
Min, Josine L.;
Mead, Daniel;
Hubbard, Tim J.;
Timpson, Nicholas J.;
Down, Thomas A.;
Soranzo, Nicole

Publication type:

Article

WormBase 2016: expanding to enable helminth genomic research.

Published in:

Nucleic Acids Research, 2016, v. 44, p. D774, doi. 10.1093/nar/gkv1217

By:

Howe, Kevin L.;
Bolt, Bruce J.;
Cain, Scott;
Chan, Juancarlos;
Chen, Wen J.;
Davis, Paul;
Done, James;
Down, Thomas;
Gao, Sibyl;
Grove, Christian;
Harris, Todd W.;
Kishore, Ranjana;
Lee, Raymond;
Lomax, Jane;
Yuling Li;
Muller, Hans-Michael;
Nakamura, Cecilia;
Nuin, Paulo;
Paulini, Michael;
Raciti, Daniela

Publication type:

Article

Systematic bias in high-throughput sequencing data and its correction by BEADS.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 15, p. e103, doi. 10.1093/nar/gkr425

By:

Cheung, Ming-Sin;
Down, Thomas A.;
Latorre, Isabel;
Ahringer, Julie

Publication type:

Article

A Comparison of Peak Callers Used for DNase-Seq Data.

Published in:

PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0096303

By:

Koohy, Hashem;
Down, Thomas A.;
Spivakov, Mikhail;
Hubbard, Tim

Publication type:

Article

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0069853

By:

Koohy, Hashem;
Down, Thomas A.;
Hubbard, Tim J.

Publication type:

Article

Genomic Targets of Brachyury (T) in Differentiating Mouse Embryonic Stem Cells.

Published in:

2012

By:

Evans, Amanda L.;
Faial, Tiago;
Gilchrist, Michael J.;
Down, Thomas;
Vallier, Ludovic;
Pedersen, Roger A.;
Wardle, Fiona C.;
Smith, James C.

Publication type:

Art Reproduction

Genome Wide Analysis of Acute Myeloid Leukemia Reveal Leukemia Specific Methylome and Subtype Specific Hypomethylation of Repeats.

Published in:

PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0033213

By:

Saied, Marwa H.;
Marzec, Jacek;
Khalid, Sabah;
Smith, Paul;
Down, Thomas A.;
Rakyan, Vardhman K.;
Molloy, Gael;
Raghavan, Manoj;
Debernardi, Silvana;
Young, Bryan D.

Publication type:

Article

Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus.

Published in:

PLoS ONE, 2010, v. 5, n. 11, p. 1, doi. 10.1371/journal.pone.0014040

By:

Bell, Christopher G.;
Finer, Sarah;
Lindgren, Cecilia M.;
Wilson, Gareth A.;
Rakyan, Vardhman K.;
Teschendorff, Andrew E.;
Akan, Pelin;
Stupka, Elia;
Down, Thomas A.;
Prokopenko, Inga;
Morison, Ian M.;
Mill, Jonathan;
Pidsley, Ruth;
Deloukas, Panos;
Frayling, Timothy M.;
Hattersley, Andrew T.;
McCarthy, Mark I.;
Beck, Stephan;
Hitman, Graham A.

Publication type:

Article

Differential DNA Methylation Correlates with Differential Expression of Angiogenic Factors in Human Heart Failure.

Published in:

PLoS ONE, 2010, v. 5, n. 1, p. 1, doi. 10.1371/journal.pone.0008564

By:

Movassagh, Mehregan;
Choy, Mun-Kit;
Goddard, Martin;
Bennett, Martin R.;
Down, Thomas A.;
Foo, Roger S.-Y.

Publication type:

Article

Binding of TFIIIC to SINE Elements Controls the Relocation of Activity-Dependent Neuronal Genes to Transcription Factories.

Published in:

PLoS Genetics, 2013, v. 9, n. 8, p. 1, doi. 10.1371/journal.pgen.1003699

By:

Crepaldi, Luca;
Policarpi, Cristina;
Coatti, Alessandro;
Sherlock, William T.;
Jongbloets, Bart C.;
Down, Thomas A.;
Riccio, Antonella

Publication type:

Article

Identification of Type 1 Diabetes-Associated DNA Methylation Variable Positions That Precede Disease Diagnosis.

Published in:

PLoS Genetics, 2011, v. 7, n. 9, p. 1, doi. 10.1371/journal.pgen.1002300

By:

Rakyan, Vardhman K.;
Beyan, Huriya;
Down, Thomas A.;
Hawa, Mohammed I.;
Maslau, Siarhei;
Aden, Deeqo;
Daunay, Antoine;
Busato, Florence;
Mein, Charles A.;
Manfras, Burkhard;
Dias, Kerith-Rae M.;
Bell, Christopher G.;
Tost, Jörg;
Boehm, Bernhard O.;
Beck, Stephan;
Leslie, R. David

Publication type:

Article

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Published in:

Nature Biotechnology, 2008, v. 26, n. 7, p. 779, doi. 10.1038/nbt1414

By:

Down, Thomas A;
Rakyan, Vardhman K;
Turner, Daniel J;
Flicek, Paul;
Li, Heng;
Kulesha, Eugene;
Gräf, Stefan;
Johnson, Nathan;
Herrero, Javier;
Tomazou, Eleni M;
Thorne, Natalie P;
Bäckdahl, Liselotte;
Herberth, Marlis;
Howe, Kevin L;
Jackson, David K;
Miretti, Marcos M;
Marioni, John C;
Birney, Ewan;
Hubbard, Tim J P;
Durbin, Richard

Publication type:

Article

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated.

Published in:

BMC Genomics, 2010, v. 11, p. 519, doi. 10.1186/1471-2164-11-519

By:

Choy, Mun-Kit;
Movassagh, Mehregan;
Goh, Hock-Guan;
Bennett, Martin R.;
Down, Thomas A.;
Foo, Roger S. Y.

Publication type:

Article

What can we learn from noncoding regions of similarity between genomes?

Published in:

BMC Bioinformatics, 2004, v. 5, p. 1, doi. 10.1186/1471-2105-5-131

By:

Down, Thomas A.;
Hubbard, Tim J. P.

Publication type:

Article