Tim Hubbard: all publications

• Publications

  • Integrating biological data - the Distributed Annotation System. BMC bioinformatics 9 Suppl 8 , S3 (2008) (Epub 22 Jul 2008) PubMed ID:(18673527)

  • Andreeva A, Howorth D, Chandonia J, Brenner S, Hubbard T, Chothia C, Murzin A. Data growth and its impact on the SCOP database: new developments. Nucleic acids research 36 (Database issue) , D419-25 (2008) (Epub 13 Nov 2007) PubMed ID:(18000004)

  • Brosch M, Swamy S, Hubbard T, Choudhary J. Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold. Molecular & cellular proteomics : MCP 7 (5) , 962-70 (2008) (Epub 23 Jan 2008) PubMed ID:(18216375)

  • Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E. Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic acids research 36 (Database issue) , D5-12 (2008) (Epub 26 Nov 2007) PubMed ID:(18039715)

  • Doğruel M, Down T, Hubbard T. NestedMICA as an ab initio protein motif discovery tool. BMC bioinformatics 9 , 19 (2008) (Epub 14 Jan 2008) PubMed ID:(18194537)

  • Down T, Rakyan V, Turner D, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou E, Thorne N, Bäckdahl L, Herberth M, Howe K, Jackson D, Miretti M, Marioni J, Birney E, Hubbard T, Durbin R, Tavaré S, Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature biotechnology 26 (7) , 779-85 (2008) PubMed ID:(18612301)

  • Flicek P, Aken B, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer S, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe K, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez X, Herrero J, Hubbard T, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S. Ensembl 2008. Nucleic acids research 36 (Database issue) , D707-14 (2008) (Epub 13 Nov 2007) PubMed ID:(18000006)

  • Rakyan V, Down T, Thorne N, Flicek P, Kulesha E, Gräf S, Tomazou E, Bäckdahl L, Johnson N, Herberth M, Howe K, Jackson D, Miretti M, Fiegler H, Marioni J, Birney E, Hubbard T, Carter N, Tavaré S, Beck S. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome research 18 (9) , 1518-29 (2008) (Epub 24 Jun 2008) PubMed ID:(18577705)

  • Uren A, Kool J, Matentzoglu K, de Ridder J, Mattison J, van Uitert M, Lagcher W, Sie D, Tanger E, Cox T, Reinders M, Hubbard T, Rogers J, Jonkers J, Wessels L, Adams D, van Lohuizen M, Berns A. Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks. Cell 133 (4) , 727-41 (2008) PubMed ID:(18485879)

  • Wilming L, Gilbert J, Howe K, Trevanion S, Hubbard T, Harrow J. The vertebrate genome annotation (Vega) database. Nucleic acids research 36 (Database issue) , D753-60 (2008) (Epub 14 Nov 2007) PubMed ID:(18003653)