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University of Cambridge > Department of Oncology > Computational Biology Group > Publications

Computational Biology Group Publications

Selected recent publications are listed below.

2008

  • Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie ME, Deloukas P, Tavaré S, Dermitzakis ET. Exploring epistatic effects between regulatory and protein-coding variation PLoS Genet 2008 Oct;4(10):e1000244. Epub 2008 Oct 31 [pubmed]
  • Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. BASH: A tool for managing BeadArray spatial artefacts Bioinformatics Oct 25 Epub ahead of print [pubmed]
  • Lynch AG, Dunning MJ, Iddawela M, Barbose-Morais NL, Ritchie ME. Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms Statistical Methods in Medical Research in press.
  • Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S, Odom DT. Species-specific transcription in mice carrying human chromosome 21 Science 2008 Oct 17;322(5900):434-8 [pubmed]
  • Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis Nat Biotechnol 2008 Jul;26(7):779-85 [pubmed]
  • Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Genome Res 2008 Sep;18(9):1518-29 [pubmed]
  • Fanshawe TR, Lynch AG, Ellis IO, Green AR, Hanka R. Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading PLoS ONE 3(8) [pubmed]
  • Marioni JC, White M, Tavaré S, Lynch AG. Hidden copy number variation in the HapMap population, PNAS 105 (29) 10067-10072 [pubmed]
  • Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavaré S, Miska EA. Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline. Mol Cell. 2008 doi.10.1016/j.molcel.2008.06.003 [publisher online]
  • Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S, Lynch AG. Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Research Notes, 2008 1:18 [publisher online]
  • Palmer RD, Barbosa-Morais NL, Gooding EL, Muralidhar B, Thornton CM, Pett MR, Roberts I, Schneider DT, Thorne N, Tavaré S, Nicholson JC, Coleman N; On behalf of The Childrens Cancer and Leukaemia Group (CCLG). Pediatric malignant germ cell tumours show characteristic transcriptome profiles, Cancer Research, 2008 Jun 1;68(11):4239-47 [pubmed]
  • Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S, Ritchie ME. Statistical issues in the analysis of Illumina data. BMC Bioinformatics 2008 9:85 [publisher online]

2007

  • Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S, Hurles ME. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol. 2007 Oct 25;8(10):R228 [pubmed]
  • Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais NL, Wilson MD, Bhattacharjee A, Young RA, Tavaré S, Lees JA, Odom DT. Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor. PLoS ONE. 2007 Oct 24;2(10):e1061 [pubmed]
  • Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C. High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol. 2007 Oct 9;8(10):R215 [pubmed]
  • Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO, Tavaré S, Caldas C, Miska EA. MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype. Genome Biol. 2007 Oct 8;8(10):R214 [pubmed]
  • Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET. Population genomics of human gene expression. Nat Genet. 2007 Oct;39(10):1217-24 [pubmed]
  • Massie CE, Adryan B, Barbosa-Morais NL, Lynch AG, Tran MG, Neal DE, Mills IG. New androgen receptor genomic targets show an interaction with the ETS1 transcription factor. EMBO Rep. 2007 Sep;8(9):871-8. [pubmed]
  • Muralidhar B, Goldstein LD, Ng G, Winder DM, Palmer RD, Gooding EL, Barbosa-Morais NL, Mukherjee G, Thorne NP, Roberts I, Pett MR, Coleman N. Global microRNA profiles in cervical squamous cell carcinoma depend on Drosha expression levels. J Pathol. 2007 Aug;212(4):368-77 [pubmed]
  • Lynch AG, Marioni JC, Tavaré S. Numbers of Copy-Number Variations and False-Negative Rates Will Be Underestimated If We Do Not Account for the Dependence between Repeated Experiments. Am J Hum Genet. 2007 Aug;81(2):418-20 [pubmed]
  • Lynch AG, Neal DE, Kelly JD, Burtt GJ, Thorne NP. Missing channels in two-colour microarray experiments: combining single-channel and two-channel data. BMC Bioinformatics 2007 Jan 25;8:26 [pubmed]
  • Dunning MJ, Smith ML, Ritchie ME, Tavaré S. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 2007 Aug 15;23(16):2183-4. Epub 2007 Jun 22 [pubmed]
  • Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavaré S, Deloukas P, Hurles ME, Dermitzakis ET. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007 Feb 9;315(5813):848-53 [pubmed]
  • Chin SF, Wang Y, Thorne NP, Teschendorff AE, Pinder SE, Vias M, Naderi A, Roberts I, Barbosa-Morais NL, Garcia MJ, Iyer NG, Kranjac T, Robertson JF, Aparicio S, Tavaré S, Ellis I, Brenton JD, Caldas C. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene 2007 Mar 22;26(13):1959-70 [pubmed]

2006

  • Dunning MJ, Thorne NP, Tavaré S. Quality control and low-level statistical analysis of Illumina BeadArrays. REVSTAT - Statistical Journal, Volume 4, Number 1, March 2006, pages 1-30 [REVSTAT pdf] or [REVSTAT online]
  • Marioni JC, Thorne NP, Tavaré S. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics, 2006 22(9):1144-6. Epub 2006 Mar 13 [pubmed]
  • Bundy JG, Iyer NG, Gentile MS, Hu D, Maia AT, Thorne NP, Brenton J, Caldas C, Brindle KM. Metabolic consequences of p300 gene deletion in human colon cancer cells. Cancer Res. 2006;66(15):7606-14 [pubmed]
  • Ibrahim AE, Thorne NP, Baird K, Barbosa-Morais NL, Tavaré S, Collins VP, Wyllie AH, Arends MJ, Brenton JD. MMASS: an optimised array-based method for assessing CpG island methylation. Nucleic Acids Res. 2006;34(20):e136. Epub 2006 Oct 13 [pubmed]

© 2008 Computational Biology Group, Department of Oncology, University of Cambridge