Selected Publications
Deonier RC, Tavaré S and Waterman MS. Computational Genome Analysis: An Introduction. New York: Springer Verlag, 2005.
Kim JY, Siegmund KD, Tavaré S and Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Med 2005; 3: 10. PubMed PDF (in UKPMC)
Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S, Deloukas P and Dermatzakis ET. Genome-wide associations of gene expression variation in humans. PLoS Gen 2005; 1: e78. PubMed PDF (in UKPMC)
Kim JY, Tavaré and Shibata D. Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proc Natl Acad Sci USA 2005; 102: 17739-17744. PubMed PDF (in UKPMC)
Marjoram P, Molitor J, Plagnol V and Tavaré S. Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 2003; 100: 15324-15328. PubMed PDF (in UKPMC)
Yatabe Y, Tavaré S and Shibata D. Investigating stem cells in human colon by using methylation patterns. Proc Natl Acad Sci USA 2001; 98: 10839-10844. PubMed PDF (in UKPMC)
Primary Research Publications
2008
Bernard F, Al-Tamimi YZ, Chatfield D, Lynch AG, Matta BF, Menon DK. Serum albumin level as a predictor of outcome in traumatic brain injury: potential for treatment. The Journal of Trauma 2008; 64:872-85
Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. BASH: A tool for managing BeadArray spatial artefacts. Bioinformatics 2008; 24:2921-2
Chu M, Siegmund KD, Hao QL, Crooks GM, Tavar&ecute; S, Shibata D. Inferring relative numbers of human leucocyte genome replications. British Journal of Haematology 2008; 141:862-71
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, Tavar&ecute; S, Miska EA. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Molecular Cell 2008; 31:79-90
Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie ME, Deloukas P, Tavar&ecute; S, Dermitzakis ET. Modifier effects between regulatory and protein-coding variation. PLoS Genetics 2008; 4:e1000244
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, Tavar&ecute; S, Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnology 2008; 26:779-785
Driver KE, Song H, Lesueur F, Ahmed S, Barbosa-Morais NL, Tyrer J, Ponder BAJ, Easton DF, Pharoah PD, Dunning AM; for the SEARCH Team. Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population. Carcinogenesis 2008; 29:333-41
Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavar&ecute; S, Ritchie ME. Statistical issues in the analysis of Illumina data. BMC Bioinformatics 2008; 9:85
Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavar&ecute; S, Lynch AG. Spike-in validation of an Illumina-specific variance stabilizing transformation. BMC Research Notes 2008; 1:18
Dwyer JP, Ritchie ME, Smyth GK, Harrap SB, Delbridge LMD, Domenighetti AA, Di Nicolantonio R. Myocardial gene expression associated with genetic cardiac hypertension in the absence of hypertension. Hypertension Research 2008; 31:451-455
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 2008; 8:e2925
Git A, Spiteri I, Blenkiron C, Dunning M, Pole JC, Chin S-F, Wang Y, Smith J, Livesey FJ, Caldas C. PMC42, a breast progenitor cancer cell line, has normal-like mRNA and miRNA transcriptomes. Breast Cancer Research 2008; 10:R54
Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, von Lindern M, Carmo-Fonseca M. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Research 2008; 36:4823-32
Grover D, Tower J, Tavaré S. O fly, where art thou? J R Soc Interface 2008 Mar 26; [Epub ahead of print]
Huggins CE, Domenighetti AA, Ritchie ME, Khalil N, Favaloro JM, Proietto J, Smyth GK, Pepe S, Delbridge LMD. Functional and metabolic remodelling in GLUT4-deficient hearts confers hyper-responsiveness to substrate intervention. Journal of Molecular and Cellular Cardiology 2008; 44:270-280
Marioni JC, White M, Tavar&ecute; S, Lynch AG. Hidden copy number variation in the HapMap population. Proceedings of National Academy of Sciences USA 2008; 105:10067-72
Michaud J, Simpson KM. Escher R, Buchet-Poyau K, Beissbarth T, Carmichael C, Ritchie ME, Schütz F, Cannon P, Liu M, Shen X, Ito Y, Raskind WH, Horwitz M, Osato M., Turner DR, Speed TP, Kavallaris M, Smyth GK, Scott HS. Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics 2008; 9:363
Palmer RD, Barbosa-Morais NL, Gooding EL, Muralidhar B, Thornton CM, Pett MR, Roberts I, Schneider DT, Thorne N, Tavar&ecute; S, Nicholson JC, Coleman N; Children's Cancer and Leukaemia Group. Pediatric malignant germ cell tumors show characteristic transcriptome profiles. Cancer Research 2008; 68:4239-47
Rakyan V, Down T, Thorne N, Flicek P, Kulesha E, Graf S, Tomazou E, Backdahl L, Johnson N, Herberth M, Howe K, Jackson D, Miretti M, Fiegler H, Marioni J, Birney E, Hubbard T, Carter N, Tavar&ecute; S, Beck S. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research 2008; 18:1518-29
Silver JD, Ritchie ME, Smyth GK. Microarray background correction: Maximum Likelihood estimation for the normal-exponential convolution. Biostatistics 2008; Dec 8 [Epub ahead of print]
Szyjka SJ, Aparicio JG, Viggiani CJ, Knott S, Xu W, Tavar&ecute; S, Aparicio OM. Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes and Development 2008; 22:1906-20
Veerakumarasivam A, Goldstein LD, Saeb-Parsy K, Scott HE, Warren A, Thorne NP, Mills IG, Venkitaraman A, Neal DE, Kelly JD. AURKA overexpression accompanies dysregulation of DNA-damage response genes in invasive urothelial cell carcinoma Cell Cycle 2008; 7:45-53
Walsh SR, Boyle JR, Lynch AG, Sadat U, Carpenter JP, Tang TY, Gaunt ME. Suprarenal endograft fixation and medium-term renal function: systematic review and meta-analysis. Journal of Vascular Surgery 2008; 47:1364-1370
Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavar&ecute; S, Odom DT. Species-specific transcription in mice carrying human chromosome 21. Science 2008; 322:434-8
2007
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 tumor subtype. Genome Biol 2007; 8(10):Article R214
Burnet NG, Lynch AG, Jefferies SJ, Price SJ, Jones PH, Antoun NM, Xuereb JH, Pohl U. High grade glioma: imaging combined with pathological grade defines management and predicts prognosis. Radiotherapy and Oncology 2007; 85:371-378.
Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, De Wiel MAV, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007; 8(10):Article R215
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 JFR, 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; 26(13):1959-1970
Chu MW, Siegmund KD, Eckstam CL, Kim JY, Yang AS, Kanel GC, Tavaré S, Shibata D. Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging. BMC Med Genet 2007; 8:Article 50
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; 2:e1061.
Dunning MJ, Smith ML, Ritchie ME, Tavaré S. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 2007; 23(16):2183-2184
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; 8:Article 26
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; 8(10):Article R228
Martin RD, Soligo C, Tavaré S. Primate origins: Implications of a cretaceous ancestry. Folia Primatol 2007; 78(5-6):277-296
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; 8(9):871-878
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; 212(4):368-377
Naderi A, Teschendorff AE, Barbosa-Morais NI, Pinder SE, Green AR, Powe DG, Robertson JFR, Aparicio S, Ellis IO, Brenton JD, Caldas C. A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene 2007; 26(10):1507-1516
Nicolas P, Kim KM, Shibata D, Tavaré S. The stem cell population of the human colon crypt: Analysis via methylation patterns. PLoS Comput Biol 2007; 3(3):364-374
Price SJ, Jena R, Green HAL, Kirkby NF, Lynch AG, Coles CE, Pickard JD, Giltard JH, Burnet NG. Early radiotherapy dose response and lack of hypersensitivity effect in normal brain tissue: a sequential dynamic susceptibility imaging study of cerebral perfusion. Clin Oncol (R Coll Radiol) 2007; 19(8):577-587
Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007; 23:2700-2707.
Skvortsov D, Abdueva D, Curtis C, Schaub B, Tavaré S. Explaining differences in saturation levels for Affymetrix GeneChip (R) arrays. Nucleic Acids Res 2007; 35(12):4154-4163
Skvortsov D, Abdueva D, Stitzer ME, Finkel SE, Tavaré S. Using expression arrays for copy number detection: an example from E. coli. BMC Bioinformatics 2007; 8:Article 203
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; 315(5813):848-853
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; 39(10):1217-1224
2006
Abdueva D, Skvortsov D, Tavaré S. Non-linear analysis of GeneChip arrays. Nucleic Acids Res 2006; 34(15):Article E105
Ibrahim AEK, Thorne NP, Baird K, Barbosa-Morais NL, Tavaré S, Collins VP, Wyllie AH, Arends MJ, Brenton JD. MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res 2006; 34(20):Article e136
Jakobsson M, Hagenblad J, Tavaré S, Sall T, Hallden C, Lind-Hallden C, Nordborg M. A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers. Mol Biol Evol 2006; 23(6):1217-1231
Jiang R, Marjoram P, Borevitz JO, Tavaré S. Inferring population parameters from single-feature polymorphism data. Genetics 2006; 173(4):2257-2267
Kim JY, Tavaré S, Shibata D. Human hair genealogies and stem cell latency. BMC Biol 2006; 4:Article 2
Marioni JC, Thorne NP, Tavaré S. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics 2006; 22(9):1144-1146
Shibata D, Tavaré S. Counting divisions in a human somatic cell tree - How, what and why? Cell Cycle 2006; 5(6):610-614
2005
Calabrese P, Mecklin JP, Jarvinen H, Aaltonen LA, Tavaré S, Shibata D. Numbers of mutations to different types of colorectal cancer. BMC Cancer 2005; 5:Article 12
Clark RM, Tavaré S, Doebley J. Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol Biol Evol 2005; 22(11):2304-2312
Innan H, Zhang KY, Marjoram P, Tavaré S, Rosenberg NA. Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics 2005; 169(3):1763-1777
Kim JY, Siegmund KD, Tavaré S, Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Med 2005; 3:Article 10
Kim JY, Tavaré S, Shibata D. Counting human somatic cell replications: Methylation mirrors endometrial stem cell divisions. Proc Natl Acad Sci U S A 2005; 102(49):17739-17744
Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S, Deloukas P, Dermitzakis ET. Genome-wide associations of gene expression variation in humans. PLoS Genet 2005; 1(6):695-704
2004
Landis GN, Abdueva D, Skvortsov D, Yang JD, Rabin BE, Carrick J, Tavaré S, Tower J. Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc Natl Acad Sci U S A 2004; 101(20):7663-7668
Other Publications
Walsh SR, Boyle JR, Lynch AG, Sadat U, Carpenter JP, Tang TY, Gaunt ME. Suprarenal endograft fixation and medium-term renal function: systematic review and meta-analysis. J Vasc Surg 2008;47(6):1364-1370.
Curtis C, Landis GN, Folk D, Wehr NB, Hoe N, Waskar M, Abdueva D, Skvortsov D, Ford D, Luu A, Badrinath A, Levine RL, Bradley TJ, Tavaré S, Tower J. Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes. Genome Biol 2007; 8(12):Article R262
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; 81(2):418-420
Shibata D, Tavaré S. Stem cell chronicles: Autobiographies within Genomes. Stem Cell Rev 2007; 3(1):94-103
Marjoram P, Tavaré S. Modern computational approaches for analysing molecular genetic variation data. Nat Rev Genet 2006; 7(10):759-770
