Simon Tavaré

Simon Tavaré

PUBLICATIONS


    Submitted

    (⭑ denotes consortium paper; § denotes equal contribution; † denotes joint senior authors)

    da Silva PH, Jamshidpey A & Tavaré S. Markov chains arising from biased random derangements. Submitted. arXiv version: 2211.13831.

    Books

  1. Deonier RC, Tavaré S & Waterman MS. Computational Genome Analysis: An Introduction. Springer Verlag, New York. 2005, 540pp.

  2. Arratia R, Barbour AD & Tavaré S. Logarithmic Combinatorial Structures: A Probabilistic Approach. 352pp, 2003. EMS Monographs in Mathematics, 1. European Mathematical Society Publishing House, Zuerich.

  3. Donnelly P & Tavaré S. (eds) Progress in Population Genetics and Human Evolution. IMA Volumes in Mathematics and its Applications, 87. Springer Verlag, Berlin. 1997, 330pp.

    4. Unsubmitted papers on arXivs

  4. Dinh KN, Vázquez-Garcia I, Chan A, Malhotra R, Weiner A, McPherson A & Tavaré S. CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution., biorXiv, 10.1101/2024.04.03.587939, 2024.

    5. In Press

  5. Ng AWT, McClurg DP, Wesley B, Zamani SA, Miremadi A, Giger O, ten Hoopen R, Devonshire G, Redmond AM, Grehan N, Blasko AG, Li X, Aparicio S, Tavaré S, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Nowicki-Osuch K & Fitzgerald RC. Disentangling oncogenic amplicons in esophageal adenocarcinoma. Nature Communications

    6. 2024

  6. da Silva PH, Jamshidpey A & Tavaré S. Another view of sequential sampling in the birth process with immigration. Journal of Mathematical Biology, 88, art. 27, 2024. https://doi.org/10.1007/s00285-023-02041-0. arXiv version: 2210.07307.

    7. 2023

  7. Melamed D, Choi A, Reilein A, Tavaré S & Kalderon D. Spatial regulation of Drosophila ovarian Follicle Stem Cell division rates and cell cycle transitions. PLoS Genetics, 19, e1010965, 2023.

  8. Kunes RZ, Yin M, Land M, Haviv D, Pe'er D & Tavaré S. Gradient estimation for binary latent variables via gradient variance clipping. Proceedings of the AAAI Conference on Artificial Intelligence, 37(7), 8405–8412, 2023. doi: 10.1609/aaai.v37i7.26013. arXiv version: 2208.06124.

  9. González-Solares EA, Dariush A, González-Fernández C, Yoldaş AK, Molaeinezhad A, Al Sa'd M, Smith L, Millar N, Whitmarsh T, Millar N, Chornay N, Falciatori I, Fatemi A, Goodwin D, Kuett L, Mulvey CM, Páez Ribes M, Qosaj F, Roth A, Sepulveda LA, Vázquez-García I, Watson S, Windhager J, Aparicio S, Bodenmiller B, Boyden E, Caldas C, Harris O, Shah SP, Tavaré S, CRUK IMAXT Grand Challenge Team, Bressan D, Hannon G & Walton NA. The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) high throughput data and analysis infrastructure. Biological Imaging, 3, e11, 2023. biorXiv version: 2021.06.22.448403v1.

  10. Nowicki-Osuch K, Zhuang L, Cheung TS, Black E, Masque-Soler N, Devonshire G, Redmond AM, Freeman A, di Pietro M, Pilonis N, Januszewicz W, O'Donovan M, Tavaré S, Shields J & Fitzgerald RC. Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia. Cancer Discovery, 13,1346–1363, 2023.

  11. da Silva PH, Jamshidpey A, McCullagh P & Tavaré S. Fisher's measure of variability in repeated samples. Bernoulli, 29, 1166–1194, 2023.

    12. 2022

  12. Lynch AG, Smith ML, Eldridge MD & Tavaré S on behalf of the OCCAMS consortium. PCR duplicate proportion estimation and consequences for DNA copy number calculations. pp 259–279 in Recent Developments in Statistics and Data Science, eds. Bispo R, Henriques-Rodrigues L, Alpizar-Jara R & de Carvalho M. Vol 398, Springer Proceedings in Mathematics & Statistics, 2022.

  13. da Silva PH, Jamshidpey A & Tavaré S. The Feller Coupling for random derangements. Stochastic Processes and their Applications, 150, 1139–1164, 2022. [Original version is arXiv:2006.04840.]

  14. Ng AWT, Contino G, Killcoyne S, Devonshire G, Hsu R, Abbas S, Su J, Redmond A, Weaver JMJ, Eldridge MD, Tavaré S, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Edwards PAW & Fitzgerald RC. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas. Communications Biology, 5, art 335, 2022.

  15. Tavaré S. A note on the Screaming Toes game. Journal of Applied Probability, 59, 118–130, 2022 [Original version: arXiv: 2006.04805].

  16. ⭑ Kuett L, Catena C, Özcan A, Plüss A, Cancer Grand Challenges IMAXT Consortium, Schraml P, Moch H, de Souza N & Bodenmiller B. Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nature Cancer, 3, 122–133, 2022.

    17. 2021

  17. Tavaré S. The magical Ewens Sampling Formula. Bulletin of the London Mathematical Society, 53, 1563–1582, 2021.

  18. ⭑ Au L, Hatipoglu E, ..., Jamal-Hanjani M on behalf of the PEACE Consortium, ..., Swanton C, Quezada SA, Turajlic S and on behalf of the TRACERx Renal Consortium. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma. Cancer Cell, 39, 1497–1518, 2021.

  19. ⭑ Abujudeh S, Zeki SS, van Lanschot MCJ, Pusung M, Weaver JMJ, Li X, Noorani A, Metz AJ, Bornschein J, Bower L, Miremadi A, Fitzgerald RC, Morrissey ER & Lynch AG. Low-cost and clinically applicable copy number profiling using repeat DNA. BMC Genomics, 23:599, 2022.

  20. ⭑ Georgopoulou D, Callari M, Rueda OM, Shea A, Martin A, Giovannetti A, Qosaj F, Dariush A, Chin S-F, Carnevalli LS, Provenzano E, Greenwood W, Lerda G, Esmaeilishirazifard E, O'Reilly M, Serra V, Bressan D, IMAXT Consortium, Mills GB, Ali HR, Cosulich SS, Hannon GJ, Bruna A & Caldas C . Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response. Nat Comm, 12, art. 1998, 2021.

  21. ⭑ Alon S, Goodwin DR, Sinha A et al. Expansion sequencing: spatially precise in situ transcriptomics in intact biological systems. Science, 371, eaax2656, 2021.

  22. Williams EH, Flint TR, Connell CM, Giglio D, Lee H, Ha T, Gablenz E, Bird N, Weaver JMJ, Potts H, Whitley CT, Bookman MA, Lynch AG, Meyer HV, Tavaré S & Janowitz T. CamGFR v2: a new model for estimating the glomerular filtration rate from standardized or non-standardized creatinine in patients with cancer. Clinical Cancer Research, 27, 1381–1390, 2021.

  23. Touloumis A, Marioni JC & Tavaré S. Hypothesis testing for the covariance matrix in high-dimensional transposable data with Kronecker product dependence structure. Statistica Sinica, 31, 1309–1329, 2021. [Original version: arXiv:1404.7684v2, 2014.]

    24. 2020

  24. ⭑ Knight WRC, McEwan R, Byrne BE, Habib W, Bott R, Zylstra J, Mahadeva U, Gossage JA & OCCAMS Consortium. Endoscopic tumour morphology impacts survival in adenocarcinoma of the oesophagus. European Journal of Surgical Oncology, 46, 2257–2261, 2020.

  25. ⭑ Litchfield K, Stanislaw S, Spain L, Gallegos LL, Rowan A, Schnidrig D, Rosenbaum H, Harle A, Au L, Hill SM, Tippu Z, Thomas J, Thompson L, Xu H, Horswell S, Barhoumi A, Jones C, Leith KF, Burgess DL, Watkins TBK, Lim E, Birkbak NJ, Lamy P, Nordentoft I, Dyrskjøt L, Pickering L, Hazell S, Jamal-Hanjani M, PEACE Consortium, Larkin J, Swanton C, Alexander NR & Turajlic S. Representative sequencing: unbiased sampling of solid tumor tissue. Cell Reports, 31, 107550, 2020.

  26. Biasci D, Thaventhiran J§ & Tavaré S§. Fibroblastic reticular cells predict response to immune checkpoint inhibitors. biorXiv, doi.org/10.1101/2020.02.19.955666, 2020.

  27. ⭑ Rahman SA,Walker RC, Lloyd MA, Grace BL, van Boxel GI, Kingma BF, Ruurda JP, van Hillegersberg R, Harris S, Parsons S, Mercer S, Griffiths EA, O'Neill JR, Turkington R, Fitzgerald RC& Underwood TJ, on behalf of the OCCAMS Consortium. Machine learning to predict early recurrence after oesophageal cancer surgery. Br J Surg, 107, 1042–1052, 2020.

  28. Perner J, Abbas S, Nowicki-Osuch K, Devonshire G, Eldridge M, Tavaré S & Fitzgerald R. The mutREAD method detects mutational signatures from low quantities of cancer DNA. Nature Communications, 11, 3166, 2020.

  29. Jammula S, Katz-Summercorn A, Li X, Linossi C, Smyth E, Killcoyne S, Biasci D, Subash VV, Abbas S, Blasko A, Devonshire G, Grantham A, Wronowski F, O'Donovan M, Grehan N, Eldridge M, Tavaré S, the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium & Fitzgerald RC. Identification of subtypes of Barrett's esophagus and esophageal adenocarcinoma based on DNA methylation profiles and integration of transcriptome and genome data. Gastroenterology, 158, 1682–1697, 2020.

  30. ⭑ Ali HR, Jackson HW, Zanotelli VRT, Danenberg E, Fischer JR, Bardwell H, Provenzano H, CRUK IMAXT Grand Challenge Team, Rueda OM, Chin S-F, Aparicio S, Caldas C & Bodenmiller B. Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer. Nature Cancer, 1, 163 –175, 2020.

  31. Dinh KN, Jaksik R, Kimmel M, Lambert A & Tavaré S. Statistical inference for the evolutionary history of cancer genomes. Statistical Science, 35, 129–144, 2020.

    32. 2019

  32. ⭑ Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T , Ting J, Grewal D, Nielsen C, Leung, S, Bojilova V, Smith M, Golovko O, Poon S, Eirew P, Kabeer F, Ruiz de Algara T, Lee SR, Taghiyar MJ, Huebner C, Ngo J, Chan T, Vatrt-Watts S, Walters P, Abrar N, Chan S, Wiens M, Martin, L Scott RW, Underhill TM, Chavez E, Steidl C, Da Costa D, Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Mar C, Cafferty F, Gelmon K, Chia S, CRUK IMAXT Grand Challenge Team, Marra MA, Hansen C, Shah SP & Aparicio S. Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing. Cell, 179, 1207–1221, 2019.

  33. Williams EH, Connell CM, Weaver JMJ, Beh I, Potts H, Whitley CT, Bird N, Al-Sayed T, Fehr M, Cathomas R, Bertelli G, Quinton A, Lewis P, Shamash J, Wilson P, Dooley M, Poole S, Bookman MA, Earl H, Jodrell D, Tavaré S, Lynch AG & Janowitz T. Multicentre validation of the CamGFR model for estimated glomerular filtration rate. JNCI Cancer Spectrum, 3, pkz068, 2019.

  34. ⭑ Mourikis TP, Benedetti L, Foxall E, Temelkovski D, Nulsen J, Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald RC, Scaffidi P, The Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium & Ciccarelli FD. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. Nature Communications, 10, art 3101, 2019.

  35. Spencer S, Bal SK, Egner W, Allen HL, Raza SI, Ma CA, Gürel M, Zhang Y, Sun G, Sabroe RA, Greene D, Rae W, Shahin T, Kania K, Ardy RC, Thian M, Staples E, Pecchia-Bekkum A, Worrall WPM, Stephens J, Brown M, Tuna S, York M, Shackley F, Kerrin D, Sargur R, Condliffe A, Tipu HN, Kuehn HS, Rosenzweig SD, Turro E, Tavaré S, Thrasher AJ, Jodrell DI, Smith KGC, Boztug K, Milner JD & Thaventhiran JED. Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses. Journal of Experimental Medicine, 216, 1986–1998, 2019.

  36. ⭑ Bornschein J, Wernisch L, Secrier M, Miremadi A, Perner J, MacRae S, O’Donovan M, Newton R, Menon S, Bower L, Eldridge MD, Devonshire G, Cheah C, Turkington R, Hardwick RH, Selgrad M, Venerito M, Malfertheiner P, OCCAMS Consortium & Fitzgerald RC. Transcriptomic profiling reveals three molecular phenotypes of adenocarcinoma at the gastro-esophageal junction. Int J Cancer, 145, 3389–3401, 2019.

  37. ⭑ Turkington RC, Knight LA, Blayney JK, Secrier M, Douglas R, Parkes EE, Sutton EK, Stevenson L, McManus D, Halliday S, Mccavigan AM, Logan GE, Walker SM, Steele CJ, Perner J, Bornschein J, Macrae S, Miremadi A, Mccarron E, McQuaid S, Arthur K, James JA, Eatock MM, O’Neill R, Noble F, Underwood TJ, Harkin P, Salto-Tellez M, Fitzgerald RC & Kennedy RD on behalf of the Oesophageal cancer clinical and Molecular Stratification (OccaMS) Study group. Immune activation by DNA damage predicts response to chemotherapy and survival in oesophageal adenocarcinoma. Gut , 68, 1918–1927, 2019.

  38. Frankell AM, Jammula S, Li X, Contino G, Killcoyne S, Abbas S, Perner J, Bower L, Devonshire G, Ococks E, Grehan N, Mok J, O'Donovan M, MacRae S, Eldridge MD, Tavaré S, Fitzgerald RC & the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium. The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic. Nat Genet, 51, 506–516, 2019.

  39. Tavaré S. The linear birth-death process: an inferential retrospective. In Branching and Applied Probability. Papers in honour of Peter Jagers. Editors Asmussen S, Klebaner F, Nerman O & Vatutin V. Adv Appl Prob, 50A, 253–269, 2019.

    40. 2018

  40. Tavaré S. The history of ABC. Chapter 2 in Handbook of Approximate Bayesian Computation. Eds. Sisson SA, Fan Y & Beaumont MA. Taylor and Francis, 2018.

  41. Griffiths RC & Tavaré S. Ancestral inference from haplotypes and mutations. Theoret Popul Biol, 122, 12–21, 2018.

  42. Arratia R, Barbour AD, Ewens WJ & Tavaré S. Simulating the component counts of combinatorial structures. Theoret Popul Biol, 122, 5–11, 2018.

  43. Nicholson AM, Olpe C, Hoyle A, Thorsen A-S, Rus T, Colombé M, Brunton-Sim R, Kemp R, Marks K, Quirke P, Malhotra S, ten Hoopen R, Ibrahim A, Lindskog C, Myers MB, Parsons B, Tavaré S, Wilkinson M, Morrissey E & Winton DJ. Fixation and spread of somatic clones in adult human colonic epithelium. Cell Stem Cell, 22, 909–918, 2018.

  44. ⭑ Sawas T, Killcoyne S, Iyer PG, Wang KK, Smyrk TC, Kisiel JB, Qin Y, Ahlquist DA, Rustgi AK, Costa RJ, Gerstung M, Fitzgerald RC & Katzka DA for the OCCAMS Consortium. Identification of prognostic phenotypes of esophageal adenocarcinoma in two independent cohorts. Gastroenterology, 155, 1720–1728, 2018.

  45. Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton HJ, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton D, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam VJ, Shah N, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, CAMCAP study group, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, The TCGA consortium, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch A, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper C & Eeles R. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet, 50, 682–692, 2018.

  46. Reilein A, Melamed D, Tavaré S & Kalderon D. Division-independent differentiation mandates proliferative competition among stem cells. Proc Natl Acad Sci USA, 115, E3182–E3191, 2018.

    47. 2017

  47. ⭑ Noble F, Lloyd MA, Turkington R, Griffiths E, O'Donovan M, O'Neill JR, Mercer S, Parsons SL, Fitzgerald RC, Underwood TJ & OCCAMS consortium. Multicentre cohort study to define and validate pathological assessment of response to neoadjuvant therapy in oesophagogastric adenocarcinoma. Br J Surg, 104, 1816–1828, 2017.

  48. Asim M, Tarish F, Zecchini HI, Sanjiv K, Gelali E, Massie CE, Baridi A, Warren AY, Zhao W, Ogris C, McDuffus L-A, Mascalchi P, Shaw G, Dev H, Wadhwa K, Wijnhoven P, Forment JV, Lyons SR, Lynch AG, O'Neill C, Zecchini VR, Rennie PS, Baniahmad A, Tavaré S, Mills IG, Galanty Y, Crosetto N, Schultz N, Neal D & Helleday T. Synthetic lethality between Androgen receptor signaling and the PARP pathway in prostate cancer. Nat Comm, 8, art 374, 2017.

  49. ⭑ Britton E, Rogerson C, Mehta S, Li Y, Li X, OCCAMS consortium, Fitzgerald RC, Ang YS & Sharrocks AD. Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma. PLoS Genet, 13, e1006879, 2017.

  50. Janowitz T§, Williams EH§, Marshall A, Ainsworth N, Thomas PB, Sammut SJ, Shepherd S, White J, Mark PB, Lynch AG, Jodrell D, Tavaré S & Earl H. A new model for estimating glomerular filtration rate in patients with cancer. J Clinical Oncology, 35, 2798–2805, 2017.

  51. ⭑ Fels Elliott DR, Perner J, Li X, Symmons MF, Verstak B, Eldridge M, Bower L, O'Donovan M, Gay NJ, OCCAMS Consortium &: Fitzgerald RC. Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis. PLoS Genet, 13, e1006808, 2017.

  52. Noorani A§, Bornschein J§, Lynch A§, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong CAJ, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S & Fitzgerald RC, on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium. A comparative analysis of whole genome sequencing of oesophageal adenocarcinoma pre- and post- chemotherapy. Genome Research, 27, 902–912, 2017.

    53. 2016

  53. Sottoriva A & Tavaré S. Population genetics of neoplasms. Pp 31–42 in Frontiers in Cancer Research: Evolutionary Foundations, Revolutionary Directions. Eds. Maley CC \& Greaves M. Springer, New York, 2016.

  54. Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O’Donovan M, Miremadi A, Yang T-P, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PAW, Lynch AG, Tavaré S & Fitzgerald RC on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium. Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance. Nature Genetics, 48, 1131–1141, 2016.

  55. Touloumis A, Marioni JC & Tavaré S. HDTD: Analyzing multi-tissue gene expression data. Bioinformatics, 32, 2193–2195, 2016.

  56. ⭑ Garcia E, Hayden A, Birts C, Britton E, Cowie A, Pickard K, Mellone M, Choh C, Derouet M, Duriez P, Noble F, White MJ, Primrose JN, Strefford JC, Rose-Zerilli M, Thomas GJ, Ang Y, Sharrocks AD, Fitzgerald RC, Underwood TJ & OCCAMS consortium. Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1. Sci Rep, 6, 32417, 2016.
    Correction: www.nature.com/articles/s41598-018-37591-7

  57. Andrews DJ, Lynch AG & Tavaré S. Using methylation patterns for reconstructing cell division dynamics: assessing validation experiments. Chapter 1, pp 3–15 in Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology – Systems & Applications. Tran Q-N & Arabnia HR, editors. Morgan Kauffman, 2016.

  58. ⭑ Behjati S, Gundem G, Wedge DC, Roberts ND, Tarpey PS, Cooke SL, Van Loo P, Alexandrov LB, Ramakrishna M, Davies H, Nik-Zainal S, Hardy C, Latimer C, Raine KM, Stebbings L, Menzies A, Jones D, Shepherd R, Butler AP, Teague JW, Jorgensen M, Khatri B, Pillay N, Shlien A, Futreal PA, Badie C, ICGC Prostate Group, McDermott U, Bova GS, Richardson AL, Flanagan AM, Stratton MR & Campbell PJ. Mutational signatures of ionizing radiation in second malignancies. Nat Commun, 7, 12605, 2016.

  59. Arratia R, Barbour AD & Tavaré S. Exploiting the Feller coupling for the Ewens sampling formula. Statistical Science, 31, 27–29, 2016.

  60. Asim M, Massie CE, Orafidiya F, Pértega-Gomes N, Warren AY, Esmaeili M, Selth LA, Zecchini HI, Luko K, Qureshi A, Baridi A, Menon S, Madhu B, Escriu C, Lyons S, Vowler SL, Zecchini VR, Shaw G, Hessenkemper W, Russell R, Mohammed H, Stefanos N, Lynch AG, Grigorenko E, D’Santos C, Taylor C, Lamb A, Sriranjan R, Yang J, Stark R, Dehm SM, Rennie PS, Carroll JS, Griffiths JR, Tavaré S, Mills IG, McEwan IJ, Baniahmad A, Tilley WD & Neal DE Choline kinase alpha as an androgen receptor chaperone and prostate cancer therapeutic target. Journal of the National Cancer Institute, 108, djv371, 2016.

    61. 2015

  61. Madhu B, Narita M, Jauhiainen A, Menon S, Stubbs M, Tavaré S, Narita M & Griffiths JR. Metabolomic changes during cellular transformation monitored by metabolite-metabolite correlation analysis and correlated gene expression. Metabolomics, 11, 1848–1863, 2015

  62. ⭑ Ross-Innes CS, Becq J, Warren A, Cheetham RK, Northen H, O'Donovan M, Malhotra S, di Pietro M, Ivakhno S, He M, Weaver JMJ, Lynch AG, Kingsbury Z, Ross M, Humphray S, Bentley D & Fitzgerald RC for the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Study Group. Whole-genome sequencing defines new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma. Nature Genetics, 47, 1038–1046, 2015

  63. Paterson AL, Weaver JMJ, Eldridge MD, Tavaré S, Fitzgerald RC & Edwards PAW, on behalf of the OCCAMs Consortium. Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis. BMC Genomics, 16: 473, 2015

  64. Ivakhno S, Frese K, Tavaré S, Iacobuzio-Donahue C & Tuveson D. Pancreatic cancer. Ch. 26 in Systems Biology of Cancer, ed. Thiagalingam S. Cambridge University Press, pp 409–420, 2015.

  65. Greenwood AK, Ardekani R, McCann SR, Dubin ME, Sullivan A, Bensussen S, Tavaré S & Peichel CL. Genetic mapping of natural variation in schooling tendency in the threespine stickleback. G3, 5, 761–769, 2015.

  66. Touloumis A, Tavaré S & Marioni JC. Testing the mean matrix in high-dimensional transposable data. Biometrics, 71, 157–166, 2015.

  67. Kirschner K§, Samarajiwa SA§, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S & Narita M. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genetics, 11, e1005053, 2015.

  68. Josephidou M, Lynch AG & Tavaré S. multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples. Nucleic Acids Research, 43, e61, 2015.

  69. Gubernator M, Slater SC, Spencer HL, Spiteri I, Sottoriva A, Riu F, Rowlinson J, Avolio E, Katare R, Mangialardi G, Oikawa A, Reni C, Campagnolo P, Spinetti G, Touloumis A, Tavaré S, Prandi F, Pesce M, Hofner M, Klemens V, Emanueli C, Angelini G & Madeddu P. The epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia. Arteriosclerosis, Thrombosis, and Vascular Biology, 35, 675–688, 2015

  70. ⭑ Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, ICGC Prostate UK Group, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC & Bova GS. The evolutionary history of lethal metastatic prostate cancer. Nature, 520, 353–357, 2015.

  71. Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker H, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer D, Cooper CS, Eeles R, Warren A, Tavaré S, Neal DE & Lynch AG. HES5 silencing is an early and recurrent change in prostate tumourigenesis. Endocrine-Related Cancer, 22, 131–144, 2015.

  72. ⭑ Vollan HKM, Rueda OM, Chin S-F, Curtis C, Turashvili G, Shah S, Lingjærde AC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, METABRIC Group, Brenton JD, Pharoah PDP, Børresen-Dale A-L, Aparicio S, Caldas C. A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Molecular Oncology, 9, 115–127, 2015.

  73. Piccirillo SGM, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis CN, Marioni JC, Tavaré S & Watts C. Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone. Cancer Research, 75, 194–202, 2015.

    74. 2014

  74. Cairns J, Lynch AG & Tavaré S. Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data. Frontiers in Genetics, 5: 399, 2014.

  75. Silva A-L, Dawson SN, Arends MJ, Guttula K, Hall N, Cameron EA, Huang TH-M , Brenton JD, Tavaré S, Bienz M & Ibrahim AEK. Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists. BMC Cancer, 14: 891, 2014.

  76. Jauhiainen A, Basetti M, Narita M, Narita M, Griffiths J & Tavaré S. Normalization of metabolomics data with applications to correlation maps. Bioinformatics, 30, 2155–2161, 2014.

  77. Weaver JMJ§, Ross-Innes CS§, Shannon N§, Lynch AG§, Forshew T, Barbera M, Murtaza M, Ong C-AJ, Lao-Sirieix P, Dunning M, Smith L, Smith ML, Anderson CM, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PAW, Rosenfeld N, Tavaré S, Fitzgerald RC, and the OCCAMS consortium. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nature Genetics, 46, 837–843, 2014.

  78. Ostrow AZ, Nellimoottil T, Knott SRV, Fox CA, Tavaré S & Aparicio OM. Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics. PLoS ONE, 9, e87647, 2014.

  79. Turro E, Astle WJ & Tavaré S. Flexible analysis of RNA-seq data using mixed effects models. Bioinformatics, 30, 180–188, 2014.

    80. 2013

  80. Fu QA, Russell S, Bray S & Tavaré S. Bayesian clustering of replicated time-course gene expression data with weak signals. Annals of Applied Statistics, 7, 1334–1361, 2013.

  81. Kozar SK§, Morrissey E§, NIcholson AM, van der Heijden M, Kemp R, Tavaré S, Vermeulen L & Winton DJ. Continuous clonal labeling defines the functional stem cell compartment in intestinal crypts and adenomas. Cell Stem Cell, 13, 626–633, 2013.

  82. Vermeulen L§, Morrissey E§, van der Heijden M, Nicholson AM, Sottoriva A, Buczacki S, Kemp R, Tavaré S & Winton DJ. Defining stem cell dynamics in models of intestinal tumor initiation. Science, 342, 995–998, 2013.

  83. Ardekani R, Greenwood AK, Peichel CL & Tavaré S. Automated quantification of the schooling behaviour of sticklebacks. EURASIP Journal on Image and Video Processing, Art 61, 2013. doi:10.1186/1687-5281-2013-61

  84. Cairns JC, Lynch AG & Tavaré S. Statistical aspects of ChIP-seq analysis. Pp 138–169 in Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, eds. Do K, Qin Z & Vannucci M. Cambridge University Press, 2013.

  85. Newman S, Howarth KD, Greenman CD, Bignell GR, Tavaré S & Edwards PAW. The relative timing of mutations in a breast cancer genome. PLoS ONE, 8, e64991, 2013.

  86. Marjoram P & Tavaré S. The coalescent. In Brenner's Encyclopedia of Genetics, 2nd Edition, Vol 2, eds. Maloy S & Hughes K. Academic Press, San Diego, pp. 54–57, 2013.

  87. Zhong Y, Nellimoottil T, Peace JM, Knott SRV, Villwock SK, Yee JM, Jancuska JM, Rege S, Tecklenburg M, Sclafani RA, Tavaré S & Aparicio OM. The level of origin firing inversely affects the rate of replication fork progression. Journal of Cell Biology, 201, 373–383, 2013.

  88. Sottoriva A§, Spiteri I§, Piccirillo SGM, Touloumis A, Collins VP, Marioni JC, Curtis CN, Watts C† & Tavaré S†. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci USA, 110, 4009–4014, 2013.

  89. Ardekani R, Tavaré S & Tower J. Assessing senescence in Drosophila using video tracking. Methods Mol Bio, 965, 501–516, 2013.

  90. Sottoriva A, Spiteri, I, Shibata D, Curtis C & Tavaré S. Single molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer Research, 73, 41–49, 2013.

  91. Housden BE, Fu A, Krejci A, Bernard F, Fischer B, Tavaré S, Russell S & Bray SJ. Transcriptional dynamics elicited by a short pulse of Notch activation involves feed-forward regulation by E(spl)/Hes genes. PLoS Genetics, 9: e1003162, 2013.

  92. Ardekani R, Biyani A, Dalton JE, Saltz JB, Arbeitman MN, Tower J, Nuzhdin S & Tavaré S. Three-dimensional tracking and behaviour monitoring of multiple fruit flies. Journal of the Royal Society Interface, 10: 20120547, 2013.

    93. 2012

  93. Ardekani R, Greenwood AK, Peichel CL & Tavaré S. Using non-local background modeling to quantify the schooling behaviour of sticklebacks. VAIB12: Workshop on Visual Observation and Analysis of Animal and Insect Behavior 2012. In conjunction with 21st International Conference on Pattern Recognition (ICPR 2012).

  94. Lynch AG, Chin S-F, Dunning MJ, Caldas C, Tavaré S & Curtis C. Calling sample mixups in cancer population studies. PLoS ONE, 7, e41815, 2012.

  95. Ardekani R, Huang YM, Sancheti P, Stanciauskas P, Tavaré S & Tower J. Using GFP video to track 3D movement and conditional gene expression in free-moving flies. PLoS ONE, 7, e40506, 2012.

  96. Chandra T, Kirschner K, Thuret J-Y, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nuñez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PAW, Lowe SW, Kimura H, Gilbert DM & Narita M. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Molecular Cell, 47, 203–214, 2012.

  97. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, METABRIC group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale A-L, Brenton JD, Tavaré S, Caldas C & Aparicio S. The genomic and transcriptomic architecture of 2000 breast tumours reveals novel subgroups. Nature, 486, 346–352, 2012.

  98. Knott SRV, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S & Aparicio OM. Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell, 148, 99–111, 2012.

    99. 2011

  99. Manolopoulou I, Legarreta L, Emerson BC, Brooks S & Tavaré S. A Bayesian approach to phylogeographic clustering. Interface Focus, 1, 909–921, 2011.

  100. Speed D & Tavaré S. Sparse partitioning: nonlinear regression with binary or tertiary predictors, with application to association studies. Ann Appl Stats, 5, 873–893, 2011.

  101. Siegmund KD, Marjoram P, Tavaré S & Shibata D High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS ONE, 6: e21657, 2011.

  102. Sottoriva A, Vermeulen L & Tavaré S. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors. PLoS Comp Bio, 7: e1001132, 2011. [doi:10.1371/journal.pcbi.1001132]

  103. Narita M, Young ARJ, Arakawa S, Samarajiwa SA, Nakashima T, Yoshida S, Hong SK, Berry LS, Reichelt S, Ferreira M, Tavaré S, Inoki K, Shimizu S & Narita M. Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science, 332, 966–970, 2011.

  104. Ibrahim AEK, Arends MJ, DeSilva AL, Wyllie AH, Gerger L, Ito Y, Vowler SL, Huang TH-M, Tavaré S, Murrell A & Brenton JD. Progressive DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic development. Gut, 60, 499–508, 2011.

  105. Cairns J, Spyrou S, Stark R, Smith ML, Lynch AG & Tavaré S. BayesPeak - An R package for analysing ChIP-seq data. Bioinformatics, 27, 713–714, 2011.

  106. Wilkinson RD, Steiper M, Soligo C, Martin R, Yang Z & Tavaré S. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Systematic Biology, 60, 16–31, 2011.

    107. 2010

  107. Ivakhno S, Royce T, Cox AJ, Evers D, Cheetham KR & Tavaré S. CNAseg -- a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics, 26, 3051–3058, 2011.

  108. Lynch AG, Hadfield J, Dunning MJ, Osborne M, Thorne NP & Tavaré S. The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment. BMC Genomics, 11: 540, 2010.

  109. Dunning MJ, Curtis CN, Barbosa-Morais NL, Caldas C, Tavaré S & Lynch AG. The importance of platform annotation in interpreting microarray data: A response to "Breast cancer molecular profiling with single sample predictors: a retrospective analysis". The Lancet Oncology, 11, 717, 2010.

  110. Sottoriva A & Tavaré S. Integrating approximate Bayesian computation with complex agent-based models for cancer research. In COMPSTAT 2010 -- Proceedings in Computational Statistics, eds. Saporta G & Lechevallier Y. Springer, Physica Verlag. pp. 57–66, 2010.

  111. Ritchie ME, Forrest MS, Dimas AS, Daelemans C, Dermitzakis ET, Deloukas P & Tavaré S. Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. BMC Bioinformatics, 11: 280, 2010.

  112. Ivakhno S & Tavaré S. CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data. Bioinformatics, 26, 1395–1402, 2010.

  113. Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, Forrest MS, Campino S, Clark TG, Stanier P, Kwiatkowski D, Deloukas P, Dermitzakis ET, Tavaré S, Moore GE & Dunham I. High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genetics, 11: 25, 2010.

  114. Barbour AD & Tavaré S. Assessing molecular variability in cancer genomes. In Probability and Mathematical Genetics: Papers in Honour of Sir John Kingman, eds. Bingham N & Goldie C. Cambridge, Cambridge University Press. pp 91–111, 2010.

  115. Smith ML, Dunning MJ, Tavaré S & Lynch AG. Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. BMC Bioinformatics 11: 208, 2010.

  116. Clark AM, Goldstein LD, Tevlin M, Tavaré S, Shaham S & Miska EA. The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nuc Acids Res. 38, 3780–3793, 2010.

  117. Barbosa-Morais NL, Dunning MJ, Samarajiwa S, Darot JFJ, Ritchie ME, Lynch AG & Tavaré S. A reannotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nuc Acids Res, 38: e17, 2010.

    118. 2009

  118. Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin S-F, Brenton J, Tavaré S & Caldas C. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics, 10: 588, 2009.

  119. Avril-Sassen S, Goldstein L, Stingl J, Blenkiron C, Le Quesne J, Spiteri I, Karagavriilidou K, Watson CJ, Tavaré S, Miska EA & Caldas C. Characterization of microRNA expression in post-natal mouse mammary gland development. BMC Genomics, 10: 548, 2009.

  120. Grover D & Tavaré S. Finding behavioral motifs in fly trajectories. Communications in Information and Systems, 9, 283–294, 2009.

  121. ⭑ Papatheodorou I, Crichton C, Morris L, Maccallum P, METABRIC Group, Davies J, Brenton JD & Caldas C. A metadata approach for clinical data management in translational genomics studies in breast cancer. BMC Medical Genomics 2: 66, 2009.

  122. Waskar M, Landis GN, Shen J, Curtis CN, Abdueva D, Skvortsov D, Tavaré S & Tower J. Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy. Aging, 1(11), 1–31, 2009.

  123. Grover D, Ford D, Brown C, Hoe N, Erdem E, Tavaré S & Tower J. Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster. PLoS ONE, 4: e7580, 2009.

  124. Knott S, Viggiani CJ, Aparicio OM & Tavaré S. Strategies for analyzing highly enriched IP-chip datasets. BMC Bioinformatics, 10: 305, 2009.

  125. Spyrou C, Stark R, Lynch AG & Tavaré S. BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics, 10: 299, 2009.

  126. Fernando H, Sewitz S, Darot J, Tavaré S, Huppert JL & Balasubramanian S. Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression. Nuc Acids Res, 37, 6716–6722, 2009.

  127. Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S & Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics, 25, 2621–2623, 2009.

  128. Siegmund KD, Marjoram P, Tavaré S & Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle, 8, 2187–2193, 2009.

  129. Tiemann-Boege I, Curtis CN, Shinde DN, Goodman DB, Tavaré S & Arnheim N. Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel. Analytical Chemistry, 81, 5770–5776, 2009.

  130. Knott S, Viggiani CJ, Tavaré S & Aparicio OM. Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes & Dev, 23, 1077–1090, 2009.

  131. Thorne NP, Marioni JC, Rakyan V, Ibrahim AEK, Massie C, Curtis C, Brenton JD, Murrell A & Tavaré S. DNA methylation arrays: Methods and analysis. In Microarray Innovations - Technology and Experimentation in Drug Discovery and Biomedical Research, Ed. G. Hardiman. Chapter 13, pp. 175–206, 2009.

  132. Grover D, Yang J, Ford D, Tavaré S & Tower J. Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes. BMC Research Notes, 2: 58, 2009.

  133. Young ARJ, Narita M, Ferreira M, Kirschner K, Sadaie M, Darot JFJ, Tavaré S, Arakawa S, Shimizu S, Watt, FM & Narita M. Autophagy mediates the mitotic-senescence transition. Genes Dev, 23, 798–803, 2009.

  134. Wilkinson RD & Tavaré S. Estimating primate divergence times by using conditioned birth-and-death processes. Theoret Popul Biol, 75, 278–295, 2009.

  135. Siegmund KD, Marjoram P, Woo Y-J, Tavaré S & Shibata D. Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci USA, 106, 4828–4833, 2009.

  136. Shen J, Curtis C, Tavaré S & Tower J. A screen of apoptosis and senescence regulatory genes for life span effects when over-expressed in Drosophila. Impact Aging, 1, 191–211, 2009.

  137. Woo Y-J, Siegmund KD, Tavaré S & Shibata D. Older individuals appear to acquire mitotically older colorectal cancers. Journal of Pathology, 217, 483–488, 2009.

  138. Jiang R, Tavaré S & Marjoram P. Population genetic inference from resequencing data. Genetics, 181, 187–197, 2009. Corrigendum: 190, 829–830, 2012.

    139. 2008

  139. Grover D, Yang J, Tavaré S & Tower J. Simultaneous tracking of fly movement and expression using GFP. BMC Biotechnology, 8: 93, 2008.

  140. Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie M, Deloukas P, Tavaré S & Dermitzakis ET. Modifier effects between regulatory and protein-coding variation. PLoS Genetics, 4 (10), e1000244, 2008.

  141. 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, 322, 434–438, 2008.

  142. Hull ML, Rangel Escareno C, Godsland J, Doig J, Johnson C, Butt RP, Phillips S, Smith SK, Tavaré S, Print CG & Charnock-Jones DS. Endometrial-peritoneal interactions during endometriotic lesion establishment. Am J Path, 173, 700–715, 2008.

  143. Marioni JC, White M, Tavaré S & Lynch AG. Hidden copy number variation in the HapMap trios. Proc Natl Acad Sci USA, 105: 10067–10072, 2008.

  144. Szyjka SJ, Aparicio JG, Viggiani CJ, Knott S, Xu W, Tavaré S & Aparicio OM. Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes Dev, 22: 1906–1920, 2008.

  145. 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 TJP, Carter NP, Tavaré S & Beck S. mPod, an integrated resource for identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research, 18, 1181–1191, 2008.

  146. 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. Molecular Cell, 31: 79–90, 2008.

  147. 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 TJP, Durbin R, Tavaré S & Beck S. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotech, 26: 779–785, 2008.

  148. Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S & Lynch AG. Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Research Notes, 1: 18, 2008.

  149. 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 Children's Cancer and Leukaemia Group (CCLG). Pediatric malignant germ cell tumours show characteristic transcriptome profiles. Cancer Research, 68: 4239–4247, 2008.

  150. Chu M, Siegmund KD, Hao Q-L, Crooks GM, Tavaré S & Shibata D. Inferring relative numbers of human leukocyte genome replications. Br. J. Haematology. 141: 862–871, 2008.

  151. Grover D, Tower J & Tavaré S. O fly, where art thou? J Roy Soc Interface, 5: 1181–1191, 2008.

  152. Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S & Ritchie ME. Statistical issues in the analysis of Illumina data. BMC Bioinformatics, 9: 85, 2008.

    153. 2007

  153. Journée M, Teschendorff AE, Absil P-A, Tavaré S & Sepulchre R. Geometric optimization methods for the analysis of gene expression data. In Principal Manifolds for Data Visualization and Dimension Reduction, Eds. A. Gorban, B. Kegl, D. Winsch, A. Zinovyev. LNCSE, Springer, pp. 271–292, 2007.

  154. 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 Biology, 8(12): R262, 2007.

  155. Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, 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 Biology, 8(10): R228, 2007.

  156. Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais N, Bhattacharjee A, Young RA, Tavaré S, Lees JA & Odom DT. Cell cycle genes are the evolutionarily conserved targets of mammalian DREAM member E2F4. PLoS ONE, 2:e1061, 2007.

  157. Blenkiron C, Goldstein LD, Thorne NP, Spiteri MI, Chin SF, Dunning M, Barbosa-Morais NL, Tavaré S, Caldas C & Miska EA. MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype. Genome Biology, 8: R214, 2007.

  158. Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa J, 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 Biology, 8: R215, 2007.

  159. Shibata D & Tavaré S. Stem cell chronicles: Autobiographies within genomes. Stem Cell Reviews, 3, 94–103.

  160. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle C, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P & Dermitzakis ET. Population genomics of human gene expression. Nat. Genet. 39, 1217–1224, 2007.

  161. Martin RD, Soligo C & Tavaré S. Primate origins: Implications of a Cretaceous ancestry. Folia Primatologica, 78, 277–296, 2007.

  162. 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 Medical Genetics, 8:50, 2007.

  163. Lynch AG, Marioni JC & Tavaré S. Numbers of CNVs and false negative rates will be underestimated if we do not account for the dependence between repeated experiments. Amer J Hum Genet, 81, 418–420, 2007.

  164. Dunning MJ, Smith ML, Ritchie ME & Tavaré S beadarray: R classes and methods for Illumina bead-based data. Bioinformatics, 23, 2183–2184, 2007.

  165. Skvortsov D, Abdueva D, Curtis CN, Schaub B & Tavaré S. Explaining differences in saturation levels for Affymetrix GeneChip arrays. Nucleic Acids Research, 35, 4154–4163, 2007.

  166. Skvortsov D, Abdueva D, Stitzer M, Finkel SA & Tavaré S. Using expression arrays for copy number detection: an example from E. coli. BMC Bioinformatics, 8(1):203, 2007.

  167. Chin S-F, Wang Y, Thorne NP, Teschendorff AE, Pinder SE, Vias M, Naderi A, Roberts I, Barbosa-Morais NL, Garcia M, Iyer NG, Kranjac T, Robertson J, Ruffalo T, Aparicio SFR, Tavaré S, Ellis I, Brenton JD & Caldas C. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene, 26, 1959–1970, 2007.

  168. Nicolas P, Kim K-M, Shibata D & Tavaré S. The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Comp Bio, 3, 364–374, 2007.

  169. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, 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, 315, 848–853, 2007.

  170. Soligo C, Will O, Tavaré S, Marshall CR & Martin RD. New light on the dates of primate origins and divergence. In Primate Origins: Adaptations and Evolution. Eds. Ravosa MJ and Dagosto M. Springer, New York, pp. 29–49, 2007. ISBN: 0-387-30335-9

    171. 2006

  171. Dunning M, Smith M, Thorne NP & Tavaré S. beadarray: an R package to analyse Illumina BeadArrays. R News, 6(5), 17–23, 2006.

  172. Xu W, Aparicio JG, Aparicio OM & Tavaré S. Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and precise identification of essential ARS consensus sequences in S. cerevisiae. BMC Genomics, 7: 276, 2006.

  173. Ibrahim AEK, 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 Research., 34: e136, 2006.

  174. Marjoram P & Tavaré S. Modern computational approaches for analysing molecular-genetic variation data. Nat. Rev. Genet., 7, 759–770, 2006.

  175. Abdueva D, Skvortsov D & Tavaré S. Non-linear analysis of GeneChip arrays. Nucleic Acids Research, 34: e105, 2006.

  176. Jiang R, Marjoram P, Borevitz JO & Tavaré S. Inferring population parameters from single-feature polymorphism data. Genetics, 173, 2257–2267, 2006.

  177. Shibata D & Tavaré S. Counting divisions in a human somatic cell tree: How, what, and why. Cell Cycle, 5, 610–614, 2006.

  178. Jakobsson M, Hagenblad J, Tavaré S, Säll T, Halldén C, Lind-Halldén C & Nordborg M. A unique recent origin of the allotetraploid species Arabidopsis suecica: evidence from nuclear DNA markers. Mol. Biol. Evol., 23, 1217–1231, 2006.
  179. Marioni JC, Thorne NP & Tavaré S. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics, 22, 1144–1146, 2006.

  180. Dunning M, Thorne NP, Camilier I, Smith ML & Tavaré S. Quality control and low-level statistical analysis of Illumina BeadArrays. REVSTAT, 4, 1–30, 2006.

  181. Arratia R, Barbour AD & Tavaré S. A tale of three couplings: Poisson-Dirichlet and GEM approximations for random permutations. Comb. Prob. Comput., 15, 31–62, 2006.

  182. Kim JY, Tavaré S & Shibata D. Human hair genealogies and stem cell latency. BMC Biology, 4:2, 2006.

  183. Millman K, Black CM, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S & Dean D. Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of associations between ompA polymorphisms and clinical phenotypes. Microbes and Infection, 8, 604–611, 2006.

    184. 2005

  184. Stranger BE, Forrest MS, Clark AG, Minichiello M, 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 Genetics, 1(6), 695–704, 2005.

  185. Kim JY, Tavaré S & Shibata D. Counting human somatic cell replications: Methylation mirrors human endometrial stem cell divisions. Proc. Natl. Acad. Sci. USA 102, 17739–17744, 2005.

  186. Clark RM, Tavaré S & Doebley J. Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Mol. Biol. Evol., 22, 2304–2312, 2005.

  187. Calabrese P, Mecklin JP, Järvinen HJ, Aaltonen LA, Tavaré S & Shibata D. Numbers of mutations to different types of colorectal cancer. BMC Cancer, 5:126, 2005.

  188. Kim JY, Siegmund KD, Tavaré S & Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Medicine, 3:10, 2005.

  189. Arratia R, Barbour AD & Tavaré S. A probabilistic approach to analytic arithmetic on algebraic function fields. Math. Proc. Camb. Phil. Soc., 139, 1–26, 2005.

  190. Tavaré S. Ancestral inference for branching processes. In Branching Processes in Biology: Variation, Growth, Extinction, eds. Haccou P, Jagers P & Vatutin V. Cambridge University Press, pp. 208–217, 2005.

  191. Innan H, Zhang K, 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, 169, 1763–1777, 2005.

    192. 2004

  192. Tavaré S. Ancestral inference in population genetics. In: Lectures on Probability Theory and Statistics. Ecole d'Etés de Probabilité de Saint-Flour XXXI -- 2001. (Ed. Picard J.) Lecture Notes in Mathematics, 1837, 1–188, 2004. Springer Verlag, New York.

  193. Landis GN, Abdueva D, Skvortsov D, Yang J, Rabin BE, Carrick J, Tavaré S & Tower J. Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA, 101, 7663–7668, 2004.

  194. Millman KL, Black CM, Johnson R, Stamm W, Jones R, Hook E, Martin D, Bolan G, Tavaré S, & Dean D. Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States. J. Bacteriol., 186, 2457–2465, 2004.

  195. Calabrese P, Tavaré S & Shibata D. Pre-tumor progression: clonal evolution of human stem cell populations. Am. J. Pathol., 164, 1337–1346, 2004.

  196. Kim K-M, Calabrese P, Tavaré S & Shibata D. Enhanced stem cell survival in familial adenomatous polyposis. Am. J. Pathol., 164, 1369-1377, 2004.

  197. Calabrese P, Tsao J-L, Yatabe Y, Salovaara R, Mecklin J-P, Järvinen HJ, Aaltonen LA, Tavaré S & Shibata D. Colorectal pre-tumor progression before and after loss of DNA mismatch repair. Am. J. Pathol., 164, 1447–1453, 2004.

  198. Plagnol V & Tavaré S. Approximate Bayesian computation and MCMC. In Monte Carlo and Quasi-Monte Carlo Methods 2002. Ed. Niederreiter H, Springer-Verlag, pp. 99–114, 2004.

    199. 2003

  199. Marjoram P, Molitor J, Plagnol V & Tavaré S. Markov chain Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. USA, 100, 15324–15328, 2003.

  200. Tavaré S. Coalescent theory. In Encyclopedia of the Human Genome, Vol. 1, ed. Cooper DN, pp. 836–845, 2003. Nature Publishing Group.

  201. Griffiths RC & Tavaré S. The genealogy of a neutral mutation. In Highly Structured Stochastic Systems. Eds. Green P, Hjort N and Richardson S, pp. 393–412, 2003. Oxford Statistical Science Series, Vol. 27, Oxford University Press.

  202. Navidi WC, Tavaré S & Arnheim N. The roles of mutation rate and selective pressure on observed levels of the human mitochondrial DNA deletion mtDNA4977 In Science and Statistics: A Festschrift for Terry Speed. Ed. Goldstein DR, IMS Lecture Notes - Monograph Series, Volume 40, pp. 247–258, 2003.

    203. 2002

  203. Tavaré S, Marshall CR, Will O, Soligo C & Martin RD. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature, 416, 726–729, 2002.

  204. Nordborg M & Tavaré S. Linkage disequilibrium: what history has to tell us. Trends in Genetics, 18, 83–90, 2002.

    205. 2001

  205. Millman KL, Tavaré S & Dean D. Recombination in the ompA gene but not the omcB gene of Chlamydia contributes to serovar-specific differences in tissue tropism, immune surveillance and persistence of the organism. J. Bacteriol., 183, 5997–6008, 2001.

  206. Yatabe Y, Tavaré S & Shibata D. Investigating stem cells in human colon by using methylation patterns. Proc. Natl. Acad. Sci., 98, 10839–10844, 2001. (With editorial.)

  207. Markovtsova L, Marjoram P & Tavaré S. On a test of Depaulis and Veuille. Mol. Biol. Evol., 18, 1132–1133, 2001.

  208. Tavaré S, Adams DC, Fedrigo O & Naylor GJP. A model for phylogenetic inference using structural and chemical covariates. Pacific Symposium on Biocomputing, 6, 215–225, 2001.

  209. Neuhauser C & Tavaré S. The coalescent. Encyclopedia of Genetics, Vol. I. Eds. Brenner S and Miller J, pp. 392–397, 2001. Academic Press, New York.

    210. 2000

  210. Marjoram P, Markovtsova L & Tavaré S. Estimation in ancestral recombination graphs using Markov chain Monte Carlo. Research Report, October 2000.

  211. Tsao JL, Yatabe Y, Salovaara R, Jarvinen HJ, Mecklin JP, Aaltonen LA, Tavaré S & Shibata D. Genetic reconstruction of individual colorectal tumor histories. Proc. Natl. Acad. Sci. USA, 97, 1236–1241, 2000.

  212. Schbath S, Bossard N & Tavaré S. The effect of non-homogeneous clone length distribution on the progress of an STS mapping project. J. Comp. Biol., 7, 47–57, 2000.

  213. Arratia R, Barbour AD & Tavaré S. The number of components in a logarithmic combinatorial structure. Ann. Appl. Prob., 10, 331–361, 2000.

  214. Markovtsova L, Marjoram P & Tavaré S. The age of a unique event polymorphism. Genetics, 156, 401–409, 2000.

  215. Markovtsova L, Marjoram P & Tavaré S. The effects of rate variation on ancestral inference in the coalescent. Genetics, 156, 1427–1436, 2000.

  216. Arratia R, Barbour AD & Tavaré S. Limits of logarithmic combinatorial structures. Ann. Probab., 28, 1620–1644, 2000.

    1999

  217. Arratia R, Barbour AD & Tavaré S. On Poisson-Dirichlet limits for random decomposable combinatorial structures. Combin. Probab. Comput., 8, 193–208, 1999.

  218. Arratia R, Barbour AD & Tavaré S. The Poisson-Dirichlet distribution and the scale-invariant Poisson process. Combin. Probab. Comput., 8, 407–416, 1999.

  219. Griffiths RC & Tavaré S. The ages of mutations in gene trees. Ann. Appl. Prob., 9, 567–590, 1999.

  220. Tsao JL, Tavaré S, Salovaara R, Jass JR, Aaltonen LA & Shibata D. Colorectal adenoma and cancer divergence: evidence of multi-lineage progression. Am. J. Pathol., 154, 1815–1824, 1999.

  221. Leeflang E, Tavaré S, Marjoram P, Neal COS, Srinidhi J, MacFarlane H, MacDonald ME, Gusella JF, de Young M, Wexler N & Arnheim N. Analysis of germline mutation spectra at the Huntington Disease locus supports a mitotic mutation mechanism. Hum. Mol. Genet., 8, 173–183, 1999.

  222. Fan F, Liu C, Tavaré S & Arnheim N. Polymorphisms in the human DNA repair gene XPF. Mutation Research Genomics, 406, 115–120, 1999.

  223. Jaruzelska J, Zietkiewicz E, Batzer M, Cole D, Moisan J-P, Scozzari R, Tavaré S & Labuda D. Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy. Genetics, 152, 1091–1101, 1999.

    224. 1998

  224. Griffiths RC & Tavaré S. The age of a mutation in a general coalescent tree. Stochastic Models, 14, 273–295, 1998.

  225. Ewens WJ & Tavaré S. The Ewens Sampling Formula. In Encyclopedia of Statistical Science, Vol. 2 update. Eds. Kotz S, Read CB and Banks DL, pp. 230–234, 1998. Wiley, New York.

  226. Leeflang EP, Tavaré S, Marjoram P, Grewal R, Neal COS & Arnheim N. Human germline mutation analysis by single genome PCR: application to dynamic mutations. Chapter 37 in Genetic instabilities and hereditary neurological diseases. Eds. Wells RD and Warren ST, pp. 543–560, 1998. Academic Press, New York.

  227. Barbour AD & Tavaré S. A rate for the Erdös-Turán law. In Combinatorics, geometry and probability. A tribute to Paul Erdös. Eds. Bollobás B and Thomason A, pp. 71–80, 1998. Cambridge University Press. (A reprinting of 1994 article below)

    1997

  228. Tavaré S, Balding DJ, Griffiths RC & Donnelly P. Inferring coalescence times for molecular sequence data. Genetics, 145, 505–518, 1997.

  229. Arratia R, Barbour AD & Tavaré S. Random combinatorial structures and prime factorizations. Notices of the American Mathematical Society, 44, 903–910, 1997.

  230. Griffiths RC & Tavaré S. Computational methods for the coalescent. Chapter 10 in Progress in Population Genetics and Human Evolution. Eds. P. Donnelly P and Tavaré S. IMA Volumes in Mathematics and its Applications, 87, 165–182, 1997. Springer Verlag, Berlin.

  231. Tavaré S & Ewens WJ. Multivariate Ewens distribution. Chapter 41 in Discrete Multivariate Distributions. Eds. Johnson NS, Kotz S and Balakrishnan N, pp. 232–246, 1997. Wiley, New York.

  232. Tavaré S. Ancestral inference from DNA sequence data. Chapter 5 in Case Studies in Mathematical Modeling: Ecology, Physiology, and Cell Biology. Eds. Othmer HG, Adler FR, Lewis MA and Dallon J, pp. 81–96, 1997. Prentice-Hall.

    1996

  233. Griffiths RC & Tavaré S. Monte Carlo inference methods in population genetics. Mathl. Comput. Modelling, 23, 141–158, 1996.

  234. Donnelly P, Tavaré S, Balding DJ & Griffiths RC. Estimating the age of the common ancestor of men from the ZFY intron. Science, 272, 1357–1359, 1996.

  235. Shenkar R, Navidi W, Tavaré S, Dang MH, Chomyn A, Attardi G, Cortopassi G & Arnheim N. The mutation rate of the human mitochondrial DNA deletion mtDNA4977. Amer. J. Hum. Gen., 59, 772–780, 1996. (With editorial.)

    1995

  236. Griffiths RC & Tavaré S. Unrooted genealogical tree probabilities in the infinitely-many-sites model. Math. Biosci., 127, 77–98, 1995.

  237. Joyce P & Tavaré S. The distribution of rare alleles. J. Math. Biol., 33, 602–618, 1995.

  238. Arratia R, Stark D & Tavaré S. Total variation asymptotics for Poisson process approximations of logarithmic combinatorial assemblies. Ann. Probab., 23, 1347–1388, 1995.

  239. Leeflang EP, Zhang L, Tavaré S, Hubert R, Srinidhi J, MacDonald ME, Myers RM, de Young M, Wexler NS, Gusella JF & Arnheim N. Single sperm analysis of the trinucleotide repeats in the Huntington's disease gene: quantification of the mutation frequency spectrum. Hum. Molec. Genet., 4, 1519–1526, 1995.

  240. Donnelly P & Tavaré S. Coalescents and genealogical structure under neutrality. Annu. Rev. Genet., 29, 401–421, 1995.

  241. Tavaré S. Calibrating the clock: using stochastic processes to measure the rate of evolution. Chapter 5 in Calculating the Secrets of Life, Eds. Lander ES and Waterman MS, pp. 114–152, 1995. National Academy Press, Washington.

    1994

  242. Raftery AE & Tavaré S. Estimation and modelling repeated patterns in high order Markov chains with
    the mixture transition distribution (MTD) model.     Applied Statistics, 43, 179–199, 1994.

  243. Arratia R & Tavaré S. Independent process approximations for random combinatorial structures. Adv. Math., 104, 90–154, 1994.

  244. Griffiths RC & Tavaré S. Simulating probability distributions in the coalescent. Theor. Popn. Biol., 46, 131–159, 1994.

  245. Barbour AD & Tavaré S. A rate for the Erdös-Turán law. Combin. Probab. Comput., 3, 167–176, 1994.

  246. Griffiths RC & Tavaré S. Sampling theory for neutral alleles in a varying environment. Phil. Trans. R. Soc. Lond. B, 344, 403–410, 1994.

  247. Griffiths RC & Tavaré S. Ancestral inference in population genetics. Statistical Science, 9, 307–319, 1994.

    1993

  248. Arratia R, Barbour AD & Tavaré S. On random polynomials over a finite field. Math. Proc. Camb. Phil. Soc., 114, 347–368, 1993.

  249. Arratia R & Tavaré S. Probability approximations via the Poisson clumping heuristic by Aldous D,
    Poisson approximation by Barbour AD, Holst L and Janson S. Ann. Probab., 21, 2269–2279, 1993. [Book Review]

    1992

  250. Joyce PJ & Tavaré S. A convergence theorem for symmetric functionals of random partitions. J. Appl. Prob., 29, 280–290, 1992.

  251. Arratia R & Tavaré S. The cycle structure of random permutations. Ann. Probab., 20, 1567–1591, 1992.

  252. Arratia R, Barbour AD & Tavaré S. Poisson process approximations for the Ewens Sampling Formula. Ann. Appl. Probab., 2, 519–535, 1992.

  253. Arratia R & Tavaré S. Limit theorems for combinatorial structures via discrete process approximations. Rand. Struct. Alg., 3, 321–345, 1992.

  254. Lundstrom R, Tavaré S & Ward RH. Estimating substitution rates from molecular data using the coalescent. Proc. Natl. Acad. Sci., USA, 89, 5961–5965, 1992.

  255. Lundstrom R, Tavaré S & Ward RH. Modelling the evolution of the human mitochondrial genome. Math. Biosci., 112, 319–336, 1992.

    1991

  256. Arratia R, Lander ES, Tavaré S & Waterman MS. Genomic mapping by anchoring random clones: a mathematical analysis. Genomics, 11, 806–827, 1991.

  257. Donnelly P, Kurtz TG & Tavaré S. On the functional central limit theorem for the Ewens sampling formula. Ann. Appl. Probab., 1, 539–545, 1991.

    1990

  258. Joyce PJ & Tavaré S. Random permutations and neutral evolution models. Stoch. Proc. and Applns., 36, 245–262, 1990.

    1989

  259. Tavaré S & Song B. Codon preference and primary sequence structure in protein coding regions. Bull. Math. Biol., 51, 95–115, 1989.

  260. Tavaré S, Ewens WJ & Joyce P. Is knowing the age-order of alleles useful in testing for selective neutrality? Genetics, 122, 705-711, 1989.

  261. Tavaré S. The genealogy of the birth, death and immigration process. Chapter 3 in Mathematical Evolutionary Theory. Ed. Feldman MW, pp. 41–56, 1989. Princeton University Press.

    1988

  262. Tavaré S & Giddings BW. Some statistical aspects of the primary structure of nucleotide sequences. Mathematical Methods for DNA Sequences. Ed. Waterman MS, pp. 117–132, 1988. CRC Press.

    1987

  263. Tavaré S. The birth process with immigration, and the genealogical structure of large populations. J. Math. Biol., 25, 161–168, 1987.

  264. Donnelly P & Tavaré S. The population genealogy of the infinitely-many neutral alleles model. J. Math. Biol., 25, 381–391, 1987.

  265. Joyce PJ & Tavaré S. Cycles, permutations and the structure of the Yule process with immigration. Stoch. Proc. and Applns., 25, 309–314, 1987.

  266. Donnelly P & Tavaré S. A genealogical description of the infinitely-many neutral alleles model. Stochastic Methods in Biology. Eds. Kimura M, Kallianpur G, Hida T. Lecture Notes in Biomathematics, 70, 27–35, 1987. Springer-Verlag.

    1986

  267. Donnelly P & Tavaré S. The ages of alleles and a coalescent. Adv. Appl. Prob., 18, 1–19, 1986. Correction:18, 1023.

  268. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences, 17, 57–86, 1986. American Mathematical Society.

    1985

  269. Tavaré S. Mathematical Methods of Applied Probability, by Hunter JJ. J. A. S. A., 80, 1071–1072, 1985. [Book Review]

    1984

  270. Saunders IW, Tavaré S & Watterson GA. On the genealogy of nested subsamples from a haploid population. Adv. Appl. Prob., 16, 471–491, 1984.

  271. Tavaré S. Lines of descent and genealogical processes, and their application in population genetics models. Theoret. Popn. Biol., 26, 119–164, 1984.

  272. Tavaré S. Genealogical and Genetic Structure, by Cannings C and Thompson EA. J. A. S. A., 79, 743–744, 1984. [Book Review]

    1983

  273. Karlin S & Tavaré S. A class of diffusion processes with killing arising in population genetics. SIAM J. Appl. Math., 43, 31–41, 1983.

  274. Tavaré S & Altham PME. Serial dependence of observations leading to contingency tables, with corrections to χ2 statistics. Biometrika, 70, 139–144, 1983.

  275. Tavaré S. Serial dependence in contingency tables. J. Royal Statist. Soc. B, 45, 100–106, 1983.

  276. Seneta E & Tavaré S. A note on models using the branching process with immigration stopped at zero. J. Appl. Prob., 20, 11–18, 1983.

  277. Seneta E & Tavaré S. Some stochastic models for plasmid copy number. Theoret. Popn. Biol., 23, 241–256, 1983.

  278. Ethier SN & Tavaré S. The proportional bettor's return on investment. J. Appl. Prob., 20, 563–573, 1983.

  279. Karlin S, Ghandhour G, Ost F, Tavaré S & Korn LJ. New approaches for computer analysis of nucleic acid sequences. Proc. Natl. Acad. Sci. USA, 80, 5660–5664, 1983.

    1982

  280. Karlin S & Tavaré S. A diffusion with killing: the time to formation of recurrent deleterious mutant genes. Stoch. Proc. and Applns., 13, 249–261, 1982.

  281. Karlin S & Tavaré S. Detecting particular genotypes in populations under non-random mating. Math. Biosci., 59, 57–75, 1982.

  282. Karlin S & Tavaré S. Linear birth and death processes with killing. J. Appl. Prob., 19, 477–487, 1982.

    1981

  283. Karlin S & Tavaré S. The detection of a recessive visible gene in finite populations. Genetical Research, 37, 22–46, 1981.

  284. Karlin S & Tavaré S. The detection of particular genotypes in finite populations. I. Natural selection effects. Theoret. Popn. Biol., 19, 187–214, 1981.

  285. Karlin S & Tavaré S. The detection of particular genotypes in finite populations. II. The effects of partial penetrance and family structure. Theoret. Popn. Biol., 19, 215–229, 1981.

  286. Pakes AG & Tavaré S. Comments on the age distribution of Markov processes. Adv. Appl. Prob., 13, 681–703, 1981.

    1980

  287. Tavaré S. Time reversal and age distributions. I. Discrete-time Markov chains. J. Appl. Prob., 17, 33–46, 1980.

    1979

  288. Oakley JR & Tavaré S. Another approach to the assessment of growth in early infancy. Developmental Medicine and Child Neurology, 21, 186–193, 1979.

  289. Tavaré S. Sojourn times for conditioned Markov chains in genetics. Theoret. Popn. Biol., 15, 108–112, 1979.

  290. Tavaré S. A note on finite continuous-time Markov chains. Biometrics, 35, 831–834, 1979.

  291. Tavaré S. Dual diffusions, killed diffusions and the age distribution problem in population genetics. Theoret. Popn. Biol., 16, 253–266, 1979.

  292. Williamson JA, Bishop DT, Tavaré CJ & Tavaré S. On the independence structure that exists within a pedigree with an application to testing for a major gene. In Progress in Clinical and Biological Research. Eds. Sing CF and Skolnick MH. 32, 271–276, 1979. AR Liss, New York.

    Newsletter Articles

  293. Dinh K, Tavaré S & Xiang Z. ABC and distributional random forests. IICD Newsletter, February 2024. cancerdynamics.columbia.edu/news/approximate-bayesian-computation-and-distributional-random-forests acrobat.adobe.com/id/urn:aaid:sc:VA6C2:c0ec8dc1-4c77-4f22-a7fa-835f93e028f1

  294. Tavaré S. Computing the exponential of a matrix. IICD Newsletter, September 2020. cancerdynamics.columbia.edu/news/iicd-newsletter-september-2020

  295. Tavaré S. The complex step method for numerical differentiation. IICD Newsletter, August 2020 cancerdynamics.columbia.edu/news/iicd-newsletter-august-2020

    296. Other Publications

  296. Lynch AG, Smith ML, Dunning MJ, Cairns JM, Barbosa-Morais NL & Tavaré S. beadarray, BASH and HULK -- tools to increase the value of Illumina BeadArray experiments. In Statistical Tools for Challenges in Bioinformatics. Eds Gusnanto A, Mardia KV & Fallaize CJ. Leeds, Leeds University Press, pp. 33–37, 2009.

  297. Lynch AG. Curtis CN & Tavaré S. Correcting for probe-design in the analysis of gene-expression microarrays. In Systems Biology & Statistical Bioinformatics. Eds. Barber S, Baxter PD & Mardia KV. Leeds, Leeds University Press, pp. 83–86, 2007.

  298. Tavaré S, Nicolas P & Shibata D. Stochastic models for the evolution of stem cells in colon crypts. In Systems Biology & Statistical Bioinformatics. Eds. Barber S, Baxter PD & Mardia KV. Leeds, Leeds University Press, pp. 61–64, 2007.

  299. Marjoram P, Markovtsova L, & Tavaré S. "I see dead people:" gene mapping via ancestral inference. Accepted draft for Genetic Analysis Workshop 12.

  300. Marjoram P, Markovtsova L & Tavaré S. Estimation in ancestral recombination graphs using Markov chain Monte Carlo. Research Report, October 2000.

  301. Markovtsova L, Marjoram P & Tavaré S. Discussion of `Inference in molecular population genetics' by Stephens and Donnelly. J. Royal Statist. Soc. B, 62, 647, 2000.

  302. Martin RD, Soligo C, Tavaré S, Will O & Marshall CR. New light on the dates of primate origins and divergence. Folia Primatol., 71, 358–359, 2000.

  303. Tavaré S. Random trees in molecular genetics. Bull. I.S.I., 52, 269–272, 1999.

  304. Tavaré S & Feng Y. Reconstructing phylogenetic trees when sites are dependent. pp. 55–57 in Proceedings of Phylogeny Workshop, DIMACS Technical Report 95-48, ed. S. Tavaré, 1995.

  305. Tavaré S. International Conference on Random Mappings, Partitions, and Permutations. Report, Adv. Appl. Prob., 24, 761–777, 1992.

  306. Tavaré S. Mathematical models in population genetics. Composite Function, 1991. (A reprinting of the 1980 Function article below)

  307. Tavaré S & Lundstrom R. Comments on `Sampling strategies for distances between DNA sequences', by Weir and Basten. Biometrics, 46, 577–582, 1990.

  308. Tavaré S & Doerge RW. An application of computer algebra to likelihood analysis. Manuscript, 19pp, 1988.

  309. Donnelly P & Tavaré S. The genealogy of the infinite alleles model. In Proceedings, First World Congress of the Bernoulli Society, 1986. VNU Sci. Press, Utrecht, pp. 701–704, 1987.

  310. Tavaré S. A genealogical view of some stochastic models in population genetics. Stoch. Proc. Applns., 19, 10, 1985.

  311. Tavaré S & Janzen T. On estimating substitution rates from pairs of homologous nucleotide sequences. Manuscript, 28pp, 1985.

  312. Tavaré S. The estimation of substitution rates and divergence times from DNA sequence data. Third Rocky Mountain Regional Conference on Medical Applications of Statistics, Preprint Volume, 89–96, 1985.

  313. Seneta E & Tavaré S. Stochastic models for plasmid copy number. First Rocky Mountain Regional Conference on Medical Applications of Statistics, Preprint Volume, 27-33, 1982.

  314. Tavaré S. Mathematical models in population genetics. Function, 4, 26-32, 1980.

  315. Tavaré S. Time reversion and age distributions. Adv. Appl. Prob., 11, 10–12, 1979.

  316. Tavaré S. Conference on ecological statistics - a summary report. J. Royal Statist. Soc. C, 27, 344–345, 1978.

  317. Tavaré S. Age distributions for Markov chains in genetics. Adv. Appl. Prob., 10, 17–19, 1978.

  318. Tavaré S. Sojourn times for conditional Markov chains in genetics. Adv. Appl. Prob., 8, 645–647, 1976.


Updated February 16 2024