Simon Tavare - Publications

Applied Mathematics: Doctor of Philosophy University of Southern California, Los Angeles, CA, United States 
Mathematics, Molecular Biology, Oncology

117 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A, Yang TP, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, et al. Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance. Nature Genetics. PMID 27595477 DOI: 10.1038/Ng.3659  1
2016 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. Erratum to: Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes. Genome Biology. 17: 93. PMID 27154433 DOI: 10.1186/s13059-016-0959-3  1
2016 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, et al. Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target. Journal of the National Cancer Institute. 108. PMID 26657335 DOI: 10.1093/Jnci/Djv371  1
2016 Arratia R, Barbour AD, Tavaré S. Exploiting the feller coupling for the ewens sampling formula Statistical Science. 31: 27-29. DOI: 10.1214/15-Sts537  1
2016 Andrews DJ, Lynch AG, Tavaré S. Using Methylation Patterns for Reconstructing Cell Division Dynamics: Assessing Validation Experiments Emerging Trends in Applications and Infrastructures For Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications. 3-15. DOI: 10.1016/B978-0-12-804203-8.00001-8  1
2015 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, et al. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. Plos Genetics. 11: e1005053. PMID 25790137 DOI: 10.1371/Journal.Pgen.1005053  1
2015 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 (Bethesda, Md.). 5: 761-9. PMID 25717151 DOI: 10.1534/G3.114.016519  1
2015 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, et al. Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia. Arteriosclerosis, Thrombosis, and Vascular Biology. 35: 675-88. PMID 25573856 DOI: 10.1161/Atvbaha.114.304989  1
2015 Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker HC, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer DS, Cooper CS, Eeles R, Warren AY, Tavaré S, et al. HES5 silencing is an early and recurrent change in prostate tumourigenesis. Endocrine-Related Cancer. 22: 131-44. PMID 25560400 DOI: 10.1530/Erc-14-0454  1
2015 Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, 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. PMID 25406193 DOI: 10.1158/0008-5472.Can-13-3131  1
2015 Paterson AL, Weaver JMJ, Eldridge MD, Tavaré S, Fitzgerald RC, Edwards PAW. Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis Bmc Genomics. 16. DOI: 10.1186/s12864-015-1685-z  1
2015 Tavaré S, Sottoriva A, Piccirillo S, Spiteri I, Touloumis A, Marioni JC, Curtis CN, Watts C. Abstract IA04: Understanding tumor heterogeneity in glioblastoma Brain. 75. DOI: 10.1158/1538-7445.Brain15-Ia04  0.4
2015 Madhu B, Narita M, Jauhiainen A, Menon S, Stubbs M, Tavaré S, Griffiths JR. Metabolomic changes during cellular transformation monitored by metabolite–metabolite correlation analysis and correlated with gene expression Metabolomics. 11: 1848-1863. DOI: 10.1007/s11306-015-0838-z  1
2014 Silva AL, Dawson SN, Arends MJ, Guttula K, Hall N, Cameron EA, Huang TH, Brenton JD, Tavaré S, Bienz M, Ibrahim AE. Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists. Bmc Cancer. 14: 891. PMID 25432628 DOI: 10.1186/1471-2407-14-891  1
2014 Weaver JM, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CA, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, et al. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nature Genetics. 46: 837-43. PMID 24952744 DOI: 10.1038/Ng.3013  1
2014 Ostrow AZ, Nellimoottil T, Knott SR, 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. PMID 24504085 DOI: 10.1371/Journal.Pone.0087647  1
2013 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 (New York, N.Y.). 342: 995-8. PMID 24264992 DOI: 10.1126/Science.1243148  1
2013 Kozar S, Morrissey E, Nicholson AM, van der Heijden M, Zecchini HI, Kemp R, Tavaré S, Vermeulen L, Winton DJ. Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas. Cell Stem Cell. 13: 626-33. PMID 24035355 DOI: 10.1016/J.Stem.2013.08.001  1
2013 Newman S, Howarth KD, Greenman CD, Bignell GR, Tavaré S, Edwards PA. The relative timing of mutations in a breast cancer genome. Plos One. 8: e64991. PMID 23762276 DOI: 10.1371/Journal.Pone.0064991  1
2013 Zhong Y, Nellimoottil T, Peace JM, Knott SR, 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. The Journal of Cell Biology. 201: 373-83. PMID 23629964 DOI: 10.1083/Jcb.201208060  1
2013 Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proceedings of the National Academy of Sciences of the United States of America. 110: 4009-14. PMID 23412337 DOI: 10.1073/Pnas.1219747110  1
2013 Housden BE, Fu AQ, 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. PMID 23300480 DOI: 10.1371/Journal.Pgen.1003162  1
2013 Ardekani R, Tavaré S, Tower J. Assessing senescence in Drosophila using video tracking. Methods in Molecular Biology (Clifton, N.J.). 965: 501-16. PMID 23296680 DOI: 10.1007/978-1-62703-239-1_33  1
2013 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: 41-9. PMID 23090114 DOI: 10.1158/0008-5472.Can-12-2273  0.6
2013 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 / the Royal Society. 10: 20120547. PMID 23034355 DOI: 10.1098/Rsif.2012.0547  1
2013 Fu AQ, Russell S, Bray SJ, Tavaré S. Bayesian clustering of replicated time-course gene expression data with weak signals Annals of Applied Statistics. 7: 1334-1361. DOI: 10.1214/13-Aoas650  1
2013 Piccirillo SGM, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis N, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavare S, Watts C. Abstract 5016: The human sub-ependymal zone harbors glioblastoma precursors and represents a distinct therapeutic target. Cancer Research. 73: 5016-5016. DOI: 10.1158/1538-7445.Am2013-5016  0.6
2012 Lynch AG, Chin SF, Dunning MJ, Caldas C, Tavaré S, Curtis C. Calling sample mix-ups in cancer population studies. Plos One. 7: e41815. PMID 22912679 DOI: 10.1371/Journal.Pone.0041815  0.72
2012 Ardekani R, Huang YM, Sancheti P, Stanciauskas R, Tavaré S, Tower J. Using GFP video to track 3D movement and conditional gene expression in free-moving flies. Plos One. 7: e40506. PMID 22829875 DOI: 10.1371/Journal.Pone.0040506  1
2012 Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, et al. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Molecular Cell. 47: 203-14. PMID 22795131 DOI: 10.1016/J.Molcel.2012.06.010  1
2012 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, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 486: 346-52. PMID 22522925 DOI: 10.1038/Nature10983  0.72
2012 Knott SR, 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. PMID 22265405 DOI: 10.1016/J.Cell.2011.12.012  1
2012 Piccirillo SGM, Spiteri I, Sottoriva A, Marko N, Tavare S, Collins P, Watts C. Abstract 3342: Tumor-initiating cells in human glioblastoma are heterogeneous populations which reside in distinct environmental niches Cancer Research. 72: 3342-3342. DOI: 10.1158/1538-7445.Am2012-3342  0.4
2012 Samarajiwa SA, Spiteri I, Lynch A, Jauhiainen A, Morrissey E, Cairns J, Narita M, Tavaré S. O039 The interferonscape: Systems biology of interferon stimulated pathways and networks Cytokine. 59: 515-516. DOI: 10.1016/J.Cyto.2012.06.076  0.4
2011 Manolopoulou I, Legarreta L, Emerson BC, Brooks S, Tavaré S. A Bayesian approach to phylogeographic clustering. Interface Focus. 1: 909-21. PMID 23226589 DOI: 10.1098/Rsfs.2011.0054  1
2011 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. PMID 21738754 DOI: 10.1371/Journal.Pone.0021657  1
2011 Sottoriva A, Vermeulen L, Tavaré S. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors. Plos Computational Biology. 7: e1001132. PMID 21573198 DOI: 10.1371/Journal.Pcbi.1001132  0.4
2011 Narita M, Young AR, Arakawa S, Samarajiwa SA, Nakashima T, Yoshida S, Hong S, Berry LS, Reichelt S, Ferreira M, Tavaré S, Inoki K, Shimizu S, Narita M. Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science (New York, N.Y.). 332: 966-70. PMID 21512002 DOI: 10.1126/Science.1205407  1
2011 Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang Z, Tavaré S. Dating primate divergences through an integrated analysis of palaeontological and molecular data. Systematic Biology. 60: 16-31. PMID 21051775 DOI: 10.1093/Sysbio/Syq054  1
2010 Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S. CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics (Oxford, England). 26: 3051-8. PMID 20966003 DOI: 10.1093/Bioinformatics/Btq587  1
2010 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. PMID 20925945 DOI: 10.1186/1471-2164-11-540  1
2010 Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S, Lynch AG. The importance of platform annotation in interpreting microarray data. The Lancet. Oncology. 11: 717. PMID 20688273 DOI: 10.1016/S1470-2045(10)70115-7  0.6
2010 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. PMID 20403199 DOI: 10.1186/1471-2156-11-25  1
2010 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. Nucleic Acids Research. 38: 3780-93. PMID 20176573 DOI: 10.1093/Nar/Gkq083  1
2010 Sottoriva A, Tavaré S. Abstract PL04-03: Cancer stem cells Cancer Prevention Research. 3. DOI: 10.1158/1940-6207.Prev-10-Pl04-03  0.4
2009 Waskar M, Landis GN, Shen J, Curtis C, Tozer K, 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: 903-36. PMID 20157574  1
2009 Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavaré S, Caldas C. The pitfalls of platform comparison: DNA copy number array technologies assessed. Bmc Genomics. 10: 588. PMID 19995423 DOI: 10.1186/1471-2164-10-588  0.72
2009 Avril-Sassen S, Goldstein LD, Stingl J, Blenkiron C, Le Quesne J, Spiteri I, Karagavriilidou K, Watson CJ, Tavaré S, Miska EA, Caldas C. Characterisation of microRNA expression in post-natal mouse mammary gland development. Bmc Genomics. 10: 548. PMID 19930549 DOI: 10.1186/1471-2164-10-548  0.4
2009 Grover D, Ford D, Brown C, Hoe N, Erdem A, Tavaré S, Tower J. Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster. Plos One. 4: e7580. PMID 19862323 DOI: 10.1371/Journal.Pone.0007580  1
2009 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. Nucleic Acids Research. 37: 6716-22. PMID 19745055 DOI: 10.1093/Nar/Gkp740  1
2009 Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (Oxford, England). 25: 2621-3. PMID 19661241 DOI: 10.1093/Bioinformatics/Btp470  1
2009 Tiemann-Boege I, Curtis C, 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: 5770-6. PMID 19601653 DOI: 10.1021/Ac900633Y  1
2009 Siegmund KD, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle (Georgetown, Tex.). 8: 2187-93. PMID 19556889 DOI: 10.4161/Cc.8.14.9151  1
2009 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. PMID 19374758 DOI: 10.1186/1756-0500-2-58  1
2009 Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D. Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proceedings of the National Academy of Sciences of the United States of America. 106: 4828-33. PMID 19261858 DOI: 10.1073/Pnas.0810276106  1
2009 Woo YJ, Siegmund KD, Tavaré S, Shibata D. Older individuals appear to acquire mitotically older colorectal cancers. The Journal of Pathology. 217: 483-8. PMID 19165870 DOI: 10.1002/Path.2506  1
2009 Jiang R, Tavaré S, Marjoram P. Population genetic inference from resequencing data. Genetics. 181: 187-97. PMID 18984575 DOI: 10.1534/Genetics.107.080630  0.72
2009 Grover D, Tavare S. Finding Behavioral Motifs in Fly Trajectories Communications in Information and Systems. 9: 283-294. DOI: 10.4310/Cis.2009.V9.N3.A5  0.92
2008 Grover D, Yang J, Tavaré S, Tower J. Simultaneous tracking of fly movement and gene expression using GFP. Bmc Biotechnology. 8: 93. PMID 19087237 DOI: 10.1186/1472-6750-8-93  1
2008 Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie ME, Deloukas P, Tavaré S, Dermitzakis ET. Modifier effects between regulatory and protein-coding variation. Plos Genetics. 4: e1000244. PMID 18974877 DOI: 10.1371/Journal.Pgen.1000244  1
2008 Hull ML, Escareno CR, Godsland JM, Doig JR, Johnson CM, Phillips SC, Smith SK, Tavaré S, Print CG, Charnock-Jones DS. Endometrial-peritoneal interactions during endometriotic lesion establishment. The American Journal of Pathology. 173: 700-15. PMID 18688027 DOI: 10.2353/Ajpath.2008.071128  1
2008 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, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnology. 26: 779-85. PMID 18612301 DOI: 10.1038/Nbt1414  1
2008 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, et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research. 18: 1518-29. PMID 18577705 DOI: 10.1101/Gr.077479.108  1
2008 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. PMID 18571451 DOI: 10.1016/J.Molcel.2008.06.003  0.72
2008 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. Pediatric malignant germ cell tumors show characteristic transcriptome profiles. Cancer Research. 68: 4239-47. PMID 18519683 DOI: 10.1158/0008-5472.Can-07-5560  1
2008 Chu M, Siegmund KD, Hao QL, Crooks GM, Tavaré S, Shibata D. Inferring relative numbers of human leucocyte genome replications. British Journal of Haematology. 141: 862-71. PMID 18410448 DOI: 10.1111/J.1365-2141.2008.07142.X  0.72
2008 Grover D, Tower J, Tavaré S. O fly, where art thou? Journal of the Royal Society, Interface / the Royal Society. 5: 1181-91. PMID 18367442 DOI: 10.1098/Rsif.2007.1333  1
2007 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: R262. PMID 18067683 DOI: 10.1186/Gb-2007-8-12-R262  1
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 Biology. 8: R228. PMID 17961237 DOI: 10.1186/Gb-2007-8-10-R228  1
2007 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. 2: e1061. PMID 17957245 DOI: 10.1371/Journal.Pone.0001061  1
2007 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, et al. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biology. 8: R215. PMID 17925008 DOI: 10.1186/Gb-2007-8-10-R215  1
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 Biology. 8: R214. PMID 17922911 DOI: 10.1186/Gb-2007-8-10-R214  1
2007 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. Nature Genetics. 39: 1217-24. PMID 17873874 DOI: 10.1038/Ng2142  1
2007 Shibata D, Tavaré S. Stem cell chronicles: autobiographies within genomes. Stem Cell Reviews. 3: 94-103. PMID 17873386 DOI: 10.1007/S12015-007-0022-6  1
2007 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. PMID 17672908 DOI: 10.1186/1471-2350-8-50  0.72
2007 Skvortsov D, Abdueva D, Stitzer ME, Finkel SE, Tavaré S. Using expression arrays for copy number detection: an example from E. coli. Bmc Bioinformatics. 8: 203. PMID 17570850 DOI: 10.1186/1471-2105-8-203  1
2007 Skvortsov D, Abdueva D, Curtis C, Schaub B, Tavaré S. Explaining differences in saturation levels for Affymetrix GeneChip arrays. Nucleic Acids Research. 35: 4154-63. PMID 17567617 DOI: 10.1093/Nar/Gkm348  1
2007 Nicolas P, Kim KM, Shibata D, Tavaré S. The stem cell population of the human colon crypt: analysis via methylation patterns. Plos Computational Biology. 3: e28. PMID 17335343 DOI: 10.1371/Journal.Pcbi.0030028  1
2007 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, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (New York, N.Y.). 315: 848-53. PMID 17289997 DOI: 10.1126/Science.1136678  1
2007 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, et al. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene. 26: 1959-70. PMID 17001317 DOI: 10.1038/Sj.Onc.1209985  1
2007 Soligo C, Will OA, Tavaré S, Marshall CR, Martin RD. New light on the dates of primate origins and divergence Primate Origins: Adaptations and Evolution. 29-49. DOI: 10.1007/978-0-387-33507-0_2  1
2006 Ibrahim AE, 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 Research. 34: e136. PMID 17041235 DOI: 10.1093/Nar/Gkl551  1
2006 Marjoram P, Tavaré S. Modern computational approaches for analysing molecular genetic variation data. Nature Reviews. Genetics. 7: 759-70. PMID 16983372 DOI: 10.1038/Nrg1961  0.72
2006 Abdueva D, Skvortsov D, Tavaré S. Non-linear analysis of GeneChip arrays. Nucleic Acids Research. 34: e105. PMID 16936321 DOI: 10.1093/Nar/Gkl435  1
2006 Jiang R, Marjoram P, Borevitz JO, Tavaré S. Inferring population parameters from single-feature polymorphism data. Genetics. 173: 2257-67. PMID 16702439 DOI: 10.1534/Genetics.105.047472  1
2006 Shibata D, Tavaré S. Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle (Georgetown, Tex.). 5: 610-4. PMID 16582617 DOI: 10.4161/Cc.5.6.2570  1
2006 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. Molecular Biology and Evolution. 23: 1217-31. PMID 16549398 DOI: 10.1093/Molbev/Msk006  1
2006 Marioni JC, Thorne NP, Tavaré S. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics (Oxford, England). 22: 1144-6. PMID 16533818 DOI: 10.1093/Bioinformatics/Btl089  1
2006 Kim JY, Tavaré S, Shibata D. Human hair genealogies and stem cell latency. Bmc Biology. 4: 2. PMID 16457718 DOI: 10.1186/1741-7007-4-2  1
2005 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 Genetics. 1: e78. PMID 16362079 DOI: 10.1371/Journal.Pgen.0010078  1
2005 Kim JY, Tavaré S, Shibata D. Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proceedings of the National Academy of Sciences of the United States of America. 102: 17739-44. PMID 16314580 DOI: 10.1073/Pnas.0503976102  1
2005 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. PMID 16202134 DOI: 10.1186/1471-2407-5-126  0.4
2005 Clark RM, Tavaré S, Doebley J. Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Molecular Biology and Evolution. 22: 2304-12. PMID 16079248 DOI: 10.1093/Molbev/Msi228  1
2005 Kim JY, Siegmund KD, Tavaré S, Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. Bmc Medicine. 3: 10. PMID 15975143 DOI: 10.1186/1741-7015-3-10  0.72
2005 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: 1763-77. PMID 15654103 DOI: 10.1534/Genetics.104.032219  1
2004 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. Proceedings of the National Academy of Sciences of the United States of America. 101: 7663-8. PMID 15136717 DOI: 10.1073/Pnas.0307605101  1
2004 Calabrese P, Tsao JL, Yatabe Y, Salovaara R, Mecklin JP, Järvinen HJ, Aaltonen LA, Tavaré S, Shibata D. Colorectal pretumor progression before and after loss of DNA mismatch repair. The American Journal of Pathology. 164: 1447-53. PMID 15039232 DOI: 10.1016/S0002-9440(10)63231-2  0.4
2004 Kim KM, Calabrese P, Tavaré S, Shibata D. Enhanced stem cell survival in familial adenomatous polyposis. The American Journal of Pathology. 164: 1369-77. PMID 15039224 DOI: 10.1016/S0002-9440(10)63223-3  1
2004 Calabrese P, Tavaré S, Shibata D. Pretumor progression: clonal evolution of human stem cell populations. The American Journal of Pathology. 164: 1337-46. PMID 15039221 DOI: 10.1016/S0002-9440(10)63220-8  1
2003 Marjoram P, Molitor J, Plagnol V, Tavare S. Markov chain Monte Carlo without likelihoods. Proceedings of the National Academy of Sciences of the United States of America. 100: 15324-8. PMID 14663152 DOI: 10.1073/Pnas.0306899100  1
2002 Nordborg M, Tavaré S. Linkage disequilibrium: what history has to tell us. Trends in Genetics : Tig. 18: 83-90. PMID 11818140 DOI: 10.1016/S0168-9525(02)02557-X  1
2001 Yatabe Y, Tavaré S, Shibata D. Investigating stem cells in human colon by using methylation patterns Proceedings of the National Academy of Sciences of the United States of America. 98: 10839-10844. PMID 11517339 DOI: 10.1073/Pnas.191225998  1
2001 Markovtsova L, Marjoram P, Tavare S. On a test of Depaulis and Veuille. Molecular Biology and Evolution. 18: 1132-3; author reply. PMID 11371600 DOI: 10.1093/Oxfordjournals.Molbev.A003883  1
2000 Markovtsova L, Marjoram P, Tavaré S. The effects of rate variation on ancestral inference in the coalescent. Genetics. 156: 1427-36. PMID 11063714  1
2000 Markovtsova L, Marjoram P, Tavaré S. The age of a unique event polymorphism. Genetics. 156: 401-9. PMID 10978303  1
2000 Tsao JL, Yatabe Y, Salovaara R, Järvinen HJ, Mecklin JP, Aaltonen LA, Tavare S, Shibata D. Genetic reconstruction of individual colorectal tumor histories Proceedings of the National Academy of Sciences of the United States of America. 97: 1236-1241. PMID 10655514 DOI: 10.1073/Pnas.97.3.1236  1
1999 Fan F, Liu CP, Tavaré S, Arnheim N. Polymorphisms in the human DNA repair gene XPF Mutation Research - Mutation Research Genomics. 406: 115-120. PMID 10479728 DOI: 10.1016/S1383-5726(99)00008-4  1
1999 Leeflang EP, Tavaré S, Marjoram P, Neal CO, Srinidhi J, MacFarlane H, MacDonald ME, Gusella JF, de Young M, Wexler NS, Arnheim N. Analysis of germline mutation spectra at the Huntington's disease locus supports a mitotic mutation mechanism. Human Molecular Genetics. 8: 173-83. PMID 9931325 DOI: 10.1093/Hmg/8.2.173  1
1999 Leeflang EP, Tavare S, Marjoram P, Neal COS, Srinidhi J, MacFarlane H, MacDonald ME, Gusella JF, De Young M, Wexler NS, Amheim N. Corrigendum: Analysis of germline mutation spectra at the Huntington's disease locus supports a mitotic mutation mechanism (Human Molecular Genetics (1999) 8 (173-183)) Human Molecular Genetics. 8: 717.  1
1996 Fu YX, Li WH, Donnelly P, Tavare S, Balding DJ, Griffiths RC, Weiss G, Von Haeseler A, Rogers J, Samollow PB, Comuzzie AG, Dorit RL, Akashi H, Gilbert W. Estimating the age of the common ancestor of men from the ZFY intron Science. 272: 1356-1362. PMID 8650550 DOI: 10.1126/Science.272.5266.1356  1
1995 Leeflang EP, Zhang L, Tavaré S, Hubert R, Srinidhi J, MacDonald ME, Myers RH, de Young M, Wexler NS, Gusella JF. Single sperm analysis of the trinucleotide repeats in the Huntington's disease gene: quantification of the mutation frequency spectrum. Human Molecular Genetics. 4: 1519-26. PMID 8541834 DOI: 10.1093/Hmg/4.9.1519  1
1994 Griffiths RC, Tavare S. Simulating Probability Distributions in the Coalescent Theoretical Population Biology. 46: 131-159. DOI: 10.1006/Tpbi.1994.1023  1
1994 Arratia R, Tavare S. Independent Process Approximations for Random Combinatorial Structures Advances in Mathematics. 104: 90-154. DOI: 10.1006/Aima.1994.1022  1
1992 Lundstrom R, Tavaré S, Ward RH. Estimating substitution rates from molecular data using the coalescent. Proceedings of the National Academy of Sciences of the United States of America. 89: 5961-5. PMID 1631081 DOI: 10.1073/Pnas.89.13.5961  1
1992 Lundstrom R, Tavaré S, Ward RH. Modeling the evolution of the human mitochondrial genome. Mathematical Biosciences. 112: 319-35. PMID 1490056 DOI: 10.1016/0025-5564(92)90030-Z  1
1989 Tavaré S, Song B. Codon preference and primary sequence structure in protein-coding regions Bulletin of Mathematical Biology. 51: 95-115. PMID 2706404 DOI: 10.1016/S0092-8240(89)80050-3  1
1983 Karlin S, Ghandour G, Ost F, Tavare S, Korn LJ. New approaches for computer analysis of nucleic acid sequences. Proceedings of the National Academy of Sciences of the United States of America. 80: 5660-4. PMID 6577449 DOI: 10.1073/Pnas.80.18.5660  1
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