Simon Tavaré

Simon Tavaré

PUBLICATIONS


    Books

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

  2. Tavaré S & Zeitouni O. Lectures on Probability Theory and Statistics. Ecole d'Etés de Probabilité de Saint-Flour XXXI -- 2001. (Ed. Picard J.) Lecture Notes in Mathematics, 1837, 2004. Springer Verlag, New York.

    Draft of ST part [pp. 1-188] Ancestral inference in population genetics.

  3. 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.

  4. 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.

    5. Submitted

  5. Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S & Odom DT. Tissue-specific transcription is directed by genome sequence in an aneuploid mouse strain carrying human chromosome 21.

  6. Grover D, Yang J, Tavaré S & Tower J. Simultaneous tracking of fly movement and expression using GFP.

  7. Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie M, Deloukas P, Tavaré S & Dermitzakis ET. Exploring epistatic effects between regulatory and protein-coding variation.

  8. Jiang R, Tavaré S & Marjoram P. Population genetic inference from resequencing data.

    9. In Press

  9. 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.

  10. 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, CRC Press.

    11. 2008

  11. 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.

  12. 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 and Development, 22: 1906-1920, 2008.

  13. 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, [Epub ahead of print], June 16, 2008

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Grover D, Tower J & Tavaré S. O fly, where art thou? J. Roy. Soc. Interface. Online March 26, 2008.

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

    21. 2007

  21. 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.

  22. 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.

  23. 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.

  24. 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.

  25. 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.

  26. 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.

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

  28. 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.

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

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

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

  32. 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.

  33. 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.

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

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. 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

    41. 2006

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

  42. 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.

  43. 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.

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

  45. Abdueva D, Skvortsov D & Tavaré S. Non-linear multi-chip expression analysis of GeneChip arrays. Nucleic Acids Research, 34, e105, 2006. [doi: 10.1093/nar/gkl435]

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

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

  48. 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.
  49. Marioni JC, Thorne NP & Tavaré S. BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics, 22, 1144-1146, 2006.

  50. 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.

  51. 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.

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

  53. 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.

    54. 2005

  54. 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.

  55. 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.

  56. 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.

  57. 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.

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

  59. 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.

  60. 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.

  61. 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.

    62. 2004

  62. 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.

  63. 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.

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

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

  66. 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.

  67. 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.

    2003

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

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

  70. 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.

  71. 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.

    2002

  72. 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.

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

    2001

  74. 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.

  75. 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.)

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

  77. 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.

  78. 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.

    2000

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

  80. 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.

  81. 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.

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

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

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

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

    1999

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

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

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

  89. 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.

  90. 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.

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

  92. 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.

  93. Tavaré S. Random trees in molecular genetics. Bull. I.S.I., 52, 269-272, 1999.

    1998

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

  95. 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.

  96. 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.

  97. 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

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

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

  100. 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.

  101. 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.

  102. 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

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

  104. 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.

  105. 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

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

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

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

  109. 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.

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

  111. 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

  112. 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.

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

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

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

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

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

    1993

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

  119. 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

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

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

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

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

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

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

    1991

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

  127. 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

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

    1989

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

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

  131. 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

  132. 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

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

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

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

  136. 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

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

  138. 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

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

    1984

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

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

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

    1983

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

  144. Tavaré S & Altham PME. Serial dependence of observations leading to contingency tables, with corrections to c2 statistics. Biometrika, 70, 139-144, 1983.

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

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

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

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

  149. 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

  150. 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.

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

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

    1981

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

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

  155. 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.

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

    1980

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

    1979

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

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

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

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

  162. 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.

    Abstracts, Conference Reports and Manuscripts

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

  164. 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.

  165. 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.

  166. Martin RD, Soligo C, Tavaré S, Will O & Marshall CR. Early primates and the effects of a fragmentary fossil record on dating evolutionary divergences. Abstracts of the International Symposium on the Evolution of Vertebrates. University of Lund, Sweden, 1999.

  167. Marshall CR, Tavaré S, Will O, Soligo C & Martin RD. Taking into account the temporal ranges of unobserved species: reconciliation of fossil and molecular clock estimates of primate origins? Geological Society of America Abstracts with Programs, 199830 (7), A-326, 1998.

  168. 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.

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

  170. Tavaré S. Mathematical models in population genetics. Composite Function, 1991. (A reprinting of article 124 below)

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

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

  173. 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.

  174. 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.

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

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

  177. 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.

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

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

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

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

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


    Updated June 3, 2008