Dinh, K.N. et al. (2025) “Approximate Bayesian computation sequential Monte Carlo via random forests,” Statistics and Computing, 35(6), p. 219. Available at: https://doi.org/10.1007/s11222-025-10748-x.

McPherson, A. et al. (2025) “Ongoing genome doubling shapes evolvability and immunity in ovarian cancer,” Nature, 644(8078), pp. 1078–1087. Available at: https://doi.org/10.1038/s41586-025-09240-3.

Dinh, K.N. et al. (2025) “CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution,” PLOS Computational Biology, 21, p. e1012902. Available at: https://doi.org/10.1371/journal.pcbi.1012902.

Tavaré, S. (2025) “Birth and death processes in phylogenetics and population genetics,” Philosophical Transactions of the Royal Society B: Biological Sciences, 380(1919), p. 20230300. Available at: https://doi.org/10.1098/rstb.2023.0300.

Ng, A.W.T. et al. (2024) “Disentangling oncogenic amplicons in esophageal adenocarcinoma,” Nature Communications, 15, p. 4074. Available at: https://doi.org/10.1038/s41467-024-47619-4.

da Silva, P.H., Jamshidpey, A. and Tavaré, S. (2024) “Another view of sequential sampling in the birth process with immigration,” Journal of Mathematical Biology, 88, p. 27. Available at: https://doi.org/10.1007/s00285-023-02041-0.

Melamed, D. et al. (2023) “Spatial regulation of Drosophila ovarian Follicle Stem Cell division rates and cell cycle transitions,” PLOS Genetics. Edited by K.M. Cadigan, 19, p. e1010965. Available at: https://doi.org/10.1371/journal.pgen.1010965.

Kunes, R.Z. et al. (2023) “Gradient Estimation for Binary Latent Variables via Gradient Variance Clipping,” Proceedings of the AAAI Conference on Artificial Intelligence, 37(7), pp. 8405–8412. Available at: https://doi.org/10.1609/aaai.v37i7.26013.

González-Solares, E.A. et al. (2023) “Imaging and Molecular Annotation of Xenographs and Tumours (IMAXT): High throughput data and analysis infrastructure,” Biological Imaging, 3, p. e11. Available at: https://doi.org/10.1017/S2633903X23000090.

Nowicki-Osuch, K. et al. (2023) “Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia,” Cancer Discovery, 13(6), pp. 1346–1363. Available at: https://doi.org/10.1158/2159-8290.CD-22-0824.

da Silva, P.H. et al. (2023) “Fisher’s measure of variability in repeated samples,” Bernoulli, 29, pp. 1166-1194. Available at: https://doi.org/10.3150/22-BEJ1494.

da Silva, P.H. et al. (2022) “Markov chains arising from biased random derangements.” arXiv. Available at: https://doi.org/10.48550/arXiv.2211.13831.

Ng, A.W.T. et al. (2022) “Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas,” Communications Biology, 5, p. 335. Available at: https://doi.org/10.1038/s42003-022-03238-7.

Tavaré, S. (2022) “A note on the Screaming Toes game,” Journal of Applied Probability, 59, pp. 118–130. Available at: https://doi.org/10.1017/jpr.2021.32.

Tavaré, S. (2021) “The magical Ewens sampling formula,” Bulletin of the London Mathematical Society, 53, pp. 1563–1582. Available at: https://doi.org/10.1112/blms.12537.

Williams, E.H. et al. (2021) “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(5), pp. 1381–1390. Available at: https://doi.org/10.1158/1078-0432.CCR-20-3201.

Touloumis, A., Marioni, J. and Tavaré, S. (2021) “Hypothesis Testing for the Covariance Matrix in High-Dimensional Transposable Data with Kronecker Product Dependence Structure,” Statistica Sinica, 31, pp. 1309–1329. Available at: https://doi.org/10.5705/ss.202018.0268.

Biasci, D., Thaventhiran, J. and Tavaré, S. (2020) “Fibroblastic reticular cells predict response to immune checkpoint inhibitors.” Immunology. Available at: https://doi.org/10.1101/2020.02.19.955666.

Perner, J. et al. (2020) “The mutREAD method detects mutational signatures from low quantities of cancer DNA,” Nature Communications, 11, p. 3166. Available at: https://doi.org/10.1038/s41467-020-16974-3.

Jammula, S. et al. (2020) “Identification of Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data,” Gastroenterology, 158, pp. 1682-1697.e1. Available at: https://doi.org/10.1053/j.gastro.2020.01.044.

Dinh, K.N. et al. (2020) “Statistical Inference for the Evolutionary History of Cancer Genomes,” Statistical Science, 35, pp. 129–144. Available at: https://doi.org/10.1214/19-STS7561.

Williams, E.H. et al. (2019) “Multicenter Validation of the CamGFR Model for Estimated Glomerular Filtration Rate,” JNCI Cancer Spectrum, 3(4), p. pkz068. Available at: https://doi.org/10.1093/jncics/pkz068.

Spencer, S. et al. (2019) “Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses,” Journal of Experimental Medicine, 216(9), pp. 1986–1998. Available at: https://doi.org/10.1084/jem.20190344.

Frankell, A.M. et al. (2019) “The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic,” Nature Genetics, 51(3), pp. 506–516. Available at: https://doi.org/10.1038/s41588-018-0331-5.

Tavaré, S. (2019) “The linear birth‒death process: an inferential retrospective,” Advances in Applied Probability, 50(A), pp. 253–269. Available at: https://doi.org/10.1017/apr.2018.84.

Griffiths, R.C. and Tavaré, S. (2018) “Ancestral inference from haplotypes and mutations,” Theoretical Population Biology, 122, pp. 12–21. Available at: https://doi.org/10.1016/j.tpb.2018.04.006.

Arratia, R. et al. (2018) “Simulating the component counts of combinatorial structures,” Theoretical Population Biology, 122, pp. 5–11. Available at: https://doi.org/10.1016/j.tpb.2018.02.002.

Nicholson, A.M. et al. (2018) “Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium,” Cell Stem Cell, 22, pp. 909-918.e8. Available at: https://doi.org/10.1016/j.stem.2018.04.020.

Wedge, D.C. et al. (2018) “Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets,” Nature Genetics, 50(5), pp. 682–692. Available at: https://doi.org/10.1038/s41588-018-0086-z.

Reilein, A. et al. (2018) “Division-independent differentiation mandates proliferative competition among stem cells,” Proceedings of the National Academy of Sciences, 115, pp. E3182–E3191. Available at: https://doi.org/10.1073/pnas.1718646115.

Asim, M. et al. (2017) “Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer,” Nature Communications, 8, p. 374. Available at: https://doi.org/10.1038/s41467-017-00393-y.

Janowitz, T  et al. (2017) “New Model for Estimating Glomerular Filtration Rate in Patients With Cancer,” Journal of Clinical Oncology, 35, pp. 2798–2805. Available at: https://doi.org/10.1200/JCO.2017.72.7578.

Noorani, A. et al. (2017) “A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy,” Genome Research, 27, pp. 902–912. Available at: https://doi.org/10.1101/gr.214296.116.

Secrier, M. et al. (2016) “Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance,” Nature Genetics, 48, pp. 1131–1141. Available at: https://doi.org/10.1038/ng.3659.

Touloumis, A., Marioni, J.C. and Tavaré, S. (2016) “HDTD: analyzing multi-tissue gene expression data,” Bioinformatics, 32, pp. 2193–2195. Available at: https://doi.org/10.1093/bioinformatics/btw224.

Arratia, R., Barbour, A.D. and Tavaré, S. (2016) “Exploiting the Feller Coupling for the Ewens Sampling Formula,” Statistical Science, 31, pp. 27–29. Available at: https://doi.org/10.1214/15-STS537.

Asim, M. et al. (2016) “Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target,” Journal of the National Cancer Institute, 108, p. djv371. Available at: https://doi.org/10.1093/jnci/djv371.

Madhu, B. et al. (2015) “Metabolomic changes during cellular transformation monitored by metabolite–metabolite correlation analysis and correlated with gene expression,” Metabolomics, 11, pp. 1848–1863. Available at: https://doi.org/10.1007/s11306-015-0838-z.

Paterson, A.L. et al. (2015) “Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis,” BMC Genomics, 16, p. 473. Available at: https://doi.org/10.1186/s12864-015-1685-z.

Greenwood, A.K. et al. (2015) “Genetic Mapping of Natural Variation in Schooling Tendency in the Threespine Stickleback,” G3: Genes|Genomes|Genetics, 5, pp. 761–769. Available at: https://doi.org/10.1534/g3.114.016519.

Touloumis, A., Tavaré, S. and Marioni, J.C. (2015) “Testing the mean matrix in high-dimensional transposable data: Testing the Mean Matrix in High-Dimensional Transposable Data,” Biometrics, 71, pp. 157–166. Available at: https://doi.org/10.1111/biom.12257.

Kirschner, K. et al. (2015) “Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53,” PLOS Genetics. Edited by J. Gil, 11, p. e1005053. Available at: https://doi.org/10.1371/journal.pgen.1005053.

Josephidou, M., et al. (2015) “multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples,” Nucleic Acids Research, 43, pp. e61–e61. Available at: https://doi.org/10.1093/nar/gkv135.

Gubernator, M. et al. (2015) “Epigenetic Profile of Human Adventitial Progenitor Cells Correlates With Therapeutic Outcomes in a Mouse Model of Limb Ischemia,” Arteriosclerosis, Thrombosis, and Vascular Biology, 35, pp. 675–688. Available at: https://doi.org/10.1161/ATVBAHA.114.304989.

Massie, C.E. et al. (2015) “HES5 silencing is an early and recurrent change in prostate tumourigenesis,” Endocrine-Related Cancer, 22(2), pp. 131–144. Available at: https://doi.org/10.1530/ERC-14-0454.

Piccirillo, S.G.M. et al. (2015) “Contributions to Drug Resistance in Glioblastoma Derived from Malignant Cells in the Sub-Ependymal Zone,” Cancer Research, 75, pp. 194–202. Available at: https://doi.org/10.1158/0008-5472.CAN-13-3131.

Silva, A.-L. et al. (2014) “Boosting Wnt activity during colorectal cancer progression through selective hypermethylation of Wnt signaling antagonists,” BMC Cancer, 14, p. 891. Available at: https://doi.org/10.1186/1471-2407-14-891.

Cairns, J. et al. (2014) “Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data,” Frontiers in Genetics, 5, p. 399. Available at: https://doi.org/10.3389/fgene.2014.00399.

Weaver, J.M.J. et al. (2014) “Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis,” Nature Genetics, 46, pp. 837–843. Available at: https://doi.org/10.1038/ng.3013.

Jauhiainen, A. et al. (2014) “Normalization of metabolomics data with applications to correlation maps,” Bioinformatics, 30, pp. 2155–2161. Available at: https://doi.org/10.1093/bioinformatics/btu175.

Ostrow, A.Z. et al. (2014) “Fkh1 and Fkh2 Bind Multiple Chromosomal Elements in the S. cerevisiae Genome with Distinct Specificities and Cell Cycle Dynamics,” PLoS ONE, 9, p. e87647. Available at: https://doi.org/10.1371/journal.pone.0087647.

Turro, E. et al. (2014) “Flexible analysis of RNA-seq data using mixed effects models,” Bioinformatics, 30, pp. 180–188. Available at: https://doi.org/10.1093/bioinformatics/btt624.

Ardekani, R. et al. (2013) “Automated quantification of the schooling behaviour of sticklebacks,” EURASIP Journal on Image and Video Processing 2013, p. 61. Available at: https://doi.org/10.1186/1687-5281-2013-61.

Vermeulen, L. et al. (2013) “Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation,” Science, 342, pp. 995–998. Available at: https://doi.org/10.1126/science.1243148.

Fu, A.Q. et al. (2013) “Bayesian clustering of replicated time-course gene expression data with weak signals,” The Annals of Applied Statistics, 7 pp. 1334–1361. Available at: https://doi.org/10.1214/13-AOAS650.

Ardekani, R. et al. (2013) “Assessing Senescence in Drosophila Using Video Tracking,” in L. Galluzzi et al. (eds.) Cell Senescence. Totowa, NJ: Humana Press (Methods in Molecular Biology), pp. 501–516. Available at: https://doi.org/10.1007/978-1-62703-239-1_33.

Kozar, S. et al. (2013) “Continuous Clonal Labeling Reveals Small Numbers of Functional Stem Cells in Intestinal Crypts and Adenomas,” Cell Stem Cell, 13, pp. 626–633. Available at: https://doi.org/10.1016/j.stem.2013.08.001.

Newman, S. et al. (2013) “The Relative Timing of Mutations in a Breast Cancer Genome,” PLoS ONE., 8, p. e64991. Available at: https://doi.org/10.1371/journal.pone.0064991.

Zhong, Y. et al. (2013) “The level of origin firing inversely affects the rate of replication fork progression,” The Journal of Cell Biology, 201, pp. 373–383. Available at: https://doi.org/10.1083/jcb.201208060.

Sottoriva, A. et al. (2013) “Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics,” Proceedings of the National Academy of Sciences, 110(10), pp. 4009–4014. Available at: https://doi.org/10.1073/pnas.1219747110.

Ardekani, R., Biyani, A., et al. (2013) “Three-dimensional tracking and behaviour monitoring of multiple fruit flies,” Journal of The Royal Society Interface, 10, p. 20120547. Available at: https://doi.org/10.1098/rsif.2012.0547.

Sottoriva, A. et al. (2013) “Single-Molecule Genomic Data Delineate Patient-Specific Tumor Profiles and Cancer Stem Cell Organization,” Cancer Research, 73(1), pp. 41–49. Available at: https://doi.org/10.1158/0008-5472.CAN-12-2273.

Housden, B.E. et al. (2013) “Transcriptional Dynamics Elicited by a Short Pulse of Notch Activation Involves Feed-Forward Regulation by E(spl)/Hes Genes,” PLoS Genetics, 9, p. e1003162. Available at: https://doi.org/10.1371/journal.pgen.1003162.

Ardekani, R., Tavaré, S. and Tower, J. (2013) “Assessing Senescence in Drosophila Using Video Tracking,” in L. Galluzzi et al. (eds.) Cell Senescence. Totowa, NJ: Humana Press (Methods in Molecular Biology), pp. 501–516. Available at: https://doi.org/10.1007/978-1-62703-239-1_33.

Cairns, J.M., Lynch, A.G. and Tavaré, S. (2013) “Statistical aspects of ChIP-seq analysis,” Advances in Statistical Bioinformatics: Models and Integrative Inference for High-throughput Data. Cambridge University Press, pp. 138–169.

Marjoram, P. and Tavaré, S. (2013) “Coalescent,” Brenner’s Encyclopedia of Genetics. Elsevier, pp. 54–57. Available at: https://doi.org/10.1016/B978-0-12-374984-0.00274-6.

Sottoriva, A. et al. (2013) “Single-Molecule Genomic Data Delineate Patient-Specific Tumor Profiles and Cancer Stem Cell Organization,” Cancer Research, 73, pp. 41–49. Available at: https://doi.org/10.1158/0008-5472.CAN-12-2273.

Lynch, A.G. et al. (2012) “Calling sample mix-ups in cancer population studies,” PLoS ONE, 7, p. e41815. Available at: https://doi.org/10.1371/journal.pone.0041815.

Ardekani, R., Huang, Y.M., et al. (2012) “Using GFP video to track 3D movement and conditional gene expression in free-moving flies,” PLoS ONE, 7, p. e40506. Available at: https://doi.org/10.1371/journal.pone.0040506.

Chandra, T. et al. (2012) “Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation,” Molecular Cell, 47, pp. 203–214. Available at: https://doi.org/10.1016/j.molcel.2012.06.010.

Curtis, C. et al. (2012) “The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups,” Nature, 486, pp. 346–352. Available at: https://doi.org/10.1038/nature10983.

Knott, S.R.V. et al. (2012) “Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae,” Cell, 148, pp. 99–111. Available at: https://doi.org/10.1016/j.cell.2011.12.012.

Manolopoulou, I. et al. (2011) “A Bayesian approach to phylogeographic clustering,” Interface Focus, 1, pp. 909–921. Available at: https://doi.org/10.1098/rsfs.2011.0054.

Speed, D. and Tavaré, S. (2011) “Sparse Partitioning: Nonlinear regression with binary or tertiary predictors, with application to association studies,” The Annals of Applied Statistics, 5, pp. 873–893. Available at: https://doi.org/10.1214/10-AOAS411.

Siegmund, K.D. et al. (2011) “High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers,” PLoS ONE, 6, p. e21657. Available at: https://doi.org/10.1371/journal.pone.0021657.

Sottoriva, A. et al. (2011) “Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors,” PLoS Computational Biology, 7, p. e1001132. Available at: https://doi.org/10.1371/journal.pcbi.1001132.

Narita, M. et al. (2011) “Spatial coupling of mTOR and autophagy augments secretory phenotypes,” Science, 332, pp. 966–970. Available at: https://doi.org/10.1126/science.1205407.

Ibrahim, A.E.K. et al. (2011) “Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression,” Gut, 60, pp. 499–508. Available at: https://doi.org/10.1136/gut.2010.223602.

Cairns, J. et al. (2011) “BayesPeak—an R package for analysing ChIP-seq data,” Bioinformatics, 27, pp. 713–714. Available at: https://doi.org/10.1093/bioinformatics/btq685.

Wilkinson, R.D. et al. (2011) “Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data,” Systematic Biology, 60(1), pp. 16–31. Available at: https://doi.org/10.1093/sysbio/syq054.

Ivakhno, S. et al. (2010) “CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data,” Bioinformatics, 26, pp. 3051–3058. Available at: https://doi.org/10.1093/bioinformatics/btq587.

Lynch, A.G. et al. (2010) “The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment,” BMC Genomics, 11(1), p. 540. Available at: https://doi.org/10.1186/1471-2164-11-540.

Ritchie, M.E. et al. (2010) “Data analysis issues for allele-specific expression using Illumina’s GoldenGate assay,” BMC Bioinformatics, 11, p. 280. Available at: https://doi.org/10.1186/1471-2105-11-280.

Ivakhno, S. and Tavaré, S. (2010) “CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data,” Bioinformatics, 26(11), pp. 1395–1402. Available at: https://doi.org/10.1093/bioinformatics/btq145.

Daelemans, C. et al. (2010) “High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta,” BMC Genetics, 11(1), p. 25. Available at: https://doi.org/10.1186/1471-2156-11-25.

Smith, M.L. et al. (2010) “Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data,” BMC Bioinformatics, 11, p. 208. Available at: https://doi.org/10.1186/1471-2105-11-208.

Clark, A.M. et al. (2010) “The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans,” Nucleic Acids Research, 38, pp. 3780–3793. Available at: https://doi.org/10.1093/nar/gkq083.

Barbosa-Morais, N.L. et al. (2010) “A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data,” Nucleic Acids Research, 38, pp. e17–e17. Available at: https://doi.org/10.1093/nar/gkp942.

Curtis, C. et al. (2009) “The pitfalls of platform comparison: DNA copy number array technologies assessed,” BMC Genomics, 10, p. 588. Available at: https://doi.org/10.1186/1471-2164-10-588.

Grover, D. et al. (2009) “Finding Behavioral Motifs in Fly Trajectories,” Communications in Information and Systems, 9, pp. 283–294. Available at: https://doi.org/10.4310/CIS.2009.v9.n3.a5.

Avril-Sassen, S. et al. (2009) “Characterisation of microRNA expression in post-natal mouse mammary gland development,” BMC Genomics, 10, p. 548. Available at: https://doi.org/10.1186/1471-2164-10-548.

Waskar, M. et al. (2009) “Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy,” Aging, 1, pp. 903–936. Available at: https://doi.org/10.18632/aging.100099.

Grover, D. et al. (2009) “Hydrogen Peroxide Stimulates Activity and Alters Behavior in Drosophila melanogaster,” PLoS ONE, 4, p. e7580. Available at: https://doi.org/10.1371/journal.pone.0007580.

Knott, S.R. et al. (2009) “Strategies for analyzing highly enriched IP-chip datasets,” BMC Bioinformatics, 10, p. 305. Available at: https://doi.org/10.1186/1471-2105-10-305.

Spyrou, C. et al. (2009) “BayesPeak: Bayesian analysis of ChIP-seq data,” BMC Bioinformatics, 10, p. 299. Available at: https://doi.org/10.1186/1471-2105-10-299.

Fernando, H. et al. (2009) “Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression,” Nucleic Acids Research, 37, pp. 6716–6722. Available at: https://doi.org/10.1093/nar/gkp740.

Ritchie, M.E. et al. (2009) “R/Bioconductor software for Illumina’s Infinium whole-genome genotyping BeadChips,” Bioinformatics, 25, pp. 2621–2623. Available at: https://doi.org/10.1093/bioinformatics/btp470.

Siegmund, K.D. et al. (2009) “Many colorectal cancers are ‘flat’ clonal expansions,” Cell Cycle, 8, pp. 2187–2193. Available at: https://doi.org/10.4161/cc.8.14.9151.

Tiemann-Boege, I. et al. (2009) “Product Length, Dye Choice, and Detection Chemistry in the Bead-Emulsion Amplification of Millions of Single DNA Molecules in Parallel,” Analytical Chemistry, 81, pp. 5770–5776. Available at: https://doi.org/10.1021/ac900633y.

Knott, S.R.V. et al. (2009) “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 & Development, 23, pp. 1077–1090. Available at: https://doi.org/10.1101/gad.1784309.

Grover, D. et al. (2009) “Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes,” BMC Research Notes, 2, p. 58. Available at: https://doi.org/10.1186/1756-0500-2-58.

Wilkinson, R.D. et al. (2009) “Estimating primate divergence times by using conditioned birth-and-death processes,” Theoretical Population Biology, 75, pp. 278–285. Available at: https://doi.org/10.1016/j.tpb.2009.02.003.

Young, A.R.J. et al. (2009) “Autophagy mediates the mitotic senescence transition,” Genes & Development, 23, pp. 798–803. Available at: https://doi.org/10.1101/gad.519709.

Siegmund, K.D. et al. (2009) “Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers,” Proceedings of the National Academy of Sciences, 106, pp. 4828–4833. Available at: https://doi.org/10.1073/pnas.0810276106.

Shen, J. et al. (2009) “A screen of apoptosis and senescence regulatory genes for life span effects when over-expressed in Drosophila,” Aging, 1(2), pp. 191–211. Available at: https://doi.org/10.18632/aging.100018.

Woo, Y.-J. et al. (2009) “Older individuals appear to acquire mitotically older colorectal cancers,” The Journal of Pathology, 217(4), pp. 483–488. Available at: https://doi.org/10.1002/path.2506.

Jiang, R. et al. (2009) “Population Genetic Inference From Resequencing Data,” Genetics, 181, pp. 187–197. Available at: https://doi.org/10.1534/genetics.107.080630.

Grover, D. et al. (2009) “Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes,” BMC Research Notes, 2, p. 58. Available at: https://doi.org/10.1186/1756-0500-2-58.

Dimas, A.S. et al. (2008) “Modifier Effects between Regulatory and Protein-Coding Variation,” PLoS Genetics, 4, p. e1000244. Available at: https://doi.org/10.1371/journal.pgen.1000244.

Wilson, M.D. et al. (2008) “Species-Specific Transcription in Mice Carrying Human Chromosome 21,” Science, 322, pp. 434–438. Available at: https://doi.org/10.1126/science.1160930.

Hull, M.L. et al. (2008) “Endometrial-Peritoneal Interactions during Endometriotic Lesion Establishment,” The American Journal of Pathology, 173, pp. 700–715. Available at: https://doi.org/10.2353/ajpath.2008.071128.

Marioni, J.C. et al. (2008) “Hidden copy number variation in the HapMap population,” Proceedings of the National Academy of Sciences, 105, pp. 10067–10072. Available at: https://doi.org/10.1073/pnas.0711252105.

Szyjka, S.J. et al. (2008) “Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae,” Genes & Development, 22, pp. 1906–1920. Available at: https://doi.org/10.1101/gad.1660408.

Rakyan, V.K. et al. (2008) “An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs),” Genome Research, 18, pp. 1518–1529. Available at: https://doi.org/10.1101/gr.077479.108.

Das, P.P. et al. (2008) “Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline,” Molecular Cell, 31, pp. 79–90. Available at: https://doi.org/10.1016/j.molcel.2008.06.003.

Down, T.A. et al. (2008) “A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis,” Nature Biotechnology, 26, pp. 779–785. Available at: https://doi.org/10.1038/nbt1414.

Dunning, M.J. et al. (2008) “Spike-in validation of an Illumina-specific variance-stabilizing transformation,” BMC Research Notes, 1, p. 18. Available at: https://doi.org/10.1186/1756-0500-1-18.

Palmer, R.D. et al. (2008) “Pediatric Malignant Germ Cell Tumors Show Characteristic Transcriptome Profiles,” Cancer Research, 68(11), pp. 4239–4247. Available at: https://doi.org/10.1158/0008-5472.CAN-07-5560.

Chu, M. et al. (2008) “Inferring relative numbers of human leucocyte genome replications,” British Journal of Haematology, 141, pp. 862–871. Available at: https://doi.org/10.1111/j.1365-2141.2008.07142.x.

Grover, D. et al. (2008) “O fly, where art thou?,” Journal of The Royal Society Interface, 5, pp. 1181–1191. Available at: https://doi.org/10.1098/rsif.2007.1333.

Dunning, M.J. et al. (2008) “Statistical issues in the analysis of Illumina data,” BMC Bioinformatics, 9, p. 85. Available at: https://doi.org/10.1186/1471-2105-9-85.

Curtis, C. et al. (2007) “Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes,” Genome Biology, 8, p. R262. Available at: https://doi.org/10.1186/gb-2007-8-12-r262.

Marioni, J.C. et al. (2007) “Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization,” Genome Biology, 8, p. R228. Available at: https://doi.org/10.1186/gb-2007-8-10-r228.

Conboy, C.M. et al. (2007) “Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor,” PLoS ONE. Edited by C. Fairhead, 2, p. e1061. Available at: https://doi.org/10.1371/journal.pone.0001061.

Chin, S.F. et al. (2007) “High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer,” Genome Biology, 8, p. R215. Available at: https://doi.org/10.1186/gb-2007-8-10-r215.

Blenkiron, C. et al. (2007) “MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype,” Genome Biology, 8, p. R214. Available at: https://doi.org/10.1186/gb-2007-8-10-r214.

Stranger, B.E. et al. (2007) “Population genomics of human gene expression,” Nature Genetics, 39, pp. 1217–1224. Available at: https://doi.org/10.1038/ng2142.

Shibata, D. et al. (2007) “Stem Cell Chronicles: Autobiographies Within Genomes,” Stem Cell Reviews, 3, pp. 94–103. Available at: https://doi.org/10.1007/s12015-007-0022-6.

Martin, R.D. et al. (2007) “Primate Origins: Implications of a Cretaceous Ancestry,” Folia Primatologica, 78, pp. 277–296. Available at: https://doi.org/10.1159/000105145.

Chu, M.W. et al. (2007) “Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging,” BMC Medical Genetics, 8, p. 50. Available at: https://doi.org/10.1186/1471-2350-8-50.

Dunning, M.J. et al. (2007) “beadarray: R classes and methods for Illumina bead-based data,” Bioinformatics, 23, pp. 2183–2184. Available at: https://doi.org/10.1093/bioinformatics/btm311.

Skvortsov, D. et al. (2007) “Explaining differences in saturation levels for Affymetrix GeneChip® arrays,” Nucleic Acids Research, 35, pp. 4154–4163. Available at: https://doi.org/10.1093/nar/gkm348.

Skvortsov, D. et al. (2007) “Using expression arrays for copy number detection: an example from E. coli,” BMC Bioinformatics, 8, p. 203. Available at: https://doi.org/10.1186/1471-2105-8-203.

Chin, S.-F. et al. (2007) “Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers,” Oncogene, 26, pp. 1959–1970. Available at: https://doi.org/10.1038/sj.onc.1209985.

Nicolas, P. et al. (2007) “The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns,” PLoS Computational Biology, 3, p. 11. Available at: https://doi.org/10.1371/journal.pcbi.0030028.

Stranger, B.E. et al. (2007) “Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes,” Science, 315, pp. 848–853. Available at: https://doi.org/10.1126/science.1136678.

Dunning, M. et al. (2006) “beadarray: An R Package to Analyse Illumina BeadArrays,” R News, 6, p. 7. Available here.

Xu, W. et al. (2006) “Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae,” BMC Genomics, 7, p. 276. Available at: https://doi.org/10.1186/1471-2164-7-276.

Ibrahim, A.E.K. et al. (2006) “MMASS: an optimized array-based method for assessing CpG island methylation,” Nucleic Acids Research, 34, pp. e136–e136. Available at: https://doi.org/10.1093/nar/gkl551.

Abdueva, D. et al. (2006) “Non-linear analysis of GeneChip arrays,” Nucleic Acids Research, 34, pp. e105–e105. Available at: https://doi.org/10.1093/nar/gkl435.

Marjoram, P. et al. (2006) “Modern computational approaches for analysing molecular genetic variation data,” Nature Reviews Genetics, 7, pp. 759–770. Available at: https://doi.org/10.1038/nrg1961.

Jiang, R. et al. (2006) “Inferring Population Parameters From Single-Feature Polymorphism Data,” Genetics, 173, pp. 2257–2267. Available at: https://doi.org/10.1534/genetics.105.047472.

Shibata, D. et al. (2006) “Counting Divisions in a Human Somatic Cell Tree: How, What and Why,” Cell Cycle, 5, pp. 610–614. Available at: https://doi.org/10.4161/cc.5.6.2570.

Millman, K. et al. (2006) “Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes,” Microbes and Infection, 8, pp. 604–611. Available at: https://doi.org/10.1016/j.micinf.2005.08.012.

Jakobsson, M. et al. (2006) “A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers,” Molecular Biology and Evolution, 23, pp. 1217–1231. Available at: https://doi.org/10.1093/molbev/msk006.

Marioni, J.C. et al. (2006) “BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data,” Bioinformatics, 22, pp. 1144–1146. Available at: https://doi.org/10.1093/bioinformatics/btl089.

Dunning, M.J. et al. (2006) “Quality control and low-level statistical analysis of Illumina BeadArrays,” REVSTAT, 4, pp. 1–30. Available at: https://doi.org/10.57805/revstat.v4i1.24.

Arratia, R. et al. (2006) “A Tale of Three Couplings: Poisson–Dirichlet and GEM Approximations for Random Permutations,” Combinatorics, Probability and Computing, 15, p. 31. Available at: https://doi.org/10.1017/S0963548305007054.

Kim, J. et al. (2006) “Human hair genalogies and stem cell latency,” BMC Biology, 4, p. Art 2. Available at: https://doi.org/10.1186/1741-7007-4-2.

Stranger, B.E. et al. (2005) “Genome-Wide Associations of Gene Expression Variation in Humans,” PLoS Genetics, 1, p. e78. Available at: https://doi.org/10.1371/journal.pgen.0010078.

Kim, J.Y. et al. (2005) “Counting human somatic cell replications: Methylation mirrors endometrial stem cell divisions,” Proc Natl Acad Sci USA, 102, pp. 17739–17744. Available at: https://doi.org/10.1073 pnas.0503976102.

Clark, R.M. et al. (2005) “Estimating a Nucleotide Substitution Rate for Maize from Polymorphism at a Major Domestication Locus,” Molecular Biology and Evolution, 22, pp. 2304–2312. Available at: https://doi.org/10.1093/molbev/msi228.

Calabrese, P. et al. (2005) “Numbers of mutations to different types of colorectal cancer,” BMC Cancer, 5, p. 126. Available at: https://doi.org/10.1186/1471-2407-5-126.

Kim, J.Y. et al. (2005) “Age-related human small intestine methylation: evidence for stem cell niches,” BMC Medicine, 3, p. 10. Available at: https://doi.org/10.1186/1741-7015-3-10.

Arratia, R. et al. (2005) “A probabilistic approach to analytic arithmetic on algebraic function fields,” Mathematical Proceedings of the Cambridge Philosophical Society, 139, pp. 1–26. Available at: https://doi.org/10.1017/S0305004105008583.

Innan, H. et al. (2005) “Statistical Tests of the Coalescent Model Based on the Haplotype Frequency Distribution and the Number of Segregating Sites,” Genetics, 169, pp. 1763–1777. Available at: https://doi.org/10.1534/genetics.104.032219.

Tavaré, S. (2004) “Ancestral inference in population genetics.” Springer Verlag, New York (Lecture Notes in Mathematics), pp. 1–188. Available at: https://link.springer.com/book/10.1007/b95197.

Landis, G.N. et al. (2004) “Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster,” Proceedings of the National Academy of Sciences, 101, pp. 7663–7668. Available at: https://doi.org/10.1073/pnas.0307605101.

Millman, K. et al. (2004) “Population-Based Genetic and Evolutionary Analysis of Chlamydia trachomatis Urogenital Strain Variation in the United States,” Journal of Bacteriology, 186, pp. 2457–2465. Available at: https://doi.org/10.1128/JB.186.8.2457-2465.2004.

Calabrese, P. et al. (2004) “Pretumor Progression: clonal evolution of human stem cell populations,” The American Journal of Pathology, 164, pp. 1337–1346. Available at: https://doi.org/10.1016/S0002-9440(10)63220-8.

Calabrese, P. et al. (2004) “Colorectal Pretumor Progression Before and After Loss of DNA Mismatch Repair,” The American Journal of Pathology, 164, pp. 1447–1453. Available at: https://doi.org/10.1016/S0002-9440(10)63231-2.

Kim, K.-M. et al. (2004) “Enhanced Stem Cell Survival in Familial Adenomatous Polyposis,” The American Journal of Pathology, 164, pp. 1369–1377. Available at: https://doi.org/10.1016/S0002-9440(10)63223-3.

Marjoram, P. et al. (2003) “Markov chain Monte Carlo without likelihoods,” Proceedings of the National Academy of Sciences, 100, pp. 15324–15328. Available at: https://doi.org/10.1073/pnas.0306899100.

Tavaré, S. et al. (2002) “Using the fossil record to estimate the age of the last common ancestor of extant primates,” Nature, 416, pp. 726-729. Available at: https://doi.org/10.1038/416726a.

Nordborg, M. et al. (2002) “Linkage disequilibrium: what history has to tell us,” Trends in Genetics, 18, pp. 83–90. Available at: https://doi.org/10.1016/S0168-9525(02)02557-X.

Millman, K.L. et al. (2001) “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,” Journal of Bacteriology, 183, pp. 5997–6008. Available at: https://doi.org/10.1128/JB.183.20.5997-6008.2001.

Yatabe, Y. et al. (2001) “Investigating stem cells in human colon by using methylation patterns,” Proceedings of the National Academy of Sciences, 98, pp. 10839–10844. Available at: https://doi.org/10.1073/pnas.191225998.

Tavaré, S. et al. (2000) “A model for phylogenetic inference using structural and chemical covariates,” Biocomputing 2001. Proceedings of the Pacific Symposium, Mauna Lani, Hawaii: WORLD SCIENTIFIC, pp. 215–225. Available at: https://doi.org/10.1142/9789814447362_0022.

Arratia, R. et al. (2000) “Limits of logarithmic combinatorial structures,” The Annals of Probability, 28, pp. 1620–1644. Available at: https://doi.org/10.1214/aop/1019160500.

Markovtsova, L. et al. (2000) “The Effects of Rate Variation on Ancestral Inference in the Coalescent,” Genetics, 156, pp. 1427–1436. Available at: https://doi.org/10.1093/genetics/156.3.1427.

Markovtsova, L. et al. (2000) “The Age of a Unique Event Polymorphism,” Genetics, 156, pp. 401–409. Available at: https://doi.org/10.1093/genetics/156.1.401.

Arratia, Richard, Barbour, A.D. and Tavaré, S. (2000) “The number of components in a logarithmic combinatorial structure,” The Annals of Applied Probability, 10, pp. 331–361. Available at: https://doi.org/10.1214/aoap/1019487347.

Schbath, S., Bossard, N. and Tavaré, S. (2000) “The Effect of Nonhomogeneous Clone Length Distribution on the Progress of an STS Mapping Project,” Journal of Computational Biology, 7, pp. 47–57. Available at: https://doi.org/10.1089/10665270050081379.

Tsao, J.-L. et al. (2000) “Genetic reconstruction of individual colorectal tumor histories,” Proceedings of the National Academy of Sciences, 97, pp. 1236–1241. Available at: https://doi.org/10.1073/pnas.97.3.1236.

Jaruzelska, J. et al. (1999) “Spatial and Temporal Distribution of the Neutral Polymorphisms in the Last ZFX Intron: Analysis of the Haplotype Structure and Genealogy,” Genetics, 152, pp. 1091–1101. Available at: https://doi.org/10.1093/genetics/152.3.1091.

Fan, F. et al. (1999) “Polymorphisms in the human DNA repair gene XPF,” Mutation Research genomics, 406, pp. 115–120. Available at: https://doi.org/10.1016/s1383-5726(99)00008-4.

Leeflang, E.P. et al. (1999) “Analysis of germline mutation spectra at the Huntington Disease locus supports a mitotic mutation mechanism,” Hum. Mol. Genet., 8, pp. 173–183. Available at: https://doi.org/10.1093/hmg/8.2.173.

Tsao, J.-L. et al. (1999) “Colorectal Adenoma and Cancer Divergence,: evidence of multi-lineage progression” The American Journal of Pathology, 154, pp. 1815–1824. Available at: https://doi.org/10.1016/S0002-9440(10)65437-5.

Griffiths, R.C. et al. (1999) “The ages of mutations in gene trees,” The Annals of Applied Probability, 9(3), pp. 567–590. Available at: https://doi.org/10.1214/aoap/1029962804.

Arratia, R. et al. (1999a) “The Poisson–Dirichlet Distribution and the Scale-Invariant Poisson Process,” Combinatorics, Probability and Computing, 8, pp. 407–416. Available at: https://doi.org/10.1017/S0963548399003910.

Arratia, R. et al. (1999b) “On Poisson–Dirichlet Limits for Random Decomposable Combinatorial Structures,” Combinatorics, Probability and Computing, 8, pp. 193–208. Available at: https://doi.org/10.1017/S0963548399003788.

Griffiths, R.C. et al. (1998) “The age of a mutation in a general coalescent tree,” Communications in Statistics. Stochastic Models, 14, pp. 273–295. Available at: https://doi.org/10.1080/15326349808807471.

Arratia, R. et al. (1997) “Random Combinatorial Structures and Prime Factorizations,” 44, p. 8. Available at: http://www.ams.org/notices/199708/index.html

Tavaré, S. et al. (1997) “Inferring coalescence times from molecular sequencing data,” Genetics, 145, pp. 505–518. Available at: https://doi.org/10.1093/genetics/145.2.505

Shenkar, R. et al. (1996) “The Mutation Rate of the Human mtDNA Deletion mtDNA4977,” Amer. J. Hum. Gen., 59, pp. 772–780. Available at: https://europepmc.org/article/pmc/pmc1914802.

Donnelly, P. et al. (1996) “Estimating the age of the common ancestor of men from the ZFY intron,” Science, 272, pp. 1357–1359. Available at: https://doi.org/10.1126/science.272.5266.1357.

Griffiths, R.C. et al. (1996) “Monte Carlo inference methods in population genetics,” Mathl. Comput. Modelling, 23, pp. 141–158. Available at: https://doi.org/10.1016/0895-7177(96)00046-5.

Donnelly, P. et al. (1995) “Coalescents and genealogical structure under neutrality,” Annu. Rev. Genet., 29, pp. 401–421. Available at: https://doi.org/10.1146/annurev.ge.29.120195.002153.

Leeflang, E. et al. (1995) “Single sperm analysis of the trinucleotide repeats in the Huntington’s disease gene: quantification of the mutation frequency spectrum,” Human Molecular Genetics, 4, pp. 1519–1526. Available at: https://doi.org/10.1093/hmg/4.9.1519.

Arratia, R. et al. (1995) “Total variation asymptotics for Poisson process approximations of logarithmic combinatorial assemblies,” Ann. Probab., 23, pp. 1347–1388. Available at: https://doi.org/10.1214/aop/1176988188

Joyce, P. et al. (1995) “The distribution of rare alleles,” Journal of Mathematical Biology, 33, pp. 602–618. Available at: https://doi.org/10.1007/BF00298645.

Griffiths, R.C. et al. (1995) “Unrooted genealogical tree probabilities in the infinitely-many-sites model,” Mathematical Biosciences, 127, pp. 77–98. Available at: https://doi.org/10.1016/0025-5564(94)00044-Z.

Griffiths, R.C. et al. (1994) “Ancestral inference in population genetics,” Statistical Science, 9, pp. 307–319. Available at: https://doi.org/10.1214/ss/1177010378

Griffiths, R.C. et al. (1994) “Sampling theory for neutral alleles in a varying environment,” Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 344(1310), pp. 403–410. Available at: https://doi.org/10.1098/rstb.1994.0079.

Barbour, A.D. et al. (1994) “A Rate for the Erdos-Turan Law,” Combinatorics, Probability and Computing, 3, pp. 167–176. Available at: https://doi.org/10.1017/S0963548300001097

Griffiths, R.C. et al. (1994) “Simulating probability distributions in the coalescent,” Theoret. Popn. Biol., 46, pp. 131–159. Available at: https://doi.org/10.1006/tpbi.1994.1023

Arratia, R. et al. (1994) “Independent Process Approximations for Random Combinatorial Structures,” Advances in Mathematics, 104(1), pp. 90–154. Available at: https://doi.org/10.1006/aima.1994.1022.

Raftery, A.E. et al. (1994) “Estimation and modelling repeated patterns in high order Markov chains with the mixture transition distribution (MTD) model,” Applied Statistics, 43, pp. 179–199. Available at: https://doi.org/10.2307/2986120

Arratia, R. et al. (1993) “On random polynomials over finite fields,” Mathematical Proceedings of the Cambridge Philosophical Society, 114, pp. 347–368. Available at: https://doi.org/10.1017/S0305004100071620.

Lundstrom, R. et al. (1992) “Modeling the evolution of the human mitochondrial genome,” Mathematical Biosciences, 112, pp. 319–335. Available at: https://doi.org/10.1016/0025-5564(92)90030-Z.

Lundstrom, R. et al. (1992) “Estimating substitution rates from molecular data using the coalescent.,” Proceedings of the National Academy of Sciences, 89, pp. 5961–5965. Available at: https://doi.org/10.1073/pnas.89.13.5961.

Arratia, R. et al. (1992) “Limit Theorems for Combinatorial Structures via Discrete Process Approximations,” Random Structures and Algorithms, 3, pp. 321–345. Available at: https://doi.org/10.1002/rsa.3240030310.

Arratia, R. et al. (1992) “Poisson process approximations for the Ewens sampling formula,” Ann. Appl. Prob., 2, pp. 519–535. Available at: https://doi.org/10.1214/aoap/1177005647

Arratia, R.A. et al. (1992) “The cycle structure of random permutations,” Ann. Probab., 20, pp. 1567–1591. Available at: https://doi.org/10.1214/aop/1176989707

Joyce, P.J. et al. (1992) “A convergence theorem for symmetric functionals of random partitions,” J. Appl. Prob., 29, pp. 280–290. Available at: https://doi.org/10.2307/3214566.

Donnelly, P. et al. (1991) “On the functional central limit theorem for the Ewens sampling formula,” Ann. Appl. Prob., 1, pp. 280–290. Available at: https://doi.org/10.1214/aoap/1177005837

Arratia, R. et al. (1991) “Genomic mapping by anchoring random clones: A mathematical analysis,” Genomics, 11, pp. 806–827. Available at: https://doi.org/10.1016/0888-7543(91)90004-X.

Joyce, P. et al. (1990) “Random permutations and neutral evolution models,” Stochastic Processes and their Applications, 36(2), pp. 245–261. Available at: https://doi.org/10.1016/0304-4149(90)90094-9.

Tavaré, S. et al. (1989) “Is Knowing the Age-Order of Alleles in a Sample Useful in Testing for Selective Neutrality?,” Genetics, 122, pp. 705–711. Available at: https://doi.org/10.1093/genetics/122.3.705

Tavaré, S. et al. (1989) “Codon preference and primary sequence structure in protein coding regions,” Bull. Math. Biol., 51, pp. 95–115. Available at: https://doi.org/10.1007/BF02458838.

Joyce, P. et al. (1987) “Cycles, permutations and the structure of the Yule process with immigration,” Stochastic Processes and their Applications, 25, pp. 309–314. Available at: https://doi.org/10.1016/0304-4149(87)90209-2.

Donnelly, P. et al. (1987) “The population genealogy of the infinitely-many neutral alleles model,” Journal of Mathematical Biology, 25(4), pp. 381–391. Available at: https://doi.org/10.1007/BF00277163.

Tavaré, S. (1987) “The birth process with immigration, and the genealogical structure of large populations,” Journal of Mathematical Biology, 25, pp. 161–168. Available at: https://doi.org/10.1007/BF00276387.

Tavaré, S. (1986) “Some probabilistic and statistical problems in the analysis of DNA sequences,” Lectures on Mathematics in the Life Sciences, 17, pp. 57–86. Available here.

Donnelly, P. et al. (1986) “The ages of alleles and a coalescent,” Adv. Appl. Prob., 18, pp. 1–19. Available at: https://doi.org/10.2307/1427237

Tavaré, S. (1984) “Line-of-descent and genealogical processes, and their applications in population genetics models,” Theoretical Population Biology, 26, pp. 119–164. Available at: https://doi.org/10.1016/0040-5809(84)90027-3.

Saunders, I.W. et al. (1984) “On the Genealogy of Nested Subsamples from a Haploid Population,” Adv. Appl. Prob., 16, pp. 471–491. Available at: https://doi.org/10.2307/1427285

Karlin, S. et al. (1983) “New approaches for computer analysis of nucleic acid sequences.,” Proceedings of the National Academy of Sciences, 80, pp. 5660–5664. Available at: https://doi.org/10.1073/pnas.80.18.5660.

Ethier, S.N. et al. (1983) “The Proportional Bettor’s Return on Investment,” J. Appl. Prob., 20, pp. 563–573. Available at: https://doi.org/10.2307/3213893.

Seneta, E. et al. (1983) “Some stochastic models for plasmid copy number,” Theoretical Population Biology, 23, pp. 241–256. Available at: https://doi.org/10.1016/0040-5809(83)90016-3.

Seneta, E. et al. (1983) “A Note on Models Using the Branching Process with Immigration Stopped at Zero,” J. Appl.Prob., 20, pp. 11–18. Available at: https://doi.org/10.2307/3213716

Tavaré, S. (1983) “Serial dependence in contingency tables,” JRSS B, 45, pp. 100–106. Available at: https://doi.org/10.1111/j.2517-6161.1983.tb01236.x

Tavaré, S. et al. (1983) “Serial dependence of observations leading to contingency tables, and corrections to chi-squared statistics,” Biometrika, 70, pp. 139–144. Available at: https://doi.org/10.1093/biomet/70.1.139

Karlin, S. et al. (1983) “A class of diffusion processes with killing arising in population genetics,” SIAM J. Appl. Math., 43, pp. 31–41. Available at: https://doi.org/10.1137/0143003

Karlin, S. et al. (1982) “Linear Birth and Death Processes with Killing,” J. Appl. Prob., 19, pp. 477–487. Available at: https://doi.org/10.2307/3213507.

Karlin, S. et al. (1982) “Detecting particular genotypes in populations under nonrandom mating,” Mathematical Biosciences, 59, pp. 57–75. Available at: https://doi.org/10.1016/0025-5564(82)90109-2.

Karlin, S. et al. (1982) “A diffusion process with killing: the time to formation of recurrent deletrious mutant genes,” Stoch. Proc. and Applns., 13, pp. 249–261.

Pakes, A.G. and Tavaré, S. (1981) “Comments on the Age Distribution of Markov Processes,” Adv. Appl. Prob., 13, pp. 681–703. Available at: https://doi.org/10.2307/1426967.

Karlin, S. et al. (1981) “The detection of particular genotypes in finite populations I. Natural selection effects,” Theoretical Population Biology, 19, pp. 187–214. Available at: https://doi.org/10.1016/0040-5809(81)90017-4.

Karlin, S. et al. (1981b) “The detection of particular genotypes in finite populations II. The effects of partial penetrance and family structure,” Theoretical Population Biology, 19, pp. 215–229. Available at: https://doi.org/10.1016/0040-5809(81)90018-6.

Karlin, S. et al. (1981) “The detection of a recessive visible gene in finite populations,” Genetical Research, 37, pp. 33–46. Available at: https://doi.org/10.1017/S0016672300019996.

Tavaré, S. (1979) “Dual diffusions, killed diffusions, and the age distribution problem in population genetics,” Theoretical Population Biology, 16, pp. 253–266. Available at: https://doi.org/10.1016/0040-5809(79)90016-9.

Tavaré, S. (1980) “Time Reversal and Age Distributions, I. Discrete-Time Markov Chains,” J. Appl. Prob., 17, pp. 33–46. Available at: https://doi.org/10.2307/3212922.

Tavaré, S. (1979) “A note on finite continuous-time Markov chains,” Biometrics, 35, pp. 831–834. Available at: https://doi.org/10.2307/2530117.

Tavaré, S. (1979) “Sojourn times for conditioned Markov chains in genetics,” Theoret. Popn. Biol., 15, pp. 108–112. Available at: https://doi.org/10.1016/0040-5809(79)90029-7.

‍Oakley, J.R. et al. (1979) “Another Approach to the Assessment of Growth in Early Infancy,” Developmental Medicine & Child Neurology, 21, pp. 186–193. Available at: https://doi.org/10.1111/j.1469-8749.1979.tb01600.x. ‍

Deonier RC, Tavaré S & Waterman MS. Computational Genome Analysis: An Introduction, 2005. Springer Verlag, New York. 540pp. ISBN: 0-387-98785-1

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

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

Lynch A.G., et al. on behalf of the OCCAMS consortium. (2022) “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. Available here.

Tavaré S. “The history of ABC”. (2018) Chapter 2 in Handbook of Approximate Bayesian Computation. Eds. Sisson SA, Fan Y & Beaumont MA. Taylor and Francis. Available here.

Sottoriva A. et al. (2016) “Population genetics of neoplasms.” Pp 31–42 in Frontiers in Cancer Research: Evolutionary Foundations, Revolutionary Directions, eds. Maley CC & Greaves M. Springer, New York. Available here.

Andrews D.J. et al. (2016) “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 Kaufmann. Available here.

Ivakhno S et al. (2015) “Pancreatic cancer”. Chapter 26, pp. 409–420 in Systems Biology of Cancer, ed. Thiagalingam S. Cambridge University Press. Available here.

Cairns J.C. et al. (2013) “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 ZS & Vannucci M. Cambridge University Press. Available here.

Marjoram P. et al. (2013) The coalescent,” pp. 54–57 in Brenner’s Encyclopedia of Genetics, 2nd Edition, Volume 2, eds. Maloy S & Hughes K, Academic Press, San Diego. Available here.

Ardekani R. et al. (2012) 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). Available here.

Sottoriva A. et al. (2010) “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. Available here.

Barbour A.D. et al. (2010) “Assessing molecular variability in cancer genomes.” In Probability and Mathematical Genetics: Papers in Honour of Sir John Kingman, eds. Bingham N & Goldie CM. Cambridge, Cambridge University Press, pp. 91-111. Available here.

Thorne N.P. et al. (2009) “DNA methylation arrays: Methods and analysis.” In Microarray Innovations: Technology and Experimentation in Drug Discovery and Biomedical Research, ed. G. Hardiman. CRC Press/Taylor and Francis, Ch. 13, pp. 175–206. Available here.

Journée M. et al. (2007) “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. Available here.

Soligo C. et al. (2007) New light on the dates of primate origins and divergence. In Primate Origins: Adaptations and Evolution. Eds. MJ Ravosa & M Dagosto. Springer Verlag, New York, pp. 29–49. ISBN: 0-387-30335-9. Available here.

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

Plagnol V. et al. (2004) “Approximate Bayesian computation and MCMC.” In Monte Carlo and Quasi-Monte Carlo Methods 2002, ed. H Niederreiter, Springer-Verlag, pp. 99–114. Available here.

Navidi W.C. et al. (2003) “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. DR Goldstein, IMS Lecture Notes – Monograph Series, Volume 40, pp. 247–258. Available here.

Tavaré S. (2003) “Coalescent theory.” In Nature Encyclopedia of the Human Genome, Vol. 1, ed. Cooper DN, pp. 836–845. Nature Publishing Group, London. Available here.

Griffiths R.C. et al. “The genealogy of a neutral mutation.” In Highly Structured Stochastic Systems. Eds. Green P, Hjort N and Richardson S, pp. 393–412. Oxford Statistical Science Series, Vol. 27, Oxford University Press. Available here.

Neuhauser C. et al. (2001) The coalescent. Encyclopedia of Genetics, Vol. I. Eds. Brenner S and Miller J, pp. 392–397. Academic Press, New York. Available here.

Barbour A.D. et al. (1998) 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. Cambridge University Press.

Leeflang E.P. et al. (1998) “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. Academic Press, New York. Available here.

Ewens W.J. et al. (1998) “The Ewens Sampling Formula.” In Encyclopedia of Statistical Science, Vol. 2 update. Eds. Kotz S, Read CB and Banks DL, pp. 230–234. Wiley, New York. Available here.

Tavaré S. (1997) “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. Prentice-Hall. Available here.

Tavaré S. et al. (1997) “Multivariate Ewens distribution. “ Chapter 41 in Discrete Multivariate Distributions. Eds. Johnson NS, Kotz S and Balakrishnan N, pp. 232-246. Wiley, New York. Available here.

Griffiths R.C. et al. (1997) “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. Springer Verlag, Berlin. Available here.

Tavaré S. (1995) “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. National Academy Press, Washington. Available here.

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

Tavaré S. et al. (1988) “Some statistical aspects of the primary structure of nucleotide sequences. “ Mathematical Methods for DNA Sequences. Ed. Waterman MS, pp. 117–132. CRC Press. Available here.

Donnelly P. et al. (1987) “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. Springer-Verlag. Available here.

Williamson J.A. et al. (1979) “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. AR Liss, New York. Available here.

Letters to the Editor

Dunning MJ. et al. (2010) “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, p. 717. Available here.

Lynch A.G. et al. (2007) “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, pp. 418–420. Available here.

Markovtsova L. et al. (2001) “On a test of Depaulis and Veuille.” Mol. Biol. Evol., 18, pp. 1132–1133. Available here.

Book Reviews

Arratia R. et al. (1993) Probability approximations via the Poisson clumping heuristic by Aldous D, Poisson approximation by Barbour AD, Holst L and Janson S. Ann. Probab., 21, pp. 2269–2279. Available here.

Tavaré S. (1985) Mathematical Methods of Applied Probability, by Hunter JJ. JASA., 80, pp. 1071–1072. Available here.

Tavaré S. (1984) Genealogical and Genetic Structure, by Cannings C and Thompson EA. JASA, 79, pp. 743–744. Available here.

Lynch A.G. et al. (2009) “beadarray, BASH and HULK – tools to increase the value of Illumina BeadArray experiments.“ In Statistical Tools for Challenges in Bioinformatics, eds. Gusnato A, Mardia KV & Fallaize CJ. Leeds, Leeds University Press, pp. 33–37. Available here.

Lynch A.G. et al. (2007) “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. Available here.

Tavaré S. et al. (2007) “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. Available here.

Marjoram P. et al. (2000) “I see dead people:” gene mapping via ancestral inference. “ Draft for Genetic Analysis Workshop 12, 2000. Available here.

Marjoram P. et al. (2000) “Estimation in ancestral recombination graphs using Markov chain Monte Carlo.” Research Report, October 2000. Available here.

Markovtsova L. et al. (2000) “Discussion of ‘Inference in molecular population genetics’ by Stephens and Donnelly. “ J. Royal Statist. Soc. B, 62, 647. Available here.

Martin R.D. et al. (2000) “New light on the dates of primate origins and divergence.” Folia Primatol., 71, 358–359. Available here.

Tavaré S. (1999) “Random trees in molecular genetics.” Bull. I.S.I., 52, 269–272. Available here.

Tavaré S & Feng Y. (1995) “Reconstructing phylogenetic trees when sites are dependent.” Pp. 55–57 in Proceedings of Phylogeny Workshop, DIMACS Technical Report 95-48, ed. S. Tavaré, 1995. [See http://dimacs.rutgers.edu/Workshops/Phylogeny/] Available here.

Tavaré S. (1992) “International Conference on Random Mappings, Partitions, and Permutations.” Report, Adv. Appl. Prob., 24, 761–777. Available here.

Tavaré S. et al. (1990) “Comments on ‘Sampling strategies for distances between DNA sequences’,” by Weir and Basten. Biometrics, 46, 577–582. Available here.

Donnelly P. et al. (1987) “The genealogy of the infinite alleles model.“ In Proceedings, First World Congress of the Bernoulli Society, 1986. VNU Sci. Press, Utrecht, pp. 701–704. Available here.

Tavaré S. (1985) “A genealogical view of some stochastic models in population genetics.” Stoch. Proc. Applns., 19, 10. Available here.

Tavaré S. et al. (1985) On estimating substitution rates from pairs of homologous nucleotide sequences. Manuscript, 28pp. Available here.

Tavaré S. (1985) “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. Available here.

Seneta E. et al. (1982) “Stochastic models for plasmid copy number. “ First Rocky Mountain Regional Conference on Medical Applications of Statistics, Preprint Volume, 27–33. Available here.

Tavaré S. (1980) “Mathematical models in population genetics.“ Function, 4, 26-32. Available here.

Tavaré S. (1979) “Time reversion and age distributions. Adv. Appl. Prob., 11, 10–12. Available here.

Tavaré S. (1979) “Conference on ecological statistics - a summary report.” J. Royal Statist. Soc. C, 27, 344–345. Available here.

Tavaré S. (1978) “Age distributions for Markov chains in genetics.” Adv. Appl. Prob., 10, 17–19. Available here.

Tavaré S. (1976) “Sojourn times for conditional Markov chains in genetics. “ Adv. Appl. Prob., 8, 645–647, 1976. Available here.