Tavaré, Simon
Overview
Works:  15 works in 83 publications in 2 languages and 1,678 library holdings 

Genres:  Conference papers and proceedings 
Roles:  Author, Editor, Creator, 958 
Classifications:  QA273.A1, 519.2 
Publication Timeline
.
Most widely held works by
Simon Tavaré
Computational genome analysis : an introduction by
Richard C Deonier(
Book
)
20 editions published between 2005 and 2007 in English and held by 355 WorldCat member libraries worldwide
"Computational Genome Analysis: An Introduction presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. This book is appropriate for a onesemester course for advanced undergraduate or beginning graduate students, and it can also introduce computational biology to computer scientists, mathematicians, or biologists who are extending their interests into this exciting field."Jacket
20 editions published between 2005 and 2007 in English and held by 355 WorldCat member libraries worldwide
"Computational Genome Analysis: An Introduction presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. This book is appropriate for a onesemester course for advanced undergraduate or beginning graduate students, and it can also introduce computational biology to computer scientists, mathematicians, or biologists who are extending their interests into this exciting field."Jacket
Lectures on probability theory and statistics : Ecole d'Eté de Probabilités de SaintFlour XXXII2002 by
Boris Tsirelson(
Book
)
29 editions published in 2004 in English and German and held by 289 WorldCat member libraries worldwide
This is yet another indispensable volume for all probabilists and collectors of the SaintFlour series, and is also of great interest for mathematical physicists. It contains two of the three lecture courses given at the 32nd Probability Summer School in SaintFlour (July 724, 2002). Boris Tsirelson's lectures introduce the notion of nonclassical noise produced by very nonlinear functions of many independent random variables, for instance singular stochastic flows or oriented percolation. Two examples are examined (noise made by a Poisson snake, the Brownian web). A new framework for the scaling limit is proposed, as well as old and new results about noises, stability, and spectral measures. Wendelin Werner's contribution gives a survey of results on conformal invariance, scaling limits and properties of some twodimensional random curves. It provides a definition and properties of the SchrammLoewner evolutions, computations (probabilities, critical exponents), the relation with critical exponents of planar Brownian motions, planar selfavoiding walks, critical percolation, looperased random walks and uniform spanning trees
29 editions published in 2004 in English and German and held by 289 WorldCat member libraries worldwide
This is yet another indispensable volume for all probabilists and collectors of the SaintFlour series, and is also of great interest for mathematical physicists. It contains two of the three lecture courses given at the 32nd Probability Summer School in SaintFlour (July 724, 2002). Boris Tsirelson's lectures introduce the notion of nonclassical noise produced by very nonlinear functions of many independent random variables, for instance singular stochastic flows or oriented percolation. Two examples are examined (noise made by a Poisson snake, the Brownian web). A new framework for the scaling limit is proposed, as well as old and new results about noises, stability, and spectral measures. Wendelin Werner's contribution gives a survey of results on conformal invariance, scaling limits and properties of some twodimensional random curves. It provides a definition and properties of the SchrammLoewner evolutions, computations (probabilities, critical exponents), the relation with critical exponents of planar Brownian motions, planar selfavoiding walks, critical percolation, looperased random walks and uniform spanning trees
Logarithmic combinatorial structures : a probabilistic approach by
Richard Arratia(
Book
)
12 editions published in 2003 in English and held by 210 WorldCat member libraries worldwide
"This book explains the similarities in asymptotic behaviour as the result of two basic properties shared by the structures: the conditioning relation and the logarithmic condition. The discussion is conducted in the language of probability, enabling the theory to be developed under rather general and explicit conditions; for the finer conclusions, Stein's method emerges as the key ingredient. The book is thus of particular interest to graduate students and researchers in both combinatorics and probability theory."
12 editions published in 2003 in English and held by 210 WorldCat member libraries worldwide
"This book explains the similarities in asymptotic behaviour as the result of two basic properties shared by the structures: the conditioning relation and the logarithmic condition. The discussion is conducted in the language of probability, enabling the theory to be developed under rather general and explicit conditions; for the finer conclusions, Stein's method emerges as the key ingredient. The book is thus of particular interest to graduate students and researchers in both combinatorics and probability theory."
Progress in population genetics and human evolution by
Peter Donnelly(
Book
)
8 editions published in 1997 in English and held by 190 WorldCat member libraries worldwide
"This book is devoted to the collection, interpretation and analysis of population genetic data. Among the topics included here are studies on human evolutionary history, molecular techniques for generating data, statistical and computational techniques for the interpretation of such data, and stochastic models for genealogy and population structure. The chapters reflect the close interaction between experimental molecular biologists and theoreticians. The book will be useful for specialists in the area, as well as mathematicians, statisticians, computer scientists and biologists wanting a brief overview of current problems in the field."Publisher's description
8 editions published in 1997 in English and held by 190 WorldCat member libraries worldwide
"This book is devoted to the collection, interpretation and analysis of population genetic data. Among the topics included here are studies on human evolutionary history, molecular techniques for generating data, statistical and computational techniques for the interpretation of such data, and stochastic models for genealogy and population structure. The chapters reflect the close interaction between experimental molecular biologists and theoreticians. The book will be useful for specialists in the area, as well as mathematicians, statisticians, computer scientists and biologists wanting a brief overview of current problems in the field."Publisher's description
Computing for comparative microbial genomics : bioinformatics for microbiologists by
David W Ussery(
)
3 editions published in 2009 in English and held by 6 WorldCat member libraries worldwide
This reference provides a coherent set of tools and a methodological framework for comparing raw DNA sequences and fully annotated genome sequences, then using these to build up and test models about groups of interacting organisms within an environment or ecological niche
3 editions published in 2009 in English and held by 6 WorldCat member libraries worldwide
This reference provides a coherent set of tools and a methodological framework for comparing raw DNA sequences and fully annotated genome sequences, then using these to build up and test models about groups of interacting organisms within an environment or ecological niche
Approches statistiques en segmentation = Statistical approaches for segmentation : application à la réannotation de génome by
Alice Cleynen(
)
1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide
We propose to model the output of transcriptome sequencing technologies (RNASeq) using the negative binomial distribution, as well as build segmentation models suited to their study at different biological scales, in the context of these technologies becoming a valuable tool for genome annotation, gene expression analysis, and newtranscript discovery. We develop a fast segmentation algorithm to analyze whole chromosomes series, and we propose two methods for estimating the number of segments, a key feature related to the number of genes expressed in the cell, should they be identified from previous experiments or discovered at this occasion. Research on precise gene annotation, and in particular comparison of transcription boundaries for individuals, naturally leads us to the statistical comparison of changepoints in independent series. To address our questions, we build tools, in a Bayesian segmentation framework, for which we are able to provide uncertainty measures. We illustrate our models, all implemented in R packages, on an RNASeq dataset from a study on yeast, and show for instance that the intron boundaries are conserved across conditions while the beginning and end of transcripts are subject to differential splicing
1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide
We propose to model the output of transcriptome sequencing technologies (RNASeq) using the negative binomial distribution, as well as build segmentation models suited to their study at different biological scales, in the context of these technologies becoming a valuable tool for genome annotation, gene expression analysis, and newtranscript discovery. We develop a fast segmentation algorithm to analyze whole chromosomes series, and we propose two methods for estimating the number of segments, a key feature related to the number of genes expressed in the cell, should they be identified from previous experiments or discovered at this occasion. Research on precise gene annotation, and in particular comparison of transcription boundaries for individuals, naturally leads us to the statistical comparison of changepoints in independent series. To address our questions, we build tools, in a Bayesian segmentation framework, for which we are able to provide uncertainty measures. We illustrate our models, all implemented in R packages, on an RNASeq dataset from a study on yeast, and show for instance that the intron boundaries are conserved across conditions while the beginning and end of transcripts are subject to differential splicing
Using the fossil record to estimate the age of the last common ancestor of extant primates by
Simon Tavaré(
)
2 editions published in 2002 in English and held by 2 WorldCat member libraries worldwide
2 editions published in 2002 in English and held by 2 WorldCat member libraries worldwide
Some results for Markov processes, with application to genetic models by
Simon Tavaré(
)
1 edition published in 1979 in English and held by 1 WorldCat member library worldwide
1 edition published in 1979 in English and held by 1 WorldCat member library worldwide
Workshop[s] in computational molecular biology, 4/15/914/14/94 : [abstracts](
Book
)
1 edition published in 1995 in English and held by 1 WorldCat member library worldwide
1 edition published in 1995 in English and held by 1 WorldCat member library worldwide
Approximate Bayesian computation and MCMC(
)
1 edition published in 2002 in Undetermined and held by 1 WorldCat member library worldwide
1 edition published in 2002 in Undetermined and held by 1 WorldCat member library worldwide
Estimation in the Mixture Transition Distribution Model for High Order Markov Chains(
Book
)
1 edition published in 1991 in English and held by 1 WorldCat member library worldwide
The mixture transition distribution (MTD) model was introduced by Raftery (1985) as a parsimonious model for highorder Markov chains. It is flexible, can represent a wide range of dependence patterns, can be physically motivated, fits data well, and appears to be a discretevalued analogue for the class of autoregressive time series models. However, estimation has presented difficulties because the parameter space is highly nonconvex, being defined by a large number of nonlinear constraints. Here we propose an efficient computational algorithm for maximum likelihood estimation which is based on a way of reducing the large number of constraints. This also allows more structured versions of the model, for example those involving structural zeros, to be fit quite easily. A way of fitting the model using GLIM is also discussed. The algorithm is applied to a sequence of wind directions, and also to two sequences of DNA bases from introns from genes of the mouse. In each case, the MTD model fits better than the conventional Markov chain model
1 edition published in 1991 in English and held by 1 WorldCat member library worldwide
The mixture transition distribution (MTD) model was introduced by Raftery (1985) as a parsimonious model for highorder Markov chains. It is flexible, can represent a wide range of dependence patterns, can be physically motivated, fits data well, and appears to be a discretevalued analogue for the class of autoregressive time series models. However, estimation has presented difficulties because the parameter space is highly nonconvex, being defined by a large number of nonlinear constraints. Here we propose an efficient computational algorithm for maximum likelihood estimation which is based on a way of reducing the large number of constraints. This also allows more structured versions of the model, for example those involving structural zeros, to be fit quite easily. A way of fitting the model using GLIM is also discussed. The algorithm is applied to a sequence of wind directions, and also to two sequences of DNA bases from introns from genes of the mouse. In each case, the MTD model fits better than the conventional Markov chain model
A tale of three couplings : PoissonDirichlet and GEM apprloximations for random permutations by
Richard Arratia(
Book
)
1 edition published in 2006 in English and held by 0 WorldCat member libraries worldwide
1 edition published in 2006 in English and held by 0 WorldCat member libraries worldwide
A probabilistic by
Richard Arratia(
Book
)
1 edition published in 2005 in English and held by 0 WorldCat member libraries worldwide
1 edition published in 2005 in English and held by 0 WorldCat member libraries worldwide
International Conference on Random Mappings, Partitions and Permutations Held in Los Angeles, California on 36 January 1992(
)
1 edition published in 1992 in English and held by 0 WorldCat member libraries worldwide
1 edition published in 1992 in English and held by 0 WorldCat member libraries worldwide
Linear birth and death processes with killing by
Samuel Karlin(
Book
)
1 edition published in 1982 in English and held by 0 WorldCat member libraries worldwide
1 edition published in 1982 in English and held by 0 WorldCat member libraries worldwide
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Related Identities
 Waterman, Michael S.
 Deonier, Richard C. 1942 Author
 Picard, Jean 1959 Editor
 Zeitouni, Ofer Editor
 Arratia, Richard Author
 Barbour, A. D.
 Donnelly, Peter 1959 Author Editor
 Deonier, Richard C. Author
 Lengauer, T. (Thomas)
 McClure, Marcella Ann
Associated Subjects
Asymptotic distribution (Probability theory) Asymptotic expansions Bioinformatics Birth and death processes (Stochastic processes) Combinatorial probabilities Computational biology Computer science Differential equations, Partial Distribution (Probability theory) Electronic data processing Finance GeneticsMathematics Human evolutionMathematics Human genetics Mathematical physics Mathematical statistics Mathematics Population geneticsMathematical models Population geneticsMathematics Population geneticsStatistical methods Potential theory (Mathematics) Probabilities Random walks (Mathematics) Statistical physics Statistics Stochastic processes