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Basic Probability Models For Dna Sequence Evolution
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Book Synopsis Probability Models for DNA Sequence Evolution by : Rick Durrett
Download or read book Probability Models for DNA Sequence Evolution written by Rick Durrett and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: "What underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences?" In approaching this question a number of probability models are introduced and anyalyzed.Throughout the book, the theory is developed in close connection with data from more than 60 experimental studies that illustrate the use of these results.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
Book Synopsis Probability Models for DNA Sequence Evolution by : Rick Durrett
Download or read book Probability Models for DNA Sequence Evolution written by Rick Durrett and published by . This book was released on 2002 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Sequence — Evolution — Function by : Eugene V. Koonin
Download or read book Sequence — Evolution — Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Book Synopsis Mathematical Models in Biology by : Elizabeth Spencer Allman
Download or read book Mathematical Models in Biology written by Elizabeth Spencer Allman and published by Cambridge University Press. This book was released on 2004 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: This introductory textbook on mathematical biology focuses on discrete models across a variety of biological subdisciplines. Biological topics treated include linear and non-linear models of populations, Markov models of molecular evolution, phylogenetic tree construction, genetics, and infectious disease models. The coverage of models of molecular evolution and phylogenetic tree construction from DNA sequence data is unique among books at this level. Computer investigations with MATLAB are incorporated throughout, in both exercises and more extensive projects, to give readers hands-on experience with the mathematical models developed. MATLAB programs accompany the text. Mathematical tools, such as matrix algebra, eigenvector analysis, and basic probability, are motivated by biological models and given self-contained developments, so that mathematical prerequisites are minimal.
Book Synopsis Handbook of Statistical Genomics by : David J. Balding
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1740 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Book Synopsis Computational Molecular Evolution by : Ziheng Yang
Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
Book Synopsis Stochastic Processes in Genetics and Evolution by : Charles J. Mode
Download or read book Stochastic Processes in Genetics and Evolution written by Charles J. Mode and published by World Scientific. This book was released on 2012 with total page 695 pages. Available in PDF, EPUB and Kindle. Book excerpt: Prologue; Acknowledgments; Contents; 1. An Introduction to Mathematical Probability with Applications in Mendelian Genetics; 1.1 Introduction; 1.2 Mathematical Probability in Mendelian Genetics; 1.3 Examples of Finite Probability Spaces; Example 1.3.1: An Equal Frequency Model; Example 1.3.2: Partitions of an Abstract Set; Example 1.3.3: A Deterministic Case; Example 1.3.4: Inheritance of Eye Color and Sex; 1.4 Elementary Combinatorial Analysis; 1.5 The Binomial Distribution; Example 1.5.1: Distribution of Boys and Girls in Families of Size N.
Book Synopsis Statistical Methods in Molecular Evolution by : Rasmus Nielsen
Download or read book Statistical Methods in Molecular Evolution written by Rasmus Nielsen and published by Springer Science & Business Media. This book was released on 2006-05-06 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. This book provides an overview of the statistical theory and methods used in studies of molecular evolution. It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. The chapters are written by the leaders of field and they will take the reader from basic introductory material to the state-of-the-art statistical methods. This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. The chapters of the book assume no advanced mathematical skills beyond basic calculus, although familiarity with basic probability theory will help the reader. Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. Rasmus Nielsen received his Ph.D. form the University of California at Berkeley in 1998 and after a postdoc at Harvard University, he assumed a faculty position in Statistical Genomics at Cornell University. He is currently an Ole Rømer Fellow at the University of Copenhagen and holds a Sloan Research Fellowship. His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. From the reviews: "...Overall this is a very useful book in an area of increasing importance." Journal of the Royal Statistical Society "I find Statistical Methods in Molecular Evolution very interesting and useful. It delves into problems that were considered very difficult just several years ago...the book is likely to stimulate the interest of statisticians that are unaware of this exciting field of applications. It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods." Marek Kimmel for the Journal of the American Statistical Association, September 2006 "Who should read this book? We suggest that anyone who deals with molecular data (who does not?) and anyone who asks evolutionary questions (who should not?) ought to consult the relevant chapters in this book." Dan Graur and Dror Berel for Biometrics, September 2006 "Coalescence theory facilitates the merger of population genetics theory with phylogenetic approaches, but still, there are mostly two camps: phylogeneticists and population geneticists. Only a few people are moving freely between them. Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. Although Nielsen did not contribute a chapter to his book, his work permeates all its chapters. This book gives an overview of his interests and current achievements in molecular evolution. In short, this book should be on your bookshelf." Peter Beerli for Evolution, 60(2), 2006
Book Synopsis Bayesian Modeling in Bioinformatics by : Dipak K. Dey
Download or read book Bayesian Modeling in Bioinformatics written by Dipak K. Dey and published by CRC Press. This book was released on 2010-09-03 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. It presents a broad overview of statistical inference, clustering, and c
Book Synopsis Plant Molecular Evolution by : J.J. Doyle
Download or read book Plant Molecular Evolution written by J.J. Doyle and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant molecular biology has produced an ever-increasing flood of data about genes and genomes. Evolutionary biology and systematics provides the context for synthesizing this information. This book brings together contributions from evolutionary biologists, systematists, developmental geneticists, biochemists, and others working on diverse aspects of plant biology whose work touches to varying degrees on plant molecular evolution. The book is organized in three parts, the first of which introduces broad topics in evolutionary biology and summarizes advances in plant molecular phylogenetics, with emphasis on model plant systems. The second segment presents a series of case studies of gene family evolution, while the third gives overviews of the evolution of important plant processes such as disease resistance, nodulation, hybridization, transposable elements and genome evolution, and polyploidy.
Book Synopsis Living Dinosaurs by : Dr. Gareth Dyke
Download or read book Living Dinosaurs written by Dr. Gareth Dyke and published by John Wiley & Sons. This book was released on 2011-02-15 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living Dinosaurs offers a snapshot of our current understanding of the origin and evolution of birds. After slumbering for more than a century, avian palaeontology has been awakened by startling new discoveries on almost every continent. Controversies about whether dinosaurs had real feathers or whether birds were related to dinosaurs have been swept away and replaced by new and more difficult questions: How old is the avian lineage? How did birds learn to fly? Which birds survived the great extinction that ended the Mesozoic Era and how did the avian genome evolve? Answers to these questions may help us understand how the different kinds of living birds are related to one another and how they evolved into their current niches. More importantly, they may help us understand what we need to do to help them survive the dramatic impacts of human activity on the planet.
Book Synopsis Reconstructing Evolution by : Olivier Gascuel
Download or read book Reconstructing Evolution written by Olivier Gascuel and published by OUP Oxford. This book was released on 2007-06-28 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolution is a complex process, acting at multiple scales, from DNA sequences and proteins to populations of species. Understanding and reconstructing evolution is of major importance in numerous subfields of biology. For example, phylogenetics and sequence evolution is central to comparative genomics, attempts to decipher genomes, and molecular epidemiology. Phylogenetics is also the focal point of large-scale international biodiversity assessment initiatives such as the 'Tree of Life' project, which aims to build the evolutionary tree for all extant species. Since the pioneering work in phylogenetics in the 1960s, models have become increasingly sophisticated to account for the inherent complexity of evolution. They rely heavily on mathematics and aim at modelling and analyzing biological phenomena such as horizontal gene transfer, heterogeneity of mutation, and speciation and extinction processes. This book presents these recent models, their biological relevance, their mathematical basis, their properties, and the algorithms to infer them from data. A number of subfields from mathematics and computer science are involved: combinatorics, graph theory, stringology, probabilistic and Markov models, information theory, statistical inference, Monte Carlo methods, continuous and discrete algorithmics. This book arises from the Mathematics of Evolution & Phylogenetics meeting at the Mathematical Institute Henri Poincaré, Paris, in June 2005 and is based on the outstanding state-of-the-art reports presented by the conference speakers. Ten chapters - based around five themes - provide a detailed overview of key topics, from the underlying concepts to the latest results, some of which are at the forefront of current research.
Book Synopsis Nonlinearly Perturbed Semi-Markov Processes by : Dmitrii Silvestrov
Download or read book Nonlinearly Perturbed Semi-Markov Processes written by Dmitrii Silvestrov and published by Springer. This book was released on 2017-09-06 with total page 151 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book presents new methods of asymptotic analysis for nonlinearly perturbed semi-Markov processes with a finite phase space. These methods are based on special time-space screening procedures for sequential phase space reduction of semi-Markov processes combined with the systematical use of operational calculus for Laurent asymptotic expansions. Effective recurrent algorithms are composed for getting asymptotic expansions, without and with explicit upper bounds for remainders, for power moments of hitting times, stationary and conditional quasi-stationary distributions for nonlinearly perturbed semi-Markov processes. These results are illustrated by asymptotic expansions for birth-death-type semi-Markov processes, which play an important role in various applications. The book will be a useful contribution to the continuing intensive studies in the area. It is an essential reference for theoretical and applied researchers in the field of stochastic processes and their applications that will contribute to continuing extensive studies in the area and remain relevant for years to come.
Book Synopsis Handbook of Computational Molecular Biology by : Srinivas Aluru
Download or read book Handbook of Computational Molecular Biology written by Srinivas Aluru and published by CRC Press. This book was released on 2005-12-21 with total page 1108 pages. Available in PDF, EPUB and Kindle. Book excerpt: The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology of
Book Synopsis An Operator Semigroup in Mathematical Genetics by : Adam Bobrowski
Download or read book An Operator Semigroup in Mathematical Genetics written by Adam Bobrowski and published by Springer. This book was released on 2015-03-16 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: This authored monograph presents a mathematical description of the time evolution of neutral genomic regions in terms of the differential Lyapunov equation. The qualitative behavior of its solutions, with respect to different mutation models and demographic patterns, can be characterized using operator semi group theory. Mutation and drift are two of the main genetic forces, which act on genes of individuals in populations. Their effects are influenced by population dynamics. This book covers the application to two mutation models: single step mutation for microsatellite loci and single-base substitutions. The effects of demographic change to the asymptotic of the distribution are also covered. The target audience primarily covers researchers and experts in the field but the book may also be beneficial for graduate students.
Book Synopsis Handbook of Statistical Genomics by : David J. Balding
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-02 with total page 1219 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
