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Probabilistic Models Of Dna Sequence Evolution With Context Dependeent Rates Of Substitution
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Book Synopsis Probabilistic Models of DNA Sequence Evolution with Context Dependent Rates of Substitution by : Jens Ledet Jensen
Download or read book Probabilistic Models of DNA Sequence Evolution with Context Dependent Rates of Substitution written by Jens Ledet Jensen and published by . This book was released on 1998 with total page 21 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Research Reports written by and published by . This book was released on 1998 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Probabilistic Models of DNA Sequence Evolution with Context Dependeent Rates of Substitution by :
Download or read book Probabilistic Models of DNA Sequence Evolution with Context Dependeent Rates of Substitution written by and published by . This book was released on 1998 with total page 21 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 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 Accounting for Dependent Evolution Among Sites by : Chris Anthony Nasrallah
Download or read book Accounting for Dependent Evolution Among Sites written by Chris Anthony Nasrallah and published by . This book was released on 2012 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Models of the evolution of DNA sequences typically assume that each position of the sequence evolves independently of all others. This assumption is unrealistic in most cases and is made either for simplicity, computational tractability, or because the nature of the dependence may not be well understood. Proteins and RNAs present instances in which the three dimensional structure of the molecules are essential for function, and introduce dependence among sites in clearly defined ways. Here I explore models that can account for dependence among sites, use them to explore the evolution of DNA sequences containing dependence both within a population and between species, and develop a new substitution model that can be used to make inferences about the strength of natural selection acting on these sequences. In the first chapter I demonstrate the importance of accounting for dependent evolution among sites for phylogenetic inference. Using a realistic model of the evolution of proteins and RNAs based on known structures, I simulate the evolution of DNA sequences in which the evolution at each site can depend on many other positions in the sequence. Using these simulated data I show that phylogenetic methods that assume sites evolve independently are impaired in their ability to infer the true topology relating the species, and I quantify the error in this estimation as a function of the strength of the dependence, the tree length, the topology, and the specific type of molecular structure. This underscores the importance of accounting for such dependent evolution among sites in studies of molecular evolution. In the second chapter I explore the dynamics of the substitution process within a population rather than between species. One of the central questions when accounting for epistatic interactions among sites is how two changes, which when taken together are neutral, can spread in a population when a single change in isolation is deleterious. This process of compensatory evolution has been explored by population genetics theory in the case when natural selection acting against the intermediate state is very strong. Here I explore the case in which natural selection against the intermediate states is moderate to weak using forward time population genetic simulations of the simplest possible case of two dependent sites. I show that when selection is weak the two substitutions can be made one at a time, that as selection increases the substitutions are made more frequently in tandem, and how these patterns are functions of population size, mutation rate, and recombination. In the third chapter I utilize the insights about the dynamics of compensatory evolution within a population from the second chapter to reexamine the evolution of dependent sites between species. I develop a new substitution model for the analysis of RNA that accounts for the probability of the different pathways to compensatory substitution. This model is interpretive, in that parameters have direct meaning with respect to the strength of natural selection acting against deleterious intermediate states. I implement this model in a Bayesian framework for parameter estimation, and demonstrate its utility for making inferences about historical selective pressures on RNA sequences using a 5S ribosomal RNA dataset. This represents the first probabilistic evolutionary model that both accounts for dependent evolution among sites and connects population genetic dynamics with substitution patterns between species. Taken together, these studies reveal a great deal about the nature of the evolutionary process when sites are not independent. They explore these processes both within a population and between species, and then use insights from one to better inform the other, attempting to connect these two historically separate approaches to the study of evolution. The advances here are not limited to RNA and proteins, but are generally applicable to any instance in which epistatic interactions can be found, from speciation genetics to the evolution of functional morphology.
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 Codon Evolution by : Gina M. Cannarozzi
Download or read book Codon Evolution written by Gina M. Cannarozzi and published by Oxford University Press. This book was released on 2012-02-23 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second part of the book focuses on codon usage bias.
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 The Phylogenetic Handbook by : Marco Salemi
Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Book Synopsis Mathematical Population Genetics 1 by : Warren J. Ewens
Download or read book Mathematical Population Genetics 1 written by Warren J. Ewens and published by Springer Science & Business Media. This book was released on 2012-10-01 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first of a planned two-volume work discussing the mathematical aspects of population genetics with an emphasis on evolutionary theory. This volume draws heavily from the author’s 1979 classic, but it has been revised and expanded to include recent topics which follow naturally from the treatment in the earlier edition, such as the theory of molecular population genetics.
Book Synopsis Handbook of Approximate Bayesian Computation by : Scott A. Sisson
Download or read book Handbook of Approximate Bayesian Computation written by Scott A. Sisson and published by CRC Press. This book was released on 2018-09-03 with total page 679 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the world becomes increasingly complex, so do the statistical models required to analyse the challenging problems ahead. For the very first time in a single volume, the Handbook of Approximate Bayesian Computation (ABC) presents an extensive overview of the theory, practice and application of ABC methods. These simple, but powerful statistical techniques, take Bayesian statistics beyond the need to specify overly simplified models, to the setting where the model is defined only as a process that generates data. This process can be arbitrarily complex, to the point where standard Bayesian techniques based on working with tractable likelihood functions would not be viable. ABC methods finesse the problem of model complexity within the Bayesian framework by exploiting modern computational power, thereby permitting approximate Bayesian analyses of models that would otherwise be impossible to implement. The Handbook of ABC provides illuminating insight into the world of Bayesian modelling for intractable models for both experts and newcomers alike. It is an essential reference book for anyone interested in learning about and implementing ABC techniques to analyse complex models in the modern world.
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 Handbook of Statistical Genetics by : David J. Balding
Download or read book Handbook of Statistical Genetics written by David J. Balding and published by John Wiley & Sons. This book was released on 2008-06-10 with total page 1616 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Handbook for Statistical Genetics is widely regarded as the reference work in the field. However, the field has developed considerably over the past three years. In particular the modeling of genetic networks has advanced considerably via the evolution of microarray analysis. As a consequence the 3rd edition of the handbook contains a much expanded section on Network Modeling, including 5 new chapters covering metabolic networks, graphical modeling and inference and simulation of pedigrees and genealogies. Other chapters new to the 3rd edition include Human Population Genetics, Genome-wide Association Studies, Family-based Association Studies, Pharmacogenetics, Epigenetics, Ethic and Insurance. As with the second Edition, the Handbook includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between the chapters, tying the different areas together. With heavy use of up-to-date examples, real-life case studies and references to web-based resources, this continues to be must-have reference in a vital area of research. Edited by the leading international authorities in the field. David Balding - Department of Epidemiology & Public Health, Imperial College An advisor for our Probability & Statistics series, Professor Balding is also a previous Wiley author, having written Weight-of-Evidence for Forensic DNA Profiles, as well as having edited the two previous editions of HSG. With over 20 years teaching experience, he’s also had dozens of articles published in numerous international journals. Martin Bishop – Head of the Bioinformatics Division at the HGMP Resource Centre As well as the first two editions of HSG, Dr Bishop has edited a number of introductory books on the application of informatics to molecular biology and genetics. He is the Associate Editor of the journal Bioinformatics and Managing Editor of Briefings in Bioinformatics. Chris Cannings – Division of Genomic Medicine, University of Sheffield With over 40 years teaching in the area, Professor Cannings has published over 100 papers and is on the editorial board of many related journals. Co-editor of the two previous editions of HSG, he also authored a book on this topic.
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 2019-09-10 with total page 1223 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 Molecular Evolution by : Roderick D.M. Page
Download or read book Molecular Evolution written by Roderick D.M. Page and published by John Wiley & Sons. This book was released on 2009-07-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
