Statistical Methods For Genome Variant Calling And Population Genetic Inference From Next Generation Sequencing Data

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Biological Sequence Analysis

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 113945739X
Total Pages : 372 pages
Book Rating : 4.1/5 (394 download)

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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.

Algorithms for Next-Generation Sequencing Data

Author : Mourad Elloumi
Publisher : Springer
ISBN 13 : 3319598260
Total Pages : 356 pages
Book Rating : 4.3/5 (195 download)

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Book Synopsis Algorithms for Next-Generation Sequencing Data by : Mourad Elloumi

Download or read book Algorithms for Next-Generation Sequencing Data written by Mourad Elloumi and published by Springer. This book was released on 2017-09-18 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 14 contributed chapters in this book survey the most recent developments in high-performance algorithms for NGS data, offering fundamental insights and technical information specifically on indexing, compression and storage; error correction; alignment; and assembly. The book will be of value to researchers, practitioners and students engaged with bioinformatics, computer science, mathematics, statistics and life sciences.

Statistical Population Genomics

Author : Julien Y Dutheil
Publisher :
ISBN 13 : 9781013271403
Total Pages : 464 pages
Book Rating : 4.2/5 (714 download)

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Book Synopsis Statistical Population Genomics by : Julien Y Dutheil

Download or read book Statistical Population Genomics written by Julien Y Dutheil and published by . This book was released on 2020-10-08 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

The Amaranth Genome

Author : Dinesh Adhikary
Publisher : Springer Nature
ISBN 13 : 3030723658
Total Pages : 181 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis The Amaranth Genome by : Dinesh Adhikary

Download or read book The Amaranth Genome written by Dinesh Adhikary and published by Springer Nature. This book was released on 2021-06-01 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

Genetic Data Analysis II

Author : Bruce S. Weir
Publisher : Sinauer
ISBN 13 :
Total Pages : 466 pages
Book Rating : 4.4/5 (91 download)

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Book Synopsis Genetic Data Analysis II by : Bruce S. Weir

Download or read book Genetic Data Analysis II written by Bruce S. Weir and published by Sinauer. This book was released on 1996 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic Data Analysis II details the statistical methodology needed to draw inferences from discrete genetic data. An emphasis is given to permutation tests, and developments in phylogenetic tree construction are reviewed.

Statistical Shape Analysis

Author : Ian L. Dryden
Publisher : John Wiley & Sons
ISBN 13 : 1119072514
Total Pages : 496 pages
Book Rating : 4.1/5 (19 download)

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Book Synopsis Statistical Shape Analysis by : Ian L. Dryden

Download or read book Statistical Shape Analysis written by Ian L. Dryden and published by John Wiley & Sons. This book was released on 2016-07-08 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: A thoroughly revised and updated edition of this introduction to modern statistical methods for shape analysis Shape analysis is an important tool in the many disciplines where objects are compared using geometrical features. Examples include comparing brain shape in schizophrenia; investigating protein molecules in bioinformatics; and describing growth of organisms in biology. This book is a significant update of the highly-regarded `Statistical Shape Analysis’ by the same authors. The new edition lays the foundations of landmark shape analysis, including geometrical concepts and statistical techniques, and extends to include analysis of curves, surfaces, images and other types of object data. Key definitions and concepts are discussed throughout, and the relative merits of different approaches are presented. The authors have included substantial new material on recent statistical developments and offer numerous examples throughout the text. Concepts are introduced in an accessible manner, while retaining sufficient detail for more specialist statisticians to appreciate the challenges and opportunities of this new field. Computer code has been included for instructional use, along with exercises to enable readers to implement the applications themselves in R and to follow the key ideas by hands-on analysis. Statistical Shape Analysis: with Applications in R will offer a valuable introduction to this fast-moving research area for statisticians and other applied scientists working in diverse areas, including archaeology, bioinformatics, biology, chemistry, computer science, medicine, morphometics and image analysis .

Mathematical Population Genetics 1

Author : Warren J. Ewens
Publisher : Springer Science & Business Media
ISBN 13 : 038721822X
Total Pages : 435 pages
Book Rating : 4.3/5 (872 download)

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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.

Molecular Plant Taxonomy

Author : Pascale Besse
Publisher : Humana
ISBN 13 : 9781627037662
Total Pages : 0 pages
Book Rating : 4.0/5 (376 download)

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Book Synopsis Molecular Plant Taxonomy by : Pascale Besse

Download or read book Molecular Plant Taxonomy written by Pascale Besse and published by Humana. This book was released on 2014-01-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant taxonomy is an ancient discipline facing new challenges with the current availability of a vast array of molecular approaches which allow reliable genealogy-based classifications. Although the primary focus of plant taxonomy is on the delimitation of species, molecular approaches also provide a better understanding of evolutionary processes, a particularly important issue for some taxonomic complex groups. Molecular Plant Taxonomy: Methods and Protocols describes laboratory protocols based on the use of nucleic acids and chromosomes for plant taxonomy, as well as guidelines for phylogenetic analysis of molecular data. Experts in the field also contribute review and application chapters that will encourage the reader to develop an integrative taxonomy approach, combining nucleic acid and cytogenetic data together with other crucial information (taxonomy, morphology, anatomy, ecology, reproductive biology, biogeography, paleobotany), which will help not only to best circumvent species delimitation but also to resolve the evolutionary processes in play. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Molecular Plant Taxonomy: Methods and Protocols seeks to provide conceptual as well as technical guidelines to plant taxonomists and geneticists.

Coalescent Theory

Author : John Wakely
Publisher : Roberts
ISBN 13 : 9780974707754
Total Pages : 0 pages
Book Rating : 4.7/5 (77 download)

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Book Synopsis Coalescent Theory by : John Wakely

Download or read book Coalescent Theory written by John Wakely and published by Roberts. This book was released on 2016-04-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook provides the foundation for molecular population genetics and genomics. It shows the conceptual framework for studies of DNA sequence variation within species, and is the source of essential tools for making inferences about mutation, recombination, population structure and natural selection from DNA sequence data.

Population Genomics: Wildlife

Author : Paul A. Hohenlohe
Publisher : Springer Nature
ISBN 13 : 3030634892
Total Pages : 559 pages
Book Rating : 4.0/5 (36 download)

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Book Synopsis Population Genomics: Wildlife by : Paul A. Hohenlohe

Download or read book Population Genomics: Wildlife written by Paul A. Hohenlohe and published by Springer Nature. This book was released on 2020-12-09 with total page 559 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics is revolutionizing wildlife biology, conservation, and management by providing key and novel insights into genetic, population and landscape-level processes in wildlife, with unprecedented power and accuracy. This pioneering book presents the advances and potential of population genomics in wildlife, outlining key population genomics concepts and questions in wildlife biology, population genomics approaches that are specifically applicable to wildlife, and application of population genomics in wildlife population and evolutionary biology, ecology, adaptation and conservation and management. It is important for students, researchers, and wildlife professionals to understand the growing set of population genomics tools that can address issues from delineation of wildlife populations to assessing their capacity to adapt to environmental change. This book brings together leading experts in wildlife population genomics to discuss the key areas of the field, as well as challenges, opportunities and future prospects of wildlife population genomics.

Next Generation Sequencing

Author : Jerzy Kulski
Publisher : BoD – Books on Demand
ISBN 13 : 9535122401
Total Pages : 466 pages
Book Rating : 4.5/5 (351 download)

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Book Synopsis Next Generation Sequencing by : Jerzy Kulski

Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

Paleogenomics

Author : Charlotte Lindqvist
Publisher : Springer
ISBN 13 : 3030047539
Total Pages : 432 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis Paleogenomics by : Charlotte Lindqvist

Download or read book Paleogenomics written by Charlotte Lindqvist and published by Springer. This book was released on 2019-01-07 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.

Algorithms for Minimization Without Derivatives

Author : Richard P. Brent
Publisher : Courier Corporation
ISBN 13 : 0486143686
Total Pages : 210 pages
Book Rating : 4.4/5 (861 download)

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Book Synopsis Algorithms for Minimization Without Derivatives by : Richard P. Brent

Download or read book Algorithms for Minimization Without Derivatives written by Richard P. Brent and published by Courier Corporation. This book was released on 2013-06-10 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: DIVOutstanding text for graduate students and research workers proposes improvements to existing algorithms, extends their related mathematical theories, and offers details on new algorithms for approximating local and global minima. /div

Genetic Dissection of Complex Traits

Author : D.C. Rao
Publisher : Academic Press
ISBN 13 : 0080569110
Total Pages : 788 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Genetic Dissection of Complex Traits by : D.C. Rao

Download or read book Genetic Dissection of Complex Traits written by D.C. Rao and published by Academic Press. This book was released on 2008-04-23 with total page 788 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of genetics is rapidly evolving and new medical breakthroughs are occuring as a result of advances in knowledge of genetics. This series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines. Five sections on the latest advances in complex traits Methods for testing with ethical, legal, and social implications Hot topics include discussions on systems biology approach to drug discovery; using comparative genomics for detecting human disease genes; computationally intensive challenges, and more

Probability Models for DNA Sequence Evolution

Author : Rick Durrett
Publisher : Springer Science & Business Media
ISBN 13 : 1475762852
Total Pages : 246 pages
Book Rating : 4.4/5 (757 download)

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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.

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429250
Total Pages : 1740 pages
Book Rating : 4.1/5 (194 download)

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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.

Evolution and Selection of Quantitative Traits

Author : Bruce Walsh
Publisher : Oxford University Press
ISBN 13 : 0192566644
Total Pages : 1504 pages
Book Rating : 4.1/5 (925 download)

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Book Synopsis Evolution and Selection of Quantitative Traits by : Bruce Walsh

Download or read book Evolution and Selection of Quantitative Traits written by Bruce Walsh and published by Oxford University Press. This book was released on 2018-06-21 with total page 1504 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative traits-be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene-usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences.