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Data Production And Analysis In Population Genomics
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Book Synopsis Data Production and Analysis in Population Genomics by : Fran Ois Pompanon
Download or read book Data Production and Analysis in Population Genomics written by Fran Ois Pompanon and published by Humana Press. This book was released on 2016-05-01 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book details protocols and methods that are applicable to species where genomic resources are scarce. It addresses how to implement the best method to obtain the required data given constraints as well as the other genetic resources already available.
Book Synopsis Population Genomics with R by : Emmanuel Paradis
Download or read book Population Genomics with R written by Emmanuel Paradis and published by CRC Press. This book was released on 2020-05-05 with total page 395 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).
Book Synopsis Human Population Genomics by : Kirk E. Lohmueller
Download or read book Human Population Genomics written by Kirk E. Lohmueller and published by Springer Nature. This book was released on 2021-03-13 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook provides a concise introduction and useful overview of the field of human population genomics, making the highly technical and contemporary aspects more accessible to students and researchers from various fields. Over the past decade, there has been a deluge of genetic variation data from the entire genome of individuals from many populations. These data have allowed an unprecedented look at human history and how natural selection has impacted humans during this journey. Simultaneously, there have been increased efforts to determine how genetic variation affects complex traits in humans. Due to technological and methodological advances, progress has been made at determining the architecture of complex traits. Split in three parts, the book starts with the basics, followed by more advanced and current research. The first part provides an introduction to essential concepts in population genetics, which are relevant for any organism. The second part covers the genetics of complex traits in humans. The third part focuses on applying these techniques and concepts to genetic variation data to learn about demographic history and natural selection in humans. This new textbook aims to serve as a gateway to modern human population genetics research for those new to the field. It provides an indispensable resource for students, researchers and practitioners from disparate areas of expertise.
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 with total page 468 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.
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 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.
Book Synopsis Population Genomics by : Om P. Rajora
Download or read book Population Genomics written by Om P. Rajora and published by Springer. This book was released on 2019-01-07 with total page 822 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics has revolutionized various disciplines of biology including population, evolutionary, ecological and conservation genetics, plant and animal breeding, human health, medicine and pharmacology by allowing to address novel and long-standing questions with unprecedented power and accuracy. It employs large-scale or genome-wide genetic information and bioinformatics to address various fundamental and applied aspects in biology and related disciplines, and provides a comprehensive genome-wide perspective and new insights that were not possible before. These advances have become possible due to the development of new and low-cost sequencing and genotyping technologies and novel statistical approaches and software, bioinformatics tools, and models. Population genomics is tremendously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations; improving the assessment of population genetic parameters or processes such as adaptive evolution, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography, and biogeography; resolving evolutionary histories and phylogenetic relationships of extant, ancient and extinct species; understanding the genomic basis of fitness, adaptation, speciation, complex ecological and economically important traits, and disease and insect resistance; facilitating forensics, genetic medicine and pharmacology; delineating conservation genetic units; and understanding the genetic effects of resource management practices, and assisting conservation and sustainable management of genetic resources. This Population Genomics book discusses the concepts, approaches, applications and promises of population genomics in addressing most of the above fundamental and applied crucial aspects in a variety of organisms from microorganisms to humans. The book provides insights into a range of emerging population genomics topics including population epigenomics, landscape genomics, seascape genomics, paleogenomics, ecological and evolutionary genomics, biogeography, demography, speciation, admixture, colonization and invasion, genomic selection, and plant and animal domestication. This book fills a vacuum in the field and is expected to become a primary reference in Population Genomics world-wide.
Book Synopsis Data Journeys in the Sciences by : Sabina Leonelli
Download or read book Data Journeys in the Sciences written by Sabina Leonelli and published by Springer Nature. This book was released on 2020-06-29 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: This groundbreaking, open access volume analyses and compares data practices across several fields through the analysis of specific cases of data journeys. It brings together leading scholars in the philosophy, history and social studies of science to achieve two goals: tracking the travel of data across different spaces, times and domains of research practice; and documenting how such journeys affect the use of data as evidence and the knowledge being produced. The volume captures the opportunities, challenges and concerns involved in making data move from the sites in which they are originally produced to sites where they can be integrated with other data, analysed and re-used for a variety of purposes. The in-depth study of data journeys provides the necessary ground to examine disciplinary, geographical and historical differences and similarities in data management, processing and interpretation, thus identifying the key conditions of possibility for the widespread data sharing associated with Big and Open Data. The chapters are ordered in sections that broadly correspond to different stages of the journeys of data, from their generation to the legitimisation of their use for specific purposes. Additionally, the preface to the volume provides a variety of alternative “roadmaps” aimed to serve the different interests and entry points of readers; and the introduction provides a substantive overview of what data journeys can teach about the methods and epistemology of research.
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.
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.
Book Synopsis Population Genetic Analyis of Entire Genomes, from SNP Discovery to Genome-wide Scans for Selection by : Mark Hamilton Wright
Download or read book Population Genetic Analyis of Entire Genomes, from SNP Discovery to Genome-wide Scans for Selection written by Mark Hamilton Wright and published by . This book was released on 2010 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: The analysis of molecular genetic data has driven the fields of molecular biology, genetics, population genetics, and quantitative genetics for over half a century. Only recently though has technology advanced to the point where molecular genetic data can be acquired cheaply and efficiently for the entire genome of several individuals enabling scientists to conduct genome-wide comparisons between several individuals or several population samples, and ask comprehensive questions regarding the nature of genetic variation in extant populations and the evolutionary forces in the population's history which generated and influenced this variation. Several challenges exist to utilizing these new technologies successfully however and in most cases both experimental optimization of laboratory protocols and the customization or de novo implementation of computational and statistical analysis methods are required to obtain adequate results. Even when the raw physical data acquired by these technologies has been successfully rendered into biologically meaningful molecular genetic data, the analysis of these large, genome-wide datasets is formidable and again requires advanced and customized methods to ask biologically motivated questions and produce conclusive results which may not have been obtainable without complete genome information. Here, I discuss two main technologies for the acquisition of genome-wide molecular data, next-generation sequencing technologies and fixed-array highly multiplexed SNP genotyping, and discuss the challenges in applying them in plant systems. Additionally, I demonstrate a population genetic analysis for the detection of recent selective sweeps in four subpopu- lations of Oryza sativa (cultivated Asian rice) and one Oryza rufipogon population (wild Asian rice) utilizing the genome-wide molecular data acquired by next-generation sequencing. The development of an improved and accurate statistical method to detect selection in population genomic analysis combined with genome-wide data in each of these subpopulations allowed the extent and location of selective sweeps in Oryza sativa subpopulations and its wild progenitor Oryza rufipogon to be quantified and compared for the first time, revealing that each cultivated subpopulation appears to have a largely unique and independent selective and domestication history, but several advantageous alleles for cultivation of rice that originated and were selected for in one subpopulation have been introduced into other subpopulations by introgression. (Abstract).
Book Synopsis The Fundamentals of Modern Statistical Genetics by : Nan M. Laird
Download or read book The Fundamentals of Modern Statistical Genetics written by Nan M. Laird and published by Springer Science & Business Media. This book was released on 2010-12-13 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the statistical models and methods that are used to understand human genetics, following the historical and recent developments of human genetics. Starting with Mendel’s first experiments to genome-wide association studies, the book describes how genetic information can be incorporated into statistical models to discover disease genes. All commonly used approaches in statistical genetics (e.g. aggregation analysis, segregation, linkage analysis, etc), are used, but the focus of the book is modern approaches to association analysis. Numerous examples illustrate key points throughout the text, both of Mendelian and complex genetic disorders. The intended audience is statisticians, biostatisticians, epidemiologists and quantitatively- oriented geneticists and health scientists wanting to learn about statistical methods for genetic analysis, whether to better analyze genetic data, or to pursue research in methodology. A background in intermediate level statistical methods is required. The authors include few mathematical derivations, and the exercises provide problems for students with a broad range of skill levels. No background in genetics is assumed.
Book Synopsis Population Genomics: Microorganisms by : Martin F. Polz
Download or read book Population Genomics: Microorganisms written by Martin F. Polz and published by Springer. This book was released on 2019-01-07 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics is a rapidly emerging field that has the potential to transform our understanding of how evolutionary forces shape genomic diversity among microbes. There have already been considerable advances in understanding gene flow and spread of adaptive traits, and in linking epidemiology with evolutionary biology. The current challenge is to find unifying evolutionary principles for organisms that display a wide range of reproductive biology – from highly clonal to promiscuous – and for which the vast majority have eluded cultivation. This requires interdisciplinary approaches that incorporate novel computational tools, testing of existing and novel population genetic models, and creative new ways of linking genetic diversity to ecological factors. This pioneering book will discuss the advances made and promises of population genomics in microorganisms, outlining some of the key theoretical and practical challenges for microbial population genomics, including defining and identifying populations, genomics-based reverse ecology and building appropriate tools to understand microbes in a variety of complex environments.
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.
Book Synopsis Genomics Data Analysis for Crop Improvement by : Priyanka Anjoy
Download or read book Genomics Data Analysis for Crop Improvement written by Priyanka Anjoy and published by Springer Nature. This book was released on 2024-02-10 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses complex problems associated with crop improvement programs, using a wide range of programming solutions, for genomics data handling and sustainable agriculture. It describes important concepts in genomics data analysis and sequence-based mapping approaches along with references. The book contains 16 chapters on recent developments in several methods of genomic data analysis for crop improvements and sustainable agriculture, all authored by eminent researchers who are experts in their fields. These chapters focus on applications of a wide range of key bioinformatics topics, including assembly, annotation, and visualization of next-generation sequencing (NGS) data; expression profiles of coding and noncoding RNA; statistical and quantitative genetics; trait-based association analysis, quantitative trait loci (QTL) mapping, and artificial intelligence in genomic studies. Real examples and case studies in the book will come in handy when applying the techniques. The relative scarcity of reference materials covering bioinformatics applications as compared with the readily available books also enhances the utility of this book. The targeted readers of the book are scientists, researchers, and bioinformaticians from genomics and advanced breeding in different areas. The book will appeal to the applied researchers engaged in crop improvements and sustainable agriculture by using bioinformatics tools, students, research project leaders, and practitioners from the various marginal disciplines and interdisciplinary research.
Book Synopsis An Introduction to Statistical Genetic Data Analysis by : Melinda C. Mills
Download or read book An Introduction to Statistical Genetic Data Analysis written by Melinda C. Mills and published by MIT Press. This book was released on 2020-02-18 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive introduction to modern applied statistical genetic data analysis, accessible to those without a background in molecular biology or genetics. Human genetic research is now relevant beyond biology, epidemiology, and the medical sciences, with applications in such fields as psychology, psychiatry, statistics, demography, sociology, and economics. With advances in computing power, the availability of data, and new techniques, it is now possible to integrate large-scale molecular genetic information into research across a broad range of topics. This book offers the first comprehensive introduction to modern applied statistical genetic data analysis that covers theory, data preparation, and analysis of molecular genetic data, with hands-on computer exercises. It is accessible to students and researchers in any empirically oriented medical, biological, or social science discipline; a background in molecular biology or genetics is not required. The book first provides foundations for statistical genetic data analysis, including a survey of fundamental concepts, primers on statistics and human evolution, and an introduction to polygenic scores. It then covers the practicalities of working with genetic data, discussing such topics as analytical challenges and data management. Finally, the book presents applications and advanced topics, including polygenic score and gene-environment interaction applications, Mendelian Randomization and instrumental variables, and ethical issues. The software and data used in the book are freely available and can be found on the book's website.
Book Synopsis Population Genomics: Crop Plants by : Om P. Rajora
Download or read book Population Genomics: Crop Plants written by Om P. Rajora and published by Springer Nature. This book was released on with total page 947 pages. Available in PDF, EPUB and Kindle. Book excerpt:
