Genomics

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Computational Genomics with R

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 43,7 Mb
Release : 2020-12-16
Category : Mathematics
ISBN : 9781498781862

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Computational Genomics with R by Altuna Akalin Pdf

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Genomics

Author : Whitney Stewart,Hans Christoph Andersson
Publisher : Twenty-First Century Books (Tm)
Page : 144 pages
File Size : 46,8 Mb
Release : 2021
Category : Genomics
ISBN : 1728401569

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Genomics by Whitney Stewart,Hans Christoph Andersson Pdf

"Since the completion of the Human Genome Project, genetic studies has transitioned into an era of discovery. This book explores the breakthroughs in research that inform our understanding of ancestry, inheritance, epigenetics, health, and medicine." --

Clinical Genomics

Author : Shashikant Kulkarni,John Pfeifer
Publisher : Academic Press
Page : 488 pages
File Size : 50,6 Mb
Release : 2014-11-10
Category : Science
ISBN : 9780124051737

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Clinical Genomics by Shashikant Kulkarni,John Pfeifer Pdf

Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing. Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm Tried and tested practice-based analysis for precision diagnosis and treatment plans Specific pipelines and meta-analysis for full range of clinically important variants

Genomics and Society

Author : Dhavendra Kumar,Ruth Chadwick
Publisher : Academic Press
Page : 438 pages
File Size : 41,5 Mb
Release : 2015-10-29
Category : Science
ISBN : 9780127999210

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Genomics and Society by Dhavendra Kumar,Ruth Chadwick Pdf

Genomics and Society; Ethical, Legal-Cultural, and Socioeconomic Implications is the first book to address the vast and thorny web of ELSI topics identified as core priorities of the NHGRI in 2011. The work addresses fundamental issues of biosociety and bioeconomy as the revolution in biology moves from research lab to healthcare system. Of particular interest to healthcare practitioners, bioethicists, and health economists, and of tangential interest to the gamut of applied social scientists investigating the societal impact of new medical paradigms, the work describes a myriad of issues around consent, confidentiality, rights, patenting, regulation, and legality in the new era of genomic medicine. Addresses the vast and thorny web of ELSI topics identified as core priorities of the NHGRI in 2011 Presents the core fundamental issues of biosociety and bioeconomy as the revolution in biology moves from research lab to healthcare system Describes a myriad of issues around consent, including confidentiality, rights, patenting, regulation, and more

Genomics

Author : Charles R. Cantor,Cassandra L. Smith
Publisher : John Wiley & Sons
Page : 621 pages
File Size : 43,7 Mb
Release : 2004-01-06
Category : Science
ISBN : 9780471461869

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Genomics by Charles R. Cantor,Cassandra L. Smith Pdf

A unique exploration of the principles and methods underlying the Human Genome Project and modern molecular genetics and biotechnology-from two top researchers In Genomics, Charles R. Cantor, former director of the Human Genome Project, and Cassandra L. Smith give the first integral overview of the strategies and technologies behind the Human Genome Project and the field of molecular genetics and biotechnology. Written with a range of readers in mind-from chemists and biologists to computer scientists and engineers-the book begins with a review of the basic properties of DNA and the chromosomes that package it in cells. The authors describe the three main techniques used in DNA analysis-hybridization, polymerase chain reaction, and electrophoresis-and present a complete exploration of DNA mapping in its many different forms. By explaining both the theoretical principles and practical foundations of modern molecular genetics to a wide audience, the book brings the scientific community closer to the ultimate goal of understanding the biological function of DNA. Genomics features: * Topical organization within chapters for easy reference * A discussion of the developing methods of sequencing, such as sequencing by hybridization (SBH) in which data is read through words instead of letters * Detailed explanations and critical evaluations of the many different types of DNA maps that can be generated-including cytogenic and restriction maps as well as interspecies cell hybrids * Informed predictions for the future of DNA sequencing

Population Genomics

Author : Om P. Rajora
Publisher : Springer
Page : 822 pages
File Size : 51,6 Mb
Release : 2019-01-07
Category : Science
ISBN : 9783030045890

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Population Genomics by Om P. Rajora Pdf

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.

Genomics Applications for the Developing World

Author : Karen E. Nelson,Barbara Jones-Nelson
Publisher : Springer Science & Business Media
Page : 364 pages
File Size : 55,7 Mb
Release : 2012-05-10
Category : Science
ISBN : 9781461421825

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Genomics Applications for the Developing World by Karen E. Nelson,Barbara Jones-Nelson Pdf

This book evolved from the editors strong belief that the information and new developments that were evolving from the rapidly growing field of genomics and that are happening primarily in the developed world have not happened at a parallel rate in the developing world. One would have hoped that by now the technologies and approaches would have been adapted on a far greater scale. In addition to this, the associated information is not always easily accessible, and is not disseminated in a format that can become a useful reference for scientists, students and others who reside in developing countries.

Introduction to Evolutionary Genomics

Author : Naruya Saitou
Publisher : Springer Science & Business Media
Page : 461 pages
File Size : 44,7 Mb
Release : 2014-01-22
Category : Computers
ISBN : 9781447153047

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Introduction to Evolutionary Genomics by Naruya Saitou Pdf

This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.

Medical and Health Genomics

Author : Dhavendra Kumar,Stylianos Antonarakis
Publisher : Academic Press
Page : 358 pages
File Size : 55,9 Mb
Release : 2016-06-04
Category : Science
ISBN : 9780127999227

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Medical and Health Genomics by Dhavendra Kumar,Stylianos Antonarakis Pdf

Medical and Health Genomics provides concise and evidence-based technical and practical information on the applied and translational aspects of genome sciences and the technologies related to non-clinical medicine and public health. Coverage is based on evolving paradigms of genomic medicine—in particular, the relation to public and population health genomics now being rapidly incorporated in health management and administration, with further implications for clinical population and disease management. Provides extensive coverage of the emergent field of health genomics and its huge relevance to healthcare management Presents user-friendly language accompanied by explanatory diagrams, figures, and many references for further study Covers the applied, but non-clinical, sciences across disease discovery, genetic analysis, genetic screening, and prevention and management Details the impact of clinical genomics across a diverse array of public and community health issues, and within a variety of global healthcare systems

Cancer Genomics

Author : Graham Dellaire,Jason N Berman,Robert J. Arceci
Publisher : Academic Press
Page : 510 pages
File Size : 53,6 Mb
Release : 2013-11-21
Category : Medical
ISBN : 9780123972743

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Cancer Genomics by Graham Dellaire,Jason N Berman,Robert J. Arceci Pdf

Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.

Ecological Genomics

Author : Christian R. Landry,Nadia Aubin-Horth
Publisher : Springer Science & Business Media
Page : 359 pages
File Size : 50,5 Mb
Release : 2013-11-25
Category : Science
ISBN : 9789400773479

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Ecological Genomics by Christian R. Landry,Nadia Aubin-Horth Pdf

Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

Introduction to Genomics

Author : Arthur Lesk
Publisher : Oxford University Press
Page : 421 pages
File Size : 49,9 Mb
Release : 2012
Category : Medical
ISBN : 9780199564354

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Introduction to Genomics by Arthur Lesk Pdf

This book covers the latest techniques that enable us to study the genome in detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism

Foundations of Comparative Genomics

Author : Arcady R. Mushegian
Publisher : Elsevier
Page : 280 pages
File Size : 46,7 Mb
Release : 2010-07-20
Category : Science
ISBN : 0080546099

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Foundations of Comparative Genomics by Arcady R. Mushegian Pdf

This book provides an overview of computational analysis of genes and genomes, and of some most notable findings that come out of this work. Foundations of Comparative Genomics presents a historical perspective, beginning with early analysis of individual gene sequences, to present day comparison of gene repertoires encoded by completely sequenced genomes. The author discusses the underlying scientific principles of comparative genomics, argues that completion of many genome sequences started a new era in biology, and provides a personal view on several state-of-the-art issues, such as systems biology and whole-genome phylogenetic reconstructions. This book is an essential reference for researchers and students in computational biology, evolutionary biology, and genetics. Presents an historic overview of genome biology and its achievements Includes topics not covered in other books such as minimal and ancestral genomes Discusses the evolutionary resilience of protein-coding genes and frequent functional convergence at the molecular level Critically reviews horizontal gene transfer and other contentious issues Covers comparative virology as a somewhat overlooked foundation of modern genome science

Genomics in Aquaculture

Author : Simon A MacKenzie,Sissel Jentoft
Publisher : Academic Press
Page : 304 pages
File Size : 51,8 Mb
Release : 2016-07-29
Category : Science
ISBN : 9780128016909

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Genomics in Aquaculture by Simon A MacKenzie,Sissel Jentoft Pdf

Genomics in Aquaculture is a concise, must-have reference that describes current advances within the field of genomics and their applications to aquaculture. Written in an accessible manner for anyone—non-specialists to experts alike—this book provides in-depth coverage of genomics spanning from genome sequencing, to transcriptomics and proteomics. It provides, for ease of learning, examples from key species most relevant to current intensive aquaculture practice. Its coverage of minority species that have a specific biological interest (e.g., Pleuronectiformes) makes this book useful for countries that are developing such species. It is a robust, practical resource that covers foundational, functional, and applied aspects of genomics in aquaculture, presenting the most current information in a field of research that is rapidly growing. Provides the latest scientific methods and technologies to maximize efficiencies for healthy fish production, with summary tables for quick reference Offers an extended glossary of technical and methodological terms to help readers better understand key biological concepts Describes state-of-the-art technologies, such as transcriptomics and epigenomics, currently under development for future perspective of the field Covers minority species that have a specific biological interest (e.g., Pleuronectiformes), making the book useful to countries developing such species

Genomic and Precision Medicine

Author : Geoffrey S. Ginsburg,Huntington F Willard,John Strickler,Matthew Stuart McKinney
Publisher : Academic Press
Page : 379 pages
File Size : 51,8 Mb
Release : 2022-04-09
Category : Science
ISBN : 9780128006535

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Genomic and Precision Medicine by Geoffrey S. Ginsburg,Huntington F Willard,John Strickler,Matthew Stuart McKinney Pdf

Genomic and Precision Medicine: Oncology, Third Edition focuses on the applications of genome discovery as research points to personalized cancer therapies. Each chapter is organized to cover the application of genomics and personalized medicine tools and technologies to a) Risk Assessment and Susceptibility, b) Diagnosis and Prognosis, c) Pharmacogenomics and Precision Therapeutics, and d) Emerging and Future Opportunities in the field. Provides a comprehensive volume written and edited by oncology genomic specialists for oncology health providers Includes succinct commentary and key learning points that will assist providers with their local needs for implementation of genomic and personalized medicine into practice Presents an up-to-date overview on major opportunities for genomic and personalized medicine in practice Covers case studies that highlight the practical use of genomics in the management of patients