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Genomics: A Revolution in Health and Disease Discovery
by Whitney Stewart Hans C. AnderssonOver the past 50 years, scientists have made incredible progress in the application of genetic research to human health care and disease treatment. Innovative tools and techniques, including gene therapy and CRISPR-Cas9 editing, can treat inherited disorders that were previously untreatable, or prevent them from happening in the first place. You can take a DNA test to learn where your ancestors are from. Police officers can use genetic evidence to identify criminals—or innocents. And some doctors are using new medical techniques for unprecedented procedures. Genomics: A Revolution in Health and Disease Discovery delves into the history, science, and ethics behind recent breakthroughs in genetic research. Authors Whitney Stewart and Hans Andersson, MD, present fascinating case studies that show how real people have benefitted from genetic research. Though the genome remains full of mysteries, researchers and doctors are working hard to uncover its secrets and find the best ways to treat patients and cure diseases. The discoveries to come will inform how we target disease treatment, how we understand our health, and how we define our very identities.
Genomics and Bioinformatics
by Tore SamuelssonWith the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.
Genomics and Breeding for Climate-Resilient Crops
by Chittaranjan KoleClimate change is expected to have a drastic impact on agronomic conditions including temperature, precipitation, soil nutrients, and the incidence of disease pests, to name a few. To face this looming threat, significant progress in developing new breeding strategies has been made over the last few decades. The first volume of Genomics and Breeding for Climate-Resilient Crops presents the basic concepts and strategies for developing climate-resilient crop varieties. Topics covered include: conservation, evaluation and utilization of biodiversity; identification of traits, genes and crops of the future; genomic and molecular tools; genetic engineering; participatory and evolutionary breeding; bioinformatics tools to support breeding; funding and networking support; and intellectual property, regulatory issues, social and political dimensions.
Genomics and Breeding for Climate-Resilient Crops: Vol. 2 Target Traits
by Chittaranjan KoleClimate change is expected to have a drastic impact on agronomic conditions including temperature, precipitation, soil nutrients, and the incidence of disease pests, to name a few. To face this looming threat, significant progress in developing new breeding strategies has been made over the last few decades. The second volume of Genomics and Breeding for Climate-Resilient Crops describes various genomic and breeding approaches for the genetic improvement of the major target traits. Topics covered include: flowering time; root traits; cold, heat and drought tolerance; water use efficiency; flooding and submergence tolerance; disease and insect resistance; nutrient use efficiency; nitrogen fixation; carbon sequestration; and greenhouse gas emissions.
Genomics and Molecular Genetics of Plant-Nematode Interactions
by Carmen Fenoll Godelieve Gheysen John JonesThis book reviews developments in the molecular biology of plant-nematode interactions that have been driven by the application of genomics tools. The book will be of interest to postgraduate students and to researchers with an interest in plant nematology and/or plant pathology more generally. A series of introductory chapters provide a biological context for the detailed reviews of all areas of plant-nematode interactions that follow and ensure that the bulk of the book is accessible to the non-specialist. A final section aims to show how these fundamental studies have provided outputs of practical relevance.
Genomics and Proteomics for Clinical Discovery and Development
by György Marko-VargaThe book is intended to be a resource for students as well as scientists in education and for the general public to learn about proteomics and genomics. Chromosomes form the basis for our genetic heritage and are the code for protein synthesis. The Human Genome Map came out in 2002, and the Proteome Sequence Map is under currently being created by a global consortia initiative. Proteome and genome building blocks already form the basis of scientific research areas as well as large parts of the pharmaceutical and biomedical industry. The book initiative will provide the background to and our current understanding of these gene and protein areas, as well as describe how cutting-edge science is using these resources to develop new medicines and new diagnostics for patient care and treatment. The book will be useful for undergraduate students as well as university students and researchers who need a good understanding of genomics and proteomics within the clinical field. The book will also be targeted at a broad public as well as readers not specialized within this field. Dr. Marko-Varga is the head of the Head of Div. Clinical Protein Science & Imaging at the Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, and Professor at the 1st Department of Surgery, Tokyo Medical University, Tokyo, Japan.
Genomics and Proteomics in Nutrition
by Carolyn D. Berdanier Naima Moustaid-MoussaWith contributions from 66 world-renowned authorities on the subject, Genomics And Proteomics In Nutrition focuses on the effect of genetic expression on protein production, establishing links between gene expression and nutrition, the influence of micro- and macronutrients on cellular homeostasis, and the relationship between diet, genetic
Genomics and Systems Biology of Mammalian Cell Culture
by Wei Shou Hu An-Ping ZengTranscriptome Analysis, by Frank Stahl, Bernd Hitzmann, Kai Mutz, Daniel Landgrebe, Miriam Lübbecke, Cornelia Kasper, Johanna Walter und Thomas Scheper Transcriptome Data Analysis for Cell Culture Processes, by Marlene Castro-Melchor, Huong Le und Wei-Shou Hu Modeling Metabolic Networks for Mammalian Cell Systems: General Considerations, Modeling Strategies, and Available Tools, by Ziomara P. Gerdtzen Metabolic Flux Analysis in Systems Biology of Mammalian Cells, by Jens Niklas und Elmar Heinzle Advancing Biopharmaceutical Process Development by System-Level Data Analysis and Integration of Omics Data, by Jochen Schaub, Christoph Clemens, Hitto Kaufmann und Torsten W. Schulz Protein Glycosylation and Its Impact on Biotechnology, by Markus Berger, Matthias Kaup und Véronique Blanchard Protein Glycosylation Control in Mammalian Cell Culture: Past Precedents and Contemporary Prospects, by Patrick Hossler Modeling of Intracellular Transport and Compartmentation, by Uwe Jandt und An-Ping Zeng Genetic Aspects of Cell Line Development from a Synthetic Biology Perspective, by L. Botezatu, S. Sievers, L. Gama-Norton, R. Schucht, H. Hauser und D. Wirth.
Genomics Applications for the Developing World
by Barbara Jones-Nelson Karen E. NelsonThis 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.
Genomics Assisted Breeding of Crops for Abiotic Stress Tolerance, Vol. II (Sustainable Development and Biodiversity #21)
by Vijay Rani Rajpal Deepmala Sehgal Avinash Kumar S. N. RainaThe abiotic stresses like drought, temperature, cold, salinity, heavy metals etc. affect a great deal on the yield performance of the agricultural crops. To cope up with these challenges, plant breeding programs world-wide are focussing on the development of stress tolerant varieties in all crop species. Significant genomic advances have been made for abiotic stress tolerance in various crop species in terms of availability of molecular markers, QTL mapping, genome-wide association studies (GWAS), genomic selection (GS) strategies, and transcriptome profiling. The broad-range of articles involving genomics and breeding approaches deepens our existing knowledge about complex traits. The chapters are written by authorities in their respective fields. This book provides comprehensive and consolidated account on the applications of the most recent findings and the progress made in genomics assisted breeding for tolerance to abiotic stresses in many important major crop species with a focus on applications of modern strategies for sustainable agriculture. The book is especially intended for students, molecular breeders and scientists working on the genomics-assisted genetic improvement of crop species for abiotic stress tolerance.
Genomics: commercial opportunities from a scientific revolution
by G. K. Dixon L. G. Copping D. LivingstoneThis title covers topical and unexplored issues relating to the commercial outcome of the genetic revolution which will be of great interest to both academia and industry. The book discusses whether the availability of genome sequence information will yie
Genomics Data Analysis: False Discovery Rates and Empirical Bayes Methods
by David R. BickelStatisticians have met the need to test hundreds or thousands of genomics hypotheses simultaneously with novel empirical Bayes methods that combine advantages of traditional Bayesian and frequentist statistics. Techniques for estimating the local false discovery rate assign probabilities of differential gene expression, genetic association, etc. without requiring subjective prior distributions. This book brings these methods to scientists while keeping the mathematics at an elementary level. Readers will learn the fundamental concepts behind local false discovery rates, preparing them to analyze their own genomics data and to critically evaluate published genomics research.Key Features:* dice games and exercises, including one using interactive software, for teaching the concepts in the classroom* examples focusing on gene expression and on genetic association data and briefly covering metabolomics data and proteomics data* gradual introduction to the mathematical equations needed* how to choose between different methods of multiple hypothesis testing* how to convert the output of genomics hypothesis testing software to estimates of local false discovery rates* guidance through the minefield of current criticisms of p values* material on non-Bayesian prior p values and posterior p values not previously published
Genomics Data Analysis for Crop Improvement (Springer Protocols Handbooks)
by Priyanka Anjoy Kuldeep Kumar Girish Chandra Kishor GaikwadThis 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.
Genomics-Enabled Learning Health Care Systems: Workshop Summary
by Sarah H. BeachyThe inclusion of genomic data in a knowledge-generating health care system infrastructure is one promising way to harness the full potential of that information to provide better patient care. In such a system, clinical practice and research influence each other with the goal of improving the efficiency and effectiveness of disease prevention, diagnosis, and treatment. To examine pragmatic approaches to incorporating genomics in learning health care systems, the Institute of Medicine Roundtable on Translating Genomic-Based Research for Health hosted a workshop which convened a variety of stakeholder groups, including commercial developers, health information technology professionals, clinical providers, academic researchers, patient groups, and government and health system representatives, to present their perspectives and participate in discussions on maximizing the value that can be obtained from genomic information. The workshop examined how a variety of systems are capturing and making use of genomic data to generate knowledge for advancing health care in the 21st century. It also sought to evaluate the challenges, opportunities, and best practices for capturing or using genomic information in knowledge-generating health care systems. "Genomics-Enabled Learning Health Care Systems" summarizes the presentations and discussion of the workshop.
Genomics-Enabled Learning Health Care Systems: Workshop Summary
by Sarah H. BeachyThe inclusion of genomic data in a knowledge-generating health care system infrastructure is one promising way to harness the full potential of that information to provide better patient care. In such a system, clinical practice and research influence each other with the goal of improving the efficiency and effectiveness of disease prevention, diagnosis, and treatment. To examine pragmatic approaches to incorporating genomics in learning health care systems, the Institute of Medicine Roundtable on Translating Genomic-Based Research for Health hosted a workshop which convened a variety of stakeholder groups, including commercial developers, health information technology professionals, clinical providers, academic researchers, patient groups, and government and health system representatives, to present their perspectives and participate in discussions on maximizing the value that can be obtained from genomic information. The workshop examined how a variety of systems are capturing and making use of genomic data to generate knowledge for advancing health care in the 21st century. It also sought to evaluate the challenges, opportunities, and best practices for capturing or using genomic information in knowledge-generating health care systems. Genomics-Enabled Learning Health Care Systems summarizes the presentations and discussion of the workshop.
Genomics in the AWS Cloud: Analyzing Genetic Code Using Amazon Web Services
by David Wall Catherine VacherPerform genome analysis and sequencing of data with Amazon Web Services Genomics in the AWS Cloud: Analyzing Genetic Code Using Amazon Web Services enables a person who has moderate familiarity with AWS Cloud to perform full genome analysis and research. Using the information in this book, you'll be able to take a FASTQ file containing raw data from a lab or a BAM file from a service provider and perform genome analysis on it. You'll also be able to identify potentially pathogenic gene sequences. Get an introduction to Whole Genome Sequencing (WGS) Make sense of WGS on AWS Master AWS services for genome analysis Some key advantages of using AWS for genomic analysis is to help researchers utilize a wide choice of compute services that can process diverse datasets in analysis pipelines. Genomic sequencers that generate raw data files are located in labs on premises and AWS provides solutions to make it easy for customers to transfer these files to AWS reliably and securely. Storing Genomics and Medical (e.g., imaging) data at different stages requires enormous storage in a cost-effective manner. Amazon Simple Storage Service (Amazon S3), Amazon Glacier, and Amazon Elastics Block Store (Amazon EBS) provide the necessary solutions to securely store, manage, and scale genomic file storage. Moreover, the storage services can interface with various compute services from AWS to process these files. Whether you're just getting started or have already been analyzing genomics data using the AWS Cloud, this book provides you with the information you need in order to use AWS services and features in the ways that will make the most sense for your genomic research.
Genomics in the Azure Cloud
by Colby T. FordThis practical guide bridges the gap between general cloud computing architecture in Microsoft Azure and scientific computing for bioinformatics and genomics. You'll get a solid understanding of the architecture patterns and services that are offered in Azure and how they might be used in your bioinformatics practice. You'll get code examples that you can reuse for your specific needs. And you'll get plenty of concrete examples to illustrate how a given service is used in a bioinformatics context.You'll also get valuable advice on how to:Use enterprise platform services to easily scale your bioinformatics workloadsOrganize, query, and analyze genomic data at scaleBuild a genomics data lake and accompanying data warehouseUse Azure Machine Learning to scale your model training, track model performance, and deploy winning modelsOrchestrate and automate processing pipelines using Azure Data Factory and DatabricksCloudify your organization's existing bioinformatics pipelines by moving your workflows to Azure high-performance compute servicesAnd more
Genomics in the Cloud: Using Docker, GATK, and WDL in Terra
by Brian O'Connor Geraldine A. Van der AuweraData in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud?With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics algorithms from the field. <p><p>This book covers: <li>Essential genomics and computing technology background <li>Basic cloud computing operations <li>Getting started with GATK, plus three major GATK Best Practices pipelines <li>Automating analysis with scripted workflows using WDL and Cromwell <li>Scaling up workflow execution in the cloud, including parallelization and cost optimization <li>Interactive analysis in the cloud using Jupyter notebooks <li>Secure collaboration and computational reproducibility using Terra
Genomics of Antibiotic Resistant Bacteria in Industrial Waste Water Treatment
by Maulin P. ShahThis book discusses the key problems and solutions with various applicable approaches to combat antibiotic-resistant genes in industrial waste water. Several genes are selected within the chapters to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology. As we have very limited knowledge of composition, dynamics and stability of microbial communities, various processes in wastewater treatment have been generally considered to be "black box." In recent years, with the development of several new high throughput sequencing platforms, metagenome sequencing strategies and bioinformatics toolboxes, the analysis of the genome of complex communities has become much more accessible and means easier.The opening of the biological wastewater treatment “black box” is not the unpleasant experience it was before. The viable, but not cultural, ceases to be the inconsequential, uncharacterizable enigma that existed today. Metagenomics leads the way for more specific studies in related fields. Finally, genomic studies of wastewater treatment microbes, in addition to their biotechnological applications, are also an excellent testing ground for variety of other ecological and environmental burns questions. Wastewater treatment plants are considered hotspots for the environmental dissemination of antimicrobial-resistant determinants. Comparative genomics of antibiotic resistant genes isolated from conventional activated sludge and biological aerated filter wastewater treatment plants is discussed.
Genomics of Chloroplasts and Mitochondria
by Ralph Bock Volker KnoopThe past decade has witnessed an explosion of our knowledge on the structure, coding capacity and evolution of the genomes of the two DNA-containing cell organelles in plants: chloroplasts (plastids) and mitochondria. Comparative genomics analyses have provided new insights into the origin of organelles by endosymbioses and uncovered an enormous evolutionary dynamics of organellar genomes. In addition, they have greatly helped to clarify phylogenetic relationships, especially in algae and early land plants with limited morphological and anatomical diversity. This book, written by leading experts, summarizes our current knowledge about plastid and mitochondrial genomes in all major groups of algae and land plants. It also includes chapters on endosymbioses, plastid and mitochondrial mutants, gene expression profiling and methods for organelle transformation. The book is designed for students and researchers in plant molecular biology, taxonomy, biotechnology and evolutionary biology.
Genomics of Crucifer's Host- Pathosystem
by Govind Singh Saharan Naresh K. Mehta Prabhu Dayal MeenaThe book deals with latest research achievements of Brassica scientists using omics approaches in understanding host-pathogen interaction, molecular detection, identification, and functional characterization of effectors/genes including pathogenomics and biometabolomics. Genomics of host-pathogen interaction is a source of information for the teachers, students, researchers, and policy makers to foster success in enhancing the Brassica production and productivity through the development of improved disease-resistant varieties with the use of omics technologies. It is a base and sound plate form for managing biological stresses of Brassica at global level. The book covers up-to-date information on genomics of host-pathogen interaction, pathogenomics of crucifers’ pathogen, and biometabolomics of host pathosystem supplemented with ample photographs, illustrations, and figures which make it stimulating, effective, and easy to comprehend for readers, researchers, biology students, teachers, and policy makers.
Genomics of Crucifer’s Host-Resistance
by Govind Singh Saharan Prabhu Dayal Meena Naresh K. MehtaThe book presents comprehensive information on fundamental, and applied knowledge for developing varieties resistant individually as well as to all the major pathogens of crucifers, such as Albugo, Alternaria, Erysiphe, Hyaloperonospora, Plasmodiophora, Leptosphaeria, Sclerotinia, Turnip mosaic virus, Verticillium, and Xanthomonas through the use of latest biotechnological approaches including identification of R genes and their incorporation into agronomically superior varieties. The chapters include the information’s viz., principles of host resistance, identification of R-genes sources, inheritance of disease resistance, host resistance signaling network system to multiple stresses. The book also covers transfer of disease resistance, and management of disease resistance. Standardized, reproducible techniques are also included for the researchers of cruciferous crops for developing resistant cultivars. The book deals with the gaps in understanding, knowledge of genomics, and offers suggestions for future research priorities in order to initiate the advance research on disease resistance. This book is immensely useful to the researchers especially Brassica breeders, teachers, extension specialists, students, industrialists, farmers, and all others who are interested to grow healthy, and profitable cruciferous crops all over the world.
Genomics of Foodborne Bacterial Pathogens
by Martin Wiedmann Wei ZhangFoodborne illnesses caused by various bacterial, viral, and fungal pathogens lead to a high number of morbidity and mortality in the U.S. and throughout the world. Recent advances in microbial genomics have significantly improved our understanding of the physiology, evolution, ecology, epidemiology, and pathogenesis of different foodborne pathogens. This book focuses on the genomics of foodborne bacterial pathogens. It begins with a brief overview of the recent advances in microbial genomics and the impact of genomics on food safety research. Then, eight chapters follow that elaborate some in-depth reviews on the genomics of several common foodborne bacterial pathogens including Bacillus, Campylobacter, Clostridium, Escherichia coli, Listeria, Salmonella, Staphylococcus, and Vibrio. Finally, the last four chapters focus on some current genomic, transcriptomic, and proteomic technologies and their applications in studying the epidemiology, evolution, and pathogenesis of foodborne bacterial pathogens. Genomics of Foodborne Bacterial Pathogens can be used as a reference by scientists and professionals in academia, government, and industry who are interested in understanding microbial genomics and using genomics tools to study foodborne bacterial pathogens. This book can also be used as a textbook for instructors and professors who teach food microbiology or microbial genomics-related courses at the post-graduate level.
Genomics of Pain and Co-Morbid Symptoms
by Susan G. Dorsey Angela R. StarkweatherThis book provides an overview of the field of pain genomics and the genomics of related, or co-occuring, symptoms, the current state-of-the-science, and challenges that remain. It brings differing views in the field together and provides examples of translational science from using cellular and rodent models to human clinical trials. This book's structure leads the reader through the physiology of pain and genomics into how pain is studied, mechanisms of acute and chronic pain, various protocols that are used throughout the field along with the pros/cons of the current methods used, and project into the future of pain genomics. This work is intended for classroom teaching, for nurses, for novice researchers in symptom science and pain research as well as students and postdoctoral fellows.
Genomics of Pattern Recognition Receptors: Applications in Oncology and Cardiovascular Diseases
by Anton G. Kutikhin Arseniy E. YuzhalinThis book offers comprehensive information on the polymorphisms of genes encoding pattern recognition receptors (PRRs). Following a short description of the general role of PRRs in the immune system, the structure and function of Toll-like and NOD-like receptors are examined in detail. The main focus is on the role of inherited variation in PRRs and their correlation to cancer and cardiovascular diseases. A review of all epidemiological investigations is included, and a concept of genomic risk markers for the prevention of various diseases is also discussed.