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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.
Genomics of Plant-Associated Bacteria
by Dennis C. Gross Ann Lichens-Park Chittaranjan KoleThis book describes how genomics has revolutionized our scientific understanding of agriculturally important plant-associated bacteria. Each chapter focuses on the genomics of particular bacteria: the first described plant pathogen, Erwinia amylovora; phytoplasmas lacking cell walls; fastidious, phloem-restricted liberibacters; Pseudomonas syringae, which is a genetically tractable model system; Xanthomonas citri, which causes a disease that can devastate citrus crops and Pseudomonas fluorescens, which can protect plants from diseases. Topics considered in this volume include the importance of horizontal gene transfer in originating new bacterial strains and species and advances in transcriptomics that allow us to describe the complex regulatory networks critical to plant-microbe interactions. The availability of the Xanthomonas oryzae genome has led to new technologies in genome editing, which will revolutionize approaches to genetic engineering, even in eukaryotes. The contributions show how genomics has greatly accelerated progress toward understanding the biology of these bacteria and how that understanding can be translated into novel crop protection methods.
Genomics of Plant-Associated Fungi: Monocot Pathogens
by Ralph A. Dean Ann Lichens-Park Chittaranjan KoleThis book describes how genomics has revolutionized our understanding of agriculturally important plant-associated fungi. It illustrates some fundamental discoveries about these eukaryotic microbes with regard to the overall structure of their genomes, their lifestyles and the molecular mechanisms that form the basis of their interactions with plants. Genomics has provided new insights into fungal lifestyles and led to practical advances in plant breeding and crop protection, such as predictions about the spread and evolution of new pathogens. This volume focuses on fungi that are important cereal and other monocot plant pathogens and includes: Pyrenophora tritici-repentis, Cochliobolus sp. , Colletotrichum sp. , Fusarium graminearum, Mycosphaerella graminicola and Mycosphaerella fijiensis, Magnaporthe oryzae, Blumeria graminis and Puccinia graminis.
Genomics of Plant-Associated Fungi and Oomycetes: Dicot Pathogens
by Ralph A. Dean Ann Lichens-Park Chittaranjan KoleThis book describes how genomics has revolutionized our understanding of agriculturally important plant-associated fungi and oomycetes. It illustrates some fundamental discoveries about these eukaryotic microbes with regard to the overall structure of their genomes, their lifestyles and the molecular mechanisms that form the basis of their interactions with plants. Genomics has provided new insights into fungal lifestyles and led to practical advances in plant breeding and crop protection, such as predictions about the spread and evolution of new pathogens. This volume focuses on fungi and oomycetes that are typical dicot plant pathogens and includes: Sclerotinia sclerotiorum, Botrytis cinerea, Alternaria sp. ,Verticillium alfalfae and Verticillium dahliae, Fusarium oxysporum, Phytophthora capsici, Phytophthora sojae, Phytophthora ramorum, Phytophthora infestans, Hyaloperonospora arabidopsidis.
Genomics of Plant Genetic Resources
by Emile Frison Andreas Graner Roberto TuberosaOur lives and well being intimately depend on the exploitation of the plant genetic resources available to our breeding programs. Therefore, more extensive exploration and effective exploitation of plant genetic resources are essential prerequisites for the release of improved cultivars. Accordingly, the remarkable progress in genomics approaches and more recently in sequencing and bioinformatics offers unprecedented opportunities for mining germplasm collections, mapping and cloning loci of interest, identifying novel alleles and deploying them for breeding purposes. This book collects 48 highly interdisciplinary articles describing how genomics improves our capacity to characterize and harness natural and artificially induced variation in order to boost crop productivity and provide consumers with high-quality food. This book will be an invaluable reference for all those interested in managing, mining and harnessing the genetic richness of plant genetic resources.
Genomics of Plant–Pathogen Interaction and the Stress Response
by Ashutosh Mani Sandeep KushwahaPlants are an indispensable part of human and animal lives for nutrition and health. But pests, diseases and abiotic stress adversely affect crop yield, which ultimately places significant pressure on society to provide food to an increasing population. Moreover, it also encourages increased chemical/pesticide usage on crops, which we see in the biomagnification of toxic and hazardous compounds polluting water bodies, soil and the environment. This condition will continue to worsen in the future due to the resistance-acquiring ability of pathogens against plant defense and chemical treatments. In addition, environmental disturbances and consumer health issues are being reported more promptly than before due to intensive use of pesticides in food production. Plant diseases affect our daily lives, as the use of insecticides and pesticides has become part of our food chain. As a result, precise disease diagnosis and management is crucial in order to avoid huge losses in plant production and related commodities. Accurate detection, precise diagnosis and proper management can play a significant role in keeping plants free from pathogens. In this book, scientists, researchers and scholars share their research knowledge, offering a valuable resource for understanding plant diseases, pathogen interaction and responses to stress through an omics perspective, contributing to further advancements in the field Diseases in plants may be caused by various factors, such as viruses, bacteria, fungi and abiotic stress. Disease causes low crop yield, production of poor-quality fruits and grains, and deficiency of nutrients, which have a direct impact on human and animal health. A genomics-based approach can be applied to disease diagnosis; disease outbreak; evolution of plant and pathogen genome for disease outbreak in relation to climate change; and development of long-term strategies for plant health and defense. This book presents an overview of omics technologies and approaches used to understand: 1) the relation between plants and their environment in terms of diseases 2) responses to abiotic stress 3) the genomics of plant–pathogen interaction 4) herbicide-resistance mechanisms 5) the epigenetics of plant–pathogen interaction 6) gene regulation during abiotic stress response 7) the oxidative stress response
Genomics of Plants and Fungi
by Hans J. Bohnert Rolf A. PradeThis volume provides technical insight on how genomics-oriented studies may be used to bring new understanding to established models of fungal development. The book helps to assess and solve problems associated with multiple copies of genes and proteins with seemingly identical functions and depicts various industrial applications. To bridge the in
Genomics of Soil- and Plant-Associated Fungi
by Mala Mukherjee Prasun K. Mukherjee Benjamin A. Horwitz Christian P. KubicekThis volume addresses the similarities and also the differences in the genomes of soil saprophytes, symbionts, and plant pathogens by using examples of fungal species to illustrate particular principles. It analyzes how the specific interactions with the hosts and the influence of the environment may have shaped genome evolution. The relevance of fungal genetic research and biotechnological applications is shown for areas such as plant pathogenesis, biomass degradation, litter decomposition, nitrogen assimilation, antibiotic production, mycoparasitism, energy, ecology, and also for soil fungi turning to human pathogens. In addition to the model organisms Neurospora and Aspergillus, the following species are covered providing a view of pathogens and mutualists: Trichoderma, Fusarium oxysporum, Cochliobolus heterostrophus, Penicillium chrysogenum, Rhizopus oryzae, Podospora anserina, Agaricomycetes, Archaeorhizomycetes and Magnaporthaceae. Ecology and potential applications have guided the choice of fungal genes to be studied and it will be fascinating to follow the trends of future sequencing projects.