Functional Genomics

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Bioinformatics and Functional Genomics

Jonathan Pevsner
Bioinformatics and Functional Genomics Book PDF

Author : Jonathan Pevsner
Publisher : John Wiley & Sons
Page : 792 pages
File Size : 54,6 Mb
Release : 2005-03-04
Category : Science
ISBN : 9780471459170

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Bioinformatics and Functional Genomics by Jonathan Pevsner Pdf

Wiley is proud to announce the publication of the first ever broad-based textbook introduction to Bioinformatics and Functional Genomics by a trained biologist, experienced researcher, and award-winning instructor. In this new text, author Jonathan Pevsner, winner of the 2001 Johns Hopkins University "Teacher of the Year" award, explains problem-solving using bioinformatic approaches using real examples such as breast cancer, HIV-1, and retinal-binding protein throughout. His book includes 375 figures and over 170 tables. Each chapter includes: Problems, discussion of Pitfalls, Boxes explaining key techniques and math/stats principles, Summary, Recommended Reading list, and URLs for freely available software. The text is suitable for professionals and students at every level, including those with little to no background in computer science.

Plant Functional Genomics

Erich Grotewold
Plant Functional Genomics Book PDF

Author : Erich Grotewold
Publisher : Springer Science & Business Media
Page : 443 pages
File Size : 48,8 Mb
Release : 2008-02-03
Category : Science
ISBN : 9781592594139

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Plant Functional Genomics by Erich Grotewold Pdf

Functional genomics is a young discipline whose origin can be traced back to the late 1980s and early 1990s, when molecular tools became available to determine the cellular functions of genes. Today, functional genomics is p- ceived as the analysis, often large-scale, that bridges the structure and organi- tion of genomes and the assessment of gene function. The completion in 2000 of the genome sequence of Arabidopsis thaliana has created a number of new and exciting challenges in plant functional genomics. The immediate task for the plant biology community is to establish the functions of the approximately 25,000 genes present in this model plant. One major issue that will remain even after this formidable task is c- pleted is establishing to what degree our understanding of the genome of one model organism, such as the dicot Arabidopsis, provides insight into the or- nization and function of genes in other plants. The genome sequence of rice, completed in 2002 as a result of the synergistic interaction of the private and public sectors, promises to significantly enrich our knowledge of the general organization of plant genomes. However, the tools available to investigate gene function in rice are lagging behind those offered by other model plant systems. Approaches available to investigate gene function become even more limited for plants other than the model systems of Arabidopsis, rice, and maize.

Yeast Functional Genomics

Frédéric Devaux
Yeast Functional Genomics Book PDF

Author : Frédéric Devaux
Publisher : Humana
Page : 0 pages
File Size : 54,9 Mb
Release : 2015-10-20
Category : Science
ISBN : 1493930788

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Yeast Functional Genomics by Frédéric Devaux Pdf

This volume provides a collection of protocols for the study of DNA-DNA contact maps, replication profiles, transcription rates, RNA secondary structures, protein-RNA interactions, ribosome profiling and quantitative proteomes and metabolomes. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Yeast Functional Genomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Next Steps for Functional Genomics

National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences
Next Steps for Functional Genomics Book PDF

Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences
Publisher : National Academies Press
Page : 201 pages
File Size : 50,9 Mb
Release : 2020-12-18
Category : Science
ISBN : 9780309676731

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Next Steps for Functional Genomics by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences Pdf

One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.

Sequence — Evolution — Function

Eugene V. Koonin,Michael Galperin
Sequence Evolution Function Book PDF

Author : Eugene V. Koonin,Michael Galperin
Publisher : Springer Science & Business Media
Page : 482 pages
File Size : 45,7 Mb
Release : 2013-06-29
Category : Science
ISBN : 9781475737837

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Sequence — Evolution — Function by Eugene V. Koonin,Michael Galperin Pdf

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Functional Genomics

Stephen P. Hunt,Frederick Livesey,Rick Livesey
Functional Genomics Book PDF

Author : Stephen P. Hunt,Frederick Livesey,Rick Livesey
Publisher : Practical Approach
Page : 275 pages
File Size : 43,8 Mb
Release : 2000
Category : Science
ISBN : 9780199637744

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Functional Genomics by Stephen P. Hunt,Frederick Livesey,Rick Livesey Pdf

Functional genomics: approaches and methodologies (F. J. Livesey, S . P. Hunt). Construction and screening of a subtractive cDNA library (A. N. Akopian, J. N. Wood). Differential display analysis of alteration in gene expression (Y.-J. Cho, P. Liang). Representational difference analysis of cDNA (M. Humbank, D. G. Schatz). Identification of differentially expressed genes by suppression subtractive hybridization (S. Desai, J. Hill, S. Trelogan, L. Diatchenko, P. D. Siebert). Gene expression analysis by cDNA microarrays (S. Mousses, M. L. Bittner, Y. Chen, R. Dougherty, A. Baxevanis, P. S. Meltzer, J. M. Trent). SADE: a microassay for serial analysis of gene expression (L. Cheval, B. Virlon, J.-M. Elalouf). Analysis of gene expression in single cells using three prime end amplification PCR (T. C. Freeman, A. K. Dixon, K. Lee, P. J. Richardson). Analysis of gene expression by two-dimensional gel electrophoresis (A. M. Tolkovsky). Proteome research: methods for protein characterization (I. Humphery-Smith, M. A. Ward). List of suppliers. Index.

Microbial Functional Genomics

Jizhong Zhou,Dorothea K. Thompson,Ying Xu,James M. Tiedje
Microbial Functional Genomics Book PDF

Author : Jizhong Zhou,Dorothea K. Thompson,Ying Xu,James M. Tiedje
Publisher : John Wiley & Sons
Page : 624 pages
File Size : 42,7 Mb
Release : 2004-03-19
Category : Science
ISBN : 0471071900

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Microbial Functional Genomics by Jizhong Zhou,Dorothea K. Thompson,Ying Xu,James M. Tiedje Pdf

Microbial Functional Genomics offers a timely summary of the principles, approaches, and applications. It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome-wide functional analysis, applied functional genomics, and future directions. An introduction will offer a definition of the field and an overview of the historical and comparative genomics aspects.

Genomics in Aquaculture

Simon A MacKenzie,Sissel Jentoft
Genomics in Aquaculture Book PDF

Author : Simon A MacKenzie,Sissel Jentoft
Publisher : Academic Press
Page : 304 pages
File Size : 55,5 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

Functional Genomics and Evolution of Photosynthetic Systems

Robert Burnap,Wim Vermaas
Functional Genomics and Evolution of Photosynthetic Systems Book PDF

Author : Robert Burnap,Wim Vermaas
Publisher : Springer Science & Business Media
Page : 426 pages
File Size : 46,9 Mb
Release : 2011-09-18
Category : Science
ISBN : 9789400715332

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Functional Genomics and Evolution of Photosynthetic Systems by Robert Burnap,Wim Vermaas Pdf

New possibilities have been brought about by the stunning number of genomic sequences becoming available for photosynthetic organisms. This new world of whole genome sequence data spans the phyla from photosynthetic microbes to algae to higher plants. These whole genome projects are intrinsically interesting, but also inform the variety of other molecular sequence databases including the recent 'meta-genomic' sequencing efforts that analyze entire communities of organisms. As impressive as they are, are obviously only the beginning of the effort to decipher the biological meaning encoded within them. This book aims to highlight progress in this direction. This book aims toward a genome-level understanding of the structure, function, and evolution of photosynthetic systems and the advantages accrued from the availability of phyletically diverse sets of gene sequences for the major components of the photosynthetic apparatus. While not meant to be fully comprehensive in terms of the topics covered, it does provide detailed views of specific cases and thereby illustrates important new directions that are being taken in this fast-moving field—a field that involves the integration of bioinformatics, molecular biology, physiology, and ecology.

Computational Genomics with R

Altuna Akalin
Computational Genomics with R Book PDF

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 40,5 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.

Functional Genomics in Aquaculture

Marco Saroglia
Functional Genomics in Aquaculture Book PDF

Author : Marco Saroglia
Publisher : John Wiley & Sons
Page : 435 pages
File Size : 44,6 Mb
Release : 2012-05-25
Category : Technology & Engineering
ISBN : 9781118350010

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Functional Genomics in Aquaculture by Marco Saroglia Pdf

Genomics has revolutionized biological research over the course of the last two decades. Genome maps of key agricultural species have offered increased understanding of the structure, organization, and evolution of animal genomes. Building upon this foundation, researchers are now emphasizing research on genome function. Published with the World Aquaculture Society, Functional Genomics in Aquaculture looks at the advances in this field as they directly relate to key traits and species in aquaculture production. Functional Genomics in Aquaculture opens with two chapters that provide a useful general introduction to the field of functional genomics. The second section of the book focuses on key production traits such as growth, development, reproduction, nutrition, and physiological response to stress and diseases. The final five chapters focus on a variety of key aquaculture species. Examples looking at our understanding of the functional genomes of salmonids, Mediterranean sea bass, Atlantic cod, catfish, shrimp, and molluscs, are included in the book. Providing valuable insights and discoveries into the functional genomes of finfish and shellfish species, Functional Genomics in Aquaculture, will be an invaluable resource to researchers and professionals in aquaculture, genetics, and animal science.

Plant Functional Genomics

Jose M. Alonso,Anna N. Stepanova
Plant Functional Genomics Book PDF

Author : Jose M. Alonso,Anna N. Stepanova
Publisher : Humana
Page : 0 pages
File Size : 55,7 Mb
Release : 2016-10-05
Category : Science
ISBN : 1493949136

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Plant Functional Genomics by Jose M. Alonso,Anna N. Stepanova Pdf

This second edition volume discusses the revolutionary development of faster and less expensive DNA sequencing technologies from the past 10 years and focuses on general technologies that can be utilized by a wide array of plant biologists to address specific questions in their favorite model systems. This book is organized into five parts. Part I examines the tools and methods required for identifying epigenetic and conformational changes at the whole-genome level. Part II presents approaches used to determine key aspects of a gene’s function, such as techniques used to identify and characterize gene regulatory networks. This is followed by a discussion of tools used to analyze the levels of mRNA, mRNA translation rates and metabolites. Part III features a compilation of forward and reverse genetic approaches that include recent implementation of high-throughput sequencing in classical methodologies such as QTL mapping. The final two parts explore strategies to facilitate and accelerate the generation and testing of functional DNA elements and basic computational tools used to facilitate the use of systems biology approached by a broad spectrum of plant researchers. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and key tips on troubleshooting and avoiding known pitfalls. Practical and timely, Plant Functional Genomics: Methods and Protocols, Second Edition highlights the latest developments in DNA sequencing technologies that are likely to continue shaping the future of functional genomics.

Advances in Animal Genomics

Sukanta Mondal,Ram Lakhan Singh
Advances in Animal Genomics Book PDF

Author : Sukanta Mondal,Ram Lakhan Singh
Publisher : Academic Press
Page : 340 pages
File Size : 52,6 Mb
Release : 2020-11-25
Category : Science
ISBN : 9780128206126

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Advances in Animal Genomics by Sukanta Mondal,Ram Lakhan Singh Pdf

Advances in Animal Genomics provides an outstanding collection of integrated strategies involving traditional and modern - omics (structural, functional, comparative and epigenomics) approaches and genomics-assisted breeding methods which animal biotechnologists can utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in livestock. Written by international experts on animal genomics, this book explores the recent advances in high-throughput, next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches which have enabled to produce huge genomic and transcriptomic resources globally on a genome-wide scale. This book is an important resource for researchers, students, educators and professionals in agriculture, veterinary and biotechnology sciences that enables them to solve problems regarding sustainable development with the help of current innovative biotechnologies. Integrates basic and advanced concepts of animal biotechnology and presents future developments Describes current high-throughput next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches for sustainable livestock production Illustrates integrated strategies to dissect and decode the molecular and gene regulatory networks involved in complex quantitative yield and stress tolerance traits in livestock Ensures readers will gain a strong grasp of biotechnology for sustainable livestock production with its well-illustrated discussion

Plant Functional Genomics

Dario Leister
Plant Functional Genomics Book PDF

Author : Dario Leister
Publisher : CRC Press
Page : 728 pages
File Size : 42,5 Mb
Release : 2004-12-28
Category : Science
ISBN : 1560229993

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Plant Functional Genomics by Dario Leister Pdf

Discover cutting-edge knowledge for engineering a more productive and environment-friendly agriculture! In Plant Functional Genomics, you’ll find a cross-section of state-of-the-art research on the biological function of plant genes and how they work together in health and disease. World-leading scientists in the field present breakthrough techniques, discuss the results of projects aimed at dissecting particular plant functions, and provide an overview on the state of functional genomics for several plant and plant-related species. With figures, tables, and illustrations, this book will help scientists, researchers, and advanced students in botany find new ways of creating novel plant forms to better serve the needs of a rapidly expanding human population. Plant Functional Genomics will increase your understanding of gene networks and systems rules, as well as gene expression during specific conditions or development or treatments. This important resource contains a wealth of data generated by various plant genome sequencing projects, including the newest results from experiments with Arabidopsis thaliana—the first plant to be completely sequenced. This book also contains innovative research on: T-DNA mutagenesis transcriptomics and metabolic profiling in plants large-scale yeast two-hybrid analyses the exceptional model system of Chlamydomonas genomics functional genomics in rice, maize, and Physcomitrella prospects for functional genomics in a new model grass chloroplast and plant mitochondrial proteomics plant transporters so much more Plant Functional Genomics will help speed up the identification and isolation of genes that might be of interest with respect to diverse biological questions. This valuable contribution to the field clarifies the challenges yet to be faced and the opportunities that could some day expand the frontiers of plant sciences.

Medical and Health Genomics

Dhavendra Kumar,Stylianos Antonarakis
Medical and Health Genomics Book PDF

Author : Dhavendra Kumar,Stylianos Antonarakis
Publisher : Academic Press
Page : 358 pages
File Size : 46,6 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