Structural and Evolutionary Genomics

Structural and Evolutionary Genomics
Author: Giorgio Bernardi
Publisher: Elsevier
Total Pages: 459
Release: 2005-12-19
Genre: Science
ISBN: 0080461875

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Structural genomics is the study of the DNA of living organisms. Evolutionary genomics is the study of the history of the genome. These subjects are closely interlinked. They are approached in this book using as a guideline the investigations carried out in the author's laboratory, relevant literature is critically reviewed and some general conclusions are presented. The author and his collaborators have studied a vast number of genomes, ranging from prokaryotes to human, using different approaches, including physical chemistry of DNA, viral integration and molecular cytogenetics. As the subtitle indicates the book discusses the fundamental importance of natural selection in shaping genomes. In terms of numbers, neutral and nearly neutral mutations represent most mutations, but a "regional" control is exerted by natural selection (essentially negative or purifying selection). A "neo-selectionist" model is proposed for genome evolution. · Summarizes the existing knowledge on genome organization and evolution in a self-contained book · Discusses important open problem, without refraining from criticism whenever appropriate

Comparative and Evolutionary Genomics of Angiosperm Trees

Comparative and Evolutionary Genomics of Angiosperm Trees
Author: Andrew Groover
Publisher: Springer
Total Pages: 379
Release: 2017-11-21
Genre: Science
ISBN: 3319493299

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Marking the change in focus of tree genomics from single species to comparative approaches, this book covers biological, genomic, and evolutionary aspects of angiosperm trees that provide information and perspectives to support researchers broadening the focus of their research. The diversity of angiosperm trees in morphology, anatomy, physiology and biochemistry has been described and cataloged by various scientific disciplines, but the molecular, genetic, and evolutionary mechanisms underlying this diversity have only recently been explored. Excitingly, advances in genomic and sequencing technologies are ushering a new era of research broadly termed comparative genomics, which simultaneously exploits and describes the evolutionary origins and genetic regulation of traits of interest. Within tree genomics, this research is already underway, as the number of complete genome sequences available for angiosperm trees is increasing at an impressive pace and the number of species for which RNAseq data are available is rapidly expanding. Because they are extensively covered by other literature and are rapidly changing, technical and computational approaches—such as the latest sequencing technologies—are not a main focus of this book. Instead, this comprehensive volume provides a valuable, broader view of tree genomics whose relevance will outlive the particulars of current-day technical approaches. The first section of the book discusses background on the evolution and diversification of angiosperm trees, as well as offers description of the salient features and diversity of the unique physiology and wood anatomy of angiosperm trees. The second section explores the two most advanced model angiosperm tree species (poplars and eucalypts) as well as species that are soon to emerge as new models. The third section describes the structural features and evolutionary histories of angiosperm tree genomes, followed by a fourth section focusing on the genomics of traits of biological, ecological, and economic interest. In summary, this book is a timely and well-referenced foundational resource for the forest tree community looking to embrace comparative approaches for the study of angiosperm trees.

Evolutionary Genomics and Systems Biology

Evolutionary Genomics and Systems Biology
Author: Gustavo Caetano-Anoll¿s
Publisher: John Wiley & Sons
Total Pages: 529
Release: 2011-09-26
Genre: Science
ISBN: 1118210719

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A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. Evolutionary Genomics and Systems Biology is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology. Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagrams—macromolecular components in interaction—in the context of genomic complements. The book also features: A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology A special section on RNA biology—translation, evolution of structure, and micro RNA and regulation of gene expression Chapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and disease Contributions by leading authorities on each topic Evolutionary Genomics and Systems Biology is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.

Evolutionary Genomics

Evolutionary Genomics
Author: Maria Anisimova
Publisher: Humana Press
Total Pages: 556
Release: 2012-03-08
Genre: Medical
ISBN: 9781617795848

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Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular BiologyTM series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses. Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.

Structural and Evolutionary Genomics

Structural and Evolutionary Genomics
Author: Giorgio Bernardi
Publisher: Gulf Professional Publishing
Total Pages: 462
Release: 2004
Genre: Medical
ISBN: 9780444512550

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Structural genomics is the study of the DNA of living organisms. Evolutionary genomics is the study of the history of the genome. These subjects are closely interlinked. They are approached in this book using as a guideline the investigations carried out in the author's laboratory, relevant literature is critically reviewed and some general conclusions are presented. The author and his collaborators have studied a vast number of genomes, ranging from prokaryotes to human, using different approaches, including physical chemistry of DNA, viral integration and molecular cytogenetics. As the subtitle indicates the book discusses the fundamental importance of natural selection in shaping genomes. In terms of numbers, neutral and nearly neutral mutations represent most mutations, but a regional control is exerted by natural selection (essentially negative or purifying selection). A neo-selectionist model is proposed for genome evolution.

Introduction to Evolutionary Genomics

Introduction to Evolutionary Genomics
Author: Naruya Saitou
Publisher:
Total Pages: 504
Release: 2018
Genre: Evolutionary genetics
ISBN: 9783319926438

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This authoritative textbook/reference presents a comprehensive introduction to the field of evolutionary genomics. The opening chapters describe the fundamental concepts in molecular biology and genome evolution for readers without any prior background in this area. This is followed by a detailed examination of genome evolution in various different groups of organisms. The text then concludes with a review of practical methods essential to researchers in the field. This updated and revised new edition also features historical perspectives on contributions to evolutionary genomics from related fields such as molecular evolution, genetics, and numerical taxonomy. Topics and features: Introduces the basics of molecular biology, covering protein structure and diversity, as well as DNA replication, transcription, and translation Examines the phylogenetic relationships of DNA sequences, and the processes of mutation, neutral evolution, and natural selection Presents a brief evolutionary history of life, surveying the key features of the genomes of prokaryotes, eukaryotes, viruses and phages, vertebrates, and humans Reviews the various biological “omic” databases, and discusses the analysis of homologous nucleotide and amino acid sequences Provides an overview of the experimental sequencing of genomes and transcriptomes, and the construction of phylogenetic trees Describes methods for estimating of evolutionary distances, and performing studies of population genetics Supplies additional supporting material at an associated website Serving as an indispensable textbook for graduate and advanced undergraduate courses on evolutionary genomics, this accessible overview will also prove invaluable to researchers from both computer science and the biological sciences seeking a primer on the field. Dr. Naruya Saitou is a Professor in the Division of Population Genetics at the National Institute of Genetics, and a Professor in the Department of Genetics at the Graduate University for Advanced Studies, Mishima, Japan. He is also a Professor in the Department of Biological Sciences at the University of Tokyo, Japan.

Structural Biology and Functional Genomics

Structural Biology and Functional Genomics
Author: E. Morton Bradbury
Publisher: Springer Science & Business Media
Total Pages: 332
Release: 1999-08-31
Genre: Medical
ISBN: 9780792357810

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Biomedical research will be revolutionised by the current efforts to sequence the human genome and the genomes of model organisms. Of the newly sequenced genes, 50% code for proteins of unknown functions, while as little as 5% of sequences in mammalian genomes code for proteins. New, genome-wide approaches are needed to draw together the knowledge that is emerging simultaneously in a number of fields of genome research. This volume is a high-level survey of the newly emerging concepts of structural biology and functional genomics for biologists, biochemists and medical researchers interested in genome research. Topics included are chromosome and chromatin organisation, novel DNA and RNA structures, DNA flexibility, supercoiling, prediction of protein functions, strategies for large scale structural analysis, and computer modelling.

Untangling Molecular Biodiversity: Explaining Unity And Diversity Principles Of Organization With Molecular Structure And Evolutionary Genomics

Untangling Molecular Biodiversity: Explaining Unity And Diversity Principles Of Organization With Molecular Structure And Evolutionary Genomics
Author: Gustavo Caetano-anolles
Publisher: World Scientific
Total Pages: 673
Release: 2020-11-20
Genre: Science
ISBN: 9814656631

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Untangling Molecular Biodiversity presents a unique global framework to explain molecular and organismal biodiversity that is grounded in evolutionary genomics. This book will tackle important questions such as the origin of life, the emergence of biochemistry, the origin of viruses, the nature of the last universal common ancestor responsible for diversified life, the role of information and thermodynamics in evolution, the reason for having three cellular domains in life, and the centrality of modules in biology.This book will explore six themes: (1) Explanatory frameworks for biological organization; (2) Evolutionary patterns and biodiversity; (3) Molecular structure and evolutionary genomics; (4) A framework of persistence strategies that borrows from engineering and systems biology; (5) Use of this framework to explain diversity in the molecular world; and (6) Exploring the origin and evolution of cells and viruses.Consequently, this book represents a very unique collection of ideas that can attract the attention of a broad readership interested in life sciences/biology.

Evolutionary Genomics

Evolutionary Genomics
Author: Maria Anisimova
Publisher:
Total Pages: 776
Release: 2020-10-08
Genre: Science
ISBN: 9781013271434

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This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.