Structural And Evolutionary Genomics

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Structural and Evolutionary Genomics

Giorgio Bernardi
Structural and Evolutionary Genomics Book PDF

Author : Giorgio Bernardi
Publisher : Elsevier
Page : 459 pages
File Size : 40,6 Mb
Release : 2005-12-19
Category : Science
ISBN : 9780080461878

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Structural and Evolutionary Genomics by Giorgio Bernardi Pdf

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

Andrew Groover,Quentin Cronk
Comparative and Evolutionary Genomics of Angiosperm Trees Book PDF

Author : Andrew Groover,Quentin Cronk
Publisher : Springer
Page : 366 pages
File Size : 54,6 Mb
Release : 2017-11-21
Category : Science
ISBN : 9783319493299

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Comparative and Evolutionary Genomics of Angiosperm Trees by Andrew Groover,Quentin Cronk Pdf

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

Maria Anisimova
Evolutionary Genomics Book PDF

Author : Maria Anisimova
Publisher : Humana Press
Page : 556 pages
File Size : 41,6 Mb
Release : 2012-03-08
Category : Medical
ISBN : 1617795844

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Evolutionary Genomics by Maria Anisimova Pdf

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.

Introduction to Evolutionary Genomics

Naruya Saitou
Introduction to Evolutionary Genomics Book PDF

Author : Naruya Saitou
Publisher : Springer Science & Business Media
Page : 476 pages
File Size : 42,7 Mb
Release : 2014-01-22
Category : Computers
ISBN : 9781447153047

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Introduction to Evolutionary Genomics by Naruya Saitou Pdf

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

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 : 48,5 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.

Evolutionary Genomics and Systems Biology

Gustavo Caetano-Anoll¿s
Evolutionary Genomics and Systems Biology Book PDF

Author : Gustavo Caetano-Anoll¿s
Publisher : John Wiley & Sons
Page : 529 pages
File Size : 45,8 Mb
Release : 2011-09-26
Category : Science
ISBN : 9781118210710

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Evolutionary Genomics and Systems Biology by Gustavo Caetano-Anoll¿s Pdf

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.

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 : 55,7 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.

Models and Algorithms for Genome Evolution

Cedric Chauve,Nadia El-Mabrouk,Eric Tannier
Models and Algorithms for Genome Evolution Book PDF

Author : Cedric Chauve,Nadia El-Mabrouk,Eric Tannier
Publisher : Springer Science & Business Media
Page : 329 pages
File Size : 40,5 Mb
Release : 2013-09-17
Category : Computers
ISBN : 9781447152989

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Models and Algorithms for Genome Evolution by Cedric Chauve,Nadia El-Mabrouk,Eric Tannier Pdf

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Introduction to Evolutionary Genomics

Naruya Saitou
Introduction to Evolutionary Genomics Book PDF

Author : Naruya Saitou
Publisher : Unknown
Page : 504 pages
File Size : 48,6 Mb
Release : 2018
Category : Evolutionary genetics
ISBN : 3319926438

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Introduction to Evolutionary Genomics by Naruya Saitou Pdf

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.

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

Gustavo Caetano-anolles
Untangling Molecular Biodiversity Explaining Unity And Diversity Principles Of Organization With Molecular Structure And Evolutionary Genomics Book PDF

Author : Gustavo Caetano-anolles
Publisher : World Scientific
Page : 673 pages
File Size : 44,9 Mb
Release : 2020-11-20
Category : Science
ISBN : 9789814656634

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Untangling Molecular Biodiversity: Explaining Unity And Diversity Principles Of Organization With Molecular Structure And Evolutionary Genomics by Gustavo Caetano-anolles Pdf

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.

Structural Approaches to Sequence Evolution

Ugo Bastolla,Markus Porto,Eduardo Roman,Michele Vendruscolo
Structural Approaches to Sequence Evolution Book PDF

Author : Ugo Bastolla,Markus Porto,Eduardo Roman,Michele Vendruscolo
Publisher : Springer Science & Business Media
Page : 375 pages
File Size : 54,5 Mb
Release : 2007-05-26
Category : Science
ISBN : 9783540353065

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Structural Approaches to Sequence Evolution by Ugo Bastolla,Markus Porto,Eduardo Roman,Michele Vendruscolo Pdf

Recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists.

Computer Analysis of Genetic Macromolecules

N. A. Kolchanov,Hwa A. Lim
Computer Analysis of Genetic Macromolecules Book PDF

Author : N. A. Kolchanov,Hwa A. Lim
Publisher : World Scientific
Page : 590 pages
File Size : 48,7 Mb
Release : 1994
Category : Science
ISBN : 9810213786

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Computer Analysis of Genetic Macromolecules by N. A. Kolchanov,Hwa A. Lim Pdf

Molecular biology and genetics are fast-growing fields with significant results and findings being reported virtually every day. Raw data from the wet lab accumulate at an astonishing rate, making it necessary to analyze the biological data with the use of computers. This book reveals how the current challenges of molecular biology and genetics are met with computer and mathematical treatments. A combined effort of the Computational Genetics and Biophysics Group (Supercomputer Computations Research Institute, USA), the Theoretical Molecular Genetics (Russian Academy of Sciences, Russia) and the Bioinformatics Group (Consiglio Nazionale delle Ricerche, Italy), many of these findings are firsthand discoveries made by these groups. The book emphasizes the fundamental principles of the structural-functional organization of the 3 major classes of genetic macromolecules: DNA, RNA and proteins. It also introduces universally applicable theoretical principles into the enormous realm of raw data and develops an integrative, theoretical computer approach to the analysis of these macromolecules to gain insights into the complexities of their function and evolution.

Evolutionary Genetics

Glenn-Peter Sætre,Mark Ravinet
Evolutionary Genetics Book PDF

Author : Glenn-Peter Sætre,Mark Ravinet
Publisher : Oxford University Press
Page : 352 pages
File Size : 51,6 Mb
Release : 2019-05-13
Category : Science
ISBN : 9780192566652

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Evolutionary Genetics by Glenn-Peter Sætre,Mark Ravinet Pdf

With recent technological advances, vast quantities of genetic and genomic data are being generated at an ever-increasing pace. The explosion in access to data has transformed the field of evolutionary genetics. A thorough understanding of evolutionary principles is essential for making sense of this, but new skill sets are also needed to handle and analyze big data. This contemporary textbook covers all the major components of modern evolutionary genetics, carefully explaining fundamental processes such as mutation, natural selection, genetic drift, and speciation. It also draws on a rich literature of exciting and inspiring examples to demonstrate the diversity of evolutionary research, including an emphasis on how evolution and selection has shaped our own species. Practical experience is essential for developing an understanding of how to use genetic and genomic data to analyze and interpret results in meaningful ways. In addition to the main text, a series of online tutorials using the R language serves as an introduction to programming, statistics, and analysis. Indeed the R environment stands out as an ideal all-purpose source platform to handle and analyze such data. The book and its online materials take full advantage of the authors' own experience in working in a post-genomic revolution world, and introduces readers to the plethora of molecular and analytical methods that have only recently become available. Evolutionary Genetics is an advanced but accessible textbook aimed principally at students of various levels (from undergraduate to postgraduate) but also for researchers looking for an updated introduction to modern evolutionary biology and genetics.

Genomes, Evolution, and Culture

Rene J. Herrera,Ralph Garcia-Bertrand,Francisco M. Salzano
Genomes Evolution and Culture Book PDF

Author : Rene J. Herrera,Ralph Garcia-Bertrand,Francisco M. Salzano
Publisher : John Wiley & Sons
Page : 280 pages
File Size : 41,5 Mb
Release : 2016-05-02
Category : Science
ISBN : 9781118876404

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Genomes, Evolution, and Culture by Rene J. Herrera,Ralph Garcia-Bertrand,Francisco M. Salzano Pdf

This book combines recent information and discoveries in the field of human molecular biology and human molecular evolution. It provides an interdisciplinary approach drawing together data from various diverse disciplines to address both the more classical anthropological content and the current more contemporary molecular focus of courses. Chapters include a history of human evolutionary genetics; the human genome structure and function; population structure and variability; gene and genomic dynamics; culture; health and disease; bioethics; future.

Elements of Evolutionary Genetics

Brian Charlesworth,Deborah Charlesworth
Elements of Evolutionary Genetics Book PDF

Author : Brian Charlesworth,Deborah Charlesworth
Publisher : Roberts
Page : 776 pages
File Size : 43,9 Mb
Release : 2010-02-03
Category : Science
ISBN : STANFORD:36105215340113

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Elements of Evolutionary Genetics by Brian Charlesworth,Deborah Charlesworth Pdf

This textbook shows readers how models of the genetic processes involved in evolution are made (including natural selection, migration, mutation, and genetic drift in finite populations), and how the models are used to interpret classical and molecular genetic data. The material is intended for advanced level undergraduate courses in genetics and evolutionary biology, graduate students in evolutionary biology and human genetics, and researchers in related fields who wish to learn evolutionary genetics. The topics covered include genetic variation, DNA sequence variability and its measurement, the different types of natural selection and their effects (e.g. the maintenance of variation, directional selection, and adaptation), the interactions between selection and mutation or migration, the description and analysis of variation at multiple sites in the genome, genetic drift, and the effects of spatial structure.