Sequence — Evolution — Function
Sequence — Evolution — Function

Author: Eugene Koonin

Publisher: Springer Science & Business Media

Published: 2002-11-30

Total Pages: 496

ISBN-13: 9781402072741

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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.

Biological Sequence Analysis
Biological Sequence Analysis

Author: Richard Durbin

Publisher: Cambridge University Press

Published: 1998-04-23

Total Pages: 372

ISBN-13: 113945739X

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Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Sequence — Evolution — Function
Sequence — Evolution — Function

Author: Eugene V. Koonin

Publisher: Springer Science & Business Media

Published: 2013-06-29

Total Pages: 482

ISBN-13: 1475737831

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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.

In the Light of Evolution
In the Light of Evolution

Author: National Academy of Sciences

Publisher:

Published: 2007

Total Pages: 388

ISBN-13:

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The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, four or five such colloquia are scheduled, typically two days in length and international in scope. Colloquia are organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. Colloquia presentations are recorded and posted on the National Academy of Sciences Sackler colloquia website and published on CD-ROM. These Colloquia are made possible by a generous gift from Mrs. Jill Sackler, in memory of her husband, Arthur M. Sackler.

Probability Models for DNA Sequence Evolution
Probability Models for DNA Sequence Evolution

Author: Rick Durrett

Publisher: Springer Science & Business Media

Published: 2013-03-09

Total Pages: 246

ISBN-13: 1475762852

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"What underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences?" In approaching this question a number of probability models are introduced and anyalyzed.Throughout the book, the theory is developed in close connection with data from more than 60 experimental studies that illustrate the use of these results.

Computational Methods in Protein Evolution
Computational Methods in Protein Evolution

Author: Tobias Sikosek

Publisher: Humana

Published: 2018-10-09

Total Pages: 0

ISBN-13: 9781493987351

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This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.

Protein Families
Protein Families

Author: Christine A. Orengo

Publisher: John Wiley & Sons

Published: 2014-02-03

Total Pages: 566

ISBN-13: 0470624221

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New insights into the evolution and nature of proteins Exploring several distinct approaches, this book describes the methods for comparing protein sequences and protein structures in order to identify homologous relationships and classify proteins and protein domains into evolutionary families. Readers will discover the common features as well as the key philosophical differences underlying the major protein classification systems, including Pfam, Panther, SCOP, and CATH. Moreover, they'll discover how these systems can be used to understand the evolution of protein families as well as understand and predict the degree to which structural and functional information are shared between relatives in a protein family. Edited and authored by leading international experts, Protein Families offers new insights into protein families that are important to medical research as well as protein families that help us understand biological systems and key biological processes such as cell signaling and the immune response. The book is divided into three sections: Section I: Concepts Underlying Protein Family Classification reviews the major strategies for identifying homologous proteins and classifying them into families. Section II: In-Depth Reviews of Protein Families focuses on some fascinating super protein families for which we have substantial amounts of sequence, structural and functional data, making it possible to trace the emergence of functionally diverse relatives. Section III: Review of Protein Families in Important Biological Systems examines protein families associated with a particular biological theme, such as the cytoskeleton. All chapters are extensively illustrated, including depictions of evolutionary relationships. References at the end of each chapter guide readers to original research papers and reviews in the field. Covering protein family classification systems alongside detailed descriptions of select protein families, this book offers biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new insight into the evolution and nature of proteins.

Plant Genomes
Plant Genomes

Author: Jean-Nicolas Volff

Publisher: Karger Medical and Scientific Publishers

Published: 2008-01-01

Total Pages: 155

ISBN-13: 3805584911

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Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.

Evolutionary Systems Biology
Evolutionary Systems Biology

Author: Orkun S. Soyer

Publisher: Springer Science & Business Media

Published: 2012-07-23

Total Pages: 459

ISBN-13: 1461435676

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The book aims to introduce the reader to the emerging field of Evolutionary Systems Biology, which approaches classical systems biology questions within an evolutionary framework. An evolutionary approach might allow understanding the significance of observed diversity, uncover “evolutionary design principles” and extend predictions made in model organisms to others. In addition, evolutionary systems biology can generate new insights into the adaptive landscape by combining molecular systems biology models and evolutionary simulations. This insight can enable the development of more detailed mechanistic evolutionary hypotheses.

The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution
The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution

Author: Sean B. Carroll

Publisher: W. W. Norton & Company

Published: 2007-08-28

Total Pages: 311

ISBN-13: 0393330516

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A geneticist discusses the role of DNA in the evolution of life on Earth, explaining how an analysis of DNA reveals a complete record of the events that have shaped each species and how it provides evidence of the validity of the theory of evolution.