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Bioinformatics for Evolutionary Biologists

Author: Bernhard Haubold

Publisher: Springer Nature

Published: 2023-02-03

Total Pages: 410

ISBN-13: 303120414X

This self-contained textbook covers fundamental aspects of sequence analysis with special emphasis on evolutionary biology, including sequence alignment, exact matching, phylogeny reconstruction, and coalescent simulation. It addresses these topics through a series of over 800 computer problems, ranging from elementary to research level, to enable learning by doing. Students solve the problems in the same computational environment used for decades in science – the Unix command line. This is available on all four major operating systems for PCs: Windows, macOS, chromeOS, and Linux. To learn using this powerful system, students analyze sample sequence data by applying generic tools, bioinformatics software, and over 50 programs specifically written for this course and available via GitHub. The solutions for all problems are included, making the book ideal for self-study. Problems are grouped into sections headed by an introduction and a list of new terms. By using practical computing to explore sequence data in an evolutionary context, the book enables readers to tackle their own computational problems.

Introduction to Computational Biology

Author: Bernhard Haubold

Publisher: Springer Science & Business Media

Published: 2006-08-09

Total Pages: 329

ISBN-13: 3764373873

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Written with the advanced undergraduate in mind, this book introduces into the field of Bioinformatics. The authors explain the computational and conceptional background to the analysis of large-scale sequence data. Many of the corresponding analysis methods are rooted in evolutionary thinking, which serves as a common thread throughout the book. The focus is on methods of comparative genomics and subjects covered include: alignments, gene finding, phylogeny, and the analysis of single nucleotide polymorphisms (SNPs). The volume contains exercises, questions & answers to selected problems.

Evolutionary Bioinformatics

Author: Donald R. Forsdyke

Publisher: Springer Science & Business Media

Published: 2010-11-11

Total Pages: 511

ISBN-13: 1441977716

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Books on bioinformatics which began appearing in the mid 80s primarily served gene-hunters, and biologists who wished to construct family trees showing tidy lines of descent. Given the great pharmaceutical industry interest in genes, this trend has continued in most subsequent texts. These deal extensively with the exciting topic of gene discovery and searching databases, but hardly consider genomes as information channels through which multiple forms and levels of information, including genic information, have passed through the generations.

Bioinformatics and Molecular Evolution

Author: Paul G. Higgs

Publisher: John Wiley & Sons

Published: 2013-04-30

Total Pages: 532

ISBN-13: 1118697065

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In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.

Evolutionary Bioinformatics

Author: Donald R. Forsdyke

Publisher: Springer

Published: 2016-04-27

Total Pages: 471

ISBN-13: 3319287559

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Now in its third edition and supplemented with more online material, this book aims to make the "new" information-based (rather than gene-based) bioinformatics intelligible both to the "bio" people and the "info" people. Books on bioinformatics have traditionally served gene-hunters, and biologists who wish to construct family trees showing tidy lines of descent. While dealing extensively with the exciting topics of gene discovery and database-searching, such books have hardly considered genomes as information channels through which multiple forms and levels of information have passed through the generations. This “new bioinformatics” contrasts with the "old" gene-based bioinformatics that so preoccupies previous texts. Forms of information that we are familiar with (mental, textual) are related to forms with which we are less familiar (hereditary). The book extends a line of evolutionary thought that leads from the nineteenth century (Darwin, Butler, Romanes, Bateson), through the twentieth (Goldschmidt, White), and into the twenty first (the final works of the late Stephen Jay Gould). Long an area of controversy, diverging views may now be reconciled.

Evolutionary Computation in Bioinformatics

Author: Gary Fogel

Publisher: Morgan Kaufmann

Published: 2003

Total Pages: 432

ISBN-13: 9781558607972

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This book offers a definitive resource that bridges biology and evolutionary computation. The authors have written an introduction to biology and bioinformatics for computer scientists, plus an introduction to evolutionary computation for biologists and for computer scientists unfamiliar with these techniques.

Evolutionary Genomics and Systems Biology

Author: Gustavo Caetano-Anollés

Publisher: Wiley-Blackwell

Published: 2010-07-08

Total Pages: 330

ISBN-13: 0470570407

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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 Biology from Concept to Application

Author: Pierre Pontarotti

Publisher: Springer Science & Business Media

Published: 2008-06-20

Total Pages: 220

ISBN-13: 3540789936

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Every biological system is the outcome of its evolution; therefore, the deciphering of its evolutionary history is of tremendous importance to understand the biology of a system. Since 1997 scientists of different disciplines have held an annual "Evolutionary Biology Meeting" at Marseille (France) in order to discuss their research developments, exchange ideas and start collaborations. Consisting of the most representative talks of the 11th meeting, this book provides an up-to-date overview of evolutionary concepts and how these concepts can be applied to a better understanding of various biological aspects. It is divided into the following four parts: Modelization of Evolution - Concepts in Evolutionary Biology - Knowledge - Applied Evolutionary Biology. This book is an invaluable source of information not only for evolutionary biologists, but also for biologists in general.

Evolutionary Biology: Mechanisms and Trends

Author: Pierre Pontarotti

Publisher: Springer Science & Business Media

Published: 2012-09-14

Total Pages: 360

ISBN-13: 3642304257

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The annual Evolutionary Biology Meetings in Marseilles serve to gather leading evolutionary biologists and other scientists using evolutionary biology concepts, e.g. for medical research. The aims of these meetings are to promote the exchange of ideas and to encourage interdisciplinary collaborations. This book collects 19 selected contributions presented at the 15th meeting, which took place in September 2011. It starts with a description of the life and work of J.B.S. Haldane, a remarkable evolutionary biologist of the 20th century. The remaining chapters are grouped under the following three themes: · New Concepts in Evolutionary Biology · Macroevolution: Mechanisms and Trends · Genome Evolution Offering an up-to-date overview of recent results in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.

Bioinformatics for Biologists

Author: Pavel Pevzner

Publisher: Cambridge University Press

Published: 2011-09-15

Total Pages: 478

ISBN-13: 1139501615

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The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. Rather than just presenting tools, the authors - each a leading scientist - engage the students' problem-solving skills, preparing them to meet the computational challenges of their life science careers.