Bioinformatics: Volume I: Data, Sequence Analysis and Evolution / Edition 1

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Overview

In this book, leading researchers in the field of Bioinformatics provide a selection of the most useful and widely applicable methods, able to be applied as is, or with minor variations, to many specific problems. Over 80 authors from around the globe contribute to the two volumes, including many leading experts in their respective subjects. They encompass topics from across the diverse field of bioinformatics through its broad scope, combining to provide an inter-disciplinary collaboration involving biologists, biochemists, physicists, mathematicians, statisticians and computer scientists.

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Editorial Reviews

Doody's Review Service
Reviewer: Basabi Rana, Ph.D.(Loyola University Stritch School of Medicine)
Description: This precise description of all current molecular biology techniques is an important addition to the field of bioinformatics.
Purpose: The purpose is to provide a "detailed description and implantation advice" about current molecular biology techniques.
Audience: According to the author, the book is written primarily for students and beginning bioinformatics researchers. The authors have fulfilled their objective. There are quite a few contributing authors, who are authorities in the field of molecular biology and bioinformatics.
Features: A wide variety of topics involving molecular biology techniques relevant for bioinformatics researchers are covered. This volume contains three sections composed of 24 chapters and an index and evolution index. Section I deals with data and databases with six chapters on data management, RNA and protein structure determination, microarray analysis, and functional annotations. Section II on sequence analysis describes sequence alignment and the methods used for discovering functional components of genomes including genes, alternative splice sites, noncoding RNAs and regulatory motifs. Section III, the largest section with 12 chapters, covers the methods of phylogenetics and evolution, describing both basic aspects of modeling of evolution and inferring trees as well as more complex issues such as drawing inferences on ancestral gene order, genome rearrangements, and ancestral interaction networks. This section ends with a chapter that describes the achievements and challenges of algorithm in phylogenetics. The authors have included both an index and an evolution index at the end, which will be very helpful to readers.
Assessment: This is a very good reference for students who are beginning level bioinformatics researchers.
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Product Details

  • ISBN-13: 9781617377303
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 5/26/2011
  • Series: Methods in Molecular Biology Series , #452
  • Edition description: Softcover reprint of hardcover 1st ed. 2008
  • Edition number: 1
  • Pages: 562

Table of Contents

Table of Contents

Bioinformatics: Volume I: Data, Sequence Analysis and Evolution

Section I: Data and Databases

Chapter 1. Managing Sequence Data
Ilene Karsch Mizrachi

Chapter 2. RNA Structure Determination by NMR
Lincoln G. Scott and Mirko Hennig

Chapter 3. Protein Structure Determination by X-ray Crystallography
Andrea Ilari and Carmelinda Savino

Chapter 4. Pre-processing of Microarray Data and Analysis of Differential Expression
Steffen Durinck

Chapter 5. Developing an Ontology
Midori A. Harris

Chapter 6. Genome Annotation
Hideya Kawaji and Yoshihide Hayashizaki

Section II: Sequence Analysis

Chapter 7. Multiple Sequence Alignment
Walter Pirovano and Jaap Heringa

Chapter 8. Finding Genes in Genome Sequence
Alice Carolyn McHardy

Chapter 9. Bioinformatics Detection of Alternative Splicing
Namshin Kim and Christopher Lee

Chapter 10. Reconsruction of full-length isoforms from Splice Graphs
Yi Xing and Christopher Lee

Chapter 11. Sequence Segmentation
Jonathan Keith

Chapter 12. Discovering Sequence Motifs
Timothy L. Bailey

Section III: Phylogenetics and Evolution

Chapter 13. Modeling Sequence Evolution
Pietro Lio and Martin Bishop

Chapter 14. Inferring Trees
Simon Whelan

Chapter 15. Detecting the Presence and Location of Selection in Proteins
Tim Massingham

Chapter 16. Phylogenetic Model Evaluation
Lars Sommer Jermiin, Vivek Jayaswal, Faisal Ababneh and John Robinson

Chapter 17. Inferring Ancestral Gene Order
Julian M. Catchen, John S. Conery and John H. Postlethwait

Chapter 18. Genome Rearrangement by the Double Cut and Join Operation
Richard Friedberg, Aaron E. Darling and Sophia Yancopoulos

Chapter 19. Inferring Ancestral Protein Interaction Networks
Jose M. Peregrin-Alvarez

Chapter 20. Computational Tools for the Analysis of Rearrangements in Mammalian Genomes
Guillaume Bourque and Glenn Tesler

Chapter 21. Detecting Lateral Genetic Transfer: a Phylogenetic Approach
Robert G. Beiko and Mark A. Ragan

Chapter 22. Detecting Genetic Recombination
Georg F. Weiller

Chapter 23. Inferring patterns of migration
Paul M.E. Bunje and Thierry Wirth

Chapter 24. Fixed-Parameter Algorithms in Phylogenetics
Jens Gramm, Arfst Nickelsen and Till Tantau

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