Understanding Bioinformatics / Edition 1

by Marketa Zvelebil

Overview

Suitable for advanced undergraduates and graduates, Understanding Bioinformatics provides a definitive guide to this vibrant and evolving discipline. The book takes a conceptual approach, guiding the reader from first principles through to an understanding of the computational techniques and the key algorithms. Understanding Bioinformatics is an invaluable companion for students from their first encounter with the subject through to more advanced studies.

The book is divided into seven sections, with the opening section introducing the basics of nucleic acids, proteins and databases. Subsequent sections are divided into 'applications' and 'theory' chapters, allowing readers to focus their attention effectively. In each section, the applications chapter provides a fast and straightforward route to understanding the main concepts and 'getting started'. Each of these is then followed by theory chapters which give greater detail and present the underlying mathematics. In Section 2, Sequence Alignments, the applications chapter shows the reader how to get started on producing and analyzing sequence alignments, and using sequences for database searching, while the next two chapters look closely at the more advanced techniques and the mathematical algorithms involved. Section 3 covers evolutionary processes and shows how bioinformatics can be used to help build phylogenetic trees. Section 4 looks at the characteristics of whole genomes. In Sections 5 and 6 the focus turns to secondary and tertiary structure - predicting structural conformation and analyzing structure-function relationships. The last section surveys methods of analyzing data from a set of genes orproteins of an organism and is rounded off with an overview of systems biology.

The emphasis throughout Understanding Bioinformatics is on guiding the reader through the subject matter. The writing style is notable for its clarity, while the extensive, full-color artwork has been designed to present the key concepts with simplicity and consistency.

Product Details

ISBN-13:	2900815340248
Publication date:	09/06/2007
Pages:	800
Product dimensions:	8.37(w) x 10.87(h) x 1.00(d)

About the Author

Marketa Zvelebil is the team leader of cancer informatics at The Breakthrough Toby Robins Breast Cancer Research Centre.

Jeremy O. Baum is an Honorary Teaching Fellow in the School of Crystallography, Birkbeck College.

Table of Contents

SECTION 1 Background Basics
1: Nucleic Acid World
2: Protein Structure
3: Dealing with Databases

SECTION 2 Sequence Alignments
4: Producing and Analyzing Sequence Alignments
5: Pairwise Sequence Alignment
6: Patterns, Profiles and Multiple Alignments

SECTION 3 Evolutionary Processes
7: Recovering Evolutionary History
8: Building Phylogenetic Trees

SECTION 4 Genome Characteristics
9: Revealing Genome Features
10: Principles of Genome Annotation

SECTION 5 Secondary Structures
11: Obtaining Secondary Structure from Sequence
12: Predicting Secondary Structures

SECTION 6 Tertiary Structures
13: Modeling Protein Structure
14: Analyzing Structure-Function Relationships

SECTION 7 Cells and Organisms
15: Proteome and Gene Expression Analysis
16: Clustering Methods and Statistics
17: Systems Biology

APPENDICES Background Theory
Appendix A: Probability and Bayesian Analysis
Appendix B: Molecular Energy Functions
Appendix C: Function Optimization

Editorial Reviews

"Congratulations on a fine book! I do not think I have seen such a comprehensive text on bioinformatics algorithms and techniques before. I think this will be an invaluable resource for the bioinformatics community and researchers of neighbouring disciplines." - Jaap Heringa, Free University, Amsterdam

"Many of the students in our program could benefit from reading this guide to genetics and molecular biology terms. Chapter 1 was well organized and easy to follow … I found that the illustrations were familiar and depicted the concepts well." - Sudha Iyengar, Case Western Reserve University, Cleveland, USA

"I found Chapter 6 to be a very detailed and informative overview of multiple alignment and pattern discovery methods for biological sequences. The level of detail was good, as were most of the explanations of the methods. I would use this chapter in an undergraduate course in bioinformatics." - Tim Bailey, University of Queensland, Australia

"This is very well done. Compared to other competing textbooks, your book will be probably the first one that explains gene finding in detail." - Sun Kim, Indiana University, Bloomington, USA

"This chapter is nicely done, an easy read for an upperclassman or graduate student. The chapter reads as a How-To in protein structure prediction." - Chris Bystroff, Rensselaer Polytechnic Institute, Troy, USA, writing about Chapter 13

"I enjoyed reading this chapter, and commend the authors on a well presented and explained introduction to the main algorithms and issues of analyzing this sort of data. The figures are useful and relevant and the techniques presented give a very good representation of the main algorithms in what is a diverse area of analysis.
I believe this chapter to be at a great level for biology graduates, and in fact any student who has not been exposed to data mining concepts previously. I commend that the algorithms have been placed in a biological contexts wherever possible making the concepts more accessible." - Jen Taylor, University of Oxford, UK, writing about Chapter 16

'Congratulations on a fine book! I do not think I have seen such a comprehensive text on bioinformatics algorithms and techniques before. I think this will be an invaluable resource for the bioinformatics community and researchers of neighbouring disciplines.' - Jaap Heringa, Free University, Amsterdam

'This is very well done. Compared to other competing textbooks, your book will be probably the first one that explains gene finding in detail.' - Sun Kim, Indiana University, Bloomington, USA

‘…provides an outstanding introduction to the main bioinformatics problems and tools, well-balanced between applications to biological problems and theory behind data processing methods… an excellent and updated book for students of Bioinformatics’ Computer Methods and Programs in Biomedicine

From the Publisher