Handbook of Computational Molecular Biology: 1st Edition (Hardback) book cover

Handbook of Computational Molecular Biology

1st Edition

Edited by Srinivas Aluru

Chapman and Hall/CRC

1,104 pages | 354 B/W Illus.

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Hardback: 9781584884064
pub: 2005-12-21
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The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology offers comprehensive, systematic coverage of the various techniques and methodologies currently available.

Accomplished researcher Srinivas Aluru leads a team of experts from around the world to produce this groundbreaking, authoritative reference. With discussions ranging from fundamental concepts to practical applications, this book details the algorithms necessary to solve novel problems and manage the massive amounts of data housed in biological databases throughout the world. Divided into eight sections for convenient searching, the handbook covers methods and algorithms for sequence alignment, string data structures, sequence assembly and clustering, genome-scale computational methods in comparative genomics, evolutionary and phylogenetic trees, microarrays and gene expression analysis, computational methods in structural biology, and bioinformatics databases and data mining.

The Handbook of Computational Molecular Biology is the first resource to integrate coverage of the broad spectrum of topics in computational biology and bioinformatics. It supplies a quick-reference guide for easy implementation and provides a strong foundation for future discoveries in the field.


“The material is well organized and documented, with good presentation and special care on typography. It is highly recommended for any researcher or graduate student interested in an insight into computational biology deeper than the practical use as “black boxes” of computer programs or web servers.”

—Arturo Rojo-Dominguez, in Bulletin of Mathematical Biology, (2007) 69: 2775-2776

“It is to the credit of the author and publisher that they have been able to put together such a complete and well organized handbook this early. …Useful to the researcher looking for either an introduction to the field in general or go learn about areas outside his particular area of expertise.”


"…valuable to those new to the field as well as more experienced researchers. The handbook has done a good job of developing major areas in the field while maintaining a well-organized structure. The 'Handbook for Computational Molecular Biology' will be a great resource to those interested in this exciting field." - Suzanne Sindi, Bioinformatics, Feb., 2007, Vol. 38, No. 3

Table of Contents

Sequence Alignments

Pairwise Sequence Alignments; Benjamin N. Jackson and Srinivas Aluru

Spliced Alignment and Similarity-Based Gene Recognition; Alexey D. Neverov, Andrey A. Mironov, and Mikhail S. Gelfand

Multiple Sequence Alignment; Osamu Gotoh, Shinsuke Yamada, and Tetsushi Yada

Parametric Sequence Alignment; David Fernández-Baca and Balaji Venkatachalam

String Data Structures

Lookup Tables, Suffix Trees and Suffix Arrays; Srinivas Aluru

Suffix Tree Applications in Computational Biology; Pang Ko and Srinivas Aluru

Enhanced Suffix Arrays and Applications; Mohamed I. Abouelhoda, Stefan Kurtz, and Enno Ohlebusch

Genome Assembly and EST Clustering

Computational Methods for Genome Assembly; Xiaoqiu Huang

Assembling the Human Genome; Richa Agarwala

Comparative Methods for Sequence Assembly; Vamsi Veeramachaneni

Information Theoretic Approach to Genome Reconstruction; Suchendra Bhandarkar, Jinling Huang, and Jonathan Arnold

Expressed Sequence Tags: Clustering and Applications; Anantharaman Kalyanaraman and Srinivas Aluru

Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data; Scott J. Emrich, Anantharaman Kalyanaraman, and Srinivas Aluru

Genome-Scale Computational Methods

Comparisons of Long Genomic Sequences: Algorithms and Applications; Michael Brudno and Inna Dubchak

Chaining Algorithms and Applications in Comparative Genomics; Enno Ohlebusch and Mohamed I. Abouelhoda

Computational Analysis of Alternative Splicing; Mikhail S. Gelfand

Human Genetic Linkage Analysis; Alejandro A. Schäffer

Combinatorial Methods for Haplotype Inference; Dan Gusfield and Steven Hecht Orzack


An Overview of Phylogeny Reconstruction; C. Randal Linder and Tandy Warnow

Consensus Trees and Supertrees; Oliver Eulenstein

Large-Scale Phylogenetic Analysis; Tandy Warnow

High-Performance Phylogeny Reconstruction; David A. Bader and Mi Yan

Microarrays and Gene Expression Analysis

Microarray Data: Annotation, Storage, Retrieval and Communication; Catherine A. Ball and Gavin Sherlock

Computational Methods for Microarray Design; Hui-Hsien Chou

Clustering Algorithms for Gene Expression Analysis; Pierre Baldi, G. Wesley Hatfield, and Li M. Fu

Biclustering Algorithms: A Survey; Amos Tanay, Roded Sharan, and Ron Shamir

Identifying Gene Regulatory Networks from Gene Expression Data; Vladimir Filkov

Modeling and Analysis of Gene Networks Using Feedback Control Theory; Hana El Samad and Mustafa Khammash

Computational Structural Biology

Predicting Protein Secondary and Supersecondary Structure; Mona Singh

Protein Structure Prediction with Lattice Models; William E. Hart and Alantha Newman

Protein Structure Determination via NMR Spectral Data; Guohui Lin, Xin Tu, and Xiang Wan

Geometric Processing of Reconstructed 3D Maps of Molecular Complexes; Chandrajit Bajaj and Zeyun Yu

In Search of Remote Homolog; Dong Xu, Ognen Duzlevski, and Xiu-Feng Wan

Biomolecular Modeling using Parallel Supercomputers; Laxmikant V. Kalé, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng

Bioinformatic Databases and Data Mining

String Search in External Memory: Data Structures and Algorithms; Paolo Ferragina

Index Structures for Approximate Matching in Sequence Databases; Tamer Kahveci and Ambuj K. Singh

Algorithms for Motif Search; Sanguthevar Rajasekaran

Data Mining in Computational Biology; Mohammed J. Zaki and Karlton Sequeira


About the Series

Chapman & Hall/CRC Computer and Information Science Series

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Subject Categories

BISAC Subject Codes/Headings:
SCIENCE / Life Sciences / Biology / General
SCIENCE / Biotechnology
SCIENCE / Life Sciences / Biology / Molecular Biology