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Volume I Computational Genomics: Large-scale pyrosequencing on the 454 GS FLX. Massively parallel short read sequencing using the Illumina Genome Analyzer. Single molecule real-time (SMRT) sequencing of PacBio RS systems. Algorithms for short read error correction. Accelerator-based techniques for short read error correction. Short-read mapping and alignment to reference genomics. Translational genomics via high-throughput sequencing. Graph-based approaches for de novo high-throughput genome assembly. Optimization-based approaches for genome assembly. Parallel methods for large-scale assembly of high-throughput sequences. Algorithms for metagenomics. RNA-seq based transcriptome analysis via high-throughput sequencing. Annotation of plant genomes using RNA-seq data. Volume II Computational Systems Biology: Synthetic expression data generation for structure learning. Simulation and analysis of biochemical networks and dynamics. Graphical editing and simulation of biochemical networks. Assessing methods for reverse engineering gene networks. Construction of gene regulatory networks. Construction and analysis of protein-protein interaction networks. Predicting protein function from protein-protein interaction networks. Analysis and comparison of biological networks. Identifying building blocks of cellular interaction networks. Extracting modules from protein interaction networks. Computational methods for structure and function analysis of biological networks. Visualization of molecular interaction networks using Cytoscape. Integrated visualization of metabolic networks. Volume III Computational Structural Biology: Algorithms for structural determination. Structure classification and comparison. Protein structure prediction. Protein dynamics. Protein interactions. Nucleic acid structure.
Praise for the First Edition: 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, Bulletin of Mathematical Biology, 2007 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 to learn about areas outside his particular area of expertise. -Books-On-Line ... 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, 2007