Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing

Presenting the fundamental algorithms and data structures that power bioinformatics workflows, this book covers a range of topics from the foundations of sequence analysis (alignments and hidden Markov models) to classical index structures (k-mer indexes, suffix arrays, and suffix trees), Burrows–Wheeler indexes, graph algorithms, network flows, and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualizations, and exercises, providing graduate students, researchers, and practitioners with a powerful algorithmic toolkit for the applications of high-throughput sequencing. An accompanying website (www.genome-scale.info) offers supporting teaching material. The second edition strengthens the toolkit by covering minimizers and other advanced data structures and their use in emerging pangenomics approaches.

Table of Contents:
Part I. Preliminaries: 1. Molecular biology and high-throughput sequencing; 2. Algorithm design; 3. Data structures; 4. Graphs; 5. Network flows; Part II. Fundamentals of Biological Sequence Analysis: 6. Alignments; 7. Hidden Markov models; Part III. Genome-Scale Index Structures: 8. Classical indexes; 9. Burrows–Wheeler indexes; Part IV. Genome-Scale Algorithms: 10. Alignment-based genome analysis; 11. Alignment-free genome analysis and comparison; 12. Compression of genome collections; 13. Fragment assembly; Part V. Applications: 14. Haplotype analysis; 15. Pangenomics; 16. Transcriptomics; 17. Metagenomics; References; Index.

About the Author :
Veli Mäkinen is Professor of Computer Science at the University of Helsinki, where he leads a research team on genome-scale algorithmics. He has taught advanced courses on algorithm design and analysis, string processing, data compression, and algorithmic genome analysis, as well as introductory courses on bioinformatics. Djamal Belazzougui is a permanent researcher at the Research Centre for Scientific and Technical Information in Algiers, Algeria. He worked in the Genome-Scale Algorithmics group at the University of Helsinki as a postdoctoral researcher from 2012 to 2015. His research topics include hashing, succinct and compressed data structures, string algorithms, and bioinformatics. Fabio Cunial is a computational scientist at the Broad Institute of MIT and Harvard. He has served as a postdoctoral researcher at the Genome-Scale Algorithmics group at the University of Helsinki as well as at the Myers lab in Dresden. Alexandru I. Tomescu is Associate Professor of Algorithmic Bioinformatics at the University of Helsinki, where he leads a research group on graph algorithms and their application to high-throughput sequencing problems. He is the recipient of a Starting Grant from the European Research Council.

Review :
'This book is very effective in addressing its intended target of graduate students in bioinformatics or computer science with a well-structured but highly accessible description of the fundamental algorithms and data structures that power standard sequence analysis workflows.' Romeo Rizzi, University of Verona