Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing
2nd Edition
Published on 12. October 2023
Book
Hardback
470 pages
978-1-009-34123-3 (ISBN)
Description
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.
Reviews / Votes
'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 VeronaMore details
Edition
2nd Revised edition
Language
English
Place of publication
Cambridge
United Kingdom
Edition type
Revised edition
Illustrations
Worked examples or Exercises; 50 Tables, black and white; 60 Halftones, black and white; 100 Line drawings, black and white
Dimensions
Height: 250 mm
Width: 171 mm
Thickness: 31 mm
Weight
980 gr
ISBN-13
978-1-009-34123-3 (9781009341233)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Classification
Other editions
Additional editions
Veli Maekinen | Djamal Belazzougui | Fabio Cunial
Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing
E-Book
09/2023
2nd Edition
Cambridge University Press
€67.99
Available for download
Previous edition
Veli Maekinen | Djamal Belazzougui | Fabio Cunial
Genome-Scale Algorithm Design
Biological Sequence Analysis in the Era of High-Throughput Sequencing
Book
05/2015
Cambridge University Press
€63.23
Article exhausted; check for reprint
Persons
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.
Content
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.