
Genome-Scale Algorithm Design
Biological Sequence Analysis in the Era of High-Throughput Sequencing
Cambridge University Press
Published on 7. May 2015
Book
Hardback
413 pages
978-1-107-07853-6 (ISBN)
Article exhausted; check for reprint
Description
High-throughput sequencing has revolutionised the field of biological sequence analysis. Its application has enabled researchers to address important biological questions, often for the first time. This book provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows-Wheeler indexes, graph algorithms and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing.
Reviews / Votes
'Genome-Scale Algorithm Design is a well-thought-out ... book that fills a gap in the recent literature ... [on algorithms] for bioinformatics. It offers a sound, clear, and rich overview of computer science methods for the challenge of today's biological sequence analysis. I [recommend] it to students as well as to researchers in the field.' Nadia Pisanti, University of Pisa 'This book will be a new reference text for string data structures and algorithms, as well as their applications in computational molecular biology and genome analysis. The technically precise style, illustrated with a great collection of well-designed examples and many exercises, makes it an ideal resource for researchers, students, and teachers.' Jens Stoye, Universitaet Bielefeld 'I think the book is really great and could envision using it in courses in bioinformatics and data compression. The book's scope, clarity, and mathematically precise, compelling explanations make the advanced topics in genome-wide bioinformatics accessible to [a] wide audience.' Christina Boucher, Colorado State University 'This book is a timely, rigorous and comprehensive systematization of the concepts and tools at the core of post-genome bioinformatics. By choosing to incorporate the principles of algorithms design most pertinent to the topic, the authors have created a rare, self-contained reference that will smoothly introduce the neophyte and assist the seasoned researcher as well as anybody who needs to understand these issues at a fundamental level. The organization of the material, the clarity of exposition and rigor of treatment make the book an ideal textbook for courses directed at a mixed audience coming from diverse, even distant backgrounds.' Alberto Apostolico, Georgia Institute of Technology 'A very timely textbook covering many recently established techniques and applications at a level of rigor befitting a computer science audience.' Paul Medvedev, Pennsylvania State UniversityMore details
Language
English
Place of publication
Cambridge
United Kingdom
Target group
Professional and scholarly
Illustrations
Worked examples or Exercises; 4 Tables, black and white; 38 Halftones, unspecified; 52 Line drawings, unspecified
Dimensions
Height: 253 mm
Width: 180 mm
Thickness: 22 mm
Weight
960 gr
ISBN-13
978-1-107-07853-6 (9781107078536)
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
New editions

Veli Maekinen | Djamal Belazzougui | Fabio Cunial
Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing
Book
10/2023
2nd Edition
Cambridge University Press
€72.00
Shipment within 15-20 days
Additional editions

Veli Maekinen | Djamal Belazzougui | Fabio Cunial
Genome-Scale Algorithm Design
Biological Sequence Analysis in the Era of High-Throughput Sequencing
E-Book
05/2015
Cambridge University Press
€52.99
Available for download

Veli Makinen
Genome-Scale Algorithm Design
Biological Sequence Analysis in the Era of High-Throughput Sequencing
E-Book
05/2015
Cambridge University Press
€45.49
Available for download
Persons
Veli Maekinen is a Professor of Computer Science at the University of Helsinki, Finland, where he heads a research group working on genome-scale algorithms as part of the Finnish Center of Excellence in Cancer Genetics Research. He has taught advanced courses on string processing, data compression, biological sequence analysis, along with introductory courses on bioinformatics. Djamal Belazzougui is a postdoctoral researcher at the University of Helsinki. His research topics include hashing, succinct and compressed data structures and string algorithms. Fabio Cunial is a postdoctoral researcher at the University of Helsinki. His research focuses on string algorithms and genome analysis. Alexandru I. Tomescu is a postdoctoral researcher at the University of Helsinki. His current research interests lie at the intersection of computational biology and computer science.
Author
University of Helsinki
University of Helsinki
University of Helsinki
University of Helsinki
Content
Notation; Preface; 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 (HMMs); Part III. Genome-Scale Index Structures: 8. Classical indexes; 9. Burrows-Wheeler indexes; Part IV. Genome-Scale Algorithms: 10. Read alignment; 11. Genome analysis and comparison; 12. Genome compression; 13. Fragment assembly; Part V. Applications: 14. Genomics; 15. Transcriptomics; 16. Metagenomics; References; Index.