Welcome to the website of the book “Genome-Scale Algorithm Design”.
High-throughput sequencing has revolutionized 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 current 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 visualizations, 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.

Target audience:


The book is available in several online bookstores, such as:

Veli Mäkinen 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.
“A very well written, research-level [...] reference for advanced string algorithms in bioinformatics, merging many established and recent results together into a coherent whole and occasionally adding some new results of its own. [...] The literature overviews are excellent. [...] The network flow chapter is particularly elegant. [...] The book makes a very authoritative impression, not just on the algorithmic side but also on the applied/biological side.”
Steven Kelk, ACM SIGACT News Review, 2016 [PDF]

“Not just a collection of chapters, but a well-thought-out, integrated book that fills a gap in the recent literature of textbooks in algorithmic bioinformatics. It offers a sound, clear, rich overview of computer science methods for the challenges of today's biological sequence analysis. I advise it to students as well as to researchers in the field.”
Nadia Pisanti, University of Pisa, Italy.

“This book will be a new reference text for string data structures and algorithms, and 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, Universität Bielefeld, Germany.

“The book is really great and I could envision using it in courses in bioinformatics and data compression. Its scope, clarity, and mathematically precise, compelling explanations make the advanced topics in genome-scale bioinformatics accessible to a wide audience.”
Christina Boucher, Colorado State University, USA.

“A timely, rigorous, 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 this an ideal textbook for courses directed at a mixed audience coming from diverse, even distant backgrounds.”
Alberto Apostolico, Georgia Tech, USA.

“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 University, USA.

Fabio, Veli and Djamal working hard (or hardly working?)
on a book chapter.

Fabio and Alex preparing for a stressful book meeting in the
Finnish countryside.


Fundamental Algorithms
for Bioinformatics
University of Verona
Spring 2017


Algorithmic Techniques
in Computational Biology
UC Riverside
Spring 2016 and Spring 2017

Algorithms for Sequence Analysis
Max Planck Institute for Informatics
2016 and 2017

Computational Biology Capstone
University of Washington
Spring 2016

Computational Genomics
Stanford University
Spring 2016

Computational Methods
for Handling Textual Data
University of Verona
PhD Course in Computer Science
Spring 2016

Sequence Analysis
Rice University
Spring 2016 and Spring 2017


Advanced Sequence Analysis
Universität Tübingen
Fall 2015

Algorithmics and Bioinformatics
Parisian Master of Research in Computer Science
Fall 2015

Algorithms for Sequence Analysis
Saarland University

Bioinformatics - On sequences,
genes and genomes
Universität Tübingen
Fall 2015

Computational Biology
Stony Brook University
Fall 2015 and Fall 2016

Computational Molecular Biology
Brown University
Fall 2015

Programming in Bioinformatics
Universitat Autònoma de Barcelona
Fall 2015 and Fall 2016