Computational Biology

Integer Linear Programming in Computational and Systems Biology An Entry-Level Text and Course

Dan Gusfield

University of California, Davis Integer linear programming is a versatile modeling and optimization technique with potential to transform biological computation. This hands-on text, designed for students, researchers, and professionals in both biology and computational fields, demonstrates applications in genomics, RNA and protein folding, DNA sequencing, phylogenetics, and more. Contents: Part I; Part II.

‘In his classic accessible teaching style, Gusfield teaches us why integer linear programming (ILP) is the most useful mathematical idea you’ve probably never heard of. Read this book to learn how what you don’t know can hurt you, and why ILP should be your new favorite method.’

Trey Ideker, University of California, San Diego

‘Once again, Dan Gusfield has written an accessible book that shows that algorithmic rigor need not be sacrificed when solving real-world problems. He explains integer linear programming in the context of real-world biology. In doing so, the reader has an enriched understanding of both algorithmic details and the challenges in modern biology.’

Russ Altman, Stanford University, California

2019 253 x 177 mm 428pp 123 b/w illus. 978-1-108-42176-8 Hardback £49.99 / US$64.99 For all formats available, see www.cambridge.org/9781108421768 Bioinformatics and Computational Biology in Drug Discovery and Development

Edited by William T. Loging

Mount Sinai School of Medicine, New York Providing a comprehensive overview of the drug discovery and development pipeline, this book focuses on the integral role that computational biology methods play in this process. Covering technological advances and their relation to drug developmental processes, readers are exposed to new methods of discovery utilising the available technology.

‘We live in transformative times and perhaps big data and analytics represent a most interesting and essential concept of today. From the telescope to the microscope, our ability to peer into complexities of life has transformed humanity. Big data is the next major step in major transition. Bioinformatics and Computational Biology in Drug Discovery and Development is a road map to an inevitable future – a future where data define disease, diagnosis and drugs. This book is an essential companion for anyone in drug development who has one foot in the present and one in the future.’

John Nosta, President, NOSTALAB

2018 244 x 170 mm 253pp 46 b/w illus. 9 colour illus. 3 tables 978-1-108-46115-3 Paperback £29.99 / US$39.99 For all formats available, see www.cambridge.org/9781108461153

Genome-Scale Algorithm Design Biological Sequence Analysis in the Era of High-Throughput Sequencing

Veli Mäkinen Djamal Belazzougui Fabio Cunial and Alexandru I. Tomescu

University of Helsinki Outlining the fundamental algorithms and data structures that power modern sequence analysis workflows, this book provides a powerful toolkit for students and researchers in bioinformatics and computer science. Its numerous examples and exercises are designed to help readers understand applications of the latest algorithm techniques, providing tools for further research. Contents: Part I. Preliminaries; Part II. Fundamentals of Biological Sequence Analysis; Part III. Genome-Scale Index Structures; Part IV. Genome-Scale Algorithms; Part V. Applications.

‘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 welldesigned examples and many exercises, makes it an ideal resource for researchers, students, and teachers.’

Jens Stoye, Universität Bielefeld

2015 247 x 174 mm 413pp 90 b/w illus. 4 tables 269 exercises 978-1-107-07853-6 Hardback £44.99 / US$64.99 For all formats available, see www.cambridge.org/9781107078536

Bayesian Evolutionary Analysis with BEAST

Alexei J. Drummond

University of Auckland

and Remco R. Bouckaert

University of Auckland A comprehensive overview of Bayesian approaches to phylogenetics using Markov chain Monte Carlo (MCMC) methods, offering theoretical insight, pragmatic advice and tools to develop further models. This title is a one-stop reference to applying the latest phylogenetic models in BEAST 2, interpreting the analyses and extending these models further. Contents: Part I. Theory; Part II. Practice; Part III. Programming.

‘Want to construct a phylogeny, add in calibrated time points or work out the past history of an epidemic? The open source package BEAST has established itself as the industry standard for all this and more. This definitive book, explaining what is under the hood, how the user can customize extensions and, most critically, a simple ‘how to’ users guide, is necessary reading for beginners and specialists alike.’

Laurence D. Hurst, University of Bath

‘In concert with the dramatic improvements to DNA sequencing technology, Bayesian inference has revolutionized population genetics, phylogenetics, and divergence time estimation. A similar impact on epidemiology appears imminent via a suite of new Bayesian methods that incorporate host and pathogen DNA sequence data into established mathematical frameworks. This book is an accessible and thorough introduction to these Bayesian procedures. However, the book does far more than explain the theory. It also includes clear guides on how to use the BEAST 2 software for performing Bayesian analyses, and how to visualize the results. Because the software is designed to be extensible, the book instructs users to write their own code to supplement the diverse methods that are already implemented in BEAST 2. This book is timely and is written by two of the leaders of the field. I highly recommend it.’

Jeff Thorne, North Carolina State University

2015 247 x 174 mm 260pp 21 b/w illus. 70 colour illus. 9 tables 978-1-107-01965-2 Hardback £42.99 / US$55.99 For all formats available, see www.cambridge.org/9781107019652