Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.
Provides an integrated picture of the latest developments in algorithmic techniques, with numerous worked examples, algorithm visualisations and exercises.
Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
This newly expanded and updated second edition of the best-selling classic continues to take the "mystery" out of designing algorithms, and analyzing their efficacy and efficiency. Expanding on the first edition, the book now serves as the primary textbook of choice for algorithm design courses while maintaining its status as the premier practical reference guide to algorithms for programmers, researchers, and students. The reader-friendly Algorithm Design Manual provides straightforward access to combinatorial algorithms technology, stressing design over analysis. The first part, Techniques, provides accessible instruction on methods for designing and analyzing computer algorithms. The second part, Resources, is intended for browsing and reference, and comprises the catalog of algorithmic resources, implementations and an extensive bibliography. NEW to the second edition: • Doubles the tutorial material and exercises over the first edition • Provides full online support for lecturers, and a completely updated and improved website component with lecture slides, audio and video • Contains a unique catalog identifying the 75 algorithmic problems that arise most often in practice, leading the reader down the right path to solve them • Includes several NEW "war stories" relating experiences from real-world applications • Provides up-to-date links leading to the very best algorithm implementations available in C, C++, and Java
Algorithm Design introduces algorithms by looking at the real-world problems that motivate them. The book teaches students a range of design and analysis techniques for problems that arise in computing applications. The text encourages an understanding of the algorithm design process and an appreciation of the role of algorithms in the broader field of computer science. The full text downloaded to your computer With eBooks you can: search for key concepts, words and phrases make highlights and notes as you study share your notes with friends eBooks are downloaded to your computer and accessible either offline through the Bookshelf (available as a free download), available online and also via the iPad and Android apps. Upon purchase, you'll gain instant access to this eBook. Time limit The eBooks products do not have an expiry date. You will continue to access your digital ebook products whilst you have your Bookshelf installed.
Computer science majors taking a non-programming-based course like discrete mathematics might ask 'Why do I need to learn this?' Written with these students in mind, this text introduces the mathematical foundations of computer science by providing a comprehensive treatment of standard technical topics while simultaneously illustrating some of the broad-ranging applications of that material throughout the field. Chapters on core topics from discrete structures – like logic, proofs, number theory, counting, probability, graphs – are augmented with around 60 'computer science connections' pages introducing their applications: for example, game trees (logic), triangulation of scenes in computer graphics (induction), the Enigma machine (counting), algorithmic bias (relations), differential privacy (probability), and paired kidney transplants (graphs). Pedagogical features include 'Why You Might Care' sections, quick-reference chapter guides and key terms and results summaries, problem-solving and writing tips, 'Taking it Further' asides with more technical details, and around 1700 exercises, 435 worked examples, and 480 figures.
Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Online Open Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors' acclaimed online course (http://coursera.org/course/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of biology and computer science students alike.Each chapter begins with a central biological question, such as "Are There Fragile Regions in the Human Genome?" or "Which DNA Patterns Play the Role of Molecular Clocks?" and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on Rosalind (http://rosalind.info), an online platform for learning bioinformatics.The textbook website (http://bioinformaticsalgorithms.org) directs readers toward additional educational materials, including video lectures and PowerPoint slides.
An introductory text that emphasizes the underlying algorithmic ideas that are driving advances in bioinformatics. This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems. The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively. An Introduction to Bioinformatics Algorithms is one of the first books on bioinformatics that can be used by students at an undergraduate level. It includes a dual table of contents, organized by algorithmic idea and biological idea; discussions of biologically relevant problems, including a detailed problem formulation and one or more solutions for each; and brief biographical sketches of leading figures in the field. These interesting vignettes offer students a glimpse of the inspirations and motivations for real work in bioinformatics, making the concepts presented in the text more concrete and the techniques more approachable.PowerPoint presentations, practical bioinformatics problems, sample code, diagrams, demonstrations, and other materials can be found at the Author's website.
