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Algorithms on Strings, Trees, and Sequences
String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.
Integer Linear Programming in Computational and Systems Biology
Integer linear programming (ILP) is a versatile modeling and optimization technique that is increasingly used in non-traditional ways in biology, with the potential to transform biological computation. However, few biologists know about it. This how-to and why-do text introduces ILP through the lens of computational and systems biology. It uses in-depth examples from genomics, phylogenetics, RNA, protein folding, network analysis, cancer, ecology, co-evolution, DNA sequencing, sequence analysis, pedigree and sibling inference, haplotyping, and more, to establish the power of ILP. This book aims to teach the logic of modeling and solving problems with ILP, and to teach the practical 'work flow' involved in using ILP in biology. Written for a wide audience, with no biological or computational prerequisites, this book is appropriate for entry-level and advanced courses aimed at biological and computational students, and as a source for specialists. Numerous exercises and accompanying software (in Python and Perl) demonstrate the concepts.
Algorithms on Strings, Trees, and Sequences
This book describes a range of string problems in computer science and molecular biology and the algorithms developed to solve them.
ReCombinatorics
When a Philadelphia girl intercepts a message about an impending British attack against her father's regiment, commanded by General Washington, in White Marsh, she travels alone by horseback to warn the Patriot army.
The Stable Marriage Problem
This book probes the stable marriage problem and its variants as a rich source of problems and ideas that illustrate both the design and analysis of efficient algorithms. It covers the most recent structural and algorithmic work on stable matching problems, simplifies and unifies many earlier proofs, strengthens several earlier results, and presents new results and more efficient algorithms.The authors develop the structure of the set of stable matchings in the stable marriage problem in a more general and algebraic context than has been done previously; they discuss the problem's structure in terms of rings of sets, which allows many of the most useful features to be seen as features of a m...
Algorithms in Bioinformatics
We are pleased to present the proceedings of the Second Workshop on Al- rithms in Bioinformatics (WABI 2002), which took place on September 17-21, 2002 in Rome, Italy. The WABI workshop was part of a three-conference me- ing, which, in addition to WABI, included the ESA and APPROX 2002. The three conferences are jointly called ALGO 2002, and were hosted by the F- ulty of Engineering, University of Rome “La Sapienza”. Seehttp://www.dis. uniroma1.it/ ̃algo02 for more details. The Workshop on Algorithms in Bioinformatics covers research in all areas of algorithmic work in bioinformatics and computational biology. The emphasis is on discrete algorithms that address important problems in mol...
Combinatorial Pattern Matching
This book constitutes the refereed proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching, CPM 2000, held in Montreal, Canada, in June 2000.The 29 revised full papers presented together with 3 invited contributions and 2 tutorial lectures were carefully reviewed and selected from 44 submissions. The papers are devoted to current theoretical and algorithmic issues of searching and matching strings and more complicated patterns such as trees, regular expression graphs, point sets and arrays as well as to advanced applications of CPM in areas such as Internet, computational biology, multimedia systems, information retrieval, data compression, and pattern recognition.
Topological Data Analysis for Genomics and Evolution
An introduction to geometric and topological methods to analyze large scale biological data; includes statistics and genomic applications.
Algorithmics of Matching Under Preferences
Matching problems with preferences are all around us OCo they arise when agents seek to be allocated to one another on the basis of ranked preferences over potential outcomes. Efficient algorithms are needed for producing matchings that optimise the satisfaction of the agents according to their preference lists.In recent years there has been a sharp increase in the study of algorithmic aspects of matching problems with preferences, partly reflecting the growing number of applications of these problems worldwide. This book describes the most important results in this area, providing a timely update to The Stable Marriage Problem: Structure and Algorithms (D Gusfield and R W Irving, MIT Press, 1989) in connection with stable matching problems, whilst also broadening the scope to include matching problems with preferences under a range of alternative optimality criteria."
