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Combinatorial Pattern Matching
This book constitutes the refereed proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching, CPM 2006, held in Barcelona, Spain in July 2006. The 33 revised full papers presented together with 3 invited talks were carefully reviewed and selected from 88 submissions. The papers are organized in topical sections on data structures, indexing data structures, probabilistic and algebraic techniques, applications in molecular biology, string matching, data compression, and dynamic programming.
Language and Automata Theory and Applications
This book constitutes the refereed proceedings of the Third International Conference on Language and Automata Theory and Applications, LATA 2009, held in Tarragona, Spain, in April 2009. The 58 revised full papers presented together with 3 invited lectures and two tutorials were carefully reviewed and selected from 121 submissions. The papers address all the various issues related to automata theory and formal languages.
Models and Methods for Biological Evolution
Biological evolution is the phenomenon concerning how species are born, are transformed or disappear over time. Its study relies on sophisticated methods that involve both mathematical modeling of the biological processes at play and the design of efficient algorithms to fit these models to genetic and morphological data. Models and Methods for Biological Evolution outlines the main methods to study evolution and provides a broad overview illustrating the variety of formal approaches used, notably including combinatorial optimization, stochastic models and statistical inference techniques. Some of the most relevant applications of these methods are detailed, concerning, for example, the study of migratory events of ancient human populations or the progression of epidemics. This book should thus be of interest to applied mathematicians interested in central problems in biology, and to biologists eager to get a deeper understanding of widely used techniques of evolutionary data analysis.
Rewriting Techniques and Applications
This book constitutes the refereed proceedings of the 10th International Conference on Rewriting Techniques and Applications, RTA-99, held in Trento, Italy in July 1999 as part of FLoC'99. The 23 revised full papers presented were carefully selected from a total of 53 submissions. Also included are four system descriptions as well as three invited contributions. Among the topics covered are constraint solving, termination, deduction and higher order rewriting, graphs, complexity, tree automata, context-sensitive rewriting, string rewriting and numeration systems, etc.
Biological Data Integration
The study of biological data is constantly undergoing profound changes. Firstly, the volume of data available has increased considerably due to new high throughput techniques used for experiments. Secondly, the remarkable progress in both computational and statistical analysis methods and infrastructures has made it possible to process these voluminous data. The resulting challenge concerns our ability to integrate these data, i.e. to use their complementary nature effectively in the hope of advancing our knowledge. Therefore, a major challenge in studying biology today is integrating data for the most exhaustive analysis possible. Biological Data Integration deals in a pedagogical way with research work in biological data science, examining both computational approaches to data integration and statistical approaches to the integration of omics data
Fundamentals of Computation Theory
This book constitutes the refereed proceedings of the 17th International Symposium Fundamentals of Computation Theory, FCT 2009, held in Wroclaw, Poland in August 2009. The 29 revised full papers were carefully reviewed and selected from 67 submissions. The papers address all current topics in computation theory such as automata and formal languages, design and analysis of algorithms, computational and structural complexity, semantics, logic, algebra and categories in computer science, circuits and networks, learning theory, specification and verification, parallel and distributed systems, concurrency theory, cryptography and cryptograhic protocols, approximation and randomized algorithms, computational geometry, quantum computation and information, bio-inspired computation.
Combinatorial Pattern Matching
This volume features select refereed proceedings from the 18th Annual Symposium on Combinatorial Pattern Matching. Collectively, the papers provide great insights into the most recent advances in combinatorial pattern matching. They are organized into topical sections covering algorithmic techniques, approximate pattern matching, data compression, computational biology, pattern analysis, suffix arrays and trees, and algorithmic techniques.
Comparative Genomics
This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel. The volume is intended for molecular biologists, biochemists and geneticists.
From Sequences to Graphs
In order to study living organisms, scientists not only study them at an overall macroscopic scale but also on a more detailed microscopic scale. This observation, pushed to its limits, consists of investigating the very center of each cell, where we find the molecules that determine the way it functions: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). In an organism, DNA carries the genetic information, which is called the genome. It is represented as four-letter sequences using the letters A, C, G and T; based on these sequences, computer methods described in this book can answer fundamental questions in bioinformatics. This book explores how to quickly find sequences of a few hundred nucleotides within a genome that may be made up of several billion, how to compare those sequences and how to reconstruct the complete sequence of a genome. It also discusses the problems of identifying bacteria in a given environment and predicting the structure of RNA based on its sequence.
