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Suffix arrays: A new method for online string searches
, 1991
"... A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that ..."
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Cited by 827 (0 self)
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A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees
Database resources of the National Center for Biotechnology Information
 Nucleic Acids Res
, 2008
"... In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez, ..."
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Cited by 964 (15 self)
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In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez,
A Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
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Cited by 584 (38 self)
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We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices according to each case. We conclude with some future work directions and open problems.
Genetic Programming
, 1997
"... Introduction Genetic programming is a domainindependent problemsolving approach in which computer programs are evolved to solve, or approximately solve, problems. Genetic programming is based on the Darwinian principle of reproduction and survival of the fittest and analogs of naturally occurring ..."
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Cited by 1051 (12 self)
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Introduction Genetic programming is a domainindependent problemsolving approach in which computer programs are evolved to solve, or approximately solve, problems. Genetic programming is based on the Darwinian principle of reproduction and survival of the fittest and analogs of naturally occurring genetic operations such as crossover (sexual recombination) and mutation. John Holland's pioneering Adaptation in Natural and Artificial Systems (1975) described how an analog of the evolutionary process can be applied to solving mathematical problems and engineering optimization problems using what is now called the genetic algorithm (GA). The genetic algorithm attempts to find a good (or best) solution to the problem by genetically breeding a population of individuals over a series of generations. In the genetic algorithm, each individual in the population represents a candidate solut
Parameterized Complexity
, 1998
"... the rapidly developing systematic connections between FPT and useful heuristic algorithms  a new and exciting bridge between the theory of computing and computing in practice. The organizers of the seminar strongly believe that knowledge of parameterized complexity techniques and results belongs ..."
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Cited by 1218 (75 self)
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the rapidly developing systematic connections between FPT and useful heuristic algorithms  a new and exciting bridge between the theory of computing and computing in practice. The organizers of the seminar strongly believe that knowledge of parameterized complexity techniques and results belongs into the toolkit of every algorithm designer. The purpose of the seminar was to bring together leading experts from all over the world, and from the diverse areas of computer science that have been attracted to this new framework. The seminar was intended as the rst larger international meeting with a specic focus on parameterized complexity, and it hopefully serves as a driving force in the development of the eld. 1 We had 49 participants from Australia, Canada, India, Israel, New Zealand, USA, and various European countries. During the workshop 25 lectures were given. Moreover, one night session was devoted to open problems and Thursday was basically used for problem discussion
Bayes Factors
, 1995
"... In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null ..."
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Cited by 1766 (74 self)
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In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is onehalf. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology and psychology.
Limma: linear models for microarray data
 Bioinformatics and Computational Biology Solutions using R and Bioconductor
, 2005
"... This free opensource software implements academic research by the authors and coworkers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.Contents ..."
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Cited by 759 (13 self)
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This free opensource software implements academic research by the authors and coworkers. If you use it, please support the project by citing the appropriate journal articles listed in Section 2.1.Contents
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fields, including bioinformatics, communication theory, statistical physics, combinatorial optimization, signal and image processing, information retrieval and statistical machine learning. Many problems that arise in specific instances — including the key problems of computing marginals and modes of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing likelihoods, marginal probabilities and most probable configurations. We describe how a wide varietyof algorithms — among them sumproduct, cluster variational methods, expectationpropagation, mean field methods, maxproduct and linear programming relaxation, as well as conic programming relaxations — can all be understood in terms of exact or approximate forms of these variational representations. The variational approach provides a complementary alternative to Markov chain Monte Carlo as a general source of approximation methods for inference in largescale statistical models.
Constraint Logic Programming: A Survey
"... Constraint Logic Programming (CLP) is a merger of two declarative paradigms: constraint solving and logic programming. Although a relatively new field, CLP has progressed in several quite different directions. In particular, the early fundamental concepts have been adapted to better serve in differe ..."
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Cited by 864 (25 self)
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Constraint Logic Programming (CLP) is a merger of two declarative paradigms: constraint solving and logic programming. Although a relatively new field, CLP has progressed in several quite different directions. In particular, the early fundamental concepts have been adapted to better serve in different areas of applications. In this survey of CLP, a primary goal is to give a systematic description of the major trends in terms of common fundamental concepts. The three main parts cover the theory, implementation issues, and programming for applications.
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