Download or read book Combinatorial Optimization and Application to DNA Sequence Analysis written by Kapil Gupta and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: With recent and continuing advances in bioinformatics, the volume of sequence data has increased tremendously. Along with this increase, there is a growing need to develop efficient algorithms to process such data in order to make useful and important discoveries. Careful analysis of genomic data will benefit science and society in numerous ways, including the understanding of protein sequence functions, early detection of diseases, and finding evolutionary relationships that exist among various organisms. Most sequence analysis problems arising from computational genomics and evolutionary biology fall into the class of NP-complete problems. Advances in exact and approximate algorithms to address these problems are critical. In this thesis, we investigate a novel graph theoretical model that deals with fundamental evolutionary problems. The model allows incorporation of the evolutionary operations ``insertion', ``deletion', and ``substitution', and various parameters such as relative distances and weights. By varying appropriate parameters and weights within the model, several important combinatorial problems can be represented, including the weighted supersequence, weighted superstring, and weighted longest common sequence problems. Consequently, our model provides a general computational framework for solving a wide variety of important and difficult biological sequencing problems, including the multiple sequence alignment problem, and the problem of finding an evolutionary ancestor of multiple sequences. In this thesis, we develop large scale combinatorial optimization techniques to solve our graph theoretical model. In particular, we formulate the problem as two distinct but related models: constrained network flow problem and weighted node packing problem. The integer programming models are solved in a branch and bound setting using simultaneous column and row generation. The methodology developed will also be useful to solve large scale integer programming problems arising in other areas such as transportation and logistics.

Download or read book Computational Methods for Next Generation Sequencing Data Analysis written by Ion Mandoiu and published by John Wiley & Sons. This book was released on 2016-09-12 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.

Download or read book Combinatorial Optimization and Applications written by Andreas Dress and published by Springer. This book was released on 2007-08-29 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Running to almost 400 pages, and featuring more than 40 papers, this work on combinatorial optimization and applications will be seen as an important addition to the literature. It constitutes the refereed proceedings of the first International Conference on Combinatorial Optimization and Applications, COCOA 2007, held in Xi'an, China in August of that year. The 29 revised full papers presented together with 8 invited papers and 2 invited presentations were carefully reviewed and selected from 114 submissions and cover both theoretical issues and practical applications.

Download or read book Combinatorial Data Analysis written by Lawrence Hubert and published by SIAM. This book was released on 2001-01-01 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combinatorial data analysis refers to methods for the study of data sets where the arrangement of objects is central.

Download or read book Combinatorial Pattern Matching written by Martin Farach-Colton and published by Springer Science & Business Media. This book was released on 1998-07-08 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a fair overview of the basic problems in Solar Physics. The authors address not only the physics that is well understood but also discuss many open questions. The lecturers' involvement in the SOHO mission guarantees a modern and up-to-date analysis of observational data and makes this volume an extremely valuable source for further research.

Download or read book Applied Combinatorics Third Edition written by Fred S. Roberts and published by CRC Press. This book was released on 2024-06-03 with total page 757 pages. Available in PDF, EPUB and Kindle. Book excerpt: The third edition of this popular text presents the tools of combinatorics for a first undergraduate course. After introducing fundamental counting rules, tools of graph theory and relations, the focus is on three basic problems of combinatorics: counting, existence, and optimization problems.

Download or read book Combinatorial Optimization and Applications written by Peter Widmayer and published by Springer. This book was released on 2013-11-21 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 7th International Conference on Combinatorial Optimization and Applications, COCOA 2013, held in Chengdu, China, in December 2013. The 36 full papers presented were carefully reviewed and selected from 72 submissions. The papers feature original research in the areas of combinatorial optimization and its applications. In addition to theoretical results there are reports on experimental and applied research of general algorithmic interest.

Download or read book Optimization Techniques for Solving Complex Problems written by Enrique Alba and published by John Wiley & Sons. This book was released on 2009-03-23 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: Real-world problems and modern optimization techniques to solve them Here, a team of international experts brings together core ideas for solving complex problems in optimization across a wide variety of real-world settings, including computer science, engineering, transportation, telecommunications, and bioinformatics. Part One—covers methodologies for complex problem solving including genetic programming, neural networks, genetic algorithms, hybrid evolutionary algorithms, and more. Part Two—delves into applications including DNA sequencing and reconstruction, location of antennae in telecommunication networks, metaheuristics, FPGAs, problems arising in telecommunication networks, image processing, time series prediction, and more. All chapters contain examples that illustrate the applications themselves as well as the actual performance of the algorithms.?Optimization Techniques for Solving Complex Problems is a valuable resource for practitioners and researchers who work with optimization in real-world settings.

Download or read book Combinatorial Optimization and Applications written by Weili Wu and published by Springer Science & Business Media. This book was released on 2010-12-09 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 4th International Conference on Combinatorial Optimization and Applications, COCOA 2010, held in Kailua-Kona, HI, USA, in December 2010. The 49 revised full papers were carefully reviewed and selected from 108 submissions.

Download or read book Applications of Combinatorial Optimization written by Vangelis Th. Paschos and published by John Wiley & Sons. This book was released on 2014-09-15 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aim to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization. Concepts of Combinatorial Optimization, is divided into three parts: - On the complexity of combinatorial optimization problems, presenting basics about worst-case and randomized complexity; - Classical solution methods, presenting the two most-known methods for solving hard combinatorial optimization problems, that are Branch-and-Bound and Dynamic Programming; - Elements from mathematical programming, presenting fundamentals from mathematical programming based methods that are in the heart of Operations Research since the origins of this field.

Download or read book Combinatorial Optimization written by Bernhard Korte and published by Springer. This book was released on 2018-03-13 with total page 701 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive textbook on combinatorial optimization places special emphasis on theoretical results and algorithms with provably good performance, in contrast to heuristics. It is based on numerous courses on combinatorial optimization and specialized topics, mostly at graduate level. This book reviews the fundamentals, covers the classical topics (paths, flows, matching, matroids, NP-completeness, approximation algorithms) in detail, and proceeds to advanced and recent topics, some of which have not appeared in a textbook before. Throughout, it contains complete but concise proofs, and also provides numerous exercises and references. This sixth edition has again been updated, revised, and significantly extended. Among other additions, there are new sections on shallow-light trees, submodular function maximization, smoothed analysis of the knapsack problem, the (ln 4+ɛ)-approximation for Steiner trees, and the VPN theorem. Thus, this book continues to represent the state of the art of combinatorial optimization.

Download or read book Combinatorial Optimization and Applications written by Zhao Zhang and published by Springer. This book was released on 2014-11-13 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 8th International Conference on Combinatorial Optimization and Applications, COCOA 2014, held on the island of Maui, Hawaii, USA, in December 2014. The 56 full papers included in the book were carefully reviewed and selected from 133 submissions. Topics covered include classic combinatorial optimization; geometric optimization; network optimization; optimization in graphs; applied optimization; CSoNet; and complexity, cryptography, and games.

Download or read book Combinatorial Optimization and Applications written by Andreas Dress and published by Springer Science & Business Media. This book was released on 2007-07-25 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Running to almost 400 pages, and featuring more than 40 papers, this work on combinatorial optimization and applications will be seen as an important addition to the literature. It constitutes the refereed proceedings of the first International Conference on Combinatorial Optimization and Applications, COCOA 2007, held in Xi'an, China in August of that year. The 29 revised full papers presented together with 8 invited papers and 2 invited presentations were carefully reviewed and selected from 114 submissions and cover both theoretical issues and practical applications.

Download or read book Applied Combinatorics written by Fred Roberts and published by CRC Press. This book was released on 2009-06-03 with total page 889 pages. Available in PDF, EPUB and Kindle. Book excerpt: Now with solutions to selected problems, Applied Combinatorics, Second Edition presents the tools of combinatorics from an applied point of view. This bestselling textbook offers numerous references to the literature of combinatorics and its applications that enable readers to delve more deeply into the topics.After introducing fundamental counting

Download or read book Dynamic Programming Multi Objective Combinatorial Optimization written by Michal Mankowski and published by Springer. This book was released on 2022-02-10 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces a fairly universal approach to the design and analysis of exact optimization algorithms for multi-objective combinatorial optimization problems. It proposes the circuits without repetitions representing the sets of feasible solutions along with the increasing and strictly increasing cost functions as a model for such problems. The book designs the algorithms for multi-stage and bi-criteria optimization and for counting the solutions in the framework of this model. As applications, this book studies eleven known combinatorial optimization problems: matrix chain multiplication, global sequence alignment, optimal paths in directed graphs, binary search trees, convex polygon triangulation, line breaking (text justification), one-dimensional clustering, optimal bitonic tour, segmented least squares, optimization of matchings in trees, and 0/1 knapsack problem. The results presented are useful for researchers in combinatorial optimization. This book is also useful as the basis for graduate courses.

Download or read book Analysis and Design of Algorithms for Combinatorial Problems written by G. Ausiello and published by Elsevier. This book was released on 1985-05-01 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combinatorial problems have been from the very beginning part of the history of mathematics. By the Sixties, the main classes of combinatorial problems had been defined. During that decade, a great number of research contributions in graph theory had been produced, which laid the foundations for most of the research in graph optimization in the following years. During the Seventies, a large number of special purpose models were developed. The impressive growth of this field since has been strongly determined by the demand of applications and influenced by the technological increases in computing power and the availability of data and software. The availability of such basic tools has led to the feasibility of the exact or well approximate solution of large scale realistic combinatorial optimization problems and has created a number of new combinatorial problems.

Download or read book Automated DNA Sequencing and Analysis written by Mark D. Adams and published by Elsevier. This book was released on 2012-12-02 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely book for DNA researchers, Automated DNA Sequencing and Analysis reviews and assesses the state of the art of automated DNA sequence analysis-from the construction of clone libraries to the developmentof laboratory and community databases. It presents the methodologies and strategies of automated DNA sequence analysis in a way that allows them to be compared and contrasted. By taking a broad view of the process of automated sequence analysis, the present volume bridges the gap between the protocols supplied with instrument and reaction kits and the finalized data presented in the research literature. It will be an invaluable aid to both small laboratories that are interested in taking maximum advantageof automated sequence resources and to groups pursuing large-scale cDNA and genomic sequencing projects. The field of automation in DAN sequencing and analysis is rapidly moving, this book fulfils those needs, reviews the history of the art and provides pointers to future development.