Download or read book On the Algorithmic Tractability of Single Nucleotide Polymorphism SNP Analysis and Related Problems written by Sebastian Wernicke and published by diplom.de. This book was released on 2014-04-02 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: Inhaltsangabe:Abstract: This work brings together two areas of science biology and informatics that have only recently been connected in the emerging (and vastly growing) research field of Bioinformatics. In order to achieve a common basis for Parts 2 and 3 of this work, Part 1 intends to introduce the computer scientist to the relevant biological background and terminology (Chapter 2), and to familiarize the biologist with the relevant topics from theoretical computer science (Chapter 3). Chapter 2 first introduces some terminology from the field of genetics, thereby defining SNPs. We then motivate the analysis of SNPs by two applications, i.e. the analysis of evolutionary development and the field of pharmacogenetics. Especially the field of pharmacogenetics is capable of having an enormous impact on medicine and the pharmaceutical industry in the near future by using SNP data to predict the efficacy of medication. Chapter 3 gives a brief introduction to the field of computational complexity. We will see and motivate how algorithms are analyzed in theoretical computer science. This will lead to the definition of complexity classes , introducing the class NP which includes computationally hard problems. Some of the hard problems in the class NP can be solved efficiently using the tool of fixed-parameter tractability, introduced at the end of this chapter. An important application of SNP data is in the analysis of the evolutionary history of species development (phylogenetic analysis part two chapters 4 and 5). As will be made plausible in Chapter 5 using SNP data is in many ways superior to previous approaches of phylogenetic analysis. In order to analyze the development of species using SNP data, an underlying model of evolution must be specified. A popular model is the so-called perfect phylogeny, but the construction of this phylogeny is a computationally hard problem when there are inconsistencies (such as read-errors or an imperfect .t to the model of perfect phylogeny) in the underlying data. Chapter 4 analyzes the problem of forbidden submatrix removal which is closely connected to constructing perfect phylogenies we will see in Chapter 5 that its computational complexity is directly related to that of constructing a perfect phylogeny from data which is partially erroneous. In this chapter, we analyze the algorithmic tractability of forbidden submatrix removal , characterizing cases where this problem is NP-complete (being [...]

Download or read book Prioritizing SNPs for Disease gene Association Studies written by Phil Hyoun Lee and published by . This book was released on 2009 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: Identifying single nucleotide polymorphisms (SNPs) that are involved in common and complex diseases, such as cancer, is a major challenge in current molecular epidemiology. Knowledge of such SNPs is expected to enable timely diagnosis, effective treatment, and, ultimately, prevention of human disease. However, the tremendous number of SNPs on the human genome, which is estimated at more than eleven million, poses challenges to obtain and analyze the information of all the SNPs. In this thesis we address the problem of selecting representative SNP markers for supporting effective disease-gene association studies. Our goal is to facilitate the genotyping and analysis procedure, associated with such studies, by providing effective prioritization methods for SNP markers based on both their allele information and functional significance. However, the problem of SNP selection has been proven to be NP-hard in general, and current selection methods impose certain restrictions and use heuristics for reducing the complexity of the problem. We thus aim to develop new heuristic algorithms and systems to advance the state-of-the-art, while relaxing the restrictions. To address this challenge, we formulate several SNP selection problems and present novel algorithms and a database system based on the two major SNP selection approaches: tag SNP selection and functional SNP selection. Furthermore, we describe an innovative approach to combine both tag SNP selection and functional SNP selection into one unified selection process. We demonstrate the improved performance of all the proposed methods using comparative studies.

Download or read book Experimental and Efficient Algorithms written by Sotiris Nikoletseas and published by Springer Science & Business Media. This book was released on 2005-04-28 with total page 637 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 4th International Workshop on Experimental and Efficient Algorithms, WEA 2005, held in Santorini Island, Greece in May 2005. The 47 revised full papers and 7 revised short papers presented together with extended abstracts of 3 invited talks were carefully reviewed and selected from 176 submissions. The book is devoted to the design, analysis, implementation, experimental evaluation, and engineering of efficient algorithms. Among the application areas addressed are most fields applying advanced algorithmic techniques, such as combinatorial optimization, approximation, graph theory, discrete mathematics, scheduling, searching, sorting, string matching, coding, networking, data mining, data analysis, etc.

Download or read book Parameterized and Exact Computation written by Dániel Marx and published by Springer. This book was released on 2012-03-09 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed post-conference proceedings of the 6th International Symposium on Parameterized and Exact Computation, IPEC 2011, in Saarbrücken, Germany, in September 2011. The 21 revised full papers presented were carefully reviewed and selected from 40 submissions. The topics addressed cover research in all aspects of parameterized and exact computation and complexity, including but not limited to new techniques for the design and analysis of parameterized and exact algorithms, fixed-parameter tractability results, parameterized complexity theory, relationship between parameterized complexity and traditional complexity classifications, applications of parameterized and exact computation, and implementation issues of parameterized and exact algorithms.

Download or read book Algorithms and Data Structures written by Frank Dehne and published by Springer Science & Business Media. This book was released on 2005-08-04 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 9th International Workshop on Algorithms and Data Structures, WADS 2005, held in Waterloo, Canada, in August 2005. The 37 revised full papers presented were carefully reviewed and selected from 90 submissions. A broad variety of topics in algorithmics and data structures is addressed including searching and sorting, approximation, graph and network computations, computational geometry, randomization, communications, combinatorial optimization, scheduling, routing, navigation, coding, and pattern matching.

Download or read book Theory and Applications of Models of Computation written by Manindra Agrawal and published by Springer. This book was released on 2008-04-30 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: This proceedings volume examines all major areas in computer science, mathematics (especially logic) and the physical sciences, especially computation, algorithms, complexity and computability theory.

Download or read book Bioinformatics Research and Applications written by Mark Borodovsky and published by Springer Science & Business Media. This book was released on 2010-05-06 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume constitutes the refereed proceedings of the 6th International Symposium on Bioinformatics Research and Applications, ISBRA 2010, held in Storrs, CT, USA, in May 2010. The 20 revised full papers and 6 invited talks presented were carefully reviewed and selected out of 57 submissions. Topics presented span all areas of bioinformatics and computational biology, including the development of experimental or commercial systems.

Download or read book Fundamentals of Parameterized Complexity written by Rodney G. Downey and published by Springer Science & Business Media. This book was released on 2013-12-03 with total page 765 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive and self-contained textbook presents an accessible overview of the state of the art of multivariate algorithmics and complexity. Increasingly, multivariate algorithmics is having significant practical impact in many application domains, with even more developments on the horizon. The text describes how the multivariate framework allows an extended dialog with a problem, enabling the reader who masters the complexity issues under discussion to use the positive and negative toolkits in their own research. Features: describes many of the standard algorithmic techniques available for establishing parametric tractability; reviews the classical hardness classes; explores the various limitations and relaxations of the methods; showcases the powerful new lower bound techniques; examines various different algorithmic solutions to the same problems, highlighting the insights to be gained from each approach; demonstrates how complexity methods and ideas have evolved over the past 25 years.

Download or read book SOFSEM 2004 Theory and Practice of Computer Science written by Peter Van Emde Boas and published by Springer. This book was released on 2003-12-22 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 30th Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2004, held in Mern, Czech Republic, in January 2004. The volume presents 10 invited lectures and 22 full papers selected from 136 submissions. Among the topics covered are computer science theory, programming theory, database systems, information systems, cognitive technologies and Web technologies.

Download or read book SOFSEM 2004 Theory and Practice of Computer Science written by P. van Emde Boas and published by Springer Science & Business Media. This book was released on 2004-01-14 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 30th Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2004, held in Merín, Czech Republic, in January 2004. The volume presents 10 invited lectures and 22 full papers selected from 136 submissions. Among the topics covered are computer science theory, programming theory, database systems, information systems, cognitive technologies and Web technologies.

Download or read book Experimental and Efficient Algorithms written by and published by . This book was released on 2005 with total page 656 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Algorithms and Data Structures written by and published by . This book was released on 2005 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book SOFSEM written by and published by . This book was released on 2004 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Analysis of Complex Disease Association Studies written by Eleftheria Zeggini and published by Academic Press. This book was released on 2010-11-17 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: According to the National Institute of Health, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. Whole genome information, when combined with clinical and other phenotype data, offers the potential for increased understanding of basic biological processes affecting human health, improvement in the prediction of disease and patient care, and ultimately the realization of the promise of personalized medicine. In addition, rapid advances in understanding the patterns of human genetic variation and maturing high-throughput, cost-effective methods for genotyping are providing powerful research tools for identifying genetic variants that contribute to health and disease. This burgeoning science merges the principles of statistics and genetics studies to make sense of the vast amounts of information available with the mapping of genomes. In order to make the most of the information available, statistical tools must be tailored and translated for the analytical issues which are original to large-scale association studies. Analysis of Complex Disease Association Studies will provide researchers with advanced biological knowledge who are entering the field of genome-wide association studies with the groundwork to apply statistical analysis tools appropriately and effectively. With the use of consistent examples throughout the work, chapters will provide readers with best practice for getting started (design), analyzing, and interpreting data according to their research interests. Frequently used tests will be highlighted and a critical analysis of the advantages and disadvantage complimented by case studies for each will provide readers with the information they need to make the right choice for their research. Additional tools including links to analysis tools, tutorials, and references will be available electronically to ensure the latest information is available. - Easy access to key information including advantages and disadvantage of tests for particular applications, identification of databases, languages and their capabilities, data management risks, frequently used tests - Extensive list of references including links to tutorial websites - Case studies and Tips and Tricks

Download or read book Theory and Applications of Models of Computation written by Jianer Chen and published by Springer. This book was released on 2009-05-12 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 6th International Conference on Theory and Applications of Models of Computation, TAMC 2009, held in Changsha, China in May 2009. The 39 full papers presented together with 7 invited papers as well as 3 plenary talks were selected from 86 submissions. The papers address the three main themes of the conference which were Computability, Complexity, and Algorithms. The conference aimed to bring together researchers with interests in theoretical computer science, algorithmic mathematics, and applications to the physical sciences.

Download or read book Genome Research written by and published by . This book was released on 2008 with total page 1494 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Bioinformatics and Computational Biology written by Sanguthevar Rajasekaran and published by Springer Science & Business Media. This book was released on 2009-03-27 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the First International on Bioinformatics and Computational Biology, BICoB 2007, held in New Orleans, LA, USA, in April 2007. The 30 revised full papers presented together with 10 invited lectures were carefully reviewed and selected from 72 initial submissions. The papers address current research in the area of bioinformatics and computational biology fostering the advancement of computing techniques and their application to life sciences in topics such as genome analysis sequence analysis, phylogenetics, structural bioinformatics, analysis of high-throughput biological data, genetics and population analysis, as well as systems biology.