Distributed and Sequential Algorithms for Bioinformatics
Distributed and Sequential Algorithms for Bioinformatics

Author: Kayhan Erciyes

Publisher: Springer

Published: 2015-10-31

Total Pages: 376

ISBN-13: 3319249665

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This unique textbook/reference presents unified coverage of bioinformatics topics relating to both biological sequences and biological networks, providing an in-depth analysis of cutting-edge distributed algorithms, as well as of relevant sequential algorithms. In addition to introducing the latest algorithms in this area, more than fifteen new distributed algorithms are also proposed. Topics and features: reviews a range of open challenges in biological sequences and networks; describes in detail both sequential and parallel/distributed algorithms for each problem; suggests approaches for distributed algorithms as possible extensions to sequential algorithms, when the distributed algorithms for the topic are scarce; proposes a number of new distributed algorithms in each chapter, to serve as potential starting points for further research; concludes each chapter with self-test exercises, a summary of the key points, a comparison of the algorithms described, and a literature review.

Parallel Computing for Bioinformatics and Computational Biology
Parallel Computing for Bioinformatics and Computational Biology

Author: Albert Y. Zomaya

Publisher: John Wiley & Sons

Published: 2006-04-21

Total Pages: 817

ISBN-13: 0471718483

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Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.

Guide to Graph Algorithms
Guide to Graph Algorithms

Author: K Erciyes

Publisher: Springer

Published: 2018-04-13

Total Pages: 475

ISBN-13: 3319732358

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This clearly structured textbook/reference presents a detailed and comprehensive review of the fundamental principles of sequential graph algorithms, approaches for NP-hard graph problems, and approximation algorithms and heuristics for such problems. The work also provides a comparative analysis of sequential, parallel and distributed graph algorithms – including algorithms for big data – and an investigation into the conversion principles between the three algorithmic methods. Topics and features: presents a comprehensive analysis of sequential graph algorithms; offers a unifying view by examining the same graph problem from each of the three paradigms of sequential, parallel and distributed algorithms; describes methods for the conversion between sequential, parallel and distributed graph algorithms; surveys methods for the analysis of large graphs and complex network applications; includes full implementation details for the problems presented throughout the text; provides additional supporting material at an accompanying website. This practical guide to the design and analysis of graph algorithms is ideal for advanced and graduate students of computer science, electrical and electronic engineering, and bioinformatics. The material covered will also be of value to any researcher familiar with the basics of discrete mathematics, graph theory and algorithms.

Biological Sequence Analysis
Biological Sequence Analysis

Author: Richard Durbin

Publisher: Cambridge University Press

Published: 1998-04-23

Total Pages: 372

ISBN-13: 113945739X

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Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Algorithms for Computational Biology
Algorithms for Computational Biology

Author: María Botón-Fernández

Publisher: Springer

Published: 2016-06-11

Total Pages: 187

ISBN-13: 3319388274

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This book constitutes the proceedings of the Third InternationalConference on Algorithms for Computational Biology, AlCoB 2016, held inTrujillo, Spain, in June 2016. The 13 full papers presented in this volume were carefully reviewed andselected from 23 submissions. They are organized in the following topical sections: biological networks and modelling; biological structure processing; phylogenetics; and sequence analysis and rearrangement. In addition one invited talk is included.

Distributed Graph Algorithms for Computer Networks
Distributed Graph Algorithms for Computer Networks

Author: Kayhan Erciyes

Publisher: Springer Science & Business Media

Published: 2013-05-16

Total Pages: 328

ISBN-13: 1447151739

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This book presents a comprehensive review of key distributed graph algorithms for computer network applications, with a particular emphasis on practical implementation. Topics and features: introduces a range of fundamental graph algorithms, covering spanning trees, graph traversal algorithms, routing algorithms, and self-stabilization; reviews graph-theoretical distributed approximation algorithms with applications in ad hoc wireless networks; describes in detail the implementation of each algorithm, with extensive use of supporting examples, and discusses their concrete network applications; examines key graph-theoretical algorithm concepts, such as dominating sets, and parameters for mobility and energy levels of nodes in wireless ad hoc networks, and provides a contemporary survey of each topic; presents a simple simulator, developed to run distributed algorithms; provides practical exercises at the end of each chapter.

Bioinformatics of the Brain
Bioinformatics of the Brain

Author: Kayhan Erciyes

Publisher: CRC Press

Published: 2024-09-25

Total Pages: 305

ISBN-13: 1040117414

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The brain consisting of billions of neurons is probably the most complex and mysterious organ of the body. Understanding the functioning of the brain in its health and disease states has baffled the researchers working in this area for many years. The diversity of brain diseases and disorders makes the analysis of brain functions an even more challenging area of research. In vitro and in vivo studies regarding the brain may be laborious, however, bioinformatics using in silico approaches may take the burden off the experimental studies and give us a clearer perspective on disease and healthy states of the brain, its functions, and disease mechanisms. Recent advancements in neuroimaging technologies, the development of high-performance computers and the development of software, algorithms and methods to analyze data obtained from various neuroimaging processes have opened new frontiers in neuroscience enabling unprecedented finer analysis of the brain functions. This relatively new approach of brain analysis which may be termed Bioinformatics of the Brain is the main subject of this volume aiming to provide a thorough review of various bioinformatics approaches for analyzing the functioning of the brain and understanding brain diseases such as neurodegenerative diseases, brain tumors, and neuropsychiatric disorders. Authors from various disciplines in this volume each focus on a different aspect aiming to expand our understanding of this area of research. Topics included are: Brain diseases and disorders Stem cell therapy of neurodegenerative diseases Tissue engineering applications of gliomas Brain tumor detection and modeling Brain tumor growth simulation Brain-computer interface Bioinformatics of brain diseases Graph-theoretical analysis of complex brain networks Brain proteomics This book is intended to aid scientists, researchers, and graduate students in carrying out interdisciplinary research in the areas of bioinformatics, bioengineering, computer engineering, software engineering, mathematics, molecular biology, genetics, and biotechnology.

Next Generation Sequencing
Next Generation Sequencing

Author: Jerzy Kulski

Publisher: BoD – Books on Demand

Published: 2016-01-14

Total Pages: 466

ISBN-13: 9535122401

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Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

Systems and Computational Biology
Systems and Computational Biology

Author: Ning-Sun Yang

Publisher: BoD – Books on Demand

Published: 2011-09-12

Total Pages: 350

ISBN-13: 9533078758

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Whereas some "microarray" or "bioinformatics" scientists among us may have been criticized as doing "cataloging research", the majority of us believe that we are sincerely exploring new scientific and technological systems to benefit human health, human food and animal feed production, and environmental protections. Indeed, we are humbled by the complexity, extent and beauty of cross-talks in various biological systems; on the other hand, we are becoming more educated and are able to start addressing honestly and skillfully the various important issues concerning translational medicine, global agriculture, and the environment. The two volumes of this book present a series of high-quality research or review articles in a timely fashion to this emerging research field of our scientific community.

Discrete Mathematics and Graph Theory
Discrete Mathematics and Graph Theory

Author: K. Erciyes

Publisher: Springer Nature

Published: 2021-01-28

Total Pages: 345

ISBN-13: 3030611159

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This textbook can serve as a comprehensive manual of discrete mathematics and graph theory for non-Computer Science majors; as a reference and study aid for professionals and researchers who have not taken any discrete math course before. It can also be used as a reference book for a course on Discrete Mathematics in Computer Science or Mathematics curricula. The study of discrete mathematics is one of the first courses on curricula in various disciplines such as Computer Science, Mathematics and Engineering education practices. Graphs are key data structures used to represent networks, chemical structures, games etc. and are increasingly used more in various applications such as bioinformatics and the Internet. Graph theory has gone through an unprecedented growth in the last few decades both in terms of theory and implementations; hence it deserves a thorough treatment which is not adequately found in any other contemporary books on discrete mathematics, whereas about 40% of this textbook is devoted to graph theory. The text follows an algorithmic approach for discrete mathematics and graph problems where applicable, to reinforce learning and to show how to implement the concepts in real-world applications.