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The de Bruijn graph was defined in 1949 to enumerate the number of closed sequences where each n-tuple appears exactly once as a window in a sequence. Through the years, the graph and its sequences have found numerous applications – in space technology, wireless communication, cryptography, parallel computation, genome assembly, DNA storage, and microbiome research, among others. Sequences and the de Bruijn Graph: Properties, Constructions, and Applications explores the foundations of theoretical mathematical concepts and the important applications to computer science, electrical engineering, and bioinformatics. The book introduces the various concepts, ideas, and techniques associated with the use of the de Bruijn Graph, providing comprehensive coverage of sequence classification, one-dimensional and two-dimensional applications, graphs, interconnected networks, layouts, and embedded systems. Researchers, graduate students, professors, and professionals working in the fields of applied mathematics, electrical engineering, computer science and bioinformatics will find this book useful. Investigates computational and engineering applications associated with the de Bruijn graph, its sequences, and their generalization Explores one-dimensional and two-dimensional sequences with special properties and their various properties and applications Introduces the rich structure of the de Bruijn graph and its sequences, in both mathematical theory and its applications to computing and engineering problems
The refereed proceedings from the 7th International Workshop on Algorithms in Bioinformatics are provided in this volume. Papers address current issues in algorithms in bioinformatics, ranging from mathematical tools to experimental studies of approximation algorithms to significant computational analyses. Biological problems examined include genetic mapping, sequence alignment and analysis, phylogeny, comparative genomics, and protein structure.
Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.
"Magical Mathematics reveals the secrets of amazing, fun-to-perform card tricks--and the profound mathematical ideas behind them--that will astound even the most accomplished magician. Persi Diaconis and Ron Graham provide easy, step-by-step instructions for each trick, explaining how to set up the effect and offering tips on what to say and do while performing it. Each card trick introduces a new mathematical idea, and varying the tricks in turn takes readers to the very threshold of today's mathematical knowledge. For example, the Gilbreath principle--a fantastic effect where the cards remain in control despite being shuffled--is found to share an intimate connection with the Mandelbrot set. Other card tricks link to the mathematical secrets of combinatorics, graph theory, number theory, topology, the Riemann hypothesis, and even Fermat's last theorem. Diaconis and Graham are mathematicians as well as skilled performers with decades of professional experience between them. In this book they share a wealth of conjuring lore, including some closely guarded secrets of legendary magicians. Magical Mathematics covers the mathematics of juggling and shows how the I Ching connects to the history of probability and magic tricks both old and new. It tells the stories--and reveals the best tricks--of the eccentric and brilliant inventors of mathematical magic. Magical Mathematics exposes old gambling secrets through the mathematics of shuffling cards, explains the classic street-gambling scam of three-card monte, traces the history of mathematical magic back to the thirteenth century and the oldest mathematical trick--and much more"-
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.
Contains 130 papers, which were selected based on originality, technical contribution, and relevance. Although the papers were not formally refereed, every attempt was made to verify the main claims. It is expected that most will appear in more complete form in scientific journals. The proceedings also includes the paper presented by invited plenary speaker Ronald Graham, as well as a portion of the papers presented by invited plenary speakers Udi Manber and Christos Papadimitriou.
This volume constitutes the refereed proceedings of the 26th International Symposium on String Processing and Information Retrieval, SPIRE 2019, held in Segovia, Spain, in October 2019. The 28 full papers and 8 short papers presented in this volume were carefully reviewed and selected from 59 submissions. They cover topics such as: data compression; information retrieval; string algorithms; algorithms; computational biology; indexing and compression; and compressed data structures.
This book constitutes the refereed proceedings of the Brazilian Symposium on Bioinformatics, BSB 2020, held in São Paulo, Brazil, in November 2020. Due to COVID-19 pandemic the conference was held virtually The 20 revised full papers and 5 short papers were carefully reviewed and selected from 45 submissions. The papers address a broad range of current topics in computational biology and bioinformatics.
This is the second edition of a popular book on combinatorics, a subject dealing with ways of arranging and distributing objects, and which involves ideas from geometry, algebra and analysis. The breadth of the theory is matched by that of its applications, which include topics as diverse as codes, circuit design and algorithm complexity. It has thus become essential for workers in many scientific fields to have some familiarity with the subject. The authors have tried to be as comprehensive as possible, dealing in a unified manner with, for example, graph theory, extremal problems, designs, colorings and codes. The depth and breadth of the coverage make the book a unique guide to the whole of the subject. The book is ideal for courses on combinatorical mathematics at the advanced undergraduate or beginning graduate level. Working mathematicians and scientists will also find it a valuable introduction and reference.
Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Online Open Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors' acclaimed online course (http://coursera.org/course/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of biology and computer science students alike.Each chapter begins with a central biological question, such as "Are There Fragile Regions in the Human Genome?" or "Which DNA Patterns Play the Role of Molecular Clocks?" and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on Rosalind (http://rosalind.info), an online platform for learning bioinformatics.The textbook website (http://bioinformaticsalgorithms.org) directs readers toward additional educational materials, including video lectures and PowerPoint slides.