Discrete And Topological Models In Molecular Biology

Author : Nataša Jonoska,Masahico Saito
Publisher : Springer Science & Business Media
Page : 522 pages
File Size : 55,9 Mb
Release : 2013-12-23
Category : Computers
ISBN : 9783642401930

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Discrete and Topological Models in Molecular Biology by Nataša Jonoska,Masahico Saito Pdf

Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.

Author : Raina Robeva
Publisher : Academic Press
Page : 382 pages
File Size : 41,7 Mb
Release : 2015-05-09
Category : Mathematics
ISBN : 9780128012710

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Algebraic and Discrete Mathematical Methods for Modern Biology by Raina Robeva Pdf

Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. Examines significant questions in modern biology and their mathematical treatments Presents important mathematical concepts and tools in the context of essential biology Features material of interest to students in both mathematics and biology Presents chapters in modular format so coverage need not follow the Table of Contents Introduces projects appropriate for undergraduate research Utilizes freely accessible software for visualization, simulation, and analysis in modern biology Requires no calculus as a prerequisite Provides a complete Solutions Manual Features a companion website with supplementary resources

Author : Stephen M. Downes
Publisher : Routledge
Page : 115 pages
File Size : 50,7 Mb
Release : 2020-07-09
Category : Philosophy
ISBN : 9781317298069

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Models and Modeling in the Sciences by Stephen M. Downes Pdf

Biologists, climate scientists, and economists all rely on models to move their work forward. In this book, Stephen M. Downes explores the use of models in these and other fields to introduce readers to the various philosophical issues that arise in scientific modeling. Readers learn that paying attention to models plays a crucial role in appraising scientific work. This book first presents a wide range of models from a number of different scientific disciplines. After assembling some illustrative examples, Downes demonstrates how models shed light on many perennial issues in philosophy of science and in philosophy in general. Reviewing the range of views on how models represent their targets introduces readers to the key issues in debates on representation, not only in science but in the arts as well. Also, standard epistemological questions are cast in new and interesting ways when readers confront the question, "What makes for a good (or bad) model?" All examples from the sciences and positions in the philosophy of science are presented in an accessible manner. The book is suitable for undergraduates with minimal experience in philosophy and an introductory undergraduate experience in science. Key features: The book serves as a highly accessible philosophical introduction to models and modeling in the sciences, presenting all philosophical and scientific issues in a nontechnical manner. Students and other readers learn to practice philosophy of science by starting with clear examples taken directly from the sciences. While not comprehensive, this book introduces the reader to a wide range of views on key issues in the philosophy of science.

Author : Dan Gusfield
Publisher : MIT Press
Page : 601 pages
File Size : 45,9 Mb
Release : 2014-07-03
Category : Mathematics
ISBN : 9780262027526

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ReCombinatorics by Dan Gusfield Pdf

When a Philadelphia girl intercepts a message about an impending British attack against her father's regiment, commanded by General Washington, in White Marsh, she travels alone by horseback to warn the Patriot army.

Author : Elizabeth Spencer Allman,John A. Rhodes
Publisher : Cambridge University Press
Page : 388 pages
File Size : 54,8 Mb
Release : 2004
Category : Mathematics
ISBN : 0521525861

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Mathematical Models in Biology by Elizabeth Spencer Allman,John A. Rhodes Pdf

This introductory textbook on mathematical biology focuses on discrete models across a variety of biological subdisciplines. Biological topics treated include linear and non-linear models of populations, Markov models of molecular evolution, phylogenetic tree construction, genetics, and infectious disease models. The coverage of models of molecular evolution and phylogenetic tree construction from DNA sequence data is unique among books at this level. Computer investigations with MATLAB are incorporated throughout, in both exercises and more extensive projects, to give readers hands-on experience with the mathematical models developed. MATLAB programs accompany the text. Mathematical tools, such as matrix algebra, eigenvector analysis, and basic probability, are motivated by biological models and given self-contained developments, so that mathematical prerequisites are minimal.

Author : Hamid R Arabnia,Quoc Nam Tran
Publisher : Morgan Kaufmann
Page : 592 pages
File Size : 46,7 Mb
Release : 2016-03-25
Category : Computers
ISBN : 9780128042595

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Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology by Hamid R Arabnia,Quoc Nam Tran Pdf

Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications covers the latest trends in the field with special emphasis on their applications. The first part covers the major areas of computational biology, development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques for the study of biological and behavioral systems. The second part covers bioinformatics, an interdisciplinary field concerned with methods for storing, retrieving, organizing, and analyzing biological data. The book also explores the software tools used to generate useful biological knowledge. The third part, on systems biology, explores how to obtain, integrate, and analyze complex datasets from multiple experimental sources using interdisciplinary tools and techniques, with the final section focusing on big data and the collection of datasets so large and complex that it becomes difficult to process using conventional database management systems or traditional data processing applications. Explores all the latest advances in this fast-developing field from an applied perspective Provides the only coherent and comprehensive treatment of the subject available Covers the algorithm development, software design, and database applications that have been developed to foster research

Author : Michele Berlingerio,Francesco Bonchi,Thomas Gärtner,Neil Hurley,Georgiana Ifrim
Publisher : Springer
Page : 866 pages
File Size : 51,9 Mb
Release : 2019-01-22
Category : Computers
ISBN : 9783030109288

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Machine Learning and Knowledge Discovery in Databases by Michele Berlingerio,Francesco Bonchi,Thomas Gärtner,Neil Hurley,Georgiana Ifrim Pdf

The three volume proceedings LNAI 11051 – 11053 constitutes the refereed proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases, ECML PKDD 2018, held in Dublin, Ireland, in September 2018. The total of 131 regular papers presented in part I and part II was carefully reviewed and selected from 535 submissions; there are 52 papers in the applied data science, nectar and demo track. The contributions were organized in topical sections named as follows: Part I: adversarial learning; anomaly and outlier detection; applications; classification; clustering and unsupervised learning; deep learningensemble methods; and evaluation. Part II: graphs; kernel methods; learning paradigms; matrix and tensor analysis; online and active learning; pattern and sequence mining; probabilistic models and statistical methods; recommender systems; and transfer learning. Part III: ADS data science applications; ADS e-commerce; ADS engineering and design; ADS financial and security; ADS health; ADS sensing and positioning; nectar track; and demo track.

Author : Raina Robeva,Matthew Macauley
Publisher : Academic Press
Page : 434 pages
File Size : 54,8 Mb
Release : 2018-10-08
Category : Mathematics
ISBN : 9780128140697

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Algebraic and Combinatorial Computational Biology by Raina Robeva,Matthew Macauley Pdf

Algebraic and Combinatorial Computational Biology introduces students and researchers to a panorama of powerful and current methods for mathematical problem-solving in modern computational biology. Presented in a modular format, each topic introduces the biological foundations of the field, covers specialized mathematical theory, and concludes by highlighting connections with ongoing research, particularly open questions. The work addresses problems from gene regulation, neuroscience, phylogenetics, molecular networks, assembly and folding of biomolecular structures, and the use of clustering methods in biology. A number of these chapters are surveys of new topics that have not been previously compiled into one unified source. These topics were selected because they highlight the use of technique from algebra and combinatorics that are becoming mainstream in the life sciences. Integrates a comprehensive selection of tools from computational biology into educational or research programs Emphasizes practical problem-solving through multiple exercises, projects and spinoff computational simulations Contains scalable material for use in undergraduate and graduate-level classes and research projects Introduces the reader to freely-available professional software Supported by illustrative datasets and adaptable computer code

Author : Dan Gusfield
Publisher : Cambridge University Press
Page : 431 pages
File Size : 54,6 Mb
Release : 2019-06-13
Category : Computers
ISBN : 9781108421768

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Integer Linear Programming in Computational and Systems Biology by Dan Gusfield Pdf

This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.

Author : Michael I. Monastyrsky
Publisher : Springer
Page : 238 pages
File Size : 48,5 Mb
Release : 2006-10-23
Category : Science
ISBN : 3540234071

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Topology in Molecular Biology by Michael I. Monastyrsky Pdf

Author : Jimmy Petean
Publisher : American Mathematical Soc.
Page : 201 pages
File Size : 50,9 Mb
Release : 2016-01-25
Category : Mathematics
ISBN : 9781470423100

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Mathematical Congress of the Americas by Jimmy Petean Pdf

This volume contains the proceedings of the First Mathematical Congress of the Americas, held from August 5-9, 2013, in Guanajuato, México. With the participation of close to 1,000 researchers from more than 40 countries, the meeting set a benchmark for mathematics in the two continents. The papers, written by some of the plenary and invited speakers, as well as winners of MCA awards, cover new developments in classic topics such as Hopf fibrations, minimal surfaces, and Markov processes, and provide recent insights on combinatorics and geometry, isospectral spherical space forms, homogenization on manifolds, and Lagrangian cobordism, as well as applications to physics and biology.

Author : Nii O. Attoh-Okine
Publisher : John Wiley & Sons
Page : 272 pages
File Size : 46,5 Mb
Release : 2017-05-12
Category : Mathematics
ISBN : 9781119229056

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Big Data and Differential Privacy by Nii O. Attoh-Okine Pdf

A comprehensive introduction to the theory and practice of contemporary data science analysis for railway track engineering Featuring a practical introduction to state-of-the-art data analysis for railway track engineering, Big Data and Differential Privacy: Analysis Strategies for Railway Track Engineering addresses common issues with the implementation of big data applications while exploring the limitations, advantages, and disadvantages of more conventional methods. In addition, the book provides a unifying approach to analyzing large volumes of data in railway track engineering using an array of proven methods and software technologies. Dr. Attoh-Okine considers some of today’s most notable applications and implementations and highlights when a particular method or algorithm is most appropriate. Throughout, the book presents numerous real-world examples to illustrate the latest railway engineering big data applications of predictive analytics, such as the Union Pacific Railroad’s use of big data to reduce train derailments, increase the velocity of shipments, and reduce emissions. In addition to providing an overview of the latest software tools used to analyze the large amount of data obtained by railways, Big Data and Differential Privacy: Analysis Strategies for Railway Track Engineering: • Features a unified framework for handling large volumes of data in railway track engineering using predictive analytics, machine learning, and data mining • Explores issues of big data and differential privacy and discusses the various advantages and disadvantages of more conventional data analysis techniques • Implements big data applications while addressing common issues in railway track maintenance • Explores the advantages and pitfalls of data analysis software such as R and Spark, as well as the Apache™ Hadoop® data collection database and its popular implementation MapReduce Big Data and Differential Privacy is a valuable resource for researchers and professionals in transportation science, railway track engineering, design engineering, operations research, and railway planning and management. The book is also appropriate for graduate courses on data analysis and data mining, transportation science, operations research, and infrastructure management. NII ATTOH-OKINE, PhD, PE is Professor in the Department of Civil and Environmental Engineering at the University of Delaware. The author of over 70 journal articles, his main areas of research include big data and data science; computational intelligence; graphical models and belief functions; civil infrastructure systems; image and signal processing; resilience engineering; and railway track analysis. Dr. Attoh-Okine has edited five books in the areas of computational intelligence, infrastructure systems and has served as an Associate Editor of various ASCE and IEEE journals.

Author : Matteo Barberis,Tomáš Helikar
Publisher : Frontiers Media SA
Page : 340 pages
File Size : 50,5 Mb
Release : 2019-08-16
Category : Electronic
ISBN : 9782889459834

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Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by Matteo Barberis,Tomáš Helikar Pdf

Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.

Author : Paolo Milazzo,Dániel Varró,Manuel Wimmer
Publisher : Springer
Page : 472 pages
File Size : 53,9 Mb
Release : 2016-11-29
Category : Computers
ISBN : 9783319502304

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Software Technologies: Applications and Foundations by Paolo Milazzo,Dániel Varró,Manuel Wimmer Pdf

This book contains the thoroughly refereed technical papers presented in six workshops collocated with the International Conference on Software Technologies: Applications and Foundations, STAF 2016, held in Vienna, Austria, in July 2016. The six workshops whose papers are included in this volume are: DataMod, GCM, HOFM, MELO, SEMS, and VeryComp. The 33 full and 3 short papers presented were carefully reviewed and selected from 53 submissions. They focus on practical and foundational advances in software technology covering a wide range of aspects including formal foundations of software technology, testing and formal analysis, graph transformations and model transformations, model driven engineering, and tools.

Author : Nataša Jonoska,Erik Winfree
Publisher : Springer Nature
Page : 442 pages
File Size : 49,7 Mb
Release : 2023-07-04
Category : Computers
ISBN : 9789811998911

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Visions of DNA Nanotechnology at 40 for the Next 40 by Nataša Jonoska,Erik Winfree Pdf

This open access book provides a unique and state-of-the-art view on DNA nanotechnology with an eye toward future developments. Intended as a tribute to Nadrian C. Seeman, who founded the field of DNA nanotechnology, the content is an exciting mixture of technical and non-technical material, reviews, tutorials, perspectives, new findings, and open questions. The book aims to inspire current researchers to sit back and think about the big picture, while also enticing new researchers to enter the field. Most of all, the book captures voices from a unique moment in time: 40 years after the publication of the first paper that envisioned DNA nanotechnology. From this vantage point, what are the untold stories, the unspoken concerns, the underlying fundamental issues, the overlooked opportunities, and the unifying grand challenges? What will help us see more clearly, see more creatively, or see farther? What is transpiring right now that could pave the way for the future? To address these questions, leading researchers have contributed 22 chapters, grouped into five sections: perspectives, chemistry and physics, structures, biochemical circuits, and spatial systems. This book will be an important reference point in the field of DNA nanotechnology, both for established researchers looking to take stock of the field and its future, and for newcomers such as graduate students and researchers in other fields who are beginning to appreciate the power and applicability of its methods.