Algebraic and Combinatorial Computational Biology
Algebraic and Combinatorial Computational Biology

Author: Raina Robeva

Publisher: Academic Press

Published: 2018-10-08

Total Pages: 436

ISBN-13: 0128140690

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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

Algebraic Statistics for Computational Biology
Algebraic Statistics for Computational Biology

Author: L. Pachter

Publisher: Cambridge University Press

Published: 2005-08-22

Total Pages: 440

ISBN-13: 9780521857000

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This book, first published in 2005, offers an introduction to the application of algebraic statistics to computational biology.

Algebraic Combinatorics for Computational Biology
Algebraic Combinatorics for Computational Biology

Author: Nicholas Karl Eriksson

Publisher:

Published: 2006

Total Pages: 250

ISBN-13: 9780542824098

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Algebraic statistics is the study of the algebraic varieties that correspond to discrete statistical models. Such statistical models are used throughout computational biology, for example to describe the evolution of DNA sequences. This perspective on statistics allows us to bring mathematical techniques to bear and also provides a source of new problems in mathematics.

Algebraic Biology
Algebraic Biology

Author: Katsuhisa Horimoto

Publisher: Springer Science & Business Media

Published: 2008-07-18

Total Pages: 256

ISBN-13: 3540851003

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This book constitutes the refereed proceedings of the Third International Conference on Algebraic Biology, AB 2008, held at the Castle of Hagenberg, Austria in July 2008 as part of the RISC Summer 2008, organized by the Research Institute for Symbolic Computation. The 14 revised full papers presented together with 3 tutorial lectures were carefully reviewed and selected from 27 submissions. The conference is the interdisciplinary forum for the presentation of research on all aspects of applications of symbolic computation (computer algebra, computational logic, and related methods) to various issues in biology and life sciences as well as other problems in biology being approached with symbolic methods.

Patterns in Permutations and Words
Patterns in Permutations and Words

Author: Sergey Kitaev

Publisher: Springer Science & Business Media

Published: 2011-08-30

Total Pages: 511

ISBN-13: 3642173330

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There has been considerable interest recently in the subject of patterns in permutations and words, a new branch of combinatorics with its roots in the works of Rotem, Rogers, and Knuth in the 1970s. Consideration of the patterns in question has been extremely interesting from the combinatorial point of view, and it has proved to be a useful language in a variety of seemingly unrelated problems, including the theory of Kazhdan—Lusztig polynomials, singularities of Schubert varieties, interval orders, Chebyshev polynomials, models in statistical mechanics, and various sorting algorithms, including sorting stacks and sortable permutations. The author collects the main results in the field in this up-to-date, comprehensive reference volume. He highlights significant achievements in the area, and points to research directions and open problems. The book will be of interest to researchers and graduate students in theoretical computer science and mathematics, in particular those working in algebraic combinatorics and combinatorics on words. It will also be of interest to specialists in other branches of mathematics, theoretical physics, and computational biology. The author collects the main results in the field in this up-to-date, comprehensive reference volume. He highlights significant achievements in the area, and points to research directions and open problems. The book will be of interest to researchers and graduate students in theoretical computer science and mathematics, in particular those working in algebraic combinatorics and combinatorics on words. It will also be of interest to specialists in other branches of mathematics, theoretical physics, and computational biology.

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R
Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Author: Gabriel Valiente

Publisher: CRC Press

Published: 2009-04-08

Total Pages: 370

ISBN-13: 1420069748

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Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic

Algebraic Biology
Algebraic Biology

Author: Hirokazu Anai

Publisher: Springer

Published: 2007-08-13

Total Pages: 390

ISBN-13: 3540734333

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This volume constitutes the refereed proceedings of the Second International Conference on Algebraic Biology. The conference served as an interdisciplinary forum for the presentation of research on all aspects of the application of symbolic computation in biology, including computer algebra, computational logic, and related methods. Papers also examine solutions to problems in biology using symbolic methods.

Discrete and Topological Models in Molecular Biology
Discrete and Topological Models in Molecular Biology

Author: Nataša Jonoska

Publisher: Springer Science & Business Media

Published: 2013-12-23

Total Pages: 522

ISBN-13: 3642401937

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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.

Algebraic and Discrete Mathematical Methods for Modern Biology
Algebraic and Discrete Mathematical Methods for Modern Biology

Author: Raina Robeva

Publisher: Academic Press

Published: 2015-05-09

Total Pages: 383

ISBN-13: 0128012714

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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

Algebraic Biology, Matrix Genetics, And Genetic Intelligence
Algebraic Biology, Matrix Genetics, And Genetic Intelligence

Author: Sergei V Petoukhov

Publisher: World Scientific

Published: 2023-08-02

Total Pages: 616

ISBN-13: 981127827X

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Historically, mathematics, probability, and statistics have been widely used in the biological sciences. Recent progress in genomics has yielded many millions of gene sequences. But what do these sequences tell us and what are the generalities and rules governed by them? It seems that we understand very little about the genetic contexts required to 'read' them. There is more to life than the genomic blueprint of each organism. Life functions within the natural laws that we know and the ones we do not know. The development of modern mathematical natural sciences is based on the use of certain mathematical tools. Mathematics can be used to understand life from the molecular to the biosphere level.This book provides the foundation and latest advances for an emerging research area that uses tools from symbolic computation, computer algebra and logic, algebraic geometry, fractal geometry, probability and statistics, and matrix algebra to formalize and solve biological problems and explore its applications in algebraic biology and code biology. It introduces highly interdisciplinary topics in biomathematics such as matrix genetics, gestalt biology, bio-antenna arrays, resonance genetics, quantum biology, and more.