Algebraic And Combinatorial Computational Biology

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Algebraic and Combinatorial Computational Biology

Raina Robeva,Matthew Macauley
Algebraic and Combinatorial Computational Biology Book PDF

Author : Raina Robeva,Matthew Macauley
Publisher : Academic Press
Page : 434 pages
File Size : 45,7 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

Algebraic Statistics for Computational Biology

L. Pachter,B. Sturmfels
Algebraic Statistics for Computational Biology Book PDF

Author : L. Pachter,B. Sturmfels
Publisher : Cambridge University Press
Page : 440 pages
File Size : 53,8 Mb
Release : 2005-08-22
Category : Mathematics
ISBN : 0521857007

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Algebraic Statistics for Computational Biology by L. Pachter,B. Sturmfels Pdf

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

Combinatorial Computational Biology of RNA

Christian Reidys
Combinatorial Computational Biology of RNA Book PDF

Author : Christian Reidys
Publisher : Springer Science & Business Media
Page : 262 pages
File Size : 55,6 Mb
Release : 2010-10-29
Category : Mathematics
ISBN : 9780387767314

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Combinatorial Computational Biology of RNA by Christian Reidys Pdf

In this monograph, new combinatorial and computational approaches in the study of RNA structures are presented which enhance both mathematics and computational biology. It begins with an introductory chapter, which motivates and sets the background of this research. In the following chapter, all the concepts are systematically developed. The reader will find * integration of more than forty research papers covering topics like, RSK-algorithm, reflection principle, singularity analysis and random graph theory * systematic presentation of the theory of pseudo-knotted RNA structures including their generating function, uniform generation as well as central and discrete limit theorems * computational biology of pseudo-knotted RNA structures, including dynamic programming paradigms and a new folding algorithm * analysis of neutral networks of pseudo knotted RNA structures and their random graph theory, including neutral paths, giant components and connectivity All algorithms presented are freely available through springer.com and implemented in C. A proofs section at the end contains the necessary technicalities. This book will serve graduate students and researchers in the fields of discrete mathematics, mathematical and computational biology. It is suitable as a textbook for a graduate course in mathematical and computational biology.

Patterns in Permutations and Words

Sergey Kitaev
Patterns in Permutations and Words Book PDF

Author : Sergey Kitaev
Publisher : Springer Science & Business Media
Page : 494 pages
File Size : 48,6 Mb
Release : 2011-08-30
Category : Computers
ISBN : 9783642173332

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Patterns in Permutations and Words by Sergey Kitaev Pdf

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.

Algebraic Biology

Hirokazu Anai,Katsuhisa Horimoto,Temur Kutsia
Algebraic Biology Book PDF

Author : Hirokazu Anai,Katsuhisa Horimoto,Temur Kutsia
Publisher : Springer
Page : 379 pages
File Size : 49,7 Mb
Release : 2007-08-13
Category : Computers
ISBN : 9783540734338

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Algebraic Biology by Hirokazu Anai,Katsuhisa Horimoto,Temur Kutsia Pdf

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.

Algebraic Biology

Katsuhisa Horimoto,Georg Regensburger,Markus Rosenkranz,Hiroshi Yoshida
Algebraic Biology Book PDF

Author : Katsuhisa Horimoto,Georg Regensburger,Markus Rosenkranz,Hiroshi Yoshida
Publisher : Springer Science & Business Media
Page : 256 pages
File Size : 40,6 Mb
Release : 2008-07-18
Category : Computers
ISBN : 9783540851004

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Algebraic Biology by Katsuhisa Horimoto,Georg Regensburger,Markus Rosenkranz,Hiroshi Yoshida Pdf

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.

Discrete and Topological Models in Molecular Biology

Nataša Jonoska,Masahico Saito
Discrete and Topological Models in Molecular Biology Book PDF

Author : Nataša Jonoska,Masahico Saito
Publisher : Springer Science & Business Media
Page : 522 pages
File Size : 54,6 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.

An Introduction to the Mathematics of Biology: with Computer Algebra Models

Edward K. Yeargers,James V. Herod,Ronald W. Shonkweiler
An Introduction to the Mathematics of Biology with Computer Algebra Models Book PDF

Author : Edward K. Yeargers,James V. Herod,Ronald W. Shonkweiler
Publisher : Springer Science & Business Media
Page : 426 pages
File Size : 52,7 Mb
Release : 2013-12-01
Category : Mathematics
ISBN : 9781475710953

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An Introduction to the Mathematics of Biology: with Computer Algebra Models by Edward K. Yeargers,James V. Herod,Ronald W. Shonkweiler Pdf

Biology is a source of fascination for most scientists, whether their training is in the life sciences or not. In particular, there is a special satisfaction in discovering an understanding of biology in the context of another science like mathematics. Fortunately there are plenty of interesting (and fun) problems in biology, and virtually all scientific disciplines have become the richer for it. For example, two major journals, Mathematical Biosciences and Journal of Mathematical Biology, have tripled in size since their inceptions 20-25 years ago. The various sciences have a great deal to give to one another, but there are still too many fences separating them. In writing this book we have adopted the philosophy that mathematical biology is not merely the intrusion of one science into another, but has a unity of its own, in which both the biology and the math ematics should be equal and complete, and should flow smoothly into and out of one another. We have taught mathematical biology with this philosophy in mind and have seen profound changes in the outlooks of our science and engineering students: The attitude of "Oh no, another pendulum on a spring problem!," or "Yet one more LCD circuit!" completely disappeared in the face of applications of mathematics in biology. There is a timeliness in calculating a protocol for ad ministering a drug.

Algebraic and Discrete Mathematical Methods for Modern Biology

Raina Robeva
Algebraic and Discrete Mathematical Methods for Modern Biology Book PDF

Author : Raina Robeva
Publisher : Academic Press
Page : 382 pages
File Size : 46,8 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

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Gabriel Valiente
Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R Book PDF

Author : Gabriel Valiente
Publisher : CRC Press
Page : 368 pages
File Size : 52,9 Mb
Release : 2009-04-08
Category : Science
ISBN : 1420069748

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Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R by Gabriel Valiente Pdf

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, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology. The book provides a well-rounded explanation of traditional issues as well as an up-to-date account of more recent developments, such as graph similarity and search. It is organized around the specific algorithmic problems that arise when dealing with structures that are commonly found in computational biology, including biological sequences, trees, and graphs. For each of these structures, the author makes a clear distinction between problems that arise in the analysis of one structure and in the comparative analysis of two or more structures. He also presents phylogenetic trees and networks as examples of trees and graphs in computational biology. This book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions of each biological problem, it includes detailed algorithmic solutions in pseudo-code, full Perl and R implementation, and pointers to other software, such as those on CPAN and CRAN.

Algebraic and Numeric Biology

Katsuhisa Horimoto,Masahiko Nakatsui,Nikolaj Popov
Algebraic and Numeric Biology Book PDF

Author : Katsuhisa Horimoto,Masahiko Nakatsui,Nikolaj Popov
Publisher : Springer Science & Business Media
Page : 193 pages
File Size : 46,8 Mb
Release : 2012-02-14
Category : Computers
ISBN : 9783642280665

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Algebraic and Numeric Biology by Katsuhisa Horimoto,Masahiko Nakatsui,Nikolaj Popov Pdf

This book constitutes the refereed proceedings of the 4th International Conference on Algebraic Biology, ANB 2010, held at the Castle of Hagenberg, Austria in July/August 2010. The conference is a follow up of the AB Conference. The 10 papers were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on mathematical modeling, system analysis and design, genomics, molecular structure analysis, automata theory, artificial intelligence, sequence analysis, automated reasoning, formal language and hybrid symbolic numerical methods.

Combinatorial Pattern Matching

Moshe Lewenstein,Gabriel Valiente
Combinatorial Pattern Matching Book PDF

Author : Moshe Lewenstein,Gabriel Valiente
Publisher : Springer
Page : 420 pages
File Size : 54,5 Mb
Release : 2006-07-01
Category : Computers
ISBN : 9783540354611

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Combinatorial Pattern Matching by Moshe Lewenstein,Gabriel Valiente Pdf

This book constitutes the refereed proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching, CPM 2006, held in Barcelona, Spain, July 2006. The book presents 33 revised full papers together with 3 invited talks, organized in topical sections on data structures, indexing data structures, probabilistic and algebraic techniques, applications in molecular biology, string matching, data compression, and dynamic programming.

Mathematics of Bioinformatics

Matthew He,Sergey Petoukhov
Mathematics of Bioinformatics Book PDF

Author : Matthew He,Sergey Petoukhov
Publisher : John Wiley & Sons
Page : 231 pages
File Size : 44,6 Mb
Release : 2011-03-16
Category : Computers
ISBN : 9781118099520

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Mathematics of Bioinformatics by Matthew He,Sergey Petoukhov Pdf

Mathematics of Bioinformatics: Theory, Methods, and Applications provides a comprehensive format for connecting and integrating information derived from mathematical methods and applying it to the understanding of biological sequences, structures, and networks. Each chapter is divided into a number of sections based on the bioinformatics topics and related mathematical theory and methods. Each topic of the section is comprised of the following three parts: an introduction to the biological problems in bioinformatics; a presentation of relevant topics of mathematical theory and methods to the bioinformatics problems introduced in the first part; an integrative overview that draws the connections and interfaces between bioinformatics problems/issues and mathematical theory/methods/applications.

Computational Molecular Biology

Peter Clote,Rolf Backofen
Computational Molecular Biology Book PDF

Author : Peter Clote,Rolf Backofen
Publisher : Wiley
Page : 304 pages
File Size : 44,7 Mb
Release : 2000-10-03
Category : Mathematics
ISBN : 0471872520

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Computational Molecular Biology by Peter Clote,Rolf Backofen Pdf

Recently molecular biology has undergone unprecedented development generating vast quantities of data needing sophisticated computational methods for analysis, processing and archiving. This requirement has given birth to the truly interdisciplinary field of computational biology, or bioinformatics, a subject reliant on both theoretical and practical contributions from statistics, mathematics, computer science and biology. * Provides the background mathematics required to understand why certain algorithms work * Guides the reader through probability theory, entropy and combinatorial optimization * In-depth coverage of molecular biology and protein structure prediction * Includes several less familiar algorithms such as DNA segmentation, quartet puzzling and DNA strand separation prediction * Includes class tested exercises useful for self-study * Source code of programs available on a Web site Primarily aimed at advanced undergraduate and graduate students from bioinformatics, computer science, statistics, mathematics and the biological sciences, this text will also interest researchers from these fields.

Combinatorial Optimization and Applications

Weili Wu,Ovidiu Daescu
Combinatorial Optimization and Applications Book PDF

Author : Weili Wu,Ovidiu Daescu
Publisher : Springer Science & Business Media
Page : 437 pages
File Size : 44,6 Mb
Release : 2010-12-09
Category : Computers
ISBN : 9783642174575

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Combinatorial Optimization and Applications by Weili Wu,Ovidiu Daescu Pdf

This book constitutes the refereed proceedings of the 4th International Conference on Combinatorial Optimization and Applications, COCOA 2010, held in Kailua-Kona, HI, USA, in December 2010. The 49 revised full papers were carefully reviewed and selected from 108 submissions.