Algebraic and Combinatorial Computational Biology PDF Download

Author: Raina Robeva
Publisher: Academic Press
ISBN: 0128140690
Category : Mathematics
Languages : en
Pages : 436

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Book Description
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: L. Pachter
Publisher: Cambridge University Press
ISBN: 9780521857000
Category : Mathematics
Languages : en
Pages : 440

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

Author: Raina Robeva
Publisher: Academic Press
ISBN: 0128012714
Category : Mathematics
Languages : en
Pages : 383

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Book Description
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: Philippe Flajolet
Publisher: Cambridge University Press
ISBN: 1139477161
Category : Mathematics
Languages : en
Pages : 825

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Book Description
Analytic combinatorics aims to enable precise quantitative predictions of the properties of large combinatorial structures. The theory has emerged over recent decades as essential both for the analysis of algorithms and for the study of scientific models in many disciplines, including probability theory, statistical physics, computational biology, and information theory. With a careful combination of symbolic enumeration methods and complex analysis, drawing heavily on generating functions, results of sweeping generality emerge that can be applied in particular to fundamental structures such as permutations, sequences, strings, walks, paths, trees, graphs and maps. This account is the definitive treatment of the topic. The authors give full coverage of the underlying mathematics and a thorough treatment of both classical and modern applications of the theory. The text is complemented with exercises, examples, appendices and notes to aid understanding. The book can be used for an advanced undergraduate or a graduate course, or for self-study.

Author: Dimitry Kozlov
Publisher: Springer Science & Business Media
ISBN: 9783540730514
Category : Mathematics
Languages : en
Pages : 416

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Book Description
This volume is the first comprehensive treatment of combinatorial algebraic topology in book form. The first part of the book constitutes a swift walk through the main tools of algebraic topology. Readers - graduate students and working mathematicians alike - will probably find particularly useful the second part, which contains an in-depth discussion of the major research techniques of combinatorial algebraic topology. Although applications are sprinkled throughout the second part, they are principal focus of the third part, which is entirely devoted to developing the topological structure theory for graph homomorphisms.

Author: Bruce R. Donald
Publisher: MIT Press
ISBN: 0262548798
Category : Science
Languages : en
Pages : 497

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Book Description
An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Author: Bhubaneswar Mishra
Publisher: Springer Science & Business Media
ISBN: 1461243440
Category : Computers
Languages : en
Pages : 427

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Book Description
Algorithmic Algebra studies some of the main algorithmic tools of computer algebra, covering such topics as Gröbner bases, characteristic sets, resultants and semialgebraic sets. The main purpose of the book is to acquaint advanced undergraduate and graduate students in computer science, engineering and mathematics with the algorithmic ideas in computer algebra so that they could do research in computational algebra or understand the algorithms underlying many popular symbolic computational systems: Mathematica, Maple or Axiom, for instance. Also, researchers in robotics, solid modeling, computational geometry and automated theorem proving community may find it useful as symbolic algebraic techniques have begun to play an important role in these areas. The book, while being self-contained, is written at an advanced level and deals with the subject at an appropriate depth. The book is accessible to computer science students with no previous algebraic training. Some mathematical readers, on the other hand, may find it interesting to see how algorithmic constructions have been used to provide fresh proofs for some classical theorems. The book also contains a large number of exercises with solutions to selected exercises, thus making it ideal as a textbook or for self-study.

Author: Nicole M. Scherer
Publisher: Springer Nature
ISBN: 3031211758
Category : Science
Languages : en
Pages : 177

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Book Description
This book constitutes the proceedings of the 15th Brazilian Symposium on Bioinformatics on Advances in Bioinformatics and Computational Biology, BSB 2022, which took place in Buzios, Brazil, in September 2022. The 10 full papers and 7 short papers presented in this volume were carefully reviewed and selected from 23 submissions. The papers focus on bioinformatics, computational biology, Biological Databases, Biological Networks, Cheminformatics, Evolutionary Genomics, Computational Proteomics, Systems Biology, Drug Design, Genomics, Machine Learning applications in Bioinformatics, Metagenomics, Molecular Docking and Modeling, Molecular Evolution and Phylogenetics, Protein Structure and Modeling, Proteomics, Transcriptomics, Single-Cell Analysis, Workflows in Bioinformatics.

Author: Sergey Kitaev
Publisher: Springer Science & Business Media
ISBN: 3642173330
Category : Computers
Languages : en
Pages : 511

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Book Description
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.

Author: Noury Bakrim
Publisher: BoD - Books on Demand
ISBN: 2322453528
Category : Mathematics
Languages : en
Pages : 70

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Book Description
This book is the third component in the ROAL model; it suggests a relation between language and mathematical models of totality relying on verifiability and observability/objectivity models of the linguistic text. In addition of the biomathematical hypothesis, rules of observability and objectivity have been extended to both objective and non-objective models toward a manifolded dimension of the structure within a field dimension of consciousness in which dwells the paradigm of the text as a meta-observability domain for language and natural/individual languages.