# Algebraic and Combinatorial Computational Biology

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## Algebraic and Combinatorial Computational Biology

Author | : Raina Robeva,Matthew Macauley |

Publsiher | : Academic Press |

Total Pages | : 434 |

Release | : 2018-10-08 |

ISBN 10 | : 0128140690 |

ISBN 13 | : 9780128140697 |

Language | : EN, FR, DE, ES & NL |

**Algebraic and Combinatorial Computational Biology Book Review:**

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

Author | : L. Pachter,B. Sturmfels |

Publsiher | : Cambridge University Press |

Total Pages | : 420 |

Release | : 2005-08-22 |

ISBN 10 | : 9780521857000 |

ISBN 13 | : 0521857007 |

Language | : EN, FR, DE, ES & NL |

**Algebraic Statistics for Computational Biology Book Review:**

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

## Patterns in Permutations and Words

Author | : Sergey Kitaev |

Publsiher | : Springer Science & Business Media |

Total Pages | : 494 |

Release | : 2011-08-30 |

ISBN 10 | : 3642173330 |

ISBN 13 | : 9783642173332 |

Language | : EN, FR, DE, ES & NL |

**Patterns in Permutations and Words Book Review:**

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.

## Exam Prep for Algebraic and Combinatorial Computational

Author | : Anonim |

Publsiher | : Unknown |

Total Pages | : 329 |

Release | : 2021 |

ISBN 10 | : |

ISBN 13 | : |

Language | : EN, FR, DE, ES & NL |

**Exam Prep for Algebraic and Combinatorial Computational Book Review:**

## Combinatorial Computational Biology of RNA

Author | : Christian Reidys |

Publsiher | : Springer Science & Business Media |

Total Pages | : 258 |

Release | : 2010-10-29 |

ISBN 10 | : 9780387767314 |

ISBN 13 | : 0387767312 |

Language | : EN, FR, DE, ES & NL |

**Combinatorial Computational Biology of RNA Book Review:**

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.

## Algebraic and Discrete Mathematical Methods for Modern Biology

Author | : Raina Robeva |

Publsiher | : Academic Press |

Total Pages | : 382 |

Release | : 2015-05-09 |

ISBN 10 | : 0128012714 |

ISBN 13 | : 9780128012710 |

Language | : EN, FR, DE, ES & NL |

**Algebraic and Discrete Mathematical Methods for Modern Biology Book Review:**

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 Computational Biology of RNA

Author | : Christian Reidys |

Publsiher | : Springer Science & Business Media |

Total Pages | : 258 |

Release | : 2010-10-29 |

ISBN 10 | : 9780387767314 |

ISBN 13 | : 0387767312 |

Language | : EN, FR, DE, ES & NL |

**Combinatorial Computational Biology of RNA Book Review:**

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.

## Mathematical Concepts and Methods in Modern Biology

Author | : Raina Robeva,Terrell Hodge |

Publsiher | : Academic Press |

Total Pages | : 372 |

Release | : 2013-02-26 |

ISBN 10 | : 0124157939 |

ISBN 13 | : 9780124157934 |

Language | : EN, FR, DE, ES & NL |

**Mathematical Concepts and Methods in Modern Biology Book Review:**

Mathematical Concepts and Methods in Modern Biology offers a quantitative framework for analyzing, predicting, and modulating the behavior of complex biological systems. The book presents important mathematical concepts, methods and tools in the context of essential questions raised in modern biology. Designed around the principles of project-based learning and problem-solving, the book considers biological topics such as neuronal networks, plant population growth, metabolic pathways, and phylogenetic tree reconstruction. The mathematical modeling tools brought to bear on these topics include Boolean and ordinary differential equations, projection matrices, agent-based modeling and several algebraic approaches. Heavy computation in some of the examples is eased by the use of freely available open-source software. Features self-contained chapters with real biological research examples using freely available computational tools Spans several mathematical techniques at basic to advanced levels Offers broad perspective on the uses of algebraic geometry/polynomial algebra in molecular systems biology

## Introduction to Computational Biology

Author | : Michael S. Waterman |

Publsiher | : CRC Press |

Total Pages | : 448 |

Release | : 2018-05-02 |

ISBN 10 | : 1351437089 |

ISBN 13 | : 9781351437080 |

Language | : EN, FR, DE, ES & NL |

**Introduction to Computational Biology Book Review:**

Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.

## A Project Based Guide to Undergraduate Research in Mathematics

Author | : Pamela E. Harris,Erik Insko,Aaron Wootton |

Publsiher | : Springer Nature |

Total Pages | : 324 |

Release | : 2020-04-17 |

ISBN 10 | : 3030378535 |

ISBN 13 | : 9783030378530 |

Language | : EN, FR, DE, ES & NL |

**A Project Based Guide to Undergraduate Research in Mathematics Book Review:**

This volume provides accessible and self-contained research problems designed for undergraduate student projects, and simultaneously promotes the development of sustainable undergraduate research programs. The chapters in this work span a variety of topical areas of pure and applied mathematics and mathematics education. Each chapter gives a self-contained introduction on a research topic with an emphasis on the specific tools and knowledge needed to create and maintain fruitful research programs for undergraduates. Some of the topics discussed include:• Disease modeling• Tropical curves and surfaces• Numerical semigroups• Mathematics EducationThis volume will primarily appeal to undergraduate students interested in pursuing research projects and faculty members seeking to mentor them. It may also aid students and faculty participating in independent studies and capstone projects.

## Analytic Combinatorics

Author | : Philippe Flajolet,Robert Sedgewick |

Publsiher | : Cambridge University Press |

Total Pages | : 329 |

Release | : 2009-01-15 |

ISBN 10 | : 1139477161 |

ISBN 13 | : 9781139477161 |

Language | : EN, FR, DE, ES & NL |

**Analytic Combinatorics Book Review:**

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.

## Computational Discrete Mathematics

Author | : Sriram Pemmaraju,Steven Skiena |

Publsiher | : Cambridge University Press |

Total Pages | : 329 |

Release | : 2009-10-15 |

ISBN 10 | : 1107268710 |

ISBN 13 | : 9781107268715 |

Language | : EN, FR, DE, ES & NL |

**Computational Discrete Mathematics Book Review:**

This book was first published in 2003. Combinatorica, an extension to the popular computer algebra system Mathematica®, is the most comprehensive software available for teaching and research applications of discrete mathematics, particularly combinatorics and graph theory. This book is the definitive reference/user's guide to Combinatorica, with examples of all 450 Combinatorica functions in action, along with the associated mathematical and algorithmic theory. The authors cover classical and advanced topics on the most important combinatorial objects: permutations, subsets, partitions, and Young tableaux, as well as all important areas of graph theory: graph construction operations, invariants, embeddings, and algorithmic graph theory. In addition to being a research tool, Combinatorica makes discrete mathematics accessible in new and exciting ways to a wide variety of people, by encouraging computational experimentation and visualization. The book contains no formal proofs, but enough discussion to understand and appreciate all the algorithms and theorems it contains.

## Computational Algebraic Geometry

Author | : HENRY SCHENCK,Hal Schenck |

Publsiher | : Cambridge University Press |

Total Pages | : 193 |

Release | : 2003-10-06 |

ISBN 10 | : 9780521536509 |

ISBN 13 | : 0521536502 |

Language | : EN, FR, DE, ES & NL |

**Computational Algebraic Geometry Book Review:**

Table of contents

## Connections Between Algebra Combinatorics and Geometry

Author | : Susan M. Cooper,Sean Sather-Wagstaff |

Publsiher | : Springer |

Total Pages | : 317 |

Release | : 2014-05-16 |

ISBN 10 | : 1493906267 |

ISBN 13 | : 9781493906260 |

Language | : EN, FR, DE, ES & NL |

**Connections Between Algebra Combinatorics and Geometry Book Review:**

Commutative algebra, combinatorics, and algebraic geometry are thriving areas of mathematical research with a rich history of interaction. Connections Between Algebra and Geometry contains lecture notes, along with exercises and solutions, from the Workshop on Connections Between Algebra and Geometry held at the University of Regina from May 29-June 1, 2012. It also contains research and survey papers from academics invited to participate in the companion Special Session on Interactions Between Algebraic Geometry and Commutative Algebra, which was part of the CMS Summer Meeting at the University of Regina held June 2–3, 2012, and the meeting Further Connections Between Algebra and Geometry, which was held at the North Dakota State University February 23, 2013. This volume highlights three mini-courses in the areas of commutative algebra and algebraic geometry: differential graded commutative algebra, secant varieties, and fat points and symbolic powers. It will serve as a useful resource for graduate students and researchers who wish to expand their knowledge of commutative algebra, algebraic geometry, combinatorics, and the intricacies of their intersection.

## Computational Biology

Author | : Scott T. Kelley,Dennis Didulo |

Publsiher | : John Wiley & Sons |

Total Pages | : 194 |

Release | : 2020-08-06 |

ISBN 10 | : 1683670035 |

ISBN 13 | : 9781683670032 |

Language | : EN, FR, DE, ES & NL |

**Computational Biology Book Review:**

An introduction to the world of bioinformatics Massive increases in computing power and the ability to routinely sequence whole genomes of living organisms have begun to fundamentally alter our understanding of biology, medicine, and agriculture. At the intersection of the growing information and genomics revolutions sits bioinformatics, which uses modern computational power to reveal patterns in biological data sets, especially DNA, RNA, and protein sequences. Computational Biology: A Hypertextbook, by Scott Kelley and Dennis Didulo, provides a wonderful introduction for anyone who wants to learn the basics of bioinformatics. This book is more than a textbook because of the wealth of online ancillary materials and how the print and electronic components are integrated to form a complete educational resource. Aspects that make Computational Biology: A Hypertextbook a unique and valuable tool for teaching and learning bioinformatics include Clear explanations of the basic biology of DNA, RNA, and proteins and how the related bioinformatics algorithms work Extensive exercises that enable students to practice with the same bioinformatics applications that are used by scientists worldwide Tutorials, sample data sets, and interactive learning tools developed with teachers in mind and field-tested by hundreds of students Online tutorials and curated web links that are accurate (instead of frustrating!) and won't lead to dead ends Online resources that work on multiple platforms and electronic devices Computational Biology: A Hypertextbook is written in an accessible voice, punctuated with humor, and designed to significantly increase computational competencies. Biology and computer science undergraduate and graduate students will thoroughly enjoy learning from this unique hypertextbook, as will anyone with an interest in exploring this burgeoning topic.

## Lectures on Algebraic Statistics

Author | : Mathias Drton,Bernd Sturmfels,Seth Sullivant |

Publsiher | : Springer Science & Business Media |

Total Pages | : 172 |

Release | : 2009-04-25 |

ISBN 10 | : 3764389052 |

ISBN 13 | : 9783764389055 |

Language | : EN, FR, DE, ES & NL |

**Lectures on Algebraic Statistics Book Review:**

How does an algebraic geometer studying secant varieties further the understanding of hypothesis tests in statistics? Why would a statistician working on factor analysis raise open problems about determinantal varieties? Connections of this type are at the heart of the new field of "algebraic statistics". In this field, mathematicians and statisticians come together to solve statistical inference problems using concepts from algebraic geometry as well as related computational and combinatorial techniques. The goal of these lectures is to introduce newcomers from the different camps to algebraic statistics. The introduction will be centered around the following three observations: many important statistical models correspond to algebraic or semi-algebraic sets of parameters; the geometry of these parameter spaces determines the behaviour of widely used statistical inference procedures; computational algebraic geometry can be used to study parameter spaces and other features of statistical models.

## Combinatorial Algorithms

Author | : Charles J. Colbourn,Roberto Grossi,Nadia Pisanti |

Publsiher | : Springer |

Total Pages | : 456 |

Release | : 2019-07-15 |

ISBN 10 | : 3030250059 |

ISBN 13 | : 9783030250058 |

Language | : EN, FR, DE, ES & NL |

**Combinatorial Algorithms Book Review:**

This book constitutes the refereed post-conference proceedings of the 30th International Workshop on Combinatorial Algorithms, IWOCA 2019, held in Pisa, Italy, in July 2019. The 36 regular papers presented in this volume were carefully reviewed and selected from 73 submissions. They cover diverse areas of combinatorical algorithms, complexity theory, graph theory and combinatorics, combinatorial optimization, cryptography and information security, algorithms on strings and graphs, graph drawing and labelling, computational algebra and geometry, computational biology, probabilistic and randomized algorithms, algorithms for big data analytics, and new paradigms of computation.

## Applications of Combinatorics and Graph Theory to the Biological and Social Sciences

Author | : Fred Roberts |

Publsiher | : Springer Science & Business Media |

Total Pages | : 345 |

Release | : 2012-12-06 |

ISBN 10 | : 1468463810 |

ISBN 13 | : 9781468463811 |

Language | : EN, FR, DE, ES & NL |

**Applications of Combinatorics and Graph Theory to the Biological and Social Sciences Book Review:**

This IMA Volume in Mathematics and its Applications Applications of Combinatorics and Graph Theory to the Biological and Social Sciences is based on the proceedings of a workshop which was an integral part of the 1987-88 IMA program on APPLIED COMBINATORICS. We are grateful to the Scientific Committee: Victor Klee (Chairman), Daniel Kleitman, Dijen Ray-Chaudhuri and Dennis Stanton for planning and implementing an exciting and stimulating year long program. We especially thank the Workshop Organizers, Joel Cohen and Fred Roberts, for organizing a workshop which brought together many of the major figures in a variety of research fields connected with the application of combinatorial ideas to the social and biological sciences. A vner Friedman Willard Miller APPLICATIONS OF COMBINATORICS AND GRAPH THEORY TO THE BIOLOGICAL AND SOCIAL SCIENCES: SEVEN FUNDAMENTAL IDEAS FRED S. RoBERTS* Abstract. To set the stage for the other papers in this volume, seven fundamental concepts which arise in the applications of combinatorics and graph theory in the biological and social sciences are described. These ideas are: RNA chains as "words" in a 4 letter alphabet; interval graphs; competition graphs or niche overlap graphs; qualitative stability; balanced signed graphs; social welfare functions; and semiorders. For each idea, some basic results are presented, some recent results are given, and some open problems are mentioned.

## Basic Phylogenetic Combinatorics

Author | : Andreas Dress,Katharina T. Huber,Jacobus Koolen |

Publsiher | : Cambridge University Press |

Total Pages | : 264 |

Release | : 2012 |

ISBN 10 | : 0521768322 |

ISBN 13 | : 9780521768320 |

Language | : EN, FR, DE, ES & NL |

**Basic Phylogenetic Combinatorics Book Review:**

Phylogenetic combinatorics is a branch of discrete applied mathematics concerned with the combinatorial description and analysis of phylogenetic trees and related mathematical structures such as phylogenetic networks and tight spans. Based on a natural conceptual framework, the book focuses on the interrelationship between the principal options for encoding phylogenetic trees: split systems, quartet systems and metrics. Such encodings provide useful options for analyzing and manipulating phylogenetic trees and networks, and are at the basis of much of phylogenetic data processing. This book highlights how each one provides a unique perspective for viewing and perceiving the combinatorial structure of a phylogenetic tree and is, simultaneously, a rich source for combinatorial analysis and theory building. Graduate students and researchers in mathematics and computer science will enjoy exploring this fascinating new area and learn how mathematics may be used to help solve topical problems arising in evolutionary biology.

## Handbook of Discrete and Computational Geometry Third Edition

Author | : Csaba D. Toth,Joseph O'Rourke,Jacob E. Goodman |

Publsiher | : CRC Press |

Total Pages | : 1928 |

Release | : 2017-11-22 |

ISBN 10 | : 1351645919 |

ISBN 13 | : 9781351645911 |

Language | : EN, FR, DE, ES & NL |

**Handbook of Discrete and Computational Geometry Third Edition Book Review:**

The Handbook of Discrete and Computational Geometry is intended as a reference book fully accessible to nonspecialists as well as specialists, covering all major aspects of both fields. The book offers the most important results and methods in discrete and computational geometry to those who use them in their work, both in the academic world—as researchers in mathematics and computer science—and in the professional world—as practitioners in ?elds as diverse as operations research, molecular biology, and robotics. Discrete geometry has contributed signi?cantly to the growth of discrete mathematics in recent years. This has been fueled partly by the advent of powerful computers and by the recent explosion of activity in the relatively young ?eld of computational geometry. This synthesis between discrete and computational geometry lies at the heart of this Handbook. A growing list of application fields includes combinatorial optimization, computer-aided design, computer graphics, crystallography, data analysis, error-correcting codes, geographic information systems, motion planning, operations research, pattern recognition, robotics, solid modeling, and tomography.