# 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.

## Algebraic Combinatorics for Computational Biology

Author | : Nicholas Karl Eriksson |

Publsiher | : Unknown |

Total Pages | : 250 |

Release | : 2006 |

ISBN 10 | : 9780542824098 |

ISBN 13 | : 0542824094 |

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

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

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.

## 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.

## 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.

## Models of the Mind

Author | : Grace Lindsay |

Publsiher | : Bloomsbury Publishing |

Total Pages | : 320 |

Release | : 2021-03-04 |

ISBN 10 | : 1472966457 |

ISBN 13 | : 9781472966452 |

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

**Models of the Mind Book Review:**

The brain is made up of 85 billion neurons, which are connected by over 100 trillion synapses. For more than a century, a diverse array of researchers has been trying to find a language that can be used to capture the essence of what these neurons do and how they communicate – and how those communications create thoughts, perceptions and actions. The language they were looking for was mathematics, and we would not be able to understand the brain as we do today without it. In Models of the Mind, author and computational neuroscientist Grace Lindsay explains how mathematical models have allowed scientists to understand and describe many of the brain's processes, including decision-making, sensory processing, quantifying memory, and more. She introduces readers to the most important concepts in modern neuroscience, and highlights the tensions that arise when the abstract world of mathematical modelling collides with the messy details of biology. Each chapter focuses on mathematical tools that have been applied in a particular area of neuroscience, progressing from the simplest building block of the brain – the individual neuron – through to circuits of interacting neurons, whole brain areas and even the behaviours that brains command. Throughout, Grace examines the history of the field, starting with experiments done on neurons in frog legs at the turn of the twentieth century and building to the large models of artificial neural networks that form the basis of modern artificial intelligence. She demonstrates the value of describing the machinery of neuroscience using the elegant language of mathematics and reveals in full the remarkable fruits of this endeavour.

## Computing and Combinatorics

Author | : Joachim Gudmundsson,Julián Mestre,Taso Viglas |

Publsiher | : Springer |

Total Pages | : 606 |

Release | : 2012-08-14 |

ISBN 10 | : 3642322417 |

ISBN 13 | : 9783642322419 |

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

**Computing and Combinatorics Book Review:**

This book constitutes the refereed proceedings of the 18th Annual International Conference on Computing and Combinatorics, held in Sydney, Australia, in August 2012. The 50 revised full papers presented were carefully reviewed and selected from 121 submissions. Topics covered are algorithms and data structures; algorithmic game theory and online algorithms; automata, languages, logic, and computability; combinatorics related to algorithms and complexity; complexity theory; computational learning theory and knowledge discovery; cryptography, reliability and security, and database theory; computational biology and bioinformatics; computational algebra, geometry, and number theory; graph drawing and information visualization; graph theory, communication networks, and optimization.

## From Linear Operators to Computational Biology

Author | : Martin Davis,Edmond Schonberg |

Publsiher | : Springer Science & Business Media |

Total Pages | : 208 |

Release | : 2012-07-28 |

ISBN 10 | : 1447142829 |

ISBN 13 | : 9781447142829 |

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

**From Linear Operators to Computational Biology Book Review:**

In his rich and varied career as a mathematician, computer scientist, and educator, Jacob T. Schwartz wrote seminal works in analysis, mathematical economics, programming languages, algorithmics, and computational geometry. In this volume of essays, his friends, students, and collaborators at the Courant Institute of Mathematical Sciences present recent results in some of the fields that Schwartz explored: quantum theory, the theory and practice of programming, program correctness and decision procedures, dextrous manipulation in Robotics, motion planning, and genomics. In addition to presenting recent results in these fields, these essays illuminate the astonishingly productive trajectory of a brilliant and original scientist and thinker.

## Phenotypic Switching

Author | : Herbert Levine,Mohit Kumar Jolly,Prakash Kulkarni,Vidyanand Nanjundiah |

Publsiher | : Academic Press |

Total Pages | : 762 |

Release | : 2020-06-10 |

ISBN 10 | : 012817997X |

ISBN 13 | : 9780128179970 |

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

**Phenotypic Switching Book Review:**

Phenotypic Switching: Implications in Biology and Medicine provides a comprehensive examination of phenotypic switching across biological systems, including underlying mechanisms, evolutionary significance, and its role in biomedical science. Contributions from international leaders discuss conceptual and theoretical aspects of phenotypic plasticity, its influence over biological development, differentiation, biodiversity, and potential applications in cancer therapy, regenerative medicine and stem cell therapy, among other treatments. Chapters discuss fundamental mechanisms of phenotypic switching, including transition states, cell fate decisions, epigenetic factors, stochasticity, protein-based inheritance, specific areas of human development and disease relevance, phenotypic plasticity in melanoma, prostate cancer, breast cancer, non-genetic heterogeneity in cancer, hepatitis C, and more. This book is essential for active researchers, basic and translational scientists, clinicians, postgraduates and students in genetics, human genomics, pathology, bioinformatics, developmental biology, evolutionary biology and adaptive opportunities in yeast. Thoroughly addresses the conceptual, experimental and translational aspects that underlie phenotypic plasticity Emphasizes quantitative approaches, nonlinear dynamics, mechanistic insights and key methodologies to advance phenotypic plasticity studies Features a diverse range of chapter contributions from international leaders in the field

## Combinatorial Pattern Matching

Author | : Moshe Lewenstein,Gabriel Valiente |

Publsiher | : Springer |

Total Pages | : 420 |

Release | : 2006-07-01 |

ISBN 10 | : 3540354611 |

ISBN 13 | : 9783540354611 |

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

**Combinatorial Pattern Matching Book Review:**

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.

## 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.

## Combinatorial Algorithms

Author | : Costas Iliopoulos,Hon Wai Leong,Wing-Kin Sung |

Publsiher | : Springer |

Total Pages | : 388 |

Release | : 2018-08-03 |

ISBN 10 | : 3319946676 |

ISBN 13 | : 9783319946672 |

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

**Combinatorial Algorithms Book Review:**

This book constitutes the refereed post-conference proceedings of the 29th International Workshop on Combinatorial Algorithms, IWOCA 2018, held in Singapore, Singapore, in July 2018. The 31 regular papers presented in this volume were carefully reviewed and selected from 69 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 randomised algorithms, algorithms for big data analytics, and new paradigms of computation.

## Algorithms on Strings Trees and Sequences

Author | : Dan Gusfield |

Publsiher | : Cambridge University Press |

Total Pages | : 135 |

Release | : 1997-05-28 |

ISBN 10 | : 1139811002 |

ISBN 13 | : 9781139811002 |

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

**Algorithms on Strings Trees and Sequences Book Review:**

String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This 1997 book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.

## 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.

## Language and Automata Theory and Applications

Author | : Adrian-Horia Dediu,Carlos Martín-Vide,Bianca Truthe |

Publsiher | : Springer |

Total Pages | : 580 |

Release | : 2013-03-15 |

ISBN 10 | : 3642370640 |

ISBN 13 | : 9783642370649 |

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

**Language and Automata Theory and Applications Book Review:**

This book constitutes the refereed proceedings of the 7th International Conference on Language and Automata Theory and Applications, LATA 2013, held in Bilbao, Spain in April 2013. The 45 revised full papers presented together with 5 invited talks were carefully reviewed and selected from 97 initial submissions. The volume features contributions from both classical theory fields and application areas (bioinformatics, systems biology, language technology, artificial intelligence, etc.). Among the topics covered are algebraic language theory; algorithms for semi-structured data mining; algorithms on automata and words; automata and logic; automata for system analysis and program verification; automata, concurrency and Petri nets; automatic structures; cellular automata; combinatorics on words; computability; computational complexity; computational linguistics; data and image compression; decidability questions on words and languages; descriptional complexity; DNA and other models of bio-inspired computing; document engineering; foundations of finite state technology; foundations of XML; fuzzy and rough languages; grammars (Chomsky hierarchy, contextual, multidimensional, unification, categorial, etc.); grammars and automata architectures; grammatical inference and algorithmic learning; graphs and graph transformation; language varieties and semigroups; language-based cryptography; language-theoretic foundations of artificial intelligence and artificial life; parallel and regulated rewriting; parsing; pattern recognition; patterns and codes; power series; quantum, chemical and optical computing; semantics; string and combinatorial issues in computational biology and bioinformatics; string processing algorithms; symbolic dynamics; symbolic neural networks; term rewriting; transducers; trees, tree languages and tree automata; weighted automata.

## Discrete and Topological Models in Molecular Biology

Author | : Nataša Jonoska,Masahico Saito |

Publsiher | : Springer Science & Business Media |

Total Pages | : 524 |

Release | : 2013-12-23 |

ISBN 10 | : 3642401937 |

ISBN 13 | : 9783642401930 |

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

**Discrete and Topological Models in Molecular Biology Book Review:**

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.

## 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.

## Language and Automata Theory and Applications

Author | : Adrian-Horia Dediu,Carlos Martín-Vide,Bianca Truthe |

Publsiher | : Springer |

Total Pages | : 580 |

Release | : 2013-02-20 |

ISBN 10 | : 9783642370632 |

ISBN 13 | : 3642370632 |

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

**Language and Automata Theory and Applications Book Review:**

This book constitutes the refereed proceedings of the 7th International Conference on Language and Automata Theory and Applications, LATA 2013, held in Bilbao, Spain in April 2013. The 45 revised full papers presented together with 5 invited talks were carefully reviewed and selected from 97 initial submissions. The volume features contributions from both classical theory fields and application areas (bioinformatics, systems biology, language technology, artificial intelligence, etc.). Among the topics covered are algebraic language theory; algorithms for semi-structured data mining; algorithms on automata and words; automata and logic; automata for system analysis and program verification; automata, concurrency and Petri nets; automatic structures; cellular automata; combinatorics on words; computability; computational complexity; computational linguistics; data and image compression; decidability questions on words and languages; descriptional complexity; DNA and other models of bio-inspired computing; document engineering; foundations of finite state technology; foundations of XML; fuzzy and rough languages; grammars (Chomsky hierarchy, contextual, multidimensional, unification, categorial, etc.); grammars and automata architectures; grammatical inference and algorithmic learning; graphs and graph transformation; language varieties and semigroups; language-based cryptography; language-theoretic foundations of artificial intelligence and artificial life; parallel and regulated rewriting; parsing; pattern recognition; patterns and codes; power series; quantum, chemical and optical computing; semantics; string and combinatorial issues in computational biology and bioinformatics; string processing algorithms; symbolic dynamics; symbolic neural networks; term rewriting; transducers; trees, tree languages and tree automata; weighted automata.

## Language and Automata Theory and Applications

Author | : Adrian-Horia Dediu,Carlos Martín-Vide,José-Luis Sierra-Rodríguez,Bianca Truthe |

Publsiher | : Springer |

Total Pages | : 614 |

Release | : 2014-02-05 |

ISBN 10 | : 3319049216 |

ISBN 13 | : 9783319049212 |

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

**Language and Automata Theory and Applications Book Review:**

This book constitutes the refereed proceedings of the 8th International Conference on Language and Automata Theory and Applications, LATA 2014, held in Madrid, Spain in March 2014. The 45 revised full papers presented together with 4 invited talks were carefully reviewed and selected from 116 submissions. The papers cover the following topics: algebraic language theory; algorithms on automata and words; automata and logic; automata for system analysis and program verification; automata, concurrency and Petri nets; automatic structures; combinatorics on words; computability; computational complexity; descriptional complexity; DNA and other models of bio-inspired computing; foundations of finite state technology; foundations of XML; grammars (Chomsky hierarchy, contextual, unification, categorial, etc.); grammatical inference and algorithmic learning; graphs and graph transformation; language varieties and semigroups; parsing; patterns; quantum, chemical and optical computing; semantics; string and combinatorial issues in computational biology and bioinformatics; string processing algorithms; symbolic dynamics; term rewriting; transducers; trees, tree languages and tree automata; weighted automata.