An Introduction to Computational Systems Biology

An Introduction to Computational Systems Biology
Author: Karthik Raman
Publisher: CRC Press
Total Pages: 359
Release: 2021-05-30
Genre: Computers
ISBN: 0429944527

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This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling Covers a broad spectrum of modelling, from static networks to dynamic models and constraint-based models Thoughtful exercises to test and enable understanding of concepts State-of-the-art chapters on exciting new developments, like community modelling and biological circuit design Emphasis on coding and software tools for systems biology Companion website featuring lecture videos, figure slides, codes, supplementary exercises, further reading, and appendices: https://ramanlab.github.io/SysBioBook/ An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.

Introduction to Computational Biology

Introduction to Computational Biology
Author: Michael S. Waterman
Publisher: CRC Press
Total Pages: 456
Release: 2018-05-02
Genre: Mathematics
ISBN: 1351437089

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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.

An Introduction to Systems Biology

An Introduction to Systems Biology
Author: Uri Alon
Publisher: CRC Press
Total Pages: 324
Release: 2006-07-07
Genre: Mathematics
ISBN: 1584886420

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Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.

Systems Biology and Bioinformatics

Systems Biology and Bioinformatics
Author: Kayvan Najarian
Publisher: CRC Press
Total Pages: 190
Release: 2009-04-13
Genre: Medical
ISBN: 1439882940

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The availability of molecular imaging and measurement systems enables today's biologists to swiftly monitor thousands of genes involved in a host of diseases, a critical factor in specialized drug development. Systems Biology and Bioinformatics: A Computational Approach provides students with a comprehensive collection of the computational methods

Mathematical Modeling in Systems Biology

Mathematical Modeling in Systems Biology
Author: Brian P. Ingalls
Publisher: MIT Press
Total Pages: 423
Release: 2022-06-07
Genre: Science
ISBN: 0262545829

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An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.

Bioinformatics

Bioinformatics
Author: Stanley I. Letovsky
Publisher: Springer Science & Business Media
Total Pages: 298
Release: 2006-06-01
Genre: Science
ISBN: 0306469030

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Bioinformatics brings computational methods to the analysis and processing of genomic data. Bioinformatics: Databases and Systems focuses on the issues of system building and data curation that dominate the day-to-day concerns of bioinformatics practitioners. Included are chapters by many of today's leading bioinformatics practitioners, describing most of the current paradigms of system building and curation, including both their strengths and weaknesses. Biological topics covered include sequence databases, metabolic pathways, phenotypes, variety collections, gene expression atlases and neuroinformatics. Species range from bacteria to mammals to plants. Software systems and technologies covered include OPM, CORBA, SRS, KLEISLI, ACEDB, Web-based integration and laboratory workflow. Bioinformatics: Databases and Systems provides a valuable introduction for newcomers to the field, and a useful reference for veterans.

Computational Systems Biology

Computational Systems Biology
Author: Andres Kriete
Publisher: Academic Press
Total Pages: 549
Release: 2013-11-26
Genre: Computers
ISBN: 0124059384

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This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

An Introduction to Systems Biology

An Introduction to Systems Biology
Author: Uri Alon
Publisher: CRC Press
Total Pages: 390
Release: 2019-07-12
Genre: Mathematics
ISBN: 1000008169

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Praise for the first edition: ... superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. – Nature [This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology ... It assumes no prior knowledge of or even interest in biology ... One final aspect that must be mentioned is the wonderful set of exercises that accompany each chapter. ... Alon’s book should become a standard part of the training of graduate students. – Physics Today Written for students and researchers, the second edition of this best-selling textbook continues to offer a clear presentation of design principles that govern the structure and behavior of biological systems. It highlights simple, recurring circuit elements that make up the regulation of cells and tissues. Rigorously classroom-tested, this edition includes new chapters on exciting advances made in the last decade. Features: Includes seven new chapters The new edition has 189 exercises, the previous edition had 66 Offers new examples relevant to human physiology and disease The book website including course videos can be found here: https://www.weizmann.ac.il/mcb/UriAlon/introduction-systems-biology-design-principles-biological-circuits.

Systems Biology: A Very Short Introduction

Systems Biology: A Very Short Introduction
Author: Eberhard O. Voit
Publisher: Oxford University Press
Total Pages: 144
Release: 2020-03-26
Genre: Science
ISBN: 0192563440

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Systems biology came about as growing numbers of engineers and scientists from other fields created algorithms which supported the analysis of biological data in incredible quantities. Whereas biologists of the past had been forced to study one item or aspect at a time, due to technical and biological limitations, it suddenly became possible to study biological phenomena within their natural contexts. This interdisciplinary field offers a holistic approach to interpreting these processes, and has been responsible for some of the most important developments in the science of human health and environmental sustainability. This Very Short Introduction outlines the exciting processes and possibilities in the new field of systems biology. Eberhard O. Voit describes how it enabled us to learn how intricately the expression of every gene is controlled, how signaling systems keep organisms running smoothly, and how complicated even the simplest cells are. He explores what this field is about, why it is needed, and how it will affect our understanding of life, particularly in the areas of personalized medicine, drug development, food and energy production, and sustainable stewardship of our environments. Throughout he considers how new tools are being provided from the fields of mathematics, computer science, engineering, physics, and chemistry to grasp the complexity of the countless interacting processes in cells which would overwhelm the cognitive and analytical capabilities of the human mind. ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable.

Introduction to Bioinformatics

Introduction to Bioinformatics
Author: Anna Tramontano
Publisher: CRC Press
Total Pages: 192
Release: 2018-10-03
Genre: Science
ISBN: 1420010883

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Guiding readers from the elucidation and analysis of a genomic sequence to the prediction of a protein structure and the identification of the molecular function, Introduction to Bioinformatics describes the rationale and limitations of the bioinformatics methods and tools that can help solve biological problems. Requiring only a limited mathematical and statistical background, the book shows how to efficiently apply these approaches to biological data and evaluate the resulting information. The author, an expert bioinformatics researcher, first addresses the ways of storing and retrieving the enormous amount of biological data produced every day and the methods of decrypting the information encoded by a genome. She then covers the tools that can detect and exploit the evolutionary and functional relationships among biological elements. Subsequent chapters illustrate how to predict the three-dimensional structure of a protein. The book concludes with a discussion of the future of bioinformatics. Even though the future will undoubtedly offer new tools for tackling problems, most of the fundamental aspects of bioinformatics will not change. This resource provides the essential information to understand bioinformatics methods, ultimately facilitating in the solution of biological problems.