Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks.

Author: Uri Alon

Publisher: CRC Press

ISBN: 9781584886426

Category: Mathematics

Page: 320

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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.

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems.

Author: Sangdun Choi

Publisher: Springer Science & Business Media

ISBN: 9781597455312

Category: Science

Page: 542

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This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Author: Uri Alon

Publisher: Chapman & Hall

ISBN: 1584886455

Category: Mathematics

Page:

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This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology.

Author: Brian P. Ingalls

Publisher: MIT Press

ISBN: 9780262018883

Category: Science

Page: 408

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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.

This book is an introduction to control in biochemical pathways.

Author: Herbert Sauro

Publisher:

ISBN: 0982477368

Category: Science

Page: 278

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This book is an introduction to control in biochemical pathways. Itintroduces students to some of the most important concepts in modern metabolic control principles. It covers the basics of metabolic controlanalysis that helps us think about how biochemical networks operate. The book should be suitable for undergraduates in their early (Junior, USA, second year UK) to mid years at college.

This book examines life not from the reductionist point of view, but rather asks the questions: what are the universal properties of living systems, and how can one construct from there a phenomenological theory of life that leads naturally ...

Author: Kunihiko Kaneko

Publisher: Springer

ISBN: 9783540326670

Category: Science

Page: 374

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This book examines life not from the reductionist point of view, but rather asks the questions: what are the universal properties of living systems, and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation is relatively non-technical to appeal to a broad spectrum of students and researchers.

Design Principles of Biological Circuits Uri Alon. modularity. In parallel, the
principles that appeared in the first edition have been refined and applied to
many more systems. Thus, every old chapter is extensively revised with new
examples ...

Author: Uri Alon

Publisher: CRC Press

ISBN: 9781000008166

Category: Mathematics

Page: 324

View: 172

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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

This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies.

Author: Lilia Alberghina

Publisher: Springer Science & Business Media

ISBN: 3540742697

Category: Computers

Page: 408

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For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.

This volume aims to provide a timely view of the state-of-the-art in systems biology.

Author: Sacha Baginsky

Publisher: Springer Science & Business Media

ISBN: 9783764374396

Category: Science

Page: 358

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This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.

An easy-to-read introductory text, comprised of concise vignettes that explain key concepts within systems biology without using jargon.

Author: Eberhard O. Voit

Publisher: Cambridge University Press

ISBN: 9781107149953

Category: Science

Page: 222

View: 961

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An easy-to-read introductory text, comprised of concise vignettes that explain key concepts within systems biology without using jargon.

Identification of the sites in MAP kinase kinase-1 phosphorylated by p74raf-1.
EMBO Journal 13:1610–1619. Alon, U. (2007). An Introduction to Systems
Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman &
Hall/CRC.

Author: Pablo A. Iglesias

Publisher: MIT Press

ISBN: 9780262013345

Category: Science

Page: 345

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A survey of how engineering techniques from control and systems theory can be used tohelp biologists understand the behavior of cellular systems.

This book provides the reader with the background and mastery of methods to execute standard systems biology tasks, understand the modern literature, and launch into specialized courses or projects that address biological questions using ...

Author: Eberhard O. Voit

Publisher: Garland Science

ISBN: 9781136215100

Category: Computers

Page: 496

View: 607

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A First Course in Systems Biology is a textbook designed for advanced undergraduate and graduate students. Its main focus is the development of computational models and their applications to diverse biological systems. Because the biological sciences have become so complex that no individual can acquire complete knowledge in any given area of specialization, the education of future systems biologists must instead develop a student's ability to retrieve, reformat, merge, and interpret complex biological information. This book provides the reader with the background and mastery of methods to execute standard systems biology tasks, understand the modern literature, and launch into specialized courses or projects that address biological questions using theoretical and computational means. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and larger-scale, often open-ended questions for further reflection.

Systems Biology in Toxicology and Environmental Health uses a systems biological perspective to detail the most recent findings that link environmental exposures to human disease, providing an overview of molecular pathways that are ...

Author: Rebecca Fry

Publisher: Academic Press

ISBN: 9780128015681

Category: Medical

Page: 284

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Systems Biology in Toxicology and Environmental Health uses a systems biological perspective to detail the most recent findings that link environmental exposures to human disease, providing an overview of molecular pathways that are essential for cellular survival after exposure to environmental toxicants, recent findings on gene-environment interactions influencing environmental agent-induced diseases, and the development of computational methods to predict susceptibility to environmental agents. Introductory chapters on molecular and cellular biology, toxicology and computational biology are included as well as an assessment of systems-based tools used to evaluate environmental health risks. Further topics include research on environmental toxicants relevant to human health and disease, various high-throughput technologies and computational methods, along with descriptions of the biological pathways associated with disease and the developmental origins of disease as they relate to environmental contaminants. Systems Biology in Toxicology and Environmental Health is an essential reference for undergraduate students, graduate students, and researchers looking for an introduction in the use of systems biology approaches to assess environmental exposures and their impacts on human health. Provides the first reference of its kind, demonstrating the application of systems biology in environmental health and toxicology Includes introductions to the diverse fields of molecular and cellular biology, toxicology, and computational biology Presents a foundation that helps users understand the connections between the environment and health effects, and the biological mechanisms that link them

New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more ...

Author: Darren J. Wilkinson

Publisher: CRC Press

ISBN: 9781439837726

Category: Mathematics

Page: 363

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Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Re-written to reflect this modern perspective, this second edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. Keeping with the spirit of the first edition, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more modular way An ancillary website provides links, resources, errata, and up-to-date information on installation and use of the associated R package More background material on the theory of Markov processes and stochastic differential equations, providing more substance for mathematically inclined readers Discussion of some of the more advanced concepts relating to stochastic kinetic models, such as random time change representations, Kolmogorov equations, Fokker-Planck equations and the linear noise approximation Simple modelling of "extrinsic" and "intrinsic" noise An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional mathematical detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Taking more of a qualitative rather than computational approach, this text presents the techniques required to undertake basic modeling of biological systems through the development and analysis of dynamical systems.

Author: Fred Brauer

Publisher: Chapman and Hall/CRC

ISBN: 1420066412

Category: Mathematics

Page: 488

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Taking more of a qualitative rather than computational approach, this text presents the techniques required to undertake basic modeling of biological systems through the development and analysis of dynamical systems. It includes many different types of applications from population biology and epidemiology. Keeping technical details to a minimum, the text only requires a basic understanding of calculus. It provides examples of problems with solutions followed by exercises to reinforce the examples. Many of the problems are somewhat challenging so as to encourage a deeper understanding and prompt the use of mathematics in learning about biology.

This book explores the use of concepts and tools from theoretical computer science to tackle the complexity of cell processes.

Author: Francois Fages

Publisher: Chapman and Hall/CRC

ISBN: 1466505842

Category: Mathematics

Page: 306

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This book explores the use of concepts and tools from theoretical computer science to tackle the complexity of cell processes. In a unified framework, it presents the different modeling formalisms of systems biology, emphasizing their formal relationships by abstraction functions and putting them into practice for building predictive models of cell functions. With exercises and computational models, the book reflects the author’s many years of researching, developing, and applying computer science methods in systems biology.

Garland, New York Alon U (2006) An introduction to systems biology: design
principles of biological circuits. Taylor & Francis, Boca Raton Altmann A,
Beerenwinkel N, Sing T, Savenkov I, D'a'umer M, Kaiser R, Rhee S-Y, Fessel WJ,
Shafer ...

Author: Frederick Marcus

Publisher: Springer Science & Business Media

ISBN: 3540783539

Category: Science

Page: 287

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Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.

This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Author: Pengcheng Fu

Publisher: John Wiley & Sons

ISBN: 0470437979

Category: Technology & Engineering

Page: 672

View: 449

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The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.

Author: Dan Gusfield

Publisher: Cambridge University Press

ISBN: 9781108421768

Category: Computers

Page: 428

View: 265

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This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.

Algorithms in Bioinformatics: A Practical Introduction Wing-Kin Sung
Bioinformatics: A Practical Approach Shui Qing Ye ... Gogol-Döring and Knut
Reinert Cancer Modelling and Simulation Luigi Preziosi Cancer Systems Biology
Edwin Wang ...

Author: Alpan Raval

Publisher: CRC Press

ISBN: 9781420010367

Category: Mathematics

Page: 335

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The new research area of genomics-inspired network biology lacks an introductory book that enables both physical/computational scientists and biologists to obtain a general yet sufficiently rigorous perspective of current thinking. Filling this gap, Introduction to Biological Networks provides a thorough introduction to genomics-inspired network biology for physical scientists and biologists involved in interdisciplinary research. The book focuses on the concept of molecular and genetic interaction networks as a paradigm for interpreting the complexity of molecular biology at a genomic scale. The authors describe the experimental methods used to discover and test networks of interaction among biological molecules. They also present computational methods for predicting the interaction networks, discuss general mechanisms of network formation and evolution, and explore the application of network approaches to important problems in biology and medicine. With many examples throughout and clear explanations of key concepts, this book is the first to offer a broad treatment of genomics-inspired network biology with sufficient mathematical and biological rigor. It gives readers a conceptual understanding of this burgeoning scientific field.