An Introduction to Systems Biology

by Uri Alon

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

An Introduction to Systems Biology

Author: Uri Alon

Publisher: CRC Press

ISBN: 1584886420

Page: 320

View: 203

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.

An Introduction to Systems Biology

by Uri Alon

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.

An Introduction to Systems Biology

Author: Uri Alon

Publisher: CRC Press

ISBN: 1000008169

Page: 324

View: 502

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

Introduction to Systems Biology

by Sangdun Choi

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

Introduction to Systems Biology

Author: Sangdun Choi

Publisher: Springer Science & Business Media

ISBN: 1597455318

Page: 542

View: 202

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.

Mathematical Modeling in Systems Biology

by Brian P. Ingalls

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

Mathematical Modeling in Systems Biology

Author: Brian P. Ingalls

Publisher: MIT Press

ISBN: 0262018888

Page: 408

View: 941

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.

Systems Biology

by Herbert Sauro

This book is an introduction to control in biochemical pathways.

Systems Biology

Author: Herbert Sauro

Publisher:

ISBN: 9780982477366

Page: 278

View: 323

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.

Systems Biology A Very Short Introduction

by Eberhard O. Voit

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.

Systems Biology A Very Short Introduction

Author: Eberhard O. Voit

Publisher: Oxford University Press

ISBN: 0192563459

Page: 144

View: 355

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.

Modeling Biomolecular Networks

by Anirvan M. Sengupta

This book describes the essentials of a mathematical description of the dynamics of biochemical networks.

Modeling Biomolecular Networks

Author: Anirvan M. Sengupta

Publisher:

ISBN: 9780198568049

Page: 208

View: 318

This book describes the essentials of a mathematical description of the dynamics of biochemical networks. It covers both deterministic and stochastic aspects of the dynamics. After providing a brief introduction to basic molecular biology, the book describes fundamentals of chemical kinetics. The chapter on signal transduction makes contact with ideas from feedback circuit analysis and signal processing. The chapter on switches and oscillators analyses in detail biological examples, both natural and synthetic. Excitable systems are introduced and contrasted with oscillators. The last chapter deals with pattern formation and development and brings us to current questions of robustness of performance of developmental networks. The book provides brief introductions to some of the mathematical tools required in the main text and in a dedicated appendix. The emphasis, throughout, is on understanding of the essential dynamical aspects rather than just on recipes to build complex models.

Life An Introduction to Complex Systems Biology

by Kunihiko Kaneko

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 ...

Life An Introduction to Complex Systems Biology

Author: Kunihiko Kaneko

Publisher: Springer

ISBN: 3540326677

Page: 374

View: 770

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.

Systems Biology

by Lilia Alberghina

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

Systems Biology

Author: Lilia Alberghina

Publisher: Springer Science & Business Media

ISBN: 9783540742692

Page: 408

View: 209

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.

Systematic

by James R. Valcourt

SYSTEMATIC is the first book to introduce general readers to systems biology, which is improving medical treatments and our understanding of living things.

Systematic

Author: James R. Valcourt

Publisher: Bloomsbury Publishing USA

ISBN: 1632860317

Page: 288

View: 846

A brilliant young scientist introduces us to the fascinating field that is changing our understanding of how the body works and the way we can approach healing. SYSTEMATIC is the first book to introduce general readers to systems biology, which is improving medical treatments and our understanding of living things. In traditional bottom-up biology, a biologist might spend years studying how a single protein works, but systems biology studies how networks of those proteins work together--how they promote health and how to remedy the situation when the system isn't functioning properly. Breakthroughs in systems biology became possible only when powerful computer technology enabled researchers to process massive amounts of data to study complete systems, and has led to progress in the study of gene regulation and inheritance, cancer drugs personalized to an individual's genetically unique tumor, insights into how the brain works, and the discovery that the bacteria and other microbes that live in the gut may drive malnutrition and obesity. Systems biology is allowing us to understand more complex phenomena than ever before. In accessible prose, SYSTEMATIC sheds light not only on how systems within the body work, but also on how research is yielding new kinds of remedies that enhance and harness the body's own defenses.

Plant Systems Biology

by Sacha Baginsky

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

Plant Systems Biology

Author: Sacha Baginsky

Publisher: Springer Science & Business Media

ISBN: 376437439X

Page: 358

View: 353

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.

The Inner Workings of Life

by Eberhard O. Voit

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

The Inner Workings of Life

Author: Eberhard O. Voit

Publisher: Cambridge University Press

ISBN: 1107149959

Page: 222

View: 850

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

Control Theory and Systems Biology

by Pablo A. Iglesias

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.

Control Theory and Systems Biology

Author: Pablo A. Iglesias

Publisher: MIT Press

ISBN: 0262013347

Page: 345

View: 963

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

A First Course in Systems Biology

by Eberhard Voit

New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law ...

A First Course in Systems Biology

Author: Eberhard Voit

Publisher: Garland Science

ISBN: 1351332937

Page: 480

View: 124

A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. 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 large-scale, often open-ended questions for further reflection.

Computational Systems Biology

by Paola Lecca

This book addresses the challenge to integrate highly diverse quantitative approaches into a unified framework by highlighting the relationships existing among network analysis, inference, and modeling.

Computational Systems Biology

Author: Paola Lecca

Publisher: Woodhead Publishing

ISBN: 0081001150

Page: 180

View: 392

Computational Systems Biology: Inference and Modelling provides an introduction to, and overview of, network analysis inference approaches which form the backbone of the model of the complex behavior of biological systems. This book addresses the challenge to integrate highly diverse quantitative approaches into a unified framework by highlighting the relationships existing among network analysis, inference, and modeling. The chapters are light in jargon and technical detail so as to make them accessible to the non-specialist reader. The book is addressed at the heterogeneous public of modelers, biologists, and computer scientists. Provides a unified presentation of network inference, analysis, and modeling Explores the connection between math and systems biology, providing a framework to learn to analyze, infer, simulate, and modulate the behavior of complex biological systems Includes chapters in modular format for learning the basics quickly and in the context of questions posed by systems biology Offers a direct style and flexible formalism all through the exposition of mathematical concepts and biological applications

Aging and Health A Systems Biology Perspective

by A.I. Yashin

Finally, the book presents an outlook for the development of interventions to delay or to reverse the features of aging.

Aging and Health A Systems Biology Perspective

Author: A.I. Yashin

Publisher: Karger Medical and Scientific Publishers

ISBN: 3318027308

Page: 206

View: 645

Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its application to biological aging. Key pathways and processes that impinge on aging are reviewed, and how they contribute to health and disease during aging is discussed. The evolution of this situation is analyzed, and the consequences for the study of genetic effects on aging are presented. Epigenetic programming of aging, as a continuation of development, creates an interface between the genome and the environment. New research into the gut microbiome describes how this interface may operate in practice with marked consequences for a variety of disorders. This analysis is bolstered by a view of the aging organism as a whole, with conclusions about the mechanisms underlying resilience of the organism to change, and is expanded with a discussion of circadian rhythms in aging. Finally, the book presents an outlook for the development of interventions to delay or to reverse the features of aging. The publication is recommended to students, researchers as well as professionals dealing with public health and public policy related to an aging society.

Systems Biology in Toxicology and Environmental Health

by Rebecca Fry

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 ...

Systems Biology in Toxicology and Environmental Health

Author: Rebecca Fry

Publisher: Academic Press

ISBN: 0128015683

Page: 284

View: 658

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

Stochastic Modelling for Systems Biology Second Edition

by Darren J. Wilkinson

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 ...

Stochastic Modelling for Systems Biology Second Edition

Author: Darren J. Wilkinson

Publisher: CRC Press

ISBN: 1439837724

Page: 363

View: 348

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.