An Introduction to Systems Biology

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: 991

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

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: 502

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.

Life An Introduction to Complex Systems Biology

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: 9783642069154

Page: 374

View: 526

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.

A First Course in Systems Biology

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: 1351332945

Page: 480

View: 957

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.

Systems Biology A Very Short Introduction

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: 552

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.

Mathematical Modeling in Systems Biology

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: 672

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 Introduction to Pathway Modeling

This is revision 1.17 (April 2020) and includes reworded chapters on model fitting including a completely new chapter on Bayesian Infernece.

Systems Biology  Introduction to Pathway Modeling

Author: Herbert Sauro

Publisher: Future Skill Software

ISBN: 9780982477373

Page: 416

View: 506

Computer models of biochemical systems are starting to play an increasingly important role in modern systems and synthetic biology. This monograph introduces students to some of the essential topics in biochemical modeling using differential equations and stochastic models. The book includes many hands-on modeling exercises using Python and examples that illustrate many important concepts, including the stoichiometric networks, building models, running simulations, model fitting, stability of systems and multicompartment systems.

An Introduction to Computational Systems Biology

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.

An Introduction to Computational Systems Biology

Author: Karthik Raman

Publisher: CRC Press

ISBN: 0429944527

Page: 358

View: 615

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.

Systems Biology and Bioinformatics

The book then reviews the basic principles of molecular and cell biology using a system-oriented approach, with a brief description of the high-throughput biological experiments that produce databases.

Systems Biology and Bioinformatics

Author: Kayvan Najarian

Publisher: CRC Press

ISBN:

Page: 166

View: 575

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 used in what is being coined the digital era of biology. Written by field experts with proven track records, this authoritative textbook first provides an introduction to systems biology and its impact on biology and medicine. The book then reviews the basic principles of molecular and cell biology using a system-oriented approach, with a brief description of the high-throughput biological experiments that produce databases. The text includes techniques to discover genes, perform nucleotide and amino acid sequence matching, and estimate static gene dynamic pathways. The book also explains how to use system-oriented models to predict the behavior of biological systems for important applications such as rational drug design. The numerous examples and problem sets allow students to confidently explore practical systems biology applications using real examples with real biological data, making Systems Biology and Bioinformatics: A Computational Approach an ideal text for senior undergraduate and first-year graduate students.

Systems Biology

This book is an introduction to control in biochemical pathways.

Systems Biology

Author: Herbert Sauro

Publisher:

ISBN: 9780982477366

Page: 278

View: 552

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.

Modeling in Systems Biology

This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Modeling in Systems Biology

Author: Ina Koch

Publisher: Springer

ISBN: 9781447125983

Page: 364

View: 225

The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Foundations of Systems Biology

To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, ...

Foundations of Systems Biology

Author: Masao Nagasaki

Publisher: Springer Science & Business Media

ISBN: 9781848820234

Page: 155

View: 487

Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi?ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like • Is the database viewable through a web browser? • Is there a licensing fee? • What is the data type (metabolic, gene regulatory, signaling, etc. )? • Is the database developed/maintained by a curator or a computer? • Is there any software for editing pathways? • Is it possible to simulate the pathway? It then goes on to introduce a speci?c such tool, that is, the fabulous “Cell - lustrator 3. 0” tool developed by the authors.

Computational Systems Biology

In particular the work focuses on the engineering of biological systems and network modeling.

Computational Systems Biology

Author: Andres Kriete

Publisher: Academic Press

ISBN: 9780124059269

Page: 533

View: 108

This book 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.

Introduction to Systems Bology

This book is a comprehensive guide to applications of mathematical and computational approaches to cell biology.

Introduction to Systems Bology

Author: Zoltan Neufeld

Publisher:

ISBN: 9781848169012

Page: 300

View: 585

This book is a comprehensive guide to applications of mathematical and computational approaches to cell biology. It provides an accessible entry route into this interdisciplinary field for students and researchers from various specialized backgrounds in biology, mathematics, physics, engineering or computer science. It gives a balanced presentation of the methodology (differential equations, dynamical systems analysis, stochastic processes, networks and optimization) and new, emerging modeling approaches, illustrated through a structured collection of case studies in which the use of mathematical and computational methods combined with experiments leads to new insights into the biological phenomena. At the end of each chapter, this is complemented with a brief overview of the relevant systems biology literature, providing links to reviews and key research publications in the particular area for further reading. In addition to the modeling approaches, the book also describes the relevant mathematical and systems biology software tools, including a set of problems and computational exercises through which the reader can gain a practical knowledge of the wide range of computational tools and model databases currently available.

Modeling Biomolecular Networks

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: 920

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.

Modeling in Systems Biology

This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Modeling in Systems Biology

Author: Ina Koch

Publisher: Springer

ISBN: 9781849964739

Page: 364

View: 267

The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Systems Biology and Bioinformatics

The book then reviews the basic principles of molecular and cell biology using a system-oriented approach, with a brief description of the high-throughput biological experiments that produce databases.

Systems Biology and Bioinformatics

Author: Kayvan Najarian

Publisher: CRC Press

ISBN: 9781138118034

Page: 190

View: 654

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 used in what is being coined the digital eraof biology. Written by field experts with proven track records, this authoritative textbook first provides an introduction to systems biology and its impact on biology and medicine. The book then reviews the basic principles of molecular and cell biology using a system-oriented approach, with a brief description of the high-throughput biological experiments that produce databases. The text includes techniques to discover genes, perform nucleotide and amino acid sequence matching, and estimate static gene dynamic pathways. The book also explains how to use system-oriented models to predict the behavior of biological systems for important applications such as rational drug design. The numerous examples and problem sets allow students to confidently explore practical systems biology applications using real examples with real biological data, making Systems Biology and Bioinformatics: A Computational Approachan ideal text for senior undergraduate and first-year graduate students.

Aging and Health A Systems Biology Perspective

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: 577

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.

Stochastic Modelling for Systems Biology Third Edition

Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book.

Stochastic Modelling for Systems Biology  Third Edition

Author: Darren J. Wilkinson

Publisher: CRC Press

ISBN: 135100090X

Page: 384

View: 198

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. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, 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. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.