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: 654

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: 216

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: 839

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: 1351332937

Page: 480

View: 734

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.

An Introduction to Computational Systems Biology

The main objective of this book is to deliver 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:

ISBN: 9781138597327

Page: 336

View: 241

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 The book 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: 9781138118034

Page: 190

View: 980

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.

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: 972

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.

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: 259

Emphasizing computational methods, Systems Biology and Bioinformatics provides an introduction to systems biology and its impact on biology and medicine. It reviews 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 methods presented include techniques to discover genes, perform nucleotide and amino acid sequence matching, and estimate static gene dynamic pathways. It also explains applications for system-oriented models to predict the behavior of biological systems.

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: 960

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 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, USA

ISBN: 0198828373

Page: 160

View: 404

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.

An Introduction to Computational Systems Biology

About the Series: This series aims to capture new developments in computational biology, as well as high-quality work summarizing or contributing to more ...

An Introduction to Computational Systems Biology

Author: Karthik Raman

Publisher: CRC Press

ISBN: 0429944527

Page: 358

View: 329

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

This book is an introduction to control in biochemical pathways.

Systems Biology

Author: Herbert Sauro

Publisher:

ISBN: 9780982477366

Page: 278

View: 342

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: 594

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.

Studyguide for Mathematical Modeling in Systems Biology

Includes all testable terms, concepts, persons, places, and events. Just the FACTS101 provides the essentials of the textbook: all of the outlines, highlights, and quizzes for your textbook with optional online comprehensive practice tests.

Studyguide for Mathematical Modeling in Systems Biology

Author: Cram101 Textbook Reviews

Publisher: Cram101

ISBN: 9781490263427

Page: 78

View: 754

Never HIGHLIGHT a Book Again! Includes all testable terms, concepts, persons, places, and events. Cram101 Just the FACTS101 studyguides gives all of the outlines, highlights, and quizzes for your textbook with optional online comprehensive practice tests. Only Cram101 is Textbook Specific. Accompanies: 9780262018883. This item is printed on demand.

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 Science & Business Media

ISBN: 9781849964746

Page: 364

View: 616

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.

Control Theory and Systems Biology

An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall/CRC. Alon, U., Surette, M. G., Barkai, N., ...

Control Theory and Systems Biology

Author: Pablo A. Iglesias

Publisher: MIT Press

ISBN: 0262013347

Page: 345

View: 224

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

An Introduction to Dynamical Systems for Biological Modeling

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.

An Introduction to Dynamical Systems for Biological Modeling

Author: Fred Brauer

Publisher: Chapman and Hall/CRC

ISBN: 9781420066418

Page: 488

View: 185

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.

The Inner Workings of Life

Written in an informal and non-technical style, this book provides an accessible introduction to systems biology.

The Inner Workings of Life

Author: Eberhard O. Voit

Publisher: Cambridge University Press

ISBN: 1316682080

Page:

View: 354

Living systems are dynamic and extremely complex and their behaviour is often hard to predict by studying their individual parts. Systems biology promises to reveal and analyse these highly connected, regulated and adaptable systems, using mathematical modelling and computational analysis. This new systems approach is already having a broad impact on biological research and has potentially far-reaching implications for our understanding of life. Written in an informal and non-technical style, this book provides an accessible introduction to systems biology. Self-contained vignettes each convey a key theme and are intended to enlighten, provoke and interest readers of different academic disciplines, but also to offer new insight to those working in the field. Using a minimum amount of jargon and no mathematics, Voit manages to convey complex ideas and give the reader a genuine sense of the excitement that systems biology brings with it, as well as the current challenges and opportunities.

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: 496

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.

Kinetic Modelling in Systems Biology

... Simulation Luigi Preziosi Computational Biology: A Statistical Mechanics ... Introduction to Systems Biology: Design Principles of Biological Circuits ...

Kinetic Modelling in Systems Biology

Author: Oleg Demin

Publisher: CRC Press

ISBN: 1420011669

Page: 360

View: 528

With more and more interest in how components of biological systems interact, it is important to understand the various aspects of systems biology. Kinetic Modelling in Systems Biology focuses on one of the main pillars in the future development of systems biology. It explores both the methods and applications of kinetic modeling in this emerging f