An Introduction to Systems Biology

An Introduction to Systems Biology

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: 1584886420

Category: Mathematics

Page: 320

View: 550

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.
Categories: Mathematics

Introduction to Systems Biology

Introduction to Systems Biology

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

View: 162

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.
Categories: Science

An Introduction to Systems Biology

An Introduction to Systems Biology

'An amplified sensitivity arising from covalent modification in biological systems', Proceedings of the National Academy of Sciences, 78(11), pp. 6840–6844. doi:10.1073/pnas.78.11.6840. Heinrich, R. and Schuster, S. 1998.

Author: Uri Alon

Publisher: CRC Press

ISBN: 9781000001327

Category: Mathematics

Page: 324

View: 489

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
Categories: Mathematics

An Introduction to Computational Systems Biology

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.

Author: Karthik Raman

Publisher:

ISBN: 1138597325

Category: Biological systems

Page: 336

View: 731

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.
Categories: Biological systems

An Introduction to Computational Systems Biology

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 established topics. Publishing a broad range of reference works, textbooks, ...

Author: Karthik Raman

Publisher: CRC Press

ISBN: 9780429944529

Category: Computers

Page: 358

View: 614

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.
Categories: Computers

Systems Biology Introduction to Pathway Modeling

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.

Author: Herbert Sauro

Publisher: Future Skill Software

ISBN: 0982477376

Category: Biological systems

Page: 416

View: 702

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.
Categories: Biological systems

Control Theory and Systems Biology

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., and Leibler, S. (1999). Robustness in bacterial chemotaxis. Nature 397:168–171.

Author: Pablo A. Iglesias

Publisher: MIT Press

ISBN: 9780262013345

Category: Science

Page: 345

View: 258

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

Systems Biology A Very Short Introduction

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.

Author: Eberhard O. Voit

Publisher: Oxford University Press

ISBN: 9780192563453

Category: Science

Page: 144

View: 154

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.
Categories: Science

Studyguide for Mathematical Modeling in Systems Biology

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.

Author: Cram101 Textbook Reviews

Publisher: Cram101

ISBN: 149026342X

Category:

Page: 78

View: 812

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.
Categories:

Kinetic Modelling in Systems Biology

Kinetic Modelling in Systems Biology

Bioinformatics: A Practical Approach Shui Qing Ye Cancer Modelling and Simulation Luigi Preziosi Computational ... in Bioinformatics Martin Gollery Introduction to Bioinformatics Anna Tramontano An Introduction to Systems Biology: ...

Author: Oleg Demin

Publisher: CRC Press

ISBN: 9781420011661

Category: Mathematics

Page: 360

View: 809

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
Categories: Mathematics

Systems Biology and Bioinformatics

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.

Author: Kayvan Najarian

Publisher: CRC Press

ISBN: 1138118036

Category:

Page: 190

View: 681

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.
Categories:

Systems Biology

Systems Biology

Algorithms in Bioinformatics: A Practical Introduction Wing-Kin Sung Bioinformatics: A Practical Approach Shui Qing Ye Biological Computation Ehud Lamm and Ron Unger Biological Sequence Analysis Using the SeqAn C++ Library Andreas ...

Author: Andreas Kremling

Publisher: CRC Press

ISBN: 9781466567894

Category: Mathematics

Page: 379

View: 727

Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.
Categories: Mathematics

Systems Biology and Livestock Science

Systems Biology and Livestock Science

BLBS088-01 te Pas September 10, 2011 4:15 Trim: 244mm×172mm Introduction to Systems Biology for Animal Scientists 21 which may be useful in reproductive physiology in land vertebrates. Interestingly, they found that not only the ...

Author: Marinus te Pas

Publisher: John Wiley & Sons

ISBN: 9780813811741

Category: Science

Page: 332

View: 777

Systems Biology is an interdisciplinary approach to the study of life made possible through the explosion of molecular data made available through the genome revolution and the simultaneous development of computational technologies that allow us to interpret these large data sets. Systems Biology has changed the way biological science views and studies life and has been implemented in research efforts across the biological sciences. Systems Biology and Livestock Science will be the first book to review the latest advances using this research methodology in efforts to improve the efficiency, health, and quality of livestock production. Systems Biology and Livestock Science opens with useful introductory chapters explaining key systems biology principles. The chapters then progress to look at specific advances in fields across livestock science. Coverage includes, but is not limited to, chapters on systems biology approaches to animal nutrition, reproduction, health and disease, and animal physiology. Written by leading researchers in the field, Systems Biology and Livestock Science, will be an invaluable resource to researchers, professionals, and advance students working in this rapidly developing discipline.
Categories: Science

Stochastic Dynamics for Systems Biology

Stochastic Dynamics for Systems Biology

Differential Equations and Mathematical Biology, Second Edition D.S. Jones, M.J. Plank, and B.D. Sleeman Dynamics of ... and Motion Amit Kessel and Nir Ben-Tal An Introduction to Systems Biology: Design Principles of Biological Circuits ...

Author: Christian Mazza

Publisher: CRC Press

ISBN: 9781466514942

Category: Mathematics

Page: 274

View: 966

Stochastic Dynamics for Systems Biology is one of the first books to provide a systematic study of the many stochastic models used in systems biology. The book shows how the mathematical models are used as technical tools for simulating biological processes and how the models lead to conceptual insights on the functioning of the cellular processing
Categories: Mathematics

Computational Systems Biology of Cancer

Computational Systems Biology of Cancer

Algorithms in Bioinformatics : A Practical Introduction Wing - Kin Sung Bioinformatics : Practical Approach Shui Qing Ye Biological Computation Ehud Lamm and Ron Unger Biological Sequence Analysis Using the SeqAn C ++ Library Andreas ...

Author: Emmanuel Barillot

Publisher: CRC Press

ISBN: 9781439831458

Category: Computers

Page: 461

View: 383

The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models-integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencin
Categories: Computers

A First Course in Systems Biology

A First Course in Systems Biology

[8] Wolkenhauer O, Kitano H & Cho K-H. An introduction to systems biology. IEEE Control Syst. Mag. 23 (2003) 38–48. [9] Westerhoff HV & Palsson BO. The evolution of molecular biology into systems biology. Nat. Biotechnol.

Author: Eberhard Voit

Publisher: Garland Science

ISBN: 9781351332941

Category: Computers

Page: 480

View: 531

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.
Categories: Computers

Stochastic Modelling for Systems Biology Second Edition

Stochastic Modelling for Systems Biology  Second Edition

Algorithms in Bioinformatics: A Practical Introduction Wing-Kin Sung Bioinformatics: A Practical Approach Shui Qing Ye Biological Computation Ehud Lamm and Ron Unger Biological Sequence Analysis Using the SeqAn C++ Library Andreas ...

Author: Darren J. Wilkinson

Publisher: CRC Press

ISBN: 9781439837764

Category: Mathematics

Page: 363

View: 718

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.
Categories: Mathematics

Systems Biology of Cell Signaling

Systems Biology of Cell Signaling

Cold Spring Harbor an Introduction to Modeling in Biology. Oxford University Laboratory Press, Cold Spring Harbor, NY, 2014. Press, Oxford, 2013. Goldbeter A. Biochemical Oscillations and Cellular Rhythms: Capra EJ, Laub MT.

Author: James E. Ferrell

Publisher: Garland Science

ISBN: 9781000430738

Category: Science

Page: 284

View: 160

How can we understand the complexity of genes, RNAs, and proteins and the associated regulatory networks? One approach is to look for recurring types of dynamical behavior. Mathematical models prove to be useful, especially models coming from theories of biochemical reactions such as ordinary differential equation models. Clever, careful experiments test these models and their basis in specific theories. This textbook aims to provide advanced students with the tools and insights needed to carry out studies of signal transduction drawing on modeling, theory, and experimentation. Early chapters summarize the basic building blocks of signaling systems: binding/dissociation, synthesis/destruction, and activation/inactivation. Subsequent chapters introduce various basic circuit devices: amplifiers, stabilizers, pulse generators, switches, stochastic spike generators, and oscillators. All chapters consistently use approaches and concepts from chemical kinetics and nonlinear dynamics, including rate-balance analysis, phase plane analysis, nullclines, linear stability analysis, stable nodes, saddles, unstable nodes, stable and unstable spirals, and bifurcations. This textbook seeks to provide quantitatively inclined biologists and biologically inclined physicists with the tools and insights needed to apply modeling and theory to interesting biological processes. Key Features: · Full-color illustration program with diagrams to help illuminate the concepts · Enables the reader to apply modeling and theory to the biological processes · Further Reading for each chapter · High-quality figures available for instructors to download
Categories: Science

Systems Biology

Systems Biology

4 Szallasi, Z., Stelling, J., Periwal, V. (2006) System Modeling in Cell Biology, The MIT Press. 5 Alon, U. (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman & Hall/CRC.

Author: Robert A. Meyers

Publisher: John Wiley & Sons

ISBN: 9783527326075

Category: Science

Page: 726

View: 720

Systems biology is a relatively new biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. Systems biology is the study of the interconnected aspect of molecular, cellular, tissue, whole animal and ecological processes, and comprises mathematical and mechanistic studies of dynamical, mesoscopic, open, spatiotemporally defined, nonlinear, complex systems that are far from thermodynamic equilibrium.
Categories: Science