Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks.
Author: Uri Alon
Publisher: CRC Press
ISBN: 9781584886426
Category: Mathematics
Page: 320
View: 828
Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.
This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems.
Author: Sangdun Choi
Publisher: Springer Science & Business Media
ISBN: 9781597455312
Category: Science
Page: 542
View: 716
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.
This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology.
Author: Brian P. Ingalls
Publisher: MIT Press
ISBN: 9780262018883
Category: Science
Page: 408
View: 987
An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.
This book 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.
Author: KARTHIK. RAMAN
Publisher: CRC Press
ISBN: 1138597325
Category:
Page: 360
View: 289
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 which will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling. Coding and software tools for systems biology. Covers the entire spectrum of modelling, from static networks, to dynamic models. Thoughtful exercises to test and enable student understanding of concepts. State-of-the-art chapters on exciting new developments, like whole-cell modelling and community modelling. The book is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.
This book examines life not from the reductionist point of view, but rather asks the questions: what are the universal properties of living systems, and how can one construct from there a phenomenological theory of life that leads naturally ...
Author: Kunihiko Kaneko
Publisher: Springer
ISBN: 9783540326670
Category: Science
Page: 374
View: 277
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.
This book is an introduction to control in biochemical pathways.
Author: Herbert Sauro
Publisher:
ISBN: 0982477368
Category: Science
Page: 278
View: 676
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.
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: 9780192563446
Category: Science
Page: 144
View: 222
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.
SYSTEMATIC is the first book to introduce general readers to systems biology, which is improving medical treatments and our understanding of living things.
Author: James R. Valcourt
Publisher: Bloomsbury Publishing USA
ISBN: 9781632860316
Category: Science
Page: 288
View: 591
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.
Garland, New York Alon U (2006) An introduction to systems biology: design
principles of biological circuits. Taylor & Francis, Boca Raton Altmann A,
Beerenwinkel N, Sing T, Savenkov I, D'a'umer M, Kaiser R, Rhee S-Y, Fessel WJ,
Shafer ...
Author: Frederick Marcus
Publisher: Springer Science & Business Media
ISBN: 3540783539
Category: Science
Page: 287
View: 875
Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.
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 ...
Author: Eberhard Voit
Publisher: Garland Science
ISBN: 9781351332941
Category: Computers
Page: 480
View: 443
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.
Algorithms in Bioinformatics: A Practical Introduction Wing-Kin Sung
Bioinformatics: A Practical Approach Shui Qing Ye ... and Mathematical Biology,
Second Edition D.S. Jones, M.J. Plank, and B.D. Sleeman Dynamics of Biological Systems ...
Author: Alpan Raval
Publisher: CRC Press
ISBN: 9781420010367
Category: Computers
Page: 335
View: 702
The new research area of genomics-inspired network biology lacks an introductory book that enables both physical/computational scientists and biologists to obtain a general yet sufficiently rigorous perspective of current thinking. Filling this gap, Introduction to Biological Networks provides a thorough introduction to genomics-inspired network bi
Biology. to. the. Non-Human. Primate. Model. of Influenza Pathogenesis and
Vaccinology Carole Baskin Abstract Nonhuman primates have ... Systems biology is a powerful tool for this purpose, because it provides a much needed
wide angle view of complex interactions taking ... Berlin Heidelberg 2012
Published Online: 14 August 2012 Contents 1 Introduction: How Systems Biology
Helps us See the.
Author: Michael G. Katze
Publisher: Springer Science & Business Media
ISBN: 9783642330995
Category: Medical
Page: 263
View: 581
First, systems biology is an inter-disciplinary approach, requiring the combined talents of biologists, mathematicians, and computer scientists. Second, systems biology is holistic, with the goal of obtaining a comprehensive understanding of the workings of biological systems. This is achieved through the acquisition of massive amounts of data by high-throughput technologies—oligonucleotide microarrays, mass spectrometry, and next-generation sequencing—and the analysis of this data through sophisticated mathematical algorithms. It is perhaps the use of mathematics, to integrate abundant and diverse types of data and to generate models of interconnected molecular networks, that best characterizes systems biology.
Inference. Frank Doyle and Douglas Lauffenburger INTRODUCTION As systems biology emerges in the post-genomic era, the emphasis is shifting from
annotation of individual genes and gene products to ascertaining how DNA-
protein and ...
Author: Marvin Cassman
Publisher: Springer Science & Business Media
ISBN: 9781402054686
Category: Mathematics
Page: 262
View: 572
This book explores Systems Biology as the understanding of biological network behaviors, and in particular their dynamic aspects, which requires the utilization of mathematical modeling tightly linked to experiment. A variety of approaches are discussed here: the identification and validation of networks, the creation of appropriate datasets, the development of tools for data acquisition and software development, and the use of modeling and simulation software in close concert with experiment.
1 Introduction As Systems Biology transforms intoone ofthemain fields in life
sciences, the number ofavailablecomputational models isgrowingatan ever
increasingpace. Atthesametime, theirsize andcomplexity are alsoincreasing.The
need to ...
Author: Monika Heiner
Publisher: Springer Science & Business Media
ISBN: 9783540885610
Category: Computers
Page: 401
View: 556
This volume contains the proceedings of the 6th Conference on Computational Methods in Systems Biology (CMSB) held in October 2008 in Rostock/ Warnemunde. ] The CMSB conference series was established in 2003 to promote the c- vergence of (1) modelers, physicists, mathematicians, and theoretical computer scientists from ?elds such as language design, concurrency theory, software ve- ?cation, and (2) molecular biologists, physicians, neuroscientists joined by their interest in a systems-level understanding of cellular physiology and pathology. Sincethistime, theconferencehastakenplaceannually. Theconferencehasbeen held in Italy, France, and the UK, and we were glad to host CMSB in Germany for the ?rst time. The summaries of the invited talks by Hidde de Jong, Jane Hillston, Koichi Takahashi, Nicolas Le Novere, and Dieter Oesterhelt are included at the - ginning of the proceedings. The 21 regular papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and ?ux analysis, and case studies. They were - lected out of more than 60 submissions by a careful reviewing process. Each paper received at least three reviews from members of the Program Committee consistingof27renownedscientistsfromsevencountries. We wouldliketothank all members of the Program Committee and the referees for the thorough and insightful reviews and the constructive discussions. Due to the number of hi- quality submissions, the decision on which papers to accept or reject was not easy. Therefore, we integrated a rebuttal phase for the ?rst tim
... a very specific regulatory role at the nutrient and oxygen availability transitions.
C. Priami (Ed.): CMSB 2006, LNBI 4210, pp. 271–284, 2006. c Springer-Verlag
Berlin Heidelberg 2006 1 Introduction The systems biology view of an organism
as.
Author: Corrado Priami
Publisher: Springer Science & Business Media
ISBN: 9783540461661
Category: Computers
Page: 322
View: 847
This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2006, held in Trento, Italy, in October 2006. The 22 fully revised papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer sciences, such as language design, concurrency theory, software engineering, and formal methods.
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.
Author: Paola Lecca
Publisher: Woodhead Publishing
ISBN: 9780081001158
Category: Science
Page: 180
View: 743
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
Systems Biology in Toxicology and Environmental Health uses a systems biological perspective to detail the most recent findings that link environmental exposures to human disease, providing an overview of molecular pathways that are ...
Author: Rebecca Fry
Publisher: Academic Press
ISBN: 9780128015681
Category: Medical
Page: 284
View: 982
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
Metabolomics and Systems Biology in Chemical analysis, e.g. via NMR, GC-MS
Table 1.1. A summary. 1.1 Introduction Personalized medicine is anticipated to
become a crucial paradigm in the future of healthcare. Key to the ability to tailor ...
Author: Oliver A.H. Jones
Publisher: CABI
ISBN: 9781780642000
Category: Science
Page: 206
View: 500
The metabolomics and systems biology approach to research can be applied to many disciplines. This book provides a solid introduction to medical metabolomics and systems biology, and demonstrates how they have been applied to studies in medicine and human health, including nutrition and pathogenic microorganisms. Following core themes of diagnosis, pathology and aetiology of disease, this book provides a reference for health care professionals interested in how to use metabolomics for medical research.
The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications.
Author: Darren J. Wilkinson
Publisher: CRC Press
ISBN: 1584885408
Category: Mathematics
Page: 280
View: 433
Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. The stochastic processes formalism provides a beautiful, elegant, and coherent foundation for chemical kinetics and there is a wealth of associated theory every bit as powerful and elegant as that for conventional continuous deterministic models. The time is right for an introductory text written from this perspective. Stochastic Modelling for Systems Biology presents an accessible introduction to stochastic modelling using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modelling biological systems. He provides a comprehensive understanding of stochastic kinetic modelling of biological networks in the systems biology context. The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications. While emphasizing the necessary probabilistic and stochastic methods, the author takes a practical approach, rooting his theoretical development in discussions of the intended application. Written with self-study in mind, the book includes technical chapters that deal with the difficult problems of inference for stochastic kinetic models from experimental data. Providing enough background information to make the subject accessible to the non-specialist, the book integrates a fairly diverse literature into a single convenient and notationally consistent source.
