An Introduction to Systems Biology

by Uri Alon

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

An Introduction to Systems Biology

Author: Uri Alon

Publisher: CRC Press

ISBN: 1584886420

Page: 320

View: 376

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.

Introduction to Systems Biology

by Sangdun Choi

SBML is based on XML, which is a standard medium for representing and
transporting data that is widely supported on the Internet, as well as in
computational biology and bioinformatics. Because SBML is tool-independent, it
enables model ...

Introduction to Systems Biology

Author: Sangdun Choi

Publisher: Springer Science & Business Media

ISBN: 1597455318

Page: 542

View: 658

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Mathematical Modeling in Systems Biology

by Brian P. Ingalls

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

Mathematical Modeling in Systems Biology

Author: Brian P. Ingalls

Publisher: MIT Press

ISBN: 0262018888

Page: 408

View: 424

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.

An Introduction to Computational Systems Biology

by KARTHIK. RAMAN

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: 9781138597327

Page: 360

View: 958

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.

Systems Biology

by Herbert Sauro

This book is an introduction to control in biochemical pathways.

Systems Biology

Author: Herbert Sauro

Publisher:

ISBN: 9780982477366

Page: 278

View: 737

This book is an introduction to control in biochemical pathways. Itintroduces students to some of the most important concepts in modern metabolic control principles. It covers the basics of metabolic controlanalysis that helps us think about how biochemical networks operate. The book should be suitable for undergraduates in their early (Junior, USA, second year UK) to mid years at college.

Systems Biology A Very Short Introduction

by Eberhard O. Voit

ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly.

Systems Biology A Very Short Introduction

Author: Eberhard O. Voit

Publisher: Oxford University Press

ISBN: 0192563440

Page: 144

View: 647

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 Systems Biology

by Uri Alon

Design Principles of Biological Circuits Uri Alon. modularity. In parallel, the
principles that appeared in the first edition have been refined and applied to
many more systems. Thus, every old chapter is extensively revised with new
examples ...

An Introduction to Systems Biology

Author: Uri Alon

Publisher: CRC Press

ISBN: 1000008169

Page: 324

View: 116

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

Systems Biology Introduction to Pathway Modeling

by Herbert Sauro

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.

A First Course in Systems Biology

by Eberhard Voit

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

A First Course in Systems Biology

Author: Eberhard Voit

Publisher: Garland Science

ISBN: 1351332945

Page: 480

View: 769

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 and Synthetic Biology

by Pengcheng Fu

This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Systems Biology and Synthetic Biology

Author: Pengcheng Fu

Publisher: John Wiley & Sons

ISBN: 9780470437971

Page: 672

View: 180

The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Introduction to Computational Biology

by Bernhard Haubold

155 . A . Krogh , M . Brown , I . S . Mian , K . Sjölander , and D . Hausser . Hidden
Markov models in computational biology . Journal of Molecular Biology , 235 :
1501 - 1531 , 1994 . 156 . G . V . Kryukov , S . Castellano , S . V . Novoselov , A .
V ...

Introduction to Computational Biology

Author: Bernhard Haubold

Publisher: Birkhäuser

ISBN:

Page: 328

View: 949

Written with the advanced undergraduate in mind, this book introduces into the field of Bioinformatics. The authors explain the computational and conceptional background to the analysis of large-scale sequence data. Many of the corresponding analysis methods are rooted in evolutionary thinking, which serves as a common thread throughout the book. The focus is on methods of comparative genomics and subjects covered include: alignments, gene finding, phylogeny, and the analysis of single nucleotide polymorphisms (SNPs). The volume contains exercises, questions & answers to selected problems.

Life An Introduction to Complex Systems Biology

by Kunihiko Kaneko

Biology. 2.1. The. Understanding. Obtained. Through. Construction. As discussed
in Chap. 1, we do not wish to investigate the detailed processes of ... Rather, our
goal is to elucidate the universal properties possessed by living systems.

Life An Introduction to Complex Systems Biology

Author: Kunihiko Kaneko

Publisher: Springer

ISBN: 3540326677

Page: 374

View: 468

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.

Bioinformatics and Systems Biology

by Frederick Marcus

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 ...

Bioinformatics and Systems Biology

Author: Frederick Marcus

Publisher: Springer Science & Business Media

ISBN: 9783540783534

Page: 287

View: 638

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.

The Challenges of Systems Biology

by Gustavo Stolovitzky

An Introduction to Systems Biology - Design Principles of Biological Circuits .
Chapman & Hall / CRC . Boca Raton . 6 . Seshasayee , A . S . N . et al . 2006 .
Transcriptional regulatory networks in bacteria : from input signals to output
responses ...

The Challenges of Systems Biology

Author: Gustavo Stolovitzky

Publisher: Wiley-Blackwell

ISBN:

Page: 316

View: 795

At a microscopic level, organisms are ruled by interacting systems of biomolecules. Historically, scientists painstakingly elucidated chains of molecular events using experiments that reveal individual interactions, although they recognized that members of different pathways frequently interact. In recent years, researchers have built richer, interconnected networks to mathematically summarize their knowledge of these interactions. This systems biology enterprise, largely stimulated by high-throughput tools like microarrays that measure mRNA levels as an indicator of gene expression, is a vital and increasingly important activity in both basic biology and in medicine. A nagging concern, however, is how accurately these networks represent the biology. For complex systems like biological networks, there are practical limits on how well even massive amounts of data can uniquely define the underlying structure and yield useful predictions of measurable events. Indeed, although its advocates call this process "reverse engineering," the topology and the detailed molecular interactions of the "inferred" networks will likely never be known with precision. This volume captures the ongoing process to assess the ability of scientists—and their computer servants—to infer networks from experimental data, by comparing their predictions to "gold-standard" networks whose structure is thought to be known. NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit www.blackwellpublishing.com/nyas. ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to the Annals online and discounts on print volumes. Please visit www.nyas.org/membership/main.asp for more information about becoming a member.

Introduction to Biological Networks

by Alpan Raval

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 ...

Introduction to Biological Networks

Author: Alpan Raval

Publisher: CRC Press

ISBN: 1420010360

Page: 335

View: 433

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

Systems Biology

by Michael G. Katze

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.

Systems Biology

Author: Michael G. Katze

Publisher: Springer Science & Business Media

ISBN: 3642330991

Page: 263

View: 889

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.

Systems Biology

by Marvin Cassman

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 ...

Systems Biology

Author: Marvin Cassman

Publisher: Springer Science & Business Media

ISBN: 1402054688

Page: 262

View: 193

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.

Computational Methods in Systems Biology

by Monika Heiner

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 ...

Computational Methods in Systems Biology

Author: Monika Heiner

Publisher: Springer Science & Business Media

ISBN: 3540885617

Page: 401

View: 639

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