A First Course In Systems Biology

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A First Course in Systems Biology

Eberhard Voit
A First Course in Systems Biology Book PDF

Author : Eberhard Voit
Publisher : Garland Science
Page : 480 pages
File Size : 43,7 Mb
Release : 2017-09-05
Category : Computers
ISBN : 9781351332941

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A First Course in Systems Biology by Eberhard Voit Pdf

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.

A First Course in Systems Biology

Eberhard O. Voit
A First Course in Systems Biology Book PDF

Author : Eberhard O. Voit
Publisher : Unknown
Page : 445 pages
File Size : 43,6 Mb
Release : 2013
Category : COMPUTERS
ISBN : 0429258518

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A First Course in Systems Biology by Eberhard O. Voit Pdf

This is a textbook designed for advanced undergraduate and graduate students. Its main focus is the development of computational models and their applications to diverse biological systems. Because the biological sciences have become so complex that no individual can acquire complete knowledge in any given area of specialization, the education of future systems biologists must instead develop a student's ability to retrieve, reformat, merge, and interpret complex biological information. This book provides the reader with the background and mastery of methods to execute standard systems biology tasks, understand the modern literature, and launch into specialized courses or projects that address biological questions using theoretical and computational means.

Systems Biology

Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald
Systems Biology Book PDF

Author : Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald
Publisher : John Wiley & Sons
Page : 504 pages
File Size : 50,5 Mb
Release : 2016-03-28
Category : Medical
ISBN : 9783527675661

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Systems Biology by Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald Pdf

This advanced textbook is tailored for an introductory course in Systems Biology and is well-suited for biologists as well as engineers and computer scientists. It comes with student-friendly reading lists and a companion website featuring a short exam prep version of the book and educational modeling programs. The text is written in an easily accessible style and includes numerous worked examples and study questions in each chapter. For this edition, a section on medical systems biology has been included.

An Introduction to Systems Biology

Uri Alon
An Introduction to Systems Biology Book PDF

Author : Uri Alon
Publisher : CRC Press
Page : 324 pages
File Size : 52,6 Mb
Release : 2006-07-07
Category : Mathematics
ISBN : 9781584886426

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An Introduction to Systems Biology by Uri Alon Pdf

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.

An Introduction to Computational Systems Biology

Karthik Raman
An Introduction to Computational Systems Biology Book PDF

Author : Karthik Raman
Publisher : CRC Press
Page : 359 pages
File Size : 44,7 Mb
Release : 2021-05-30
Category : Computers
ISBN : 9780429944529

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An Introduction to Computational Systems Biology by Karthik Raman Pdf

Emphasises a hands-on approach to modelling Strong emphasis on 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 Current chapters on exciting new developments like whole-cell modelling and community modelling

Biological Modeling and Simulation

Russell Schwartz
Biological Modeling and Simulation Book PDF

Author : Russell Schwartz
Publisher : MIT Press
Page : 403 pages
File Size : 41,9 Mb
Release : 2008-07-25
Category : Science
ISBN : 9780262195843

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Biological Modeling and Simulation by Russell Schwartz Pdf

A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.

An Introduction to Systems Biology

Uri Alon
An Introduction to Systems Biology Book PDF

Author : Uri Alon
Publisher : CRC Press
Page : 324 pages
File Size : 41,8 Mb
Release : 2019-07-12
Category : Mathematics
ISBN : 9781000001327

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An Introduction to Systems Biology by Uri Alon Pdf

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

Bioinformatics for Systems Biology

Stephen Krawetz
Bioinformatics for Systems Biology Book PDF

Author : Stephen Krawetz
Publisher : Springer Science & Business Media
Page : 639 pages
File Size : 52,8 Mb
Release : 2008-12-11
Category : Science
ISBN : 9781597454407

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Bioinformatics for Systems Biology by Stephen Krawetz Pdf

Bioinformatics for Systems Biology bridges and unifies many disciplines. It presents the life scientist, computational biologist, and mathematician with a common framework. Only by linking the groups together may the true life sciences revolution move forward.

Integer Linear Programming in Computational and Systems Biology

Dan Gusfield
Integer Linear Programming in Computational and Systems Biology Book PDF

Author : Dan Gusfield
Publisher : Cambridge University Press
Page : 431 pages
File Size : 55,7 Mb
Release : 2019-06-13
Category : Computers
ISBN : 9781108421768

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Integer Linear Programming in Computational and Systems Biology by Dan Gusfield Pdf

This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.

Systems Biology

Bernhard Palsson
Systems Biology Book PDF

Author : Bernhard Palsson
Publisher : Cambridge University Press
Page : 551 pages
File Size : 51,8 Mb
Release : 2015-01-26
Category : Medical
ISBN : 9781107038851

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Systems Biology by Bernhard Palsson Pdf

The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

Life: An Introduction to Complex Systems Biology

Kunihiko Kaneko
Life An Introduction to Complex Systems Biology Book PDF

Author : Kunihiko Kaneko
Publisher : Springer
Page : 374 pages
File Size : 48,5 Mb
Release : 2006-09-14
Category : Science
ISBN : 9783540326670

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Life: An Introduction to Complex Systems Biology by Kunihiko Kaneko Pdf

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.

Fundamentals of Systems Biology

Markus W. Covert
Fundamentals of Systems Biology Book PDF

Author : Markus W. Covert
Publisher : CRC Press
Page : 367 pages
File Size : 44,8 Mb
Release : 2017-10-19
Category : Technology & Engineering
ISBN : 9781498728478

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Fundamentals of Systems Biology by Markus W. Covert Pdf

For decades biology has focused on decoding cellular processes one gene at a time, but many of the most pressing biological questions, as well as diseases such as cancer and heart disease, are related to complex systems involving the interaction of hundreds, or even thousands, of gene products and other factors. How do we begin to understand this complexity? Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models introduces students to methods they can use to tackle complex systems head-on, carefully walking them through studies that comprise the foundation and frontier of systems biology. The first section of the book focuses on bringing students quickly up to speed with a variety of modeling methods in the context of a synthetic biological circuit. This innovative approach builds intuition about the strengths and weaknesses of each method and becomes critical in the book’s second half, where much more complicated network models are addressed—including transcriptional, signaling, metabolic, and even integrated multi-network models. The approach makes the work much more accessible to novices (undergraduates, medical students, and biologists new to mathematical modeling) while still having much to offer experienced modelers--whether their interests are microbes, organs, whole organisms, diseases, synthetic biology, or just about any field that investigates living systems.

Stochastic Modelling for Systems Biology

Darren J. Wilkinson
Stochastic Modelling for Systems Biology Book PDF

Author : Darren J. Wilkinson
Publisher : CRC Press
Page : 296 pages
File Size : 55,8 Mb
Release : 2006-04-18
Category : Mathematics
ISBN : 1584885408

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Stochastic Modelling for Systems Biology by Darren J. Wilkinson Pdf

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.

Systems Biology

Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald,Hans Lehrach,Ralf Herwig
Systems Biology Book PDF

Author : Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald,Hans Lehrach,Ralf Herwig
Publisher : John Wiley & Sons
Page : 593 pages
File Size : 42,8 Mb
Release : 2011-09-19
Category : Medical
ISBN : 9783527644971

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Systems Biology by Edda Klipp,Wolfram Liebermeister,Christoph Wierling,Axel Kowald,Hans Lehrach,Ralf Herwig Pdf

This advanced textbook is tailored to the needs of introductory course in Systems Biology. It has a compagnion website (WWW.WILEY-VCH.DE/HOME/SYSTEMSBIOLOGY) with solutions to questions in the book and several additional extensive working models. The book is related to the very successful previous title 'Systems Biology in Practice' and has incorporated the feedback and suggestions from many lecturers worldwide. The book addresses biologists as well as engineers and computer scientists. The interdisciplinary team of acclaimed authors worked closely together to ensure a comprehensive coverage with no overlaps in a homogenous and compelling style.

Systems Biology

Andreas Kremling
Systems Biology Book PDF

Author : Andreas Kremling
Publisher : CRC Press
Page : 382 pages
File Size : 46,7 Mb
Release : 2013-11-12
Category : Mathematics
ISBN : 9781466567894

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Systems Biology by Andreas Kremling Pdf

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.