Fundamentals Of Network Biology

Fundamentals Of Network Biology

Author: Zhang Wenjun

Publisher: World Scientific

Published: 2018-05-16

Total Pages: 568

ISBN-13: 1786345102

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As the first comprehensive title on network biology, this book covers a wide range of subjects including scientific fundamentals (graphs, networks, etc) of network biology, construction and analysis of biological networks, methods for identifying crucial nodes in biological networks, link prediction, flow analysis, network dynamics, evolution, simulation and control, ecological networks, social networks, molecular and cellular networks, network pharmacology and network toxicology, big data analytics, and more. Across 12 parts and 26 chapters, with Matlab codes provided for most models and algorithms, this self-contained title provides an in-depth and complete insight on network biology. It is a valuable read for high-level undergraduates and postgraduates in the areas of biology, ecology, environmental sciences, medical science, computational science, applied mathematics, and social science. Contents: Mathematical Fundamentals: Fundamentals of Graph TheoryGraph AlgorithmsFundamentals of Network TheoryOther FundamentalsCrucial Nodes/Subnetworks/Modules, Network Types, and Structural Comparison: Identification of Crucial Nodes and Subnetworks/ModulesDetection of Network TypesComparison of Network StructureNetwork Dynamics, Evolution, Simulation and Control: Network DynamicsNetwork Robustness and Sensitivity AnalysisNetwork ControlNetwork EvolutionCellular AutomataSelf-OrganizationAgent-based ModelingFlow Analysis: Flow/Flux AnalysisLink and Node Prediction: Link Prediction: Sampling-based MethodsLink Prediction: Structure- and Perturbation-based MethodsLink Prediction: Node-Similarity-based MethodsNode PredictionNetwork Construction: Construction of Biological NetworksPharmacological and Toxicological Networks: Network Pharmacology and ToxicologyEcological Networks: Food WebsMicroscopic Networks: Molecular and Cellular NetworksSocial Networks: Social Network AnalysisSoftware: Software for Network AnalysisBig Data Analytics: Big Data Analytics for Network Biology Readership: Advanced undergraduates and graduate students and researchers in biology, ecology, pharmacology, applied mathematics, computational science, etc. Keywords: Network Biology;Network Analysis;Food Webs;Molecular Networks;Social Networks;Network Pharmacology;Link Prediction;Network Dynamics;Big Data Analytics;Software;Models;Algorithms;Nodes;LinksReview:0


Book Synopsis Fundamentals Of Network Biology by : Zhang Wenjun

Download or read book Fundamentals Of Network Biology written by Zhang Wenjun and published by World Scientific. This book was released on 2018-05-16 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the first comprehensive title on network biology, this book covers a wide range of subjects including scientific fundamentals (graphs, networks, etc) of network biology, construction and analysis of biological networks, methods for identifying crucial nodes in biological networks, link prediction, flow analysis, network dynamics, evolution, simulation and control, ecological networks, social networks, molecular and cellular networks, network pharmacology and network toxicology, big data analytics, and more. Across 12 parts and 26 chapters, with Matlab codes provided for most models and algorithms, this self-contained title provides an in-depth and complete insight on network biology. It is a valuable read for high-level undergraduates and postgraduates in the areas of biology, ecology, environmental sciences, medical science, computational science, applied mathematics, and social science. Contents: Mathematical Fundamentals: Fundamentals of Graph TheoryGraph AlgorithmsFundamentals of Network TheoryOther FundamentalsCrucial Nodes/Subnetworks/Modules, Network Types, and Structural Comparison: Identification of Crucial Nodes and Subnetworks/ModulesDetection of Network TypesComparison of Network StructureNetwork Dynamics, Evolution, Simulation and Control: Network DynamicsNetwork Robustness and Sensitivity AnalysisNetwork ControlNetwork EvolutionCellular AutomataSelf-OrganizationAgent-based ModelingFlow Analysis: Flow/Flux AnalysisLink and Node Prediction: Link Prediction: Sampling-based MethodsLink Prediction: Structure- and Perturbation-based MethodsLink Prediction: Node-Similarity-based MethodsNode PredictionNetwork Construction: Construction of Biological NetworksPharmacological and Toxicological Networks: Network Pharmacology and ToxicologyEcological Networks: Food WebsMicroscopic Networks: Molecular and Cellular NetworksSocial Networks: Social Network AnalysisSoftware: Software for Network AnalysisBig Data Analytics: Big Data Analytics for Network Biology Readership: Advanced undergraduates and graduate students and researchers in biology, ecology, pharmacology, applied mathematics, computational science, etc. Keywords: Network Biology;Network Analysis;Food Webs;Molecular Networks;Social Networks;Network Pharmacology;Link Prediction;Network Dynamics;Big Data Analytics;Software;Models;Algorithms;Nodes;LinksReview:0

A First Course in Network Science

A First Course in Network Science

Author: Filippo Menczer

Publisher: Cambridge University Press

Published: 2020-01-30

Total Pages: 275

ISBN-13: 1108579612

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Networks are everywhere: networks of friends, transportation networks and the Web. Neurons in our brains and proteins within our bodies form networks that determine our intelligence and survival. This modern, accessible textbook introduces the basics of network science for a wide range of job sectors from management to marketing, from biology to engineering, and from neuroscience to the social sciences. Students will develop important, practical skills and learn to write code for using networks in their areas of interest - even as they are just learning to program with Python. Extensive sets of tutorials and homework problems provide plenty of hands-on practice and longer programming tutorials online further enhance students' programming skills. This intuitive and direct approach makes the book ideal for a first course, aimed at a wide audience without a strong background in mathematics or computing but with a desire to learn the fundamentals and applications of network science.


Book Synopsis A First Course in Network Science by : Filippo Menczer

Download or read book A First Course in Network Science written by Filippo Menczer and published by Cambridge University Press. This book was released on 2020-01-30 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: Networks are everywhere: networks of friends, transportation networks and the Web. Neurons in our brains and proteins within our bodies form networks that determine our intelligence and survival. This modern, accessible textbook introduces the basics of network science for a wide range of job sectors from management to marketing, from biology to engineering, and from neuroscience to the social sciences. Students will develop important, practical skills and learn to write code for using networks in their areas of interest - even as they are just learning to program with Python. Extensive sets of tutorials and homework problems provide plenty of hands-on practice and longer programming tutorials online further enhance students' programming skills. This intuitive and direct approach makes the book ideal for a first course, aimed at a wide audience without a strong background in mathematics or computing but with a desire to learn the fundamentals and applications of network science.

Introduction to Biological Networks

Introduction to Biological Networks

Author: Alpan Raval

Publisher: CRC Press

Published: 2016-04-19

Total Pages: 329

ISBN-13: 1420010360

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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


Book Synopsis Introduction to Biological Networks by : Alpan Raval

Download or read book Introduction to Biological Networks written by Alpan Raval and published by CRC Press. This book was released on 2016-04-19 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Fundamentals of Systems Biology

Fundamentals of Systems Biology

Author: Markus W. Covert

Publisher: CRC Press

Published: 2017-10-19

Total Pages: 367

ISBN-13: 1498728472

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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.


Book Synopsis Fundamentals of Systems Biology by : Markus W. Covert

Download or read book Fundamentals of Systems Biology written by Markus W. Covert and published by CRC Press. This book was released on 2017-10-19 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Statistical and Evolutionary Analysis of Biological Networks

Statistical and Evolutionary Analysis of Biological Networks

Author: Michael P. H. Stumpf

Publisher: World Scientific

Published: 2010

Total Pages: 179

ISBN-13: 1848164335

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Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolutionary theory and tools in the understanding of biological networks. The book is divided into comprehensive and self-contained chapters, each of which focuses on an important biological network type, explains concepts and theory and illustrates how these can be used to obtain insight into biologically relevant processes and questions. There are chapters covering metabolic, transcriptomic, protein interaction and epidemiological networks as well as chapters that deal with theoretical and conceptual material. The authors, who contribute to the book, are active, highly regarded and well-known in the network community.


Book Synopsis Statistical and Evolutionary Analysis of Biological Networks by : Michael P. H. Stumpf

Download or read book Statistical and Evolutionary Analysis of Biological Networks written by Michael P. H. Stumpf and published by World Scientific. This book was released on 2010 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolutionary theory and tools in the understanding of biological networks. The book is divided into comprehensive and self-contained chapters, each of which focuses on an important biological network type, explains concepts and theory and illustrates how these can be used to obtain insight into biologically relevant processes and questions. There are chapters covering metabolic, transcriptomic, protein interaction and epidemiological networks as well as chapters that deal with theoretical and conceptual material. The authors, who contribute to the book, are active, highly regarded and well-known in the network community.

Networks of Networks in Biology

Networks of Networks in Biology

Author: Narsis A. Kiani

Publisher: Cambridge University Press

Published: 2021-04

Total Pages: 215

ISBN-13: 1108428878

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Introduces network inspired approaches for the analysis and integration of large, heterogeneous data sets in the life sciences.


Book Synopsis Networks of Networks in Biology by : Narsis A. Kiani

Download or read book Networks of Networks in Biology written by Narsis A. Kiani and published by Cambridge University Press. This book was released on 2021-04 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduces network inspired approaches for the analysis and integration of large, heterogeneous data sets in the life sciences.

Networks

Networks

Author: Mark Newman

Publisher: OUP Oxford

Published: 2010-03-25

Total Pages: 789

ISBN-13: 0191500704

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The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availability of inexpensive computers have made it possible to gather and analyze network data on a large scale, and the development of a variety of new theoretical tools has allowed us to extract new knowledge from many different kinds of networks. The study of networks is broadly interdisciplinary and important developments have occurred in many fields, including mathematics, physics, computer and information sciences, biology, and the social sciences. This book brings together for the first time the most important breakthroughs in each of these fields and presents them in a coherent fashion, highlighting the strong interconnections between work in different areas. Subjects covered include the measurement and structure of networks in many branches of science, methods for analyzing network data, including methods developed in physics, statistics, and sociology, the fundamentals of graph theory, computer algorithms, and spectral methods, mathematical models of networks, including random graph models and generative models, and theories of dynamical processes taking place on networks.


Book Synopsis Networks by : Mark Newman

Download or read book Networks written by Mark Newman and published by OUP Oxford. This book was released on 2010-03-25 with total page 789 pages. Available in PDF, EPUB and Kindle. Book excerpt: The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availability of inexpensive computers have made it possible to gather and analyze network data on a large scale, and the development of a variety of new theoretical tools has allowed us to extract new knowledge from many different kinds of networks. The study of networks is broadly interdisciplinary and important developments have occurred in many fields, including mathematics, physics, computer and information sciences, biology, and the social sciences. This book brings together for the first time the most important breakthroughs in each of these fields and presents them in a coherent fashion, highlighting the strong interconnections between work in different areas. Subjects covered include the measurement and structure of networks in many branches of science, methods for analyzing network data, including methods developed in physics, statistics, and sociology, the fundamentals of graph theory, computer algorithms, and spectral methods, mathematical models of networks, including random graph models and generative models, and theories of dynamical processes taking place on networks.

Biological Networks

Biological Networks

Author: Fran‡ois K‚pŠs

Publisher: World Scientific

Published: 2007

Total Pages: 531

ISBN-13: 981270695X

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This volume presents a timely and comprehensive overview of biological networks at all organization levels in the spirit of the complex system approach. It discusses the transversal issues and fundamental principles as well as the overall structure, dynamics, and modeling of a wide array of biological networks at the molecular, cellular, and population levels. Anchored in both empirical data and a strong theoretical background, the book therefore lends valuable credence to the complex systems approach.


Book Synopsis Biological Networks by : Fran‡ois K‚pŠs

Download or read book Biological Networks written by Fran‡ois K‚pŠs and published by World Scientific. This book was released on 2007 with total page 531 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a timely and comprehensive overview of biological networks at all organization levels in the spirit of the complex system approach. It discusses the transversal issues and fundamental principles as well as the overall structure, dynamics, and modeling of a wide array of biological networks at the molecular, cellular, and population levels. Anchored in both empirical data and a strong theoretical background, the book therefore lends valuable credence to the complex systems approach.

Network Biology

Network Biology

Author: Gerard Cagney

Publisher: Humana Press

Published: 2011-08-31

Total Pages: 437

ISBN-13: 9781617792779

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While extremely large datasets describing gene sequences, mRNA transcripts, protein abundance, and metabolite concentrations are increasingly commonplace, these represent only starting ‘parts lists’ that are usually insufficient to unlock mechanistic insights on their own right. Fortunately, as Network Biology: Methods and Applications examines, concepts emerging from the study of biological entities such as networks (e.g. functional interactions linking genes, proteins, metabolites, etc.) suggest that order rather than chaos prevails, with such principles as modular and hierarchical organization, reactive information-driven causal-response behaviours, systems robustness, co-evolution, and self-organization guiding the way. This volume presents detailed, practical descriptions of the experimental and computational approaches currently prevalent in network biology as written by practiced experts in the field. Written in the highly successful Methods in Molecular BiologyTM series format, relevant chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and accessible, Network Biology: Methods and Applications provides an ensemble of procedures that will be of great value to a broad assortment of readers, ranging from graduate students to seasoned professionals looking to polish their skill sets.


Book Synopsis Network Biology by : Gerard Cagney

Download or read book Network Biology written by Gerard Cagney and published by Humana Press. This book was released on 2011-08-31 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: While extremely large datasets describing gene sequences, mRNA transcripts, protein abundance, and metabolite concentrations are increasingly commonplace, these represent only starting ‘parts lists’ that are usually insufficient to unlock mechanistic insights on their own right. Fortunately, as Network Biology: Methods and Applications examines, concepts emerging from the study of biological entities such as networks (e.g. functional interactions linking genes, proteins, metabolites, etc.) suggest that order rather than chaos prevails, with such principles as modular and hierarchical organization, reactive information-driven causal-response behaviours, systems robustness, co-evolution, and self-organization guiding the way. This volume presents detailed, practical descriptions of the experimental and computational approaches currently prevalent in network biology as written by practiced experts in the field. Written in the highly successful Methods in Molecular BiologyTM series format, relevant chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and accessible, Network Biology: Methods and Applications provides an ensemble of procedures that will be of great value to a broad assortment of readers, ranging from graduate students to seasoned professionals looking to polish their skill sets.

Fundamentals of Complex Networks

Fundamentals of Complex Networks

Author: Guanrong Chen

Publisher: John Wiley & Sons

Published: 2015-06-29

Total Pages: 384

ISBN-13: 1118718119

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Complex networks such as the Internet, WWW, transportation networks, power grids, biological neural networks, and scientific cooperation networks of all kinds provide challenges for future technological development. • The first systematic presentation of dynamical evolving networks, with many up-to-date applications and homework projects to enhance study • The authors are all very active and well-known in the rapidly evolving field of complex networks • Complex networks are becoming an increasingly important area of research • Presented in a logical, constructive style, from basic through to complex, examining algorithms, through to construct networks and research challenges of the future


Book Synopsis Fundamentals of Complex Networks by : Guanrong Chen

Download or read book Fundamentals of Complex Networks written by Guanrong Chen and published by John Wiley & Sons. This book was released on 2015-06-29 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex networks such as the Internet, WWW, transportation networks, power grids, biological neural networks, and scientific cooperation networks of all kinds provide challenges for future technological development. • The first systematic presentation of dynamical evolving networks, with many up-to-date applications and homework projects to enhance study • The authors are all very active and well-known in the rapidly evolving field of complex networks • Complex networks are becoming an increasingly important area of research • Presented in a logical, constructive style, from basic through to complex, examining algorithms, through to construct networks and research challenges of the future