Analysis Of Biological Networks

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Analysis of Biological Networks

Björn H. Junker,Falk Schreiber
Analysis of Biological Networks Book PDF

Author : Björn H. Junker,Falk Schreiber
Publisher : John Wiley & Sons
Page : 278 pages
File Size : 45,6 Mb
Release : 2011-09-20
Category : Computers
ISBN : 9781118209912

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Analysis of Biological Networks by Björn H. Junker,Falk Schreiber Pdf

An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.

Biological Network Analysis

Pietro Hiram Guzzi,Swarup Roy
Biological Network Analysis Book PDF

Author : Pietro Hiram Guzzi,Swarup Roy
Publisher : Elsevier
Page : 212 pages
File Size : 50,9 Mb
Release : 2020-05-11
Category : Science
ISBN : 9780128193518

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Biological Network Analysis by Pietro Hiram Guzzi,Swarup Roy Pdf

Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes Includes a discussion of various graph theoretic and data analytics approaches

Statistical and Evolutionary Analysis of Biological Networks

Michael P. H. Stumpf,Carsten Wiuf
Statistical and Evolutionary Analysis of Biological Networks Book PDF

Author : Michael P. H. Stumpf,Carsten Wiuf
Publisher : World Scientific
Page : 179 pages
File Size : 42,7 Mb
Release : 2010
Category : Science
ISBN : 9781848164338

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Statistical and Evolutionary Analysis of Biological Networks by Michael P. H. Stumpf,Carsten Wiuf Pdf

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.

Biological Networks and Pathway Analysis

Tatiana V. Tatarinova,Yuri Nikolsky
Biological Networks and Pathway Analysis Book PDF

Author : Tatiana V. Tatarinova,Yuri Nikolsky
Publisher : Humana
Page : 0 pages
File Size : 42,9 Mb
Release : 2018-08-03
Category : Science
ISBN : 1493983725

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Biological Networks and Pathway Analysis by Tatiana V. Tatarinova,Yuri Nikolsky Pdf

In this volume, expert practitioners present a compilation of methods of functional data analysis (often referred to as “systems biology”) and its applications in drug discovery, medicine, and basic disease research. It covers such important issues as the elucidation of protein, compound and gene interactions, as well as analytical tools, including networks, interactome and ontologies, and clinical applications of functional analysis. As a volume in the highly successful Methods in Molecular Biology series, this work provides detailed description and hands-on implementation advice. Reputable, comprehensive, and cutting-edge, Biological Networks and Pathway Analysis presents both “wet lab” experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.

Networks of Networks in Biology

Narsis A. Kiani,David Gomez-Cabrero,Ginestra Bianconi
Networks of Networks in Biology Book PDF

Author : Narsis A. Kiani,David Gomez-Cabrero,Ginestra Bianconi
Publisher : Cambridge University Press
Page : 215 pages
File Size : 44,8 Mb
Release : 2021-04
Category : Computers
ISBN : 9781108428873

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Networks of Networks in Biology by Narsis A. Kiani,David Gomez-Cabrero,Ginestra Bianconi Pdf

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

Recent Advances in Biological Network Analysis

Byung-Jun Yoon,Xiaoning Qian
Recent Advances in Biological Network Analysis Book PDF

Author : Byung-Jun Yoon,Xiaoning Qian
Publisher : Springer Nature
Page : 220 pages
File Size : 53,5 Mb
Release : 2021-01-13
Category : Medical
ISBN : 9783030571733

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Recent Advances in Biological Network Analysis by Byung-Jun Yoon,Xiaoning Qian Pdf

This book reviews recent advances in the emerging field of computational network biology with special emphasis on comparative network analysis and network module detection. The chapters in this volume are contributed by leading international researchers in computational network biology and offer in-depth insight on the latest techniques in network alignment, network clustering, and network module detection. Chapters discuss the advantages of the respective techniques and present the current challenges and open problems in the field. Recent Advances in Biological Network Analysis: Comparative Network Analysis and Network Module Detection will serve as a great resource for graduate students, academics, and researchers who are currently working in areas relevant to computational network biology or wish to learn more about the field. Data scientists whose work involves the analysis of graphs, networks, and other types of data with topological structure or relations can also benefit from the book's insights.

Thermodynamic Network Analysis of Biological Systems

J. Schnakenberg
Thermodynamic Network Analysis of Biological Systems Book PDF

Author : J. Schnakenberg
Publisher : Springer Science & Business Media
Page : 157 pages
File Size : 52,9 Mb
Release : 2012-12-06
Category : Science
ISBN : 9783642679711

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Thermodynamic Network Analysis of Biological Systems by J. Schnakenberg Pdf

The first edition of this book was greeted with broad interest from readers en gaged in various disciplines of biophysics. I received many stimulating and en couraging responses, however, some of the book's reviewers wanted to stress the fact that an extensive literature of network theory was not included or reported in the book. But the main aspect of the book is intended to be substantive rather than methodical: networks simply serve as a remedy for doing some first steps in analysing and modelling complex biological systems. For an advanced stage in the investigation of a particular system it may be appropriate to replace the pheno menological network method by more detailed techniques like statistical equations or computer simulations. According to this intention, the second edition of the book has been enlarged by further biological examples for network analysis, not by more network theory. There is a completely new section on a network model for photoreception. For this section I am obliged to J. Tiedge who did most of the detailed calculation and to my colleague Professor Stieve with whom we have had a very fruitful cooperation. Also I would like to mention that this work has been sponsored by the "Deutsche Forschungsgemei nschaft" i n the "Sonderforschungsberei ch 160". Recent results for excitable systems represented by feedback networks have also been included in the second edition, especially for limit cycle networks.

Weighted Network Analysis

Steve Horvath
Weighted Network Analysis Book PDF

Author : Steve Horvath
Publisher : Springer Science & Business Media
Page : 433 pages
File Size : 41,8 Mb
Release : 2011-04-30
Category : Science
ISBN : 9781441988195

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Weighted Network Analysis by Steve Horvath Pdf

High-throughput measurements of gene expression and genetic marker data facilitate systems biologic and systems genetic data analysis strategies. Gene co-expression networks have been used to study a variety of biological systems, bridging the gap from individual genes to biologically or clinically important emergent phenotypes.

Biological Networks

Fran‡ois K‚pŠs
Biological Networks Book PDF

Author : Fran‡ois K‚pŠs
Publisher : World Scientific
Page : 531 pages
File Size : 42,5 Mb
Release : 2007
Category : Science
ISBN : 9789812706959

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Biological Networks by Fran‡ois K‚pŠs Pdf

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.

Handbook on Biological Networks

Stefano Boccaletti,Vito Latora,Yamir Moreno
Handbook on Biological Networks Book PDF

Author : Stefano Boccaletti,Vito Latora,Yamir Moreno
Publisher : World Scientific
Page : 465 pages
File Size : 47,6 Mb
Release : 2010
Category : Science
ISBN : 9789812838797

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Handbook on Biological Networks by Stefano Boccaletti,Vito Latora,Yamir Moreno Pdf

Networked systems are all around us. The accumulated evidence of systems as complex as a cell cannot be fully understood by studying only their isolated constituents, giving rise to a new area of interest in research ? the study of complex networks. In a broad sense, biological networks have been one of the most studied networks, and the field has benefited from many important contributions. By understanding and modeling the structure of a biological network, a better perception of its dynamical and functional behavior is to be expected. This unique book compiles the most relevant results and novel insights provided by network theory in the biological sciences, ranging from the structure and dynamics of the brain to cellular and protein networks and to population-level biology.

Computational Network Analysis with R

Matthias Dehmer,Yongtang Shi,Frank Emmert-Streib
Computational Network Analysis with R Book PDF

Author : Matthias Dehmer,Yongtang Shi,Frank Emmert-Streib
Publisher : John Wiley & Sons
Page : 364 pages
File Size : 40,5 Mb
Release : 2016-12-12
Category : Medical
ISBN : 9783527339587

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Computational Network Analysis with R by Matthias Dehmer,Yongtang Shi,Frank Emmert-Streib Pdf

This new title in the well-established "Quantitative Network Biology" series includes innovative and existing methods for analyzing network data in such areas as network biology and chemoinformatics. With its easy-to-follow introduction to the theoretical background and application-oriented chapters, the book demonstrates that R is a powerful language for statistically analyzing networks and for solving such large-scale phenomena as network sampling and bootstrapping. Written by editors and authors with an excellent track record in the field, this is the ultimate reference for R in Network Analysis.

Complex Networks

Eli Ben-Naim,Hans Frauenfelder,Zoltan Toroczkai
Complex Networks Book PDF

Author : Eli Ben-Naim,Hans Frauenfelder,Zoltan Toroczkai
Publisher : Springer Science & Business Media
Page : 548 pages
File Size : 43,9 Mb
Release : 2004-09-01
Category : Science
ISBN : 3540223541

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Complex Networks by Eli Ben-Naim,Hans Frauenfelder,Zoltan Toroczkai Pdf

This volume is devoted to the applications of techniques from statistical physics to the characterization and modeling of complex networks. The first two parts of the book concern theory and modeling of networks, the last two parts survey applications to a wide variety of natural and artificial networks. The tutorial reviews that form this book are aimed at students and newcomers to the field, and will also constitute a modern and comprehensive reference for experts. To this aim, all contributions have been carefully peer-reviewed not only for scientific content but also for self-consistency and readability.

New Frontiers of Network Analysis in Systems Biology

Avi Ma'ayan,Ben D. MacArthur
New Frontiers of Network Analysis in Systems Biology Book PDF

Author : Avi Ma'ayan,Ben D. MacArthur
Publisher : Springer Science & Business Media
Page : 204 pages
File Size : 51,9 Mb
Release : 2012-06-25
Category : Medical
ISBN : 9789400743304

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New Frontiers of Network Analysis in Systems Biology by Avi Ma'ayan,Ben D. MacArthur Pdf

The rapidly developing field of systems biology is influencing many aspects of biological research and is expected to transform biomedicine. Some emerging offshoots and specialized branches in systems biology are receiving particular attention and are becoming highly active areas of research. This collection of invited reviews describes some of the latest cutting-edge experimental and computational advances in these emerging sub-fields of systems biology. In particular, this collection focuses on the study of mammalian embryonic stem cells; new technologies involving mass-spectrometry proteomics; single cell measurements; methods for modeling complex stochastic systems; network-based classification algorithms; and the revolutionary emerging field of systems pharmacology.

Network Biology

Gerard Cagney,Andrew Emili
Network Biology Book PDF

Author : Gerard Cagney,Andrew Emili
Publisher : Humana Press
Page : 0 pages
File Size : 55,5 Mb
Release : 2011-09-28
Category : Science
ISBN : 1617792756

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Network Biology by Gerard Cagney,Andrew Emili Pdf

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 Network Biology

Zhang Wenjun
Fundamentals Of Network Biology Book PDF

Author : Zhang Wenjun
Publisher : World Scientific
Page : 568 pages
File Size : 51,5 Mb
Release : 2018-05-16
Category : Science
ISBN : 9781786345103

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Fundamentals Of Network Biology by Zhang Wenjun Pdf

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