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 : 45,7 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.

Introduction to Biological Networks

Alpan Raval,Animesh Ray
Introduction to Biological Networks Book PDF

Author : Alpan Raval,Animesh Ray
Publisher : CRC Press
Page : 329 pages
File Size : 42,9 Mb
Release : 2016-04-19
Category : Computers
ISBN : 9781420010367

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Introduction to Biological Networks by Alpan Raval,Animesh Ray Pdf

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

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 : 54,9 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

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 : 44,5 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.

Biological Networks

Francois Kepes
Biological Networks Book PDF

Author : Francois Kepes
Publisher : World Scientific
Page : 531 pages
File Size : 40,7 Mb
Release : 2007
Category : Medical
ISBN : 9789812772367

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Biological Networks by Francois Kepes Pdf

This volume presents a timely and comprehensive overview of biological networks at all organization levels in the spirit of the complex systems 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. Sample Chapter(s). Chapter 1: Scale-Free Networks in Biology (821 KB). Contents: Scale-Free Networks in Biology (E Almaas et al.); Modularity in Biological Networks (R V Sol(r) et al.); Inference of Biological Regulatory Networks: Machine Learning Approaches (F d''Alch(r)-Buc); Transcriptional Networks (F K(r)p s); Protein Interaction Networks (K Tan & T Ideker); Metabolic Networks (D A Fell); Heterogeneous Molecular Networks (V Schnchter); Evolution of Regulatory Networks (A Veron et al.); Complexity in Neuronal Networks (Y Fr(r)gnac et al.); Networks of the Immune System (R E Callard & J Stark); A History of the Study of Ecological Networks (L-F Bersier); Dynamic Network Models of Ecological Diversity, Complexity, and Nonlinear Persistence (R J Williams & N D Martinez); Infection Transmission through Networks (J S Koopman). Readership: Graduate students and industry experts in systems biology and complex systems; biologists; chemists; physicists; mathematicians; computer scientists

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 : 45,7 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.

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 : 43,5 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.

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 : 53,9 Mb
Release : 2010
Category : Mathematics
ISBN : 9781848164345

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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. Sample Chapter(s). Chapter 1: A Network Analysis Primer (350 KB). Contents: A Network Analysis Primer (M P H Stumpf & C Wiuf); Evolutionary Analysis of Protein Interaction Networks (C Wiuf & O Ratmann); Motifs in Biological Networks (F Schreiber & H SchwAbbermeyer); Bayesian Analysis of Biological Networks: Clusters, Motifs, Cross-Species Correlations (J Berg & M Lnssig); Network Concepts and Epidemiological Models (R R Kao & I Z Kiss); Evolutionary Origin and Consequences of Design Properties of Metabolic Networks (T Pfeiffer & S Bonhoeffer); Protein Interactions from an Evolutionary Perspective (F Pazos & A Valencia); Statistical Null Models for Biological Network Analysis (W P Kelly et al.). Readership: Academics, researchers, postgraduates and advanced undergraduates in bioinformatics. Biologists, mathematicians/statisticians, physicists and computer scientists.

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 : 48,9 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.

Handbook on Biological Networks

Stefano Boccaletti
Handbook on Biological Networks Book PDF

Author : Stefano Boccaletti
Publisher : World Scientific
Page : 465 pages
File Size : 42,6 Mb
Release : 2010
Category : Mathematics
ISBN : 9789812838803

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Handbook on Biological Networks by Stefano Boccaletti 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 OCo 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. Sample Chapter(s). Chapter 1: Introduction (61 KB). Contents: Networks at the Cellular Level: The Structural Network Properties of Biological Systems (M Brilli & P Li); Dynamics of Multicellular Synthetic Gene Networks (E Ullner et al.); Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level (J Thakar & R Albert); Complexity of Boolean Dynamics in Simple Models of Signaling Networks and in Real Genetic Networks (A D az-Guilera & R ulvarez-Buylla); Geometry and Topology of Folding Landscapes (L Bongini & L Casetti); Elastic Network Models for Biomolecular Dynamics: Theory and Application to Membrane Proteins and Viruses (T R Lezon et al.); Metabolic Networks (M C Palumbo et al.); Brain Networks: The Human Brain Network (O Sporns); Brain Network Analysis from High-Resolution EEG Signals (F De Vico Fallani & F Babiloni); An Optimization Approach to the Structure of the Neuronal layout of C elegans (A Arenas et al.); Cultured Neuronal Networks Express Complex Patterns of Activity and Morphological Memory (N Raichman et al.); Synchrony and Precise Timing in Complex Neural Networks (R-M Memmesheimer & M Timme); Networks at the Individual and Population Levels: Ideas for Moving Beyond Structure to Dynamics of Ecological Networks (D B Stouffer et al.); Evolutionary Models for Simple Biosystems (F Bagnoli); Evolution of Cooperation in Adaptive Social Networks (S Van Segbroeck et al.); From Animal Collectives and Complex Networks to Decentralized Motion Control Strategies (A Buscarino et al.); Interplay of Network State and Topology in Epidemic Dynamics (T Gross). Readership: Advanced undergraduates, graduate students and researchers interested in the study of complex networks in a wide range of biological processes and systems."

Dynamic Biological Networks

Ronald M. Harris-Warrick
Dynamic Biological Networks Book PDF

Author : Ronald M. Harris-Warrick
Publisher : MIT Press
Page : 366 pages
File Size : 41,9 Mb
Release : 1992
Category : Crustacea
ISBN : 0262082144

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Dynamic Biological Networks by Ronald M. Harris-Warrick Pdf

This introduction to the crustacean stomatogastric nervous system (STNS) describes some of the best-understood neural networks in the animal kingdom at cellular, network, behavioural, comparative and evolutionary levels of analysis.

Biological Networks in Human Health and Disease

Romana Ishrat
Biological Networks in Human Health and Disease Book PDF

Author : Romana Ishrat
Publisher : Springer Nature
Page : 132 pages
File Size : 46,8 Mb
Release : 2023-10-13
Category : Science
ISBN : 9789819942428

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Biological Networks in Human Health and Disease by Romana Ishrat Pdf

This book presents methods and tools of network biology and bioinformatics for understanding the disease dynamics and identification of drug targets. The initial section of chapters introduce the theoretical aspects followed by the different applications for construction and analysis of biological networks, methods for identifying crucial nodes in networks, and network dynamics. The book covers the latest advances in the network medicine, exploring the different types of biological networks, and their applications. It further reviews the role of R language in the network-based approaches that help in understanding biological systems and identifying biological functions. Towards the end, the book explores the recent developments and applications in machine learning and its potential for advancing network biology. Finally, the book elucidates a comprehensive yet a representative description of challenges associated with the understanding of disease dynamics using network biology. Given its scope, the book is intended for researchers and advanced postgraduate students of bioinformatics, computational biology, and medical sciences. ​

Summarizing Biological Networks

Sourav S. Bhowmick,Boon-Siew Seah
Summarizing Biological Networks Book PDF

Author : Sourav S. Bhowmick,Boon-Siew Seah
Publisher : Springer
Page : 146 pages
File Size : 47,6 Mb
Release : 2017-04-17
Category : Computers
ISBN : 9783319546216

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Summarizing Biological Networks by Sourav S. Bhowmick,Boon-Siew Seah Pdf

This book focuses on the data mining, systems biology, and bioinformatics computational methods that can be used to summarize biological networks. Specifically, it discusses an array of techniques related to biological network clustering, network summarization, and differential network analysis which enable readers to uncover the functional and topological organization hidden in a large biological network. The authors also examine crucial open research problems in this arena. Academics, researchers, and advanced-level students will find this book to be a comprehensive and exceptional resource for understanding computational techniques and their applications for a summary of biological networks.

Clustering Challenges in Biological Networks

Sergiy Butenko,W. Art Chaovalitwongse,Panos M. Pardalos
Clustering Challenges in Biological Networks Book PDF

Author : Sergiy Butenko,W. Art Chaovalitwongse,Panos M. Pardalos
Publisher : World Scientific
Page : 347 pages
File Size : 48,7 Mb
Release : 2009
Category : Science
ISBN : 9789812771650

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Clustering Challenges in Biological Networks by Sergiy Butenko,W. Art Chaovalitwongse,Panos M. Pardalos Pdf

This text offers introductory knowledge of a wide range of clustering and other quantitative techniques used to solve biological problems.

Discriminative Pattern Discovery on Biological Networks

Fabio Fassetti,Simona E. Rombo,Cristina Serrao
Discriminative Pattern Discovery on Biological Networks Book PDF

Author : Fabio Fassetti,Simona E. Rombo,Cristina Serrao
Publisher : Springer
Page : 45 pages
File Size : 45,8 Mb
Release : 2017-09-01
Category : Computers
ISBN : 9783319634777

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Discriminative Pattern Discovery on Biological Networks by Fabio Fassetti,Simona E. Rombo,Cristina Serrao Pdf

This work provides a review of biological networks as a model for analysis, presenting and discussing a number of illuminating analyses. Biological networks are an effective model for providing insights about biological mechanisms. Networks with different characteristics are employed for representing different scenarios. This powerful model allows analysts to perform many kinds of analyses which can be mined to provide interesting information about underlying biological behaviors. The text also covers techniques for discovering exceptional patterns, such as a pattern accounting for local similarities and also collaborative effects involving interactions between multiple actors (for example genes). Among these exceptional patterns, of particular interest are discriminative patterns, namely those which are able to discriminate between two input populations (for example healthy/unhealthy samples). In addition, the work includes a discussion on the most recent proposal on discovering discriminative patterns, in which there is a labeled network for each sample, resulting in a database of networks representing a sample set. This enables the analyst to achieve a much finer analysis than with traditional techniques, which are only able to consider an aggregated network of each population.