Biological Network Analysis

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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 : 55,5 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.

Weighted Network Analysis

Steve Horvath
Weighted Network Analysis Book PDF

Author : Steve Horvath
Publisher : Springer Science & Business Media
Page : 433 pages
File Size : 47,7 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.

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 : 40,9 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.

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 : 53,9 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.

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 : 42,8 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

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 : 45,9 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.

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 : 54,6 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.

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 : 43,6 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.

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 : 49,7 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.

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 : 52,8 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 : 42,7 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.

Analyzing Network Data in Biology and Medicine

Nataša Pržulj
Analyzing Network Data in Biology and Medicine Book PDF

Author : Nataša Pržulj
Publisher : Cambridge University Press
Page : 647 pages
File Size : 45,8 Mb
Release : 2019-03-28
Category : Language Arts & Disciplines
ISBN : 9781108432238

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Analyzing Network Data in Biology and Medicine by Nataša Pržulj Pdf

Introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning, using real-world biological and medical examples.

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 : 50,8 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

Network Analysis Literacy

Katharina A. Zweig
Network Analysis Literacy Book PDF

Author : Katharina A. Zweig
Publisher : Springer Science & Business Media
Page : 535 pages
File Size : 45,6 Mb
Release : 2016-10-26
Category : Computers
ISBN : 9783709107416

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Network Analysis Literacy by Katharina A. Zweig Pdf

This book presents a perspective of network analysis as a tool to find and quantify significant structures in the interaction patterns between different types of entities. Moreover, network analysis provides the basic means to relate these structures to properties of the entities. It has proven itself to be useful for the analysis of biological and social networks, but also for networks describing complex systems in economy, psychology, geography, and various other fields. Today, network analysis packages in the open-source platform R and other open-source software projects enable scientists from all fields to quickly apply network analytic methods to their data sets. Altogether, these applications offer such a wealth of network analytic methods that it can be overwhelming for someone just entering this field. This book provides a road map through this jungle of network analytic methods, offers advice on how to pick the best method for a given network analytic project, and how to avoid common pitfalls. It introduces the methods which are most often used to analyze complex networks, e.g., different global network measures, types of random graph models, centrality indices, and networks motifs. In addition to introducing these methods, the central focus is on network analysis literacy – the competence to decide when to use which of these methods for which type of question. Furthermore, the book intends to increase the reader's competence to read original literature on network analysis by providing a glossary and intensive translation of formal notation and mathematical symbols in everyday speech. Different aspects of network analysis literacy – understanding formal definitions, programming tasks, or the analysis of structural measures and their interpretation – are deepened in various exercises with provided solutions. This text is an excellent, if not the best starting point for all scientists who want to harness the power of network analysis for their field of expertise.

Networks in Systems Biology

Fabricio Alves Barbosa da Silva,Nicolas Carels,Marcelo Trindade dos Santos,Francisco José Pereira Lopes
Networks in Systems Biology Book PDF

Author : Fabricio Alves Barbosa da Silva,Nicolas Carels,Marcelo Trindade dos Santos,Francisco José Pereira Lopes
Publisher : Springer Nature
Page : 381 pages
File Size : 43,5 Mb
Release : 2020-10-03
Category : Computers
ISBN : 9783030518622

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Networks in Systems Biology by Fabricio Alves Barbosa da Silva,Nicolas Carels,Marcelo Trindade dos Santos,Francisco José Pereira Lopes Pdf

This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.