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Biological Network Analysis

Biological Network Analysis
Trends, Approaches, Graph Theory, and Algorithms

by Pietro Hiram Guzzi,Swarup Roy

  • Publisher : Academic Press
  • Release : 2020-05-26
  • Pages : 210
  • ISBN : 0128193506
  • Language : En, Es, Fr & De
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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

Analysis of Biological Networks

Analysis of Biological Networks
A Book

by Björn H. Junker,Falk Schreiber

  • Publisher : John Wiley & Sons
  • Release : 2011-09-20
  • Pages : 368
  • ISBN : 1118209915
  • Language : En, Es, Fr & De
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An introduction to biological networks and methods for theiranalysis Analysis of Biological Networks is the first book of itskind to provide readers with a comprehensive introduction to thestructural analysis of biological networks at the interface ofbiology and computer science. The book begins with a brief overviewof biological networks and graph theory/graph algorithms and goeson to explore: global network properties, network centralities,network motifs, network clustering, Petri nets, signal transductionand gene regulation networks, protein interaction networks,metabolic networks, phylogenetic networks, ecological networks, andcorrelation networks. Analysis of Biological Networks is a self-containedintroduction to this important research topic, assumes no expertknowledge in computer science or biology, and is accessible toprofessionals and students alike. Each chapter concludes with asummary of main points and with exercises for readers to test theirunderstanding of the material presented. Additionally, an FTP sitewith links to author-provided data for the book is available fordeeper study. This book is suitable as a resource for researchers in computerscience, biology, bioinformatics, advanced biochemistry, and thelife sciences, and also serves as an ideal reference text forgraduate-level courses in bioinformatics and biologicalresearch.

Weighted Network Analysis

Weighted Network Analysis
Applications in Genomics and Systems Biology

by Steve Horvath

  • Publisher : Springer Science & Business Media
  • Release : 2011-04-30
  • Pages : 421
  • ISBN : 9781441988195
  • Language : En, Es, Fr & De
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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.

Computational Network Analysis with R

Computational Network Analysis with R
Applications in Biology, Medicine and Chemistry

by Matthias Dehmer,Yongtang Shi,Frank Emmert-Streib

  • Publisher : John Wiley & Sons
  • Release : 2016-12-12
  • Pages : 368
  • ISBN : 3527339582
  • Language : En, Es, Fr & De
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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.

Statistical and Evolutionary Analysis of Biological Networks

Statistical and Evolutionary Analysis of Biological Networks
A Book

by Michael P. H. Stumpf,Carsten Wiuf

  • Publisher : World Scientific
  • Release : 2010
  • Pages : 170
  • ISBN : 1848164335
  • Language : En, Es, Fr & De
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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.

Thermodynamic Network Analysis of Biological Systems

Thermodynamic Network Analysis of Biological Systems
A Book

by J. Schnakenberg

  • Publisher : Springer Science & Business Media
  • Release : 2012-12-06
  • Pages : 150
  • ISBN : 3642679714
  • Language : En, Es, Fr & De
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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.

Analysis of Biological Networks

Analysis of Biological Networks
A Book

by Björn H. Junker,Falk Schreiber

  • Publisher : John Wiley & Sons
  • Release : 2008-03-14
  • Pages : 392
  • ISBN : 9780470253465
  • Language : En, Es, Fr & De
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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

Introduction to Biological Networks
A Book

by Alpan Raval,Animesh Ray

  • Publisher : CRC Press
  • Release : 2016-04-19
  • Pages : 335
  • ISBN : 1420010360
  • Language : En, Es, Fr & De
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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

Recent Advances in Biological Network Analysis

Recent Advances in Biological Network Analysis
Comparative Network Analysis and Network Module Detection

by Byung-Jun Yoon,Xiaoning Qian

  • Publisher : Springer
  • Release : 2021-03-10
  • Pages : 217
  • ISBN : 9783030571726
  • Language : En, Es, Fr & De
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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.

Analyzing Network Data in Biology and Medicine

Analyzing Network Data in Biology and Medicine
An Interdisciplinary Textbook for Biological, Medical and Computational Scientists

by Nata a Pr ulj,Nataša Pržulj

  • Publisher : Cambridge University Press
  • Release : 2019-03-28
  • Pages : 672
  • ISBN : 1108432239
  • Language : En, Es, Fr & De
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Introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning, using real-world biological and medical examples.

Biological Networks and Pathway Analysis

Biological Networks and Pathway Analysis
A Book

by Tatiana V. Tatarinova,Yuri Nikolsky

  • Publisher : Humana Press
  • Release : 2017-08-29
  • Pages : 509
  • ISBN : 9781493970254
  • Language : En, Es, Fr & De
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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.

Applied Statistics for Network Biology

Applied Statistics for Network Biology
Methods in Systems Biology

by Matthias Dehmer,Frank Emmert-Streib,Armin Graber,Armindo Salvador

  • Publisher : John Wiley & Sons
  • Release : 2011-04-08
  • Pages : 478
  • ISBN : 9783527638086
  • Language : En, Es, Fr & De
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The book introduces to the reader a number of cutting edge statistical methods which can e used for the analysis of genomic, proteomic and metabolomic data sets. In particular in the field of systems biology, researchers are trying to analyze as many data as possible in a given biological system (such as a cell or an organ). The appropriate statistical evaluation of these large scale data is critical for the correct interpretation and different experimental approaches require different approaches for the statistical analysis of these data. This book is written by biostatisticians and mathematicians but aimed as a valuable guide for the experimental researcher as well computational biologists who often lack an appropriate background in statistical analysis.

Network Biology

Network Biology
A Book

by Intawat Nookaew

  • Publisher : Springer
  • Release : 2017-05-03
  • Pages : 202
  • ISBN : 3319564609
  • Language : En, Es, Fr & De
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This book review series presents current trends in modern biotechnology. The aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science. Volumes are organized topically and provide a comprehensive discussion of developments in the respective field over the past 3-5 years. The series also discusses new discoveries and applications. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. In general, special volumes are edited by well-known guest editors. The series editor and publisher will however always be pleased to receive suggestions and supplementary information. Manuscripts are accepted in English.

Methods in Bioengineering

Methods in Bioengineering
Systems Analysis of Biological Networks

by Arul Jayaraman,Juergen Hahn

  • Publisher : Artech House
  • Release : 2009
  • Pages : 316
  • ISBN : 1596934069
  • Language : En, Es, Fr & De
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"This cutting-edge volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to: design of state-of-the art methods for analyzing biological systems Implement experimental approaches for investigating cellular behavior in health and disease; use algorithms and modeling techniques for quantitatively describing biomedical problems; and integrate experimental and computational approaches for a more complete view of biological systems." --Book Jacket.

Artificial Neural Networks in Biological and Environmental Analysis

Artificial Neural Networks in Biological and Environmental Analysis
A Book

by Grady Hanrahan

  • Publisher : CRC Press
  • Release : 2011-01-18
  • Pages : 214
  • ISBN : 9781439812594
  • Language : En, Es, Fr & De
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Originating from models of biological neural systems, artificial neural networks (ANN) are the cornerstones of artificial intelligence research. Catalyzed by the upsurge in computational power and availability, and made widely accessible with the co-evolution of software, algorithms, and methodologies, artificial neural networks have had a profound impact in the elucidation of complex biological, chemical, and environmental processes. Artificial Neural Networks in Biological and Environmental Analysis provides an in-depth and timely perspective on the fundamental, technological, and applied aspects of computational neural networks. Presenting the basic principles of neural networks together with applications in the field, the book stimulates communication and partnership among scientists in fields as diverse as biology, chemistry, mathematics, medicine, and environmental science. This interdisciplinary discourse is essential not only for the success of independent and collaborative research and teaching programs, but also for the continued interest in the use of neural network tools in scientific inquiry. The book covers: A brief history of computational neural network models in relation to brain function Neural network operations, including neuron connectivity and layer arrangement Basic building blocks of model design, selection, and application from a statistical perspective Neurofuzzy systems, neuro-genetic systems, and neuro-fuzzy-genetic systems Function of neural networks in the study of complex natural processes Scientists deal with very complicated systems, much of the inner workings of which are frequently unknown to researchers. Using only simple, linear mathematical methods, information that is needed to truly understand natural systems may be lost. The development of new algorithms to model such processes is needed, and ANNs can play a major role. Balancing basic principles and diverse applications, this text introduces newcomers to the field and reviews recent developments of interest to active neural network practitioners.

The Structure of Complex Networks

The Structure of Complex Networks
Theory and Applications

by Ernesto Estrada

  • Publisher : Oxford University Press
  • Release : 2012
  • Pages : 465
  • ISBN : 019959175X
  • Language : En, Es, Fr & De
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The book integrates approaches from mathematics, physics and computer sciences to analyse the organisation of complex networks. Every organisational principle of networks is defined, quantified and then analysed for its influences on the properties and functions of molecular, biological, ecological and social networks.

Biological Networks

Biological Networks
A Book

by Francois Kepes

  • Publisher : World Scientific
  • Release : 2007
  • Pages : 516
  • ISBN : 9812772367
  • Language : En, Es, Fr & De
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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 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

Emergence of Communication in Socio-Biological Networks

Emergence of Communication in Socio-Biological Networks
A Book

by Anamaria Berea

  • Publisher : Springer
  • Release : 2017-12-16
  • Pages : 88
  • ISBN : 331964565X
  • Language : En, Es, Fr & De
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This book integrates current advances in biology, economics of information and linguistics research through applications using agent-based modeling and social network analysis to develop scenarios of communication and language emergence in the social aspects of biological communications. The book presents a model of communication emergence that can be applied both to human and non-human living organism networks. The model is based on economic concepts and individual behavior fundamental for the study of trust and reputation networks in social science, particularly in economics; it is also based on the theory of the emergence of norms and historical path dependence that has been influential in institutional economics. Also included are mathematical models and code for agent-based models to explore various scenarios of language evolution, as well as a computer application that explores language and communication in biological versus social organisms, and the emergence of various meanings and grammars in human networks. Emergence of Communication in Socio-Biological Networks offers both a completely novel approach to communication emergence and language evolution and provides a path for the reader to explore various scenarios of language and communication that are not constrained to the human networks alone. By illustrating how computational social science and the complex systems approach can incorporate multiple disciplines and offer an integrated theory-model approach to the evolution of language, the book will be of interest to researchers working with computational linguistics, mathematical linguistics, and complex systems.

Knowledge Discovery in Proteomics

Knowledge Discovery in Proteomics
A Book

by Igor Jurisica,Dennis Wigle

  • Publisher : CRC Press
  • Release : 2005-09-02
  • Pages : 360
  • ISBN : 1420035169
  • Language : En, Es, Fr & De
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Multi-modal representations, the lack of complete and consistent domain theories, rapid evolution of domain knowledge, high dimensionality, and large amounts of missing information - these are challenges inherent in modern proteomics. As our understanding of protein structure and function becomes ever more complicated, we have reached a point where

Protein Networks and Pathway Analysis

Protein Networks and Pathway Analysis
A Book

by Yuri Nikolsky,Julie Bryant

  • Publisher : Humana Press
  • Release : 2011-11-30
  • Pages : 410
  • ISBN : 9781617794889
  • Language : En, Es, Fr & De
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From the beginning of the OMICs biology era, science has been pursuing the reduction of the complex "genome-wide" assays in order to understand the essential biology that lies beneath it. In Protein Networks and Pathway Analysis, 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. The volume is divided into three convenient sections, covering the elucidation of protein, compound and gene interactions, analytical tools, including networks, interactome and ontologies, and applications of functional analysis. As a volume in the highly successful Methods in Molecular BiologyTM series, this work provides detailed descriptions and hands-on implementation advice. Authoritative and cutting-edge, Protein 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.