Application of Network Theoretic Approaches in Biology

Application of Network Theoretic Approaches in Biology

Author: Rinku Sharma

Publisher: Frontiers Media SA

Published: 2023-08-25

Total Pages: 121

ISBN-13: 2832531679

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The biological complexity essentially includes and involves processes that are mediated through explicitly non-linear interactions that are often typically entangled in nature. These comprise a myriad of interactions among a vast number of entities such as genes, proteins, metabolites, and species, widely varying in scale. These interactions render biological systems across spatial and temporal scales as complex adaptive systems having features like: self-organisation, modularity, emergence, non-linear interactions, collective response and adaptation. The theory of complex networks offers an appropriate formal framework for modelling such complex systems. The enormous wealth of biological data generated by high-throughput techniques, as also through empirical investigations can be analysed using the aforementioned formal framework to obtain important insights into biological complexity.The concept of networks can be used:1) to explore the relationships between entities resulting in network generation; 2) to guide the analytic procedure based on existing network(s) as prior knowledge; and 3) to analyze the prior network(s) regarding their topology and attributes. Complex networks, being ubiquitous, permeate the biological systems across spatial and temporal scales. The objective of this collection is to highlight some very salient features of such inherent complexity in biological systems by adopting a network theoretic perspective. The anticipated pay-off is obtaining a deeper insight explicitly into the systems-level interactions and the emergent complex behaviour of the systems. Also, investigating the propulsive forces which lend various networks with akin topological characteristics that would help to merge vivid information related to various molecular interactions into a single framework, thereby permitting a structural perspective of the cellular dynamics.The application may include – exploring the disease/environmental stress response and trait mechanism using different omics platforms, candidate gene discovery and validation, network-guided discovery and deployment of omics approaches in biology; modern genetic improvement methods for delivering genes in addition to high throughput and precise phenotyping methodologies, exploring the disease/environmental stress response mechanism, marker re-prioritization, network-guided biomarker discovery etc.


Biological Network Analysis

Biological Network Analysis

Author: Pietro Hiram Guzzi

Publisher: Elsevier

Published: 2020-05-11

Total Pages: 212

ISBN-13: 0128193514

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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


Networks in Cell Biology

Networks in Cell Biology

Author: Mark Buchanan

Publisher: Cambridge University Press

Published: 2010-05-13

Total Pages: 282

ISBN-13: 0521882737

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Key introductory text for graduate students and researchers in physics, biology and biochemistry.


Computational Network Theory

Computational Network Theory

Author: Matthias Dehmer

Publisher: John Wiley & Sons

Published: 2015-11-16

Total Pages: 278

ISBN-13: 3527337245

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This comprehensive introduction to computational network theory as a branch of network theory builds on the understanding that such networks are a tool to derive or verify hypotheses by applying computational techniques to large scale network data. The highly experienced team of editors and high-profile authors from around the world present and explain a number of methods that are representative of computational network theory, derived from graph theory, as well as computational and statistical techniques. With its coherent structure and homogenous style, this reference is equally suitable for courses on computational networks.


Fundamentals Of Network Biology

Fundamentals Of Network Biology

Author: Wenjun Zhang

Publisher: World Scientific

Published: 2018-05-18

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.


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.


Computational Network Analysis with R

Computational Network Analysis with R

Author: Matthias Dehmer

Publisher: John Wiley & Sons

Published: 2016-12-12

Total Pages: 364

ISBN-13: 3527339582

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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.


Social Network Analysis

Social Network Analysis

Author: Mohammad Gouse Galety

Publisher: John Wiley & Sons

Published: 2022-04-28

Total Pages: 260

ISBN-13: 1119836735

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SOCIAL NETWORK ANALYSIS As social media dominates our lives in increasing intensity, the need for developers to understand the theory and applications is ongoing as well. This book serves that purpose. Social network analysis is the solicitation of network science on social networks, and social occurrences are denoted and premeditated by data on coinciding pairs as the entities of opinion. The book features: Social network analysis from a computational perspective using python to show the significance of fundamental facets of network theory and the various metrics used to measure the social network. An understanding of network analysis and motivations to model phenomena as networks. Real-world networks established with human-related data frequently display social properties, i.e., patterns in the graph from which human behavioral patterns can be analyzed and extracted. Exemplifies information cascades that spread through an underlying social network to achieve widespread adoption. Network analysis that offers an appreciation method to health systems and services to illustrate, diagnose, and analyze networks in health systems. The social web has developed a significant social and interactive data source that pays exceptional attention to social science and humanities research. The benefits of artificial intelligence enable social media platforms to meet an increasing number of users and yield the biggest marketplace, thus helping social networking analysis distribute better customer understanding and aiding marketers to target the right customers. Audience The book will interest computer scientists, AI researchers, IT and software engineers, mathematicians.


Analysis of Biological Networks

Analysis of Biological Networks

Author: Björn H. Junker

Publisher: John Wiley & Sons

Published: 2011-09-20

Total Pages: 278

ISBN-13: 1118209915

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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.


Biomolecular Networks

Biomolecular Networks

Author: Luonan Chen

Publisher: John Wiley & Sons

Published: 2009-06-29

Total Pages: 416

ISBN-13: 9780470488058

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Alternative techniques and tools for analyzing biomolecular networks With the recent rapid advances in molecular biology, high-throughput experimental methods have resulted in enormous amounts of data that can be used to study biomolecular networks in living organisms. With this development has come recognition of the fact that a complicated living organism cannot be fully understood by merely analyzing individual components. Rather, it is the interactions of components or biomolecular networks that are ultimately responsible for an organism's form and function. This book addresses the important need for a new set of computational tools to reveal essential biological mechanisms from a systems biology approach. Readers will get comprehensive coverage of analyzing biomolecular networks in cellular systems based on available experimental data with an emphasis on the aspects of network, system, integration, and engineering. Each topic is treated in depth with specific biological problems and novel computational methods: GENE NETWORKS—Transcriptional regulation; reconstruction of gene regulatory networks; and inference of transcriptional regulatory networks PROTEIN INTERACTION NETWORKS—Prediction of protein-protein interactions; topological structure of biomolecular networks; alignment of biomolecular networks; and network-based prediction of protein function METABOLIC NETWORKS AND SIGNALING NETWORKS—Analysis, reconstruction, and applications of metabolic networks; modeling and inference of signaling networks; and other topics and new trends In addition to theoretical results and methods, many computational software tools are referenced and available from the authors' Web sites. Biomolecular Networks is an indispensable reference for researchers and graduate students in bioinformatics, computational biology, systems biology, computer science, and applied mathematics.