Modeling And Analysis Of Bio Molecular Networks

Author : Jinhu Lü,Pei Wang
Publisher : Springer Nature
Page : 464 pages
File Size : 48,6 Mb
Release : 2020-12-06
Category : Science
ISBN : 9789811591440

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Modeling and Analysis of Bio-molecular Networks by Jinhu Lü,Pei Wang Pdf

This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.

Author : Luonan Chen,Ruiqi Wang,Chunguang Li,Kazuyuki Aihara
Publisher : Springer Science & Business Media
Page : 343 pages
File Size : 45,7 Mb
Release : 2010-07-05
Category : Technology & Engineering
ISBN : 9781849962148

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Modeling Biomolecular Networks in Cells by Luonan Chen,Ruiqi Wang,Chunguang Li,Kazuyuki Aihara Pdf

Modeling Biomolecular Networks in Cells shows how the interaction between the molecular components of basic living organisms can be modelled mathematically and the models used to create artificial biological entities within cells. Such forward engineering is a difficult task but the nonlinear dynamical methods espoused in this book simplify the biology so that it can be successfully understood and the synthesis of simple biological oscillators and rhythm-generators made feasible. Such simple units can then be co-ordinated using intercellular signal biomolecules. The formation of such man-made multicellular networks with a view to the production of biosensors, logic gates, new forms of integrated circuitry based on "gene-chips" and even biological computers is an important step in the design of faster and more flexible "electronics". The book also provides theoretical frameworks and tools with which to analyze the nonlinear dynamical phenomena which arise from the connection of building units in a biomolecular network.

Author : Bhaskar DasGupta,Jie Liang
Publisher : John Wiley & Sons
Page : 264 pages
File Size : 42,6 Mb
Release : 2016-01-06
Category : Science
ISBN : 9781119162261

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Models and Algorithms for Biomolecules and Molecular Networks by Bhaskar DasGupta,Jie Liang Pdf

By providing expositions to modeling principles, theories, computational solutions, and open problems, this reference presents a full scope on relevant biological phenomena, modeling frameworks, technical challenges, and algorithms. Up-to-date developments of structures of biomolecules, systems biology, advanced models, and algorithms Sampling techniques for estimating evolutionary rates and generating molecular structures Accurate computation of probability landscape of stochastic networks, solving discrete chemical master equations End-of-chapter exercises

Author : Heinz Koeppl,Douglas Densmore,Gianluca Setti,Mario di Bernardo
Publisher : Springer Science & Business Media
Page : 407 pages
File Size : 49,9 Mb
Release : 2011-05-21
Category : Technology & Engineering
ISBN : 9781441967664

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Design and Analysis of Biomolecular Circuits by Heinz Koeppl,Douglas Densmore,Gianluca Setti,Mario di Bernardo Pdf

The book deals with engineering aspects of the two emerging and intertwined fields of synthetic and systems biology. Both fields hold promise to revolutionize the way molecular biology research is done, the way today’s drug discovery works and the way bio-engineering is done. Both fields stress the importance of building and characterizing small bio-molecular networks in order to synthesize incrementally and understand large complex networks inside living cells. Reminiscent of computer-aided design (CAD) of electronic circuits, abstraction is believed to be the key concept to achieve this goal. It allows hiding the overwhelming complexity of cellular processes by encapsulating network parts into abstract modules. This book provides a unique perspective on how concepts and methods from CAD of electronic circuits can be leveraged to overcome complexity barrier perceived in synthetic and systems biology.

Author : Luonan Chen,Rui-Sheng Wang,Xiang-Sun Zhang
Publisher : John Wiley & Sons
Page : 416 pages
File Size : 51,8 Mb
Release : 2009-06-29
Category : Computers
ISBN : 0470488050

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Biomolecular Networks by Luonan Chen,Rui-Sheng Wang,Xiang-Sun Zhang Pdf

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.

Author : Zoran Nikoloski,Sergio Grimbs
Publisher : Walter de Gruyter
Page : 510 pages
File Size : 51,5 Mb
Release : 2014-07
Category : Molecular biology
ISBN : 3119165417

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Network-Based Molecular Biology by Zoran Nikoloski,Sergio Grimbs Pdf

This book provides problems and solutions for integrating high-throughput experimental data with structured biological knowledge. It includes classical and novel graph-theoretic and statistical/probabilistic approaches allowing adequate study of complex molecular networks, the possibility to posit and test biologically meaningful hypotheses and to carry out independent network-based research in computational/systems biology and bioinformatics.

Author : Mehmet Koyutürk,Shankar Subramaniam,Ananth Grama
Publisher : Springer Science & Business Media
Page : 228 pages
File Size : 47,5 Mb
Release : 2011-09-22
Category : Science
ISBN : 1461403200

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Functional Coherence of Molecular Networks in Bioinformatics by Mehmet Koyutürk,Shankar Subramaniam,Ananth Grama Pdf

Molecular networks provide descriptions of the organization of various biological processes, including cellular signaling, metabolism, and genetic regulation. Knowledge on molecular networks is commonly used for systems level analysis of biological function; research and method development in this area has grown tremendously in the past few years. This book will provide a detailed review of existing knowledge on the functional characterization of biological networks. In 15 chapters authored by an international group of prolific systems biology and bioinformatics researchers, it will organize, conceptualize, and summarize the existing core of research results and computational methods on understanding biological function from a network perspective.

Author : Fabricio Alves Barbosa da Silva,Nicolas Carels,Marcelo Trindade dos Santos,Francisco José Pereira Lopes
Publisher : Springer Nature
Page : 381 pages
File Size : 40,5 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.

Author : Elisabetta De Maria
Publisher : John Wiley & Sons
Page : 468 pages
File Size : 50,7 Mb
Release : 2022-11-18
Category : Science
ISBN : 9781119716587

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Systems Biology Modelling and Analysis by Elisabetta De Maria Pdf

Systems Biology Modelling and Analysis Describes important modelling and computational methods for systems biology research to enable practitioners to select and use the most suitable technique Systems Biology Modelling and Analysis provides an overview of state-of-the-art techniques and introduces related tools and practices to formalize models and automate reasoning for systems biology. The authors present and compare the main formal methods used in systems biology for modelling biological networks, including discussion of their advantages, drawbacks, and main applications. Each chapter includes an intuitive presentation of the specific formalism, a brief history of the formalism and of its applications in systems biology, a formal description of the formalism and its variants, at least one realistic case study, some applications of formal techniques to validate and make deep analysis of models encoded with the formalism, and a discussion on the kind of biological systems for which the formalism is suited, along with concrete ideas on its possible evolution. Edited by a highly qualified expert with significant experience in the field, some of the methods and techniques covered in Systems Biology Modelling and Analysis include: Petri nets, an important tool for studying different aspects of biological systems, ranging from simple signaling pathways to metabolic networks and beyond Pathway Logic, a formal, rule-based system and interactive viewer for developing executable models of cellular processes Boolean networks, a mathematical model which has been widely used for decades in the context of biological regulation networks Answer Set Programming (ASP), which has proven to be a strong logic programming paradigm to deal with the inherent complexity of biological models For systems biologists, biochemists, bioinformaticians, molecular biologists, pharmacologists, and computer scientists, Systems Biology Modelling and Analysis is a comprehensive all-in-one resource to understand and harness the field’s current models and techniques while also preparing for their potential developments in coming years with the help of the author’s expert insight.

Author : James M. Bower,Hamid Bolouri
Publisher : MIT Press
Page : 386 pages
File Size : 54,8 Mb
Release : 2001
Category : Computers
ISBN : 0262524236

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Computational Modeling of Genetic and Biochemical Networks by James M. Bower,Hamid Bolouri Pdf

How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.

Author : Hamid Bolouri
Publisher : World Scientific Publishing Company
Page : 340 pages
File Size : 50,8 Mb
Release : 2008-08-13
Category : Science
ISBN : 9781848168183

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Computational Modeling of Gene Regulatory Networks — A Primer by Hamid Bolouri Pdf

This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.

Author : Irit Gat-Viks
Publisher : Unknown
Page : 103 pages
File Size : 51,9 Mb
Release : 2007
Category : Electronic
ISBN : OCLC:234127416

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Computational Analysis of Molecular Networks by Irit Gat-Viks Pdf

Author : Stefano Boccaletti
Publisher : World Scientific
Page : 465 pages
File Size : 55,8 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."

Author : Pietro Hiram Guzzi,Swarup Roy
Publisher : Elsevier
Page : 212 pages
File Size : 50,7 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

Author : Corrado Priami,Melissa J Morine
Publisher : World Scientific
Page : 432 pages
File Size : 46,7 Mb
Release : 2015-01-29
Category : Science
ISBN : 9781783266890

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Analysis of Biological Systems by Corrado Priami,Melissa J Morine Pdf

Modeling is fast becoming fundamental to understanding the processes that define biological systems. High-throughput technologies are producing increasing quantities of data that require an ever-expanding toolset for their effective analysis and interpretation. Analysis of high-throughput data in the context of a molecular interaction network is particularly informative as it has the potential to reveal the most relevant network modules with respect to a phenotype or biological process of interest. Analysis of Biological Systems collects classical material on analysis, modeling and simulation, thereby acting as a unique point of reference. The joint application of statistical techniques to extract knowledge from big data and map it into mechanistic models is a current challenge of the field, and the reader will learn how to build and use models even if they have no computing or math background. An in-depth analysis of the currently available technologies, and a comparison between them, is also included. Unlike other reference books, this in-depth analysis is extended even to the field of language-based modeling. The overall result is an indispensable, self-contained and systematic approach to a rapidly expanding field of science. Contents:Algorithmic Systems BiologySetting the ContextSystems and ModelsStatic Modeling TechnologiesDynamic Modeling TechnologiesLanguage-based ModelingDynamic Modeling ProcessSimulationPerspectives and ConclusionsAppendix A: Basic MathAppendix B: Probability and StatisticsAppendix C: Semantics of Modeling Languages Readership: Graduate students in computer science, physics, mathematics or engineering or biology-related fields who want to better understand how to develop and use models of biological systems. Practitioners in systems biology who want to understand algorithmic modeling and algorithmic systems biology. Key Features:The book jointly deals with static (statistical) and dynamic (simulation) technologies making it a strong reference for who wants to approach real systems biology problemsThe content of the book is the result of more than ten years application of the material in university courses and to industrial-level problems in systems pharmacology and systems nutritionThere is no reference work available for the field of language-based modeling that is studied in depth in this bookKeywords:Modeling;Simulation;Network Analysis;Systems Biology;Systems Nutrition;Systems Pharmacology;Stochastic Models;Programming Biology;Multivariate Analysis