Download or read book Towards Structure and Dynamics of Metabolic Networks written by Sergio Grimbs and published by . This book was released on 2009 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Structure and Dynamics of Networks written by Mark Newman and published by Princeton University Press. This book was released on 2006-05-07 with total page 593 pages. Available in PDF, EPUB and Kindle. Book excerpt: From the Internet to networks of friendship, disease transmission, and even terrorism, the concept--and the reality--of networks has come to pervade modern society. But what exactly is a network? What different types of networks are there? Why are they interesting, and what can they tell us? In recent years, scientists from a range of fields--including mathematics, physics, computer science, sociology, and biology--have been pursuing these questions and building a new "science of networks." This book brings together for the first time a set of seminal articles representing research from across these disciplines. It is an ideal sourcebook for the key research in this fast-growing field. The book is organized into four sections, each preceded by an editors' introduction summarizing its contents and general theme. The first section sets the stage by discussing some of the historical antecedents of contemporary research in the area. From there the book moves to the empirical side of the science of networks before turning to the foundational modeling ideas that have been the focus of much subsequent activity. The book closes by taking the reader to the cutting edge of network science--the relationship between network structure and system dynamics. From network robustness to the spread of disease, this section offers a potpourri of topics on this rapidly expanding frontier of the new science.
Download or read book Large Scale Structure And Dynamics Of Complex Networks From Information Technology To Finance And Natural Science written by Alessandro Vespignani and published by World Scientific. This book was released on 2007-06-28 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the culmination of three years of research effort on a multidisciplinary project in which physicists, mathematicians, computer scientists and social scientists worked together to arrive at a unifying picture of complex networks. The contributed chapters form a reference for the various problems in data analysis visualization and modeling of complex networks.
Download or read book A Network Based Approach to Cell Metabolism written by Oriol Güell and published by Springer. This book was released on 2017-08-16 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis uses a systems-level approach to study the cellular metabolism, unveiling new mechanisms and responses that were impossible to reach with traditional reductionists procedures. The results reported here have a potential application in areas like metabolic engineering and disease treatment. They could also be used in determining the accuracy of the gene essentiality of new genome-scale reconstructions. Different methods and techniques, within the contexts of Systems Biology and the field known as Complex Networks Analysis have been applied in this work to show different features of the robustness of metabolic networks. The specific issues addressed here range from pure topological aspec ts of the networks themselves to the balance of biochemical fluxes.
Download or read book Dynamic Analysis and Design of Metabolic Networks written by Shyamsundhar Srinivasan and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical models of biological networks play an important role in metabolic engineering through their ability to provide a complete systems level understanding of the numerous interactions that govern metabolism, and consequently cellular function. Models of metabolism are extensively used to design these networks to achieve various engineering and pharmacological objectives. Constraint-based models of metabolism assume that metabolism operates under a pseudo steady state and represent them only in terms of their reaction stoichiometry and fluxes. The numerous regulatory interactions that constitute metabolism are not considered, and the dynamics of the networks cannot be deciphered using constraint-based models. In contrast, kinetic models can represent all of the interactions in the metabolic network, and also facilitate studying the dynamic characteristics of metabolism. Nonetheless, computational limitations encountered during various stages of kinetic model development and use limit their widespread adoption for model-based prediction and design. This thesis aims to address some of these limitations using the metabolism of Escherichia coli as an example. First, we demonstrate the use of kinetic models to characterize the steady state behaviour of a bistable metabolic network with a positive feedback loop, and to design this bistable network to produce at the highest possible steady state. Next, we explore the use of metabolic network topology and structure to assess the ability of the network to exhibit more than one steady state. We also show how this assessment can be used to design networks with either monostable or multistable topologies. Finally, we develop two scalable frameworks to assess the structural identifiability and estimability of parameters in a kinetic model of a metabolic network, based on steady state data. The application of these frameworks to determine the quality and quantity of experiments necessary to generate the steady state data required for estimating all model parameters is also shown. The methods developed and demonstrated in this thesis aim to improve the adoption of kinetic models to design metabolic networks exhibiting bistability. They also provide alternative avenues for parameter estimation in kinetic models using steady state data, while reducing the quantity of time course data needed for kinetic model parameter estimation.
Download or read book Gene Regulation and Metabolism written by Julio Collado-Vides and published by MIT Press. This book was released on 2002 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of current computational approaches to metabolism and gene regulation.
Download or read book Plant Metabolic Networks written by Jörg Schwender and published by Springer Science & Business Media. This book was released on 2009-06-12 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants are the basis for human nutrition and of increasing interest for the chemical industry as a source of chemical feed stocks. Fuels derived from plant biomass will increasingly replace fossil fuels in the future. In order to increase crop productivity, design new plant products, and create new energy crops, there is need for methods of qualitative and quantitative analysis of metabolism which are able to guide the rational re-design of metabolic networks. In this book, recent advances in qualitative and quantitative analysis of metabolism are summarized to give an overview of the current state of knowledge. Principles of the analysis of network structure, flux analysis, and kinetic modeling are described. Analytical methods necessary to produce the data needed for metabolic flux analysis and for kinetic modeling are described. The analysis of larger metabolic networks is only possible by using computer assistance. Therefore each chapter of the book shall also describe software available for this purpose.
Download or read book The Evolutionary Strategies that Shape Ecosystems written by J. Philip Grime and published by John Wiley & Sons. This book was released on 2012-03-26 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: THE EVOLUTIONARY STRATEGIES THAT SHAPE ECOSYSTEMS In 1837 a young Charles Darwin took his notebook, wrote “I think”, and then sketched a rudimentary, stick-like tree. Each branch of Darwin’s tree of life told a story of survival and adaptation – adaptation of animals and plants not just to the environment but also to life with other living things. However, more than 150 years since Darwin published his singular idea of natural selection, the science of ecology has yet to account for how contrasting evolutionary outcomes affect the ability of organisms to coexist in communities and to regulate ecosystem functioning. In this book Philip Grime and Simon Pierce explain how evidence from across the world is revealing that, beneath the wealth of apparently limitless and bewildering variation in detailed structure and functioning, the essential biology of all organisms is subject to the same set of basic interacting constraints on life-history and physiology. The inescapable resulting predicament during the evolution of every species is that, according to habitat, each must adopt a predictable compromise with regard to how they use the resources at their disposal in order to survive. The compromise involves the investment of resources in either the effort to acquire more resources, the tolerance of factors that reduce metabolic performance, or reproduction. This three-way trade-off is the irreducible core of the universal adaptive strategy theory which Grime and Pierce use to investigate how two environmental filters selecting, respectively, for convergence and divergence in organism function determine the identity of organisms in communities, and ultimately how different evolutionary strategies affect the functioning of ecosystems. This book refl ects an historic phase in which evolutionary processes are finally moving centre stage in the effort to unify ecological theory, and animal, plant and microbial ecology have begun to find a common theoretical framework. Companion website This book has a companion website www.wiley.com/go/grime/evolutionarystrategies with Figures and Tables from the book for downloading.
Download or read book Metabolic Network Analysis written by T.P. Jayadev Reddy and published by Daya Books. This book was released on 2007-03-02 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolism Is A Set Of Chemical Reactions, Used By Living Organisms To Process Chemical Compounds In Order To Take Energy, Extract Building Blocks And Eliminate Toxic Compounds. It Comprises The Network Of Interactions That Provide Energy And Building Blocks For Cells And Organisms, A Network Sustaining The Living And Allowing It To Grow And Reproduce. Understanding The Nature And Functions Of Metabolic Networks Is Imperative To Biology, Toxicology And Medicine. With The Sequencing Of Complete Genomes, It Is Now Possible To Reconstruct The Network Of Biochemical Reactions In Many Organisms, From Bacteria To Human. This Book Examines How Biological Components Interact And Form Metabolic Networks, And How These Networks Generate Cell Functions Corresponding To Observable Phenotypes. It Describes How To Model Metabolic Networks, How To Determine Their Properties, And How To Relate These To Phenotypic Functions. It Will Be A Highly Beneficial Reference Tool For Researchers And Scholars In All Areas Of Life Sciences. Contents Chapter 1: Biology Of Cellular Networks; Chapter 2: Characteristics Of Metabolic Networks; Chapter 3: Signalling Pathways; Chapter 4: Networks In Genomics And Proteomics; Chapter 5: Modelling Of Biological Network; Chapter 6: Pathway Analysis In Metabolic Networks; Chapter 7: Topological Features Of Metabolic Networks; Chapter 8: Structure Of Expanding Metabolic Networks; Chapter 9: Modularity In Metabolic Networks; Chapter 10: Connectivity In Metabolic Networks; Chapter 11: Metabolic Network Interactions; Chapter 12: Microbial Metabolic Networks; Chapter 13: Protein Interaction Networks; Chapter 14: Implications Of Human Metabolome; Chapter 15: Metabolic Network Prediction; Chapter 16: Algebraic Comparison Of Metabolic Networks; Chapter 17: Regulation Of Metabolic Pathways.
Download or read book Systems Biology of Metabolic and Signaling Networks written by Miguel A. Aon and published by Springer Science & Business Media. This book was released on 2013-10-22 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology represents a new paradigm aiming at a whole-organism-level understanding of biological phenomena, emphasizing interconnections and functional interrelationships rather than component parts. The study of network properties, and how they control and regulate behavior from the cellular to organism level, constitutes a main focus of Systems Biology. This book addresses from a novel perspective a major unsolved biological problem: understanding how a cell works and what goes wrong in pathology. The task undertaken by the authors is in equal parts conceptual and methodological, integrative and analytical, experimental and theoretical, qualitative and quantitative, didactic and comprehensive. Essentially, they unravel the spatio-temporal unfolding of interacting mass-energy and information networks at the cellular and organ levels, as well as its modulation through activation or repression by signaling networks to produce a certain phenotype or (patho)physiological response. Starting with the historical roots, in thirteen chapters this work explores the Systems Biology of signaling networks, cellular structures and fluxes, organ and microorganism functions. In doing so, it establishes the basis of a 21st century approach to biological complexity.
Download or read book Ecological Networks written by Mercedes Pascual and published by Oxford University Press. This book was released on 2006 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: Food webs are one of the most useful, and challenging, objects of study in ecology. These networks of predator-prey interactions, conjured in Darwin's image of a "tangled bank," provide a paradigmatic example of complex adaptive systems. This book is based on a February 2004 Santa Fe Institute workshop. Its authors treat the ecology of predator-prey interactions, food web theory, structure and dynamics. The book explores the boundaries of what is known of the relationship between structure and dynamics in ecological networks and will define directions for future developments in this field.
Download or read book Yeast Systems Biology written by Juan I. Castrillo and published by Humana Press. This book was released on 2011-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems. Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine. These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases. Written for the highly successful Methods in Molecular BiologyTM series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results. Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all ‘omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.
Download or read book Dynamics On and Of Complex Networks written by Niloy Ganguly and published by Springer Science & Business Media. This book was released on 2009-06-20 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: This self-contained book systematically explores the statistical dynamics on and of complex networks having relevance across a large number of scientific disciplines. The theories related to complex networks are increasingly being used by researchers for their usefulness in harnessing the most difficult problems of a particular discipline. The book is a collection of surveys and cutting-edge research contributions exploring the interdisciplinary relationship of dynamics on and of complex networks. Topics covered include complex networks found in nature—genetic pathways, ecological networks, linguistic systems, and social systems—as well as man-made systems such as the World Wide Web and peer-to-peer networks. The contributed chapters in this volume are intended to promote cross-fertilization in several research areas, and will be valuable to newcomers in the field, experienced researchers, practitioners, and graduate students interested in systems exhibiting an underlying complex network structure in disciplines such as computer science, biology, statistical physics, nonlinear dynamics, linguistics, and the social sciences.
Download or read book Handbook on Biological Networks written by Stefano Boccaletti and published by World Scientific. This book was released on 2010 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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."
Download or read book Biological Networks written by Francois Kepes and published by World Scientific. This book was released on 2007 with total page 531 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Large Scale Structure and Dynamics of Complex Networks written by Guido Caldarelli and published by World Scientific. This book was released on 2007 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the culmination of three years of research effort on a multidisciplinary project in which physicists, mathematicians, computer scientists and social scientists worked together to arrive at a unifying picture of complex networks. The contributed chapters form a reference for the various problems in data analysis visualization and modeling of complex networks.
Download or read book Networks in Nature written by Sumeet Agarwal and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis we propose some new approaches to the study of complex networks, and apply them to multiple domains, focusing in particular on protein-protein interaction networks. We begin by examining the roles of individual proteins; specifically, the influential idea of 'date' and 'party' hubs. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. We show that the observations underlying this proposal appear to have been largely illusory, and that topological properties of hubs do not in general correlate with interactor co-expression, thus undermining the primary basis for the categorisation. However, we find significant correlations between interaction centrality and the functional similarity of the interacting proteins, indicating that it might be useful to conceive of roles for protein-protein interactions, as opposed to individual proteins. The observation that examining just one or a few network properties can be misleading motivates us to attempt to develop a more holistic methodology for network investigation. A wide variety of diagnostics of network structure exist, but studies typically employ only small, largely arbitrarily selected subsets of these. Here we simultaneously investigate many networks using many diagnostics in a data-driven fashion, and demonstrate how this approach serves to organise both networks and diagnostics, as well as to relate network structure to functionally relevant characteristics in a variety of settings. These include finding fast estimators for the solution of hard graph problems, discovering evolutionarily significant aspects of metabolic networks, detecting structural constraints on particular network types, and constructing summary statistics for efficient model-fitting to networks. We use the last mentioned to suggest that duplication-divergence is a feasible mechanism for protein-protein interaction evolution, and that interactions may rewire faster in yeast than in larger genomes like human and fruit fly. Our results help to illuminate protein-protein interaction networks in multiple ways, as well as providing some insight into structure-function relationships in other types of networks. We believe the methodology outlined here can serve as a general-purpose, data-driven approach to aid in the understanding of networked systems.
