A New Kind of Computational Biology: Cellular Automata Based Models for Genomics and Proteomics, Pal Chaudhuri Parimal, Ghosh Soumyabrata, Dutta Adip
Автор: Rudolph Miguel Название: Genomics and Proteomics: Functional and Computational Aspects ISBN: 168286765X ISBN-13(EAN): 9781682867655 Издательство: Неизвестно Рейтинг: Цена: 23655.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions.In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.
Описание: Bringing together leading experts in the field of network data analysis, this text introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning. Using real-world biological and medical examples, applications of these theories are discussed and creative thinking is encouraged in the analysis of such complex network data sets.
Описание: Part I: Stochastic Chemical Reactions.- Test Models for Statistical Inference: Two-Dimensional Reaction Systems Displaying Limit Cycle Bifurcations and Bistability.- Importance Sampling for Metastable and Multiscale Dynamical Systems.- Multiscale Simulation of Stochastic Reaction-diffusion Networks.- Part II: Stochastic Numerical Approaches, Algorithms and Coarse-Grained Simulations.- Numerical Methods for Ergodic SDEs: When Stochastic Integration Meets Geometric Integration.-Stability and Strong Convergence for Spatial Stochastic Kinetics.- The T cells in an Ageing Virtual Mouse.- Part III: Analysis of Stochastic Dynamical Systems for Modeling Cell Biology.- Model reduction for Stochastic Reaction Systems.- ZI-closure Scheme: A Method to Solve and Study Stochastic Reaction Networks.- Deterministic and Stochastic Becker-Dцring Equations: Past and Recent Mathematical Developments.- Coagulation-Fragmentation with a Finite Number of Particles: Models, Stochastic Analysis and Applications to Telomere Clustering and Viral Capsid Assembly.- A Review of Stochastic and Delay Simulation Approaches in both Time and Space in Computational Cell Biology.- Part IV: Diffusion Processes and Stochastic Modeling.- Recent Mathematical Models of Axonal Transport.- Stochastic Models for Evolving Cellular Populations of Mitochondria: Disease, Development, and Ageing.- Modeling and Stochastic Analysis of the Single Photon Response.- A Phenomenological Spatial Model for Macro-ecological Patterns in Species-rich Ecosystems.
Описание: Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions.In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.
Автор: Parimal Pal Chaudhuri; Soumyabrata Ghosh; Adip Dut Название: A New Kind of Computational Biology ISBN: 9811316384 ISBN-13(EAN): 9789811316388 Издательство: Springer Рейтинг: Цена: 6986.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology. The book adopts a hands-on, “do-it-yourself” approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical ‘rules’ observed in biology. In a single framework, the authors have presented two branches of science – Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results.This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question – ‘Are life and the universe nothing but a collection of continuous systems processing information’.
Автор: Khawaja Husnain Haider Название: Stem Cells - From Drug to Drug Discovery ISBN: 3110496283 ISBN-13(EAN): 9783110496284 Издательство: Walter de Gruyter Цена: 18586.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: Stem cell based therapy is a 21st century approach of therapeutic intervention which epitomizes a shift from conventional symptomatic treatment strategy to addressing the root cause of the disease process. This is especially a hope for the patients suffering from diseases such as Alzheimer, diabetes, myocardial infarction and other diseases which have always been considered as incurable. Moreover, stem cells provide excellent in vitro disease models for drug development. This book is a compilation of the bench experience of experts from various research labs involved in the cutting edge area of research, describing the use of stem cells both as part of the combinatorial therapeutic intervention approach and as tools (disease model) during drug development.
Автор: Ian Moore Название: Principles of Proteomics ISBN: 1680945335 ISBN-13(EAN): 9781680945331 Издательство: Mare Nostrum (Eurospan) Рейтинг: Цена: 18183.00 р. Наличие на складе: Нет в наличии.
Описание: Proteomics is the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context. The proteome is not constant; it differs from cell to cell and changes over time. This text is intended to give the molecular biologist a rudimentary understanding of the technologies behind proteomics and their application to address biological questions.
Описание: What every neuroscientist should know about the mathematical modeling of excitable cells. Combining empirical physiology and nonlinear dynamics, this text provides an introduction to the simulation and modeling of dynamic phenomena in cell biology and neuroscience. It introduces mathematical modeling techniques alongside cellular electrophysiology. Topics include membrane transport and diffusion, the biophysics of excitable membranes, the gating of voltage and ligand-gated ion channels, intracellular calcium signalling, and electrical bursting in neurons and other excitable cell types. It introduces mathematical modeling techniques such as ordinary differential equations, phase plane, and bifurcation analysis of single-compartment neuron models. With analytical and computational problem sets, this book is suitable for life sciences majors, in biology to neuroscience, with one year of calculus, as well as graduate students looking for a primer on membrane excitability and calcium signalling.
Описание: This second edition integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular, cellular and evolutionary biology.
Описание: The increased and widespread availability of large network data resources in recent years has resulted in the increased need for effective methods for the analysis of these networks. The challenge is to detect patterns that provide a better understanding of the data. However, this is not a straight forward task because of the size of the data sets and the computer power required for the analyses. The solution is to devise methods for approximately answering the questions posed, and these methods will vary depending on the data sets under scrutiny. This cutting-edge text introduces graph and network theory, cluster analysis and machine learning, before discussing the thought processes and creativity involved in the analysis of large-scale biological and medical data sets, using a wide range of real-life examples. Bringing together leading experts, this inter-disciplinary text provides an ideal introduction to and insight into the field of network data analysis.
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