Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-21 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.

Download or read book Genomic Control Process written by Isabelle S. Peter and published by Academic Press. This book was released on 2015-01-21 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. - Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life - Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework - Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature - Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type - Demonstrates the causal power of system-level understanding of genomic control process - Conceptually organizes a constellation of complex and diverse biological phenomena - Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models - Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Download or read book Gene Network Inference written by Alberto Fuente and published by Springer Science & Business Media. This book was released on 2014-01-03 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.

Download or read book Genomic Signal Processing written by Ilya Shmulevich and published by Princeton University Press. This book was released on 2014-09-08 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathematical definitions and propositions for the main elements of GSP and by paying attention to the validity of models relative to the data. Ilya Shmulevich and Edward Dougherty cover real-world situations and explain their mathematical modeling in relation to systems biology and systems medicine. Genomic Signal Processing makes a major contribution to computational biology, systems biology, and translational genomics by providing a self-contained explanation of the fundamental mathematical issues facing researchers in four areas: classification, clustering, network modeling, and network intervention.

Download or read book Information Processing and Biological Systems written by Samuli Niiranen and published by Springer Science & Business Media. This book was released on 2011-03-10 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living beings require constant information processing for survival. In cells, information is being processed and propagated at various levels, from the gene regulatory network to chemical pathways, to the interaction with the environment. How this is achieved and how information is coded is still poorly understood. For example, what a cell interprets as information in the temporal level of an mRNA and what is interpreted as noise remains an open question. Recently, information theoretical methods and other tools, developed in the context of engineering and natural sciences, have been applied to study diverse biological processes. This book covers the latest findings on how information is processed in various biological processes, ranging from information processing and propagation in gene regulatory networks to information processing in natural language. An overview is presented of the state-of-the-art in information processing in biological systems and the opinion of current leaders in this research field on future research directions.

Download or read book Simulated Annealing written by Marcos Sales Guerra Tsuzuki and published by BoD – Books on Demand. This book was released on 2012-10-17 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents state of the art contributes to Simulated Annealing (SA) that is a well-known probabilistic meta-heuristic. It is used to solve discrete and continuous optimization problems. The significant advantage of SA over other solution methods has made it a practical solution method for solving complex optimization problems. Book is consisted of 13 chapters, classified in single and multiple objectives applications and it provides the reader with the knowledge of SA and several applications. We encourage readers to explore SA in their work, mainly because it is simple and can determine extremely very good results.

Download or read book Exploring Discrete Dynamics written by Andrew Wuensche and published by Luniver Press. This book was released on 2011 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: EXPLORING DISCRETE DYNAMICS is a comprehensive guide to studying cellular automata and discrete dynamical networks with the classic software Discrete Dynamics Laboratory (DDLab). These collective networks are at the core of complexity and emergent self-organisation. With interactive graphics, DDLab is able to explore an huge diversity of behaviour -- mostly terra incognita -- space-time patters, but also basins of attraction, mathematical objects representing the convergent flow in state-space. Applications range within physics, mathematics, biology, cognition, society, economics and computation, and more specifically in neural and genetic networks, artificial life, and a theory of memory.

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 ? 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.

Download or read book Handbook of Research on Computational Methodologies in Gene Regulatory Networks written by Das, Sanjoy and published by IGI Global. This book was released on 2009-10-31 with total page 740 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.

Download or read book Computational Modeling of Gene Regulatory Networks written by Hamid Bolouri and published by Imperial College Press. This book was released on 2008 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book The Origins of Order written by Stuart A. Kauffman and published by Oxford University Press. This book was released on 1993-06-10 with total page 958 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order that is widely observed throughout nature Kauffman argues that self-organization plays an important role in the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt are poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biological science itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences.

Download or read book Genes Signals written by Mark Ptashne and published by CSHL Press. This book was released on 2002 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: P. 103.

Download or read book Systems Medicine written by and published by Academic Press. This book was released on 2020-08-24 with total page 1571 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information

Download or read book Biological Network Analysis written by Pietro Hiram Guzzi and published by Elsevier. This book was released on 2020-05-11 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Logical Modeling of Cellular Processes From Software Development to Network Dynamics written by Matteo Barberis and published by Frontiers Media SA. This book was released on 2019-08-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.

Download or read book Wetware written by Dennis Bray and published by Yale University Press. This book was released on 2009-05-26 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: “A beautifully written journey into the mechanics of the world of the cell, and even beyond, exploring the analogy with computers in a surprising way” (Denis Noble, author of Dance to the Tune of Life). How does a single-cell creature, such as an amoeba, lead such a sophisticated life? How does it hunt living prey, respond to lights, sounds, and smells, and display complex sequences of movements without the benefit of a nervous system? This book offers a startling and original answer. In clear, jargon-free language, Dennis Bray taps the findings from the discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis for all distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence. In Wetware, Bray offers imaginative, wide-ranging, and perceptive critiques of robotics and complexity theory, as well as many entertaining and telling anecdotes. For the general reader, the practicing scientist, and all others with an interest in the nature of life, this book is an exciting portal to some of biology’s latest discoveries and ideas. “Drawing on the similarities between Pac-Man and an amoeba and efforts to model the human brain, this absorbing read shows that biologists and engineers have a lot to learn from working together.” —Discover magazine “Wetware will get the reader thinking.” —Science magazine

Download or read book Pulsed Neural Networks written by Wolfgang Maass and published by MIT Press. This book was released on 2001-01-26 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most practical applications of artificial neural networks are based on a computational model involving the propagation of continuous variables from one processing unit to the next. In recent years, data from neurobiological experiments have made it increasingly clear that biological neural networks, which communicate through pulses, use the timing of the pulses to transmit information and perform computation. This realization has stimulated significant research on pulsed neural networks, including theoretical analyses and model development, neurobiological modeling, and hardware implementation. This book presents the complete spectrum of current research in pulsed neural networks and includes the most important work from many of the key scientists in the field. Terrence J. Sejnowski's foreword, "Neural Pulse Coding," presents an overview of the topic. The first half of the book consists of longer tutorial articles spanning neurobiology, theory, algorithms, and hardware. The second half contains a larger number of shorter research chapters that present more advanced concepts. The contributors use consistent notation and terminology throughout the book. Contributors Peter S. Burge, Stephen R. Deiss, Rodney J. Douglas, John G. Elias, Wulfram Gerstner, Alister Hamilton, David Horn, Axel Jahnke, Richard Kempter, Wolfgang Maass, Alessandro Mortara, Alan F. Murray, David P. M. Northmore, Irit Opher, Kostas A. Papathanasiou, Michael Recce, Barry J. P. Rising, Ulrich Roth, Tim Schönauer, Terrence J. Sejnowski, John Shawe-Taylor, Max R. van Daalen, J. Leo van Hemmen, Philippe Venier, Hermann Wagner, Adrian M. Whatley, Anthony M. Zador