Boolean Networks As Predictive Models Of Emergent Biological Behaviors

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Boolean Networks as Predictive Models of Emergent Biological Behaviors

Author : Jordan C. Rozum
Publisher : Cambridge University Press
ISBN 13 : 1009292943
Total Pages : 118 pages
Book Rating : 4.0/5 (92 download)

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Book Synopsis Boolean Networks as Predictive Models of Emergent Biological Behaviors by : Jordan C. Rozum

Download or read book Boolean Networks as Predictive Models of Emergent Biological Behaviors written by Jordan C. Rozum and published by Cambridge University Press. This book was released on 2024-03-28 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions – from molecules in gene regulatory networks to species in ecological networks – and the often-incomplete state of system knowledge, such as the unknown values of kinetic parameters for biochemical reactions. Boolean networks have emerged as a powerful tool for modeling these systems. This Element provides a methodological overview of Boolean network models of biological systems. After a brief introduction, the authors describe the process of building, analyzing, and validating a Boolean model. They then present the use of the model to make predictions about the system's response to perturbations and about how to control its behavior. The Element emphasizes the interplay between structural and dynamical properties of Boolean networks and illustrates them in three case studies from disparate levels of biological organization.

Probabilistic Boolean Networks

Author : Ilya Shmulevich
Publisher : SIAM
ISBN 13 : 0898717639
Total Pages : 277 pages
Book Rating : 4.8/5 (987 download)

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Book Synopsis Probabilistic Boolean Networks by : Ilya Shmulevich

Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-01 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first comprehensive treatment of probabilistic Boolean networks (PBNs), an important model class for studying genetic regulatory networks. This book covers basic model properties, including the relationships between network structure and dynamics, steady-state analysis, and relationships to other model classes." "Researchers in mathematics, computer science, and engineering are exposed to important applications in systems biology and presented with ample opportunities for developing new approaches and methods. The book is also appropriate for advanced undergraduates, graduate students, and scientists working in the fields of computational biology, genomic signal processing, control and systems theory, and computer science.

Logic Synthesis for Genetic Diseases

Author : Pey-Chang Kent Lin
Publisher : Springer Science & Business Media
ISBN 13 : 146149429X
Total Pages : 100 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Logic Synthesis for Genetic Diseases by : Pey-Chang Kent Lin

Download or read book Logic Synthesis for Genetic Diseases written by Pey-Chang Kent Lin and published by Springer Science & Business Media. This book was released on 2013-10-31 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book brings to bear a body of logic synthesis techniques, in order to contribute to the analysis and control of Boolean Networks (BN) for modeling genetic diseases such as cancer. The authors provide several VLSI logic techniques to model the genetic disease behavior as a BN, with powerful implicit enumeration techniques. Coverage also includes techniques from VLSI testing to control a faulty BN, transforming its behavior to a healthy BN, potentially aiding in efforts to find the best candidates for treatment of genetic diseases.

Algorithms For Analysis, Inference, And Control Of Boolean Networks

Author : Akutsu Tatsuya
Publisher : World Scientific
ISBN 13 : 9813233443
Total Pages : 228 pages
Book Rating : 4.8/5 (132 download)

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Book Synopsis Algorithms For Analysis, Inference, And Control Of Boolean Networks by : Akutsu Tatsuya

Download or read book Algorithms For Analysis, Inference, And Control Of Boolean Networks written by Akutsu Tatsuya and published by World Scientific. This book was released on 2018-02-13 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Boolean network (BN) is a mathematical model of genetic networks and other biological networks. Although extensive studies have been done on BNs from a viewpoint of complex systems, not so many studies have been undertaken from a computational viewpoint. This book presents rigorous algorithmic results on important computational problems on BNs, which include inference of a BN, detection of singleton and periodic attractors in a BN, and control of a BN. This book also presents algorithmic results on fundamental computational problems on probabilistic Boolean networks and a Boolean model of metabolic networks. Although most contents of the book are based on the work by the author and collaborators, other important computational results and techniques are also reviewed or explained. Contents: Preliminaries Boolean Networks Detection of Attractors Detection of Singleton Attractors Detection of Periodic Attractors Identification of Boolean Networks Control of Boolean Networks Predecessor and Observability Problems Semi-Tensor Product Approach Analysis of Metabolic Networks Probabilistic Boolean Networks Identification of Probabilistic Boolean Networks Control of Probabilistic Boolean Networks Readership: Graduate students and researchers working on string theory and related topics. Keywords: Boolean Networks;Bioinformatics;Systems Biology;Combinatorial Algorithms;AttractorsReview: Key Features: Unique book focusing on computational aspects of Boolean networks Provide computational foundations on Boolean networks Contain recent and up-to-date results on algorithms for Boolean networks

Comprehensive Biotechnology

Author :
Publisher : Elsevier
ISBN 13 : 0444640479
Total Pages : 4876 pages
Book Rating : 4.4/5 (446 download)

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Book Synopsis Comprehensive Biotechnology by :

Download or read book Comprehensive Biotechnology written by and published by Elsevier. This book was released on 2019-07-17 with total page 4876 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive Biotechnology, Third Edition, Six Volume Set unifies, in a single source, a huge amount of information in this growing field. The book covers scientific fundamentals, along with engineering considerations and applications in industry, agriculture, medicine, the environment and socio-economics, including the related government regulatory overviews. This new edition builds on the solid basis provided by previous editions, incorporating all recent advances in the field since the second edition was published in 2011. Offers researchers a one-stop shop for information on the subject of biotechnology Provides in-depth treatment of relevant topics from recognized authorities, including the contributions of a Nobel laureate Presents the perspective of researchers in different fields, such as biochemistry, agriculture, engineering, biomedicine and environmental science

Bio-inspired Information and Communication Technologies

Author : Adriana Compagnoni
Publisher : Springer
ISBN 13 : 3030242021
Total Pages : 209 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis Bio-inspired Information and Communication Technologies by : Adriana Compagnoni

Download or read book Bio-inspired Information and Communication Technologies written by Adriana Compagnoni and published by Springer. This book was released on 2019-07-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed conference proceedings of the 11th International Conference on Bio-Inspired Information and Communications Technologies, held in Pittsburgh, PA, USA, in March 2019. The 13 revised full papers and 2 short papers were selected from 29 submissions. Past iterations of the conference have attracted contributions in Direct Bioinspiration (physical biological materials and systems used within technology) as well as Indirect Bioinspiration (biological principles, processes and mechanisms used within the design and application of technology). This year, the scope has expanded to include a third thrust: Foundational Bioinspiration (bioinspired aspects of game theory, evolution, information theory, and philosophy of science).

Comprehensive Medicinal Chemistry III

Author :
Publisher : Elsevier
ISBN 13 : 0128032014
Total Pages : 4609 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Comprehensive Medicinal Chemistry III by :

Download or read book Comprehensive Medicinal Chemistry III written by and published by Elsevier. This book was released on 2017-06-03 with total page 4609 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive Medicinal Chemistry III, Eight Volume Set provides a contemporary and forward-looking critical analysis and summary of recent developments, emerging trends, and recently identified new areas where medicinal chemistry is having an impact. The discipline of medicinal chemistry continues to evolve as it adapts to new opportunities and strives to solve new challenges. These include drug targeting, biomolecular therapeutics, development of chemical biology tools, data collection and analysis, in silico models as predictors for biological properties, identification and validation of new targets, approaches to quantify target engagement, new methods for synthesis of drug candidates such as green chemistry, development of novel scaffolds for drug discovery, and the role of regulatory agencies in drug discovery. Reviews the strategies, technologies, principles, and applications of modern medicinal chemistry Provides a global and current perspective of today's drug discovery process and discusses the major therapeutic classes and targets Includes a unique collection of case studies and personal assays reviewing the discovery and development of key drugs

Bioinformatics for Immunomics

Author : Darren D.R. Flower
Publisher : Springer
ISBN 13 : 1441905405
Total Pages : 192 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Bioinformatics for Immunomics by : Darren D.R. Flower

Download or read book Bioinformatics for Immunomics written by Darren D.R. Flower and published by Springer. This book was released on 2009-10-03 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: Like many words, the term “immunomics” equates to different ideas contingent on context. For a brief span, immunomics meant the study of the Immunome, of which there were, in turn, several different definitions. A now largely defunct meaning rendered the Immunome as the set of antigenic peptides or immunogenic proteins within a single microorganism – be that virus, bacteria, fungus, or parasite – or microbial population, or antigenic or allergenic proteins and peptides derived from the environment as a whole, containing also proteins from eukaryotic sources. However, times have changed and the meaning of immunomics has also changed. Other newer definitions of the Immunome have come to focus on the plethora of immunological receptors and accessory molecules that comprise the host immune arsenal. Today, Immunomics or immunogenomics is now most often used as a synonym for high-throughput genome-based immunology. This is the study of aspects of the immune system using high-throughput techniques within a conc- tual landscape borne of both clinical and biophysical thinking.

An Introduction to Transfer Entropy

Author : Terry Bossomaier
Publisher : Springer
ISBN 13 : 3319432222
Total Pages : 190 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis An Introduction to Transfer Entropy by : Terry Bossomaier

Download or read book An Introduction to Transfer Entropy written by Terry Bossomaier and published by Springer. This book was released on 2016-11-15 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book considers a relatively new metric in complex systems, transfer entropy, derived from a series of measurements, usually a time series. After a qualitative introduction and a chapter that explains the key ideas from statistics required to understand the text, the authors then present information theory and transfer entropy in depth. A key feature of the approach is the authors' work to show the relationship between information flow and complexity. The later chapters demonstrate information transfer in canonical systems, and applications, for example in neuroscience and in finance. The book will be of value to advanced undergraduate and graduate students and researchers in the areas of computer science, neuroscience, physics, and engineering.

Artificial Immune Systems

Author : Hugues Bersini
Publisher : Springer Science & Business Media
ISBN 13 : 3540377492
Total Pages : 471 pages
Book Rating : 4.5/5 (43 download)

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Book Synopsis Artificial Immune Systems by : Hugues Bersini

Download or read book Artificial Immune Systems written by Hugues Bersini and published by Springer Science & Business Media. This book was released on 2006-08-30 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 5th International Conference on Artificial Immune Systems, ICARIS 2006. The book presents 34 revised full papers, are organized in topical sections on computer simulation of classical immunology, computer simulation of idiotypic network, immunoinformatics conceptual papers, pattern recognition type of application, optimization type of application, control and time-series type of application, danger theory inspired application, and text mining application.

Systems Immunology

Author : Jayajit Das
Publisher : CRC Press
ISBN 13 : 1498717411
Total Pages : 355 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Systems Immunology by : Jayajit Das

Download or read book Systems Immunology written by Jayajit Das and published by CRC Press. This book was released on 2018-09-03 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Taken together, the body of information contained in this book provides readers with a bird’s-eye view of different aspects of exciting work at the convergence of disciplines that will ultimately lead to a future where we understand how immunity is regulated, and how we can harness this knowledge toward practical ends that reduce human suffering. I commend the editors for putting this volume together." –Arup K. Chakraborty, Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA New experimental techniques in immunology have produced large and complex data sets that require quantitative modeling for analysis. This book provides a complete overview of computational immunology, from basic concepts to mathematical modeling at the single molecule, cellular, organism, and population levels. It showcases modern mechanistic models and their use in making predictions, designing experiments, and elucidating underlying biochemical processes. It begins with an introduction to data analysis, approximations, and assumptions used in model building. Core chapters address models and methods for studying immune responses, with fundamental concepts clearly defined. Readers from immunology, quantitative biology, and applied physics will benefit from the following: Fundamental principles of computational immunology and modern quantitative methods for studying immune response at the single molecule, cellular, organism, and population levels. An overview of basic concepts in modeling and data analysis. Coverage of topics where mechanistic modeling has contributed substantially to current understanding. Discussion of genetic diversity of the immune system, cell signaling in the immune system, immune response at the cell population scale, and ecology of host-pathogen interactions.

Algebraic and Discrete Mathematical Methods for Modern Biology

Author : Raina Robeva
Publisher : Academic Press
ISBN 13 : 0128012714
Total Pages : 382 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Algebraic and Discrete Mathematical Methods for Modern Biology by : Raina Robeva

Download or read book Algebraic and Discrete Mathematical Methods for Modern Biology written by Raina Robeva and published by Academic Press. This book was released on 2015-05-09 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. Examines significant questions in modern biology and their mathematical treatments Presents important mathematical concepts and tools in the context of essential biology Features material of interest to students in both mathematics and biology Presents chapters in modular format so coverage need not follow the Table of Contents Introduces projects appropriate for undergraduate research Utilizes freely accessible software for visualization, simulation, and analysis in modern biology Requires no calculus as a prerequisite Provides a complete Solutions Manual Features a companion website with supplementary resources

AI Game Development

Author : Alex J. Champandard
Publisher : New Riders
ISBN 13 : 9781592730049
Total Pages : 772 pages
Book Rating : 4.7/5 (3 download)

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Book Synopsis AI Game Development by : Alex J. Champandard

Download or read book AI Game Development written by Alex J. Champandard and published by New Riders. This book was released on 2003 with total page 772 pages. Available in PDF, EPUB and Kindle. Book excerpt: With game players expecting greater intelligence, efficiency, and realism with non-player characters, AI plays an ever-increasing important role in game development. This is a tremendous challenge for game developers in methodology, software design, and programming. Creating autonomous synthetic creatures that can adapt in games requires a different kind of understanding of AI than the classical approach used by current game programmers. The Nouvelle Game AI approach presented in this book focuses on creating embodied "animats" that behave in an intelligent and realistic manner. In particular, learning AI is generating much interest among the game development community, as these modern techniques can be used to optimize the development process. Book jacket.

Individual-based Modeling and Ecology

Author : Volker Grimm
Publisher : Princeton University Press
ISBN 13 : 1400850622
Total Pages : 445 pages
Book Rating : 4.4/5 (8 download)

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Book Synopsis Individual-based Modeling and Ecology by : Volker Grimm

Download or read book Individual-based Modeling and Ecology written by Volker Grimm and published by Princeton University Press. This book was released on 2013-11-28 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: Individual-based models are an exciting and widely used new tool for ecology. These computational models allow scientists to explore the mechanisms through which population and ecosystem ecology arises from how individuals interact with each other and their environment. This book provides the first in-depth treatment of individual-based modeling and its use to develop theoretical understanding of how ecological systems work, an approach the authors call "individual-based ecology.? Grimm and Railsback start with a general primer on modeling: how to design models that are as simple as possible while still allowing specific problems to be solved, and how to move efficiently through a cycle of pattern-oriented model design, implementation, and analysis. Next, they address the problems of theory and conceptual framework for individual-based ecology: What is "theory"? That is, how do we develop reusable models of how system dynamics arise from characteristics of individuals? What conceptual framework do we use when the classical differential equation framework no longer applies? An extensive review illustrates the ecological problems that have been addressed with individual-based models. The authors then identify how the mechanics of building and using individual-based models differ from those of traditional science, and provide guidance on formulating, programming, and analyzing models. This book will be helpful to ecologists interested in modeling, and to other scientists interested in agent-based modeling.

Handbook of Systems Biology

Author : Marian Walhout
Publisher : Academic Press
ISBN 13 : 012385945X
Total Pages : 552 pages
Book Rating : 4.1/5 (238 download)

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Book Synopsis Handbook of Systems Biology by : Marian Walhout

Download or read book Handbook of Systems Biology written by Marian Walhout and published by Academic Press. This book was released on 2012-12-31 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress overall, and in the creation of new fields in particular, is discussed in 'boxes' within each chapter to relate to appropriate topics. 2013 Honorable Mention for Single Volume Reference in Science from the Association of American Publishers' PROSE Awards Emphasizes the interdisciplinary nature of systems biology with contributions from leaders in a variety of disciplines Includes the latest research developments in human and animal models to assist with translational research Presents biological and computational aspects of the science side-by-side to facilitate collaboration between computational and biological researchers

Information Processing and Biological Systems

Author : Samuli Niiranen
Publisher : Springer Science & Business Media
ISBN 13 : 3642196217
Total Pages : 230 pages
Book Rating : 4.6/5 (421 download)

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Book Synopsis Information Processing and Biological Systems by : Samuli Niiranen

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 230 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.

Reconstructing Networks

Author : Giulio Cimini
Publisher : Cambridge University Press
ISBN 13 : 110880876X
Total Pages : 106 pages
Book Rating : 4.1/5 (88 download)

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Book Synopsis Reconstructing Networks by : Giulio Cimini

Download or read book Reconstructing Networks written by Giulio Cimini and published by Cambridge University Press. This book was released on 2021-09-09 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex networks datasets often come with the problem of missing information: interactions data that have not been measured or discovered, may be affected by errors, or are simply hidden because of privacy issues. This Element provides an overview of the ideas, methods and techniques to deal with this problem and that together define the field of network reconstruction. Given the extent of the subject, the authors focus on the inference methods rooted in statistical physics and information theory. The discussion is organized according to the different scales of the reconstruction task, that is, whether the goal is to reconstruct the macroscopic structure of the network, to infer its mesoscale properties, or to predict the individual microscopic connections.