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Dynamic Directionality Of Cell States In Boolean Gene Regulatory Networks
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Book Synopsis Dynamic Directionality of Cell States in Boolean Gene Regulatory Networks by : Ioanna Deni
Download or read book Dynamic Directionality of Cell States in Boolean Gene Regulatory Networks written by Ioanna Deni and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This project studies the dynamics of three Boolean gene regulatory networks for B and T cell differentiation and proposes an original gene regulatory network for larval fat body remodeling in Drosophila. The difference between the limited number of attractors in the gene regulatory networks and the many transient states that lead to the attractors can be seen as analogous to the finite number of phenotypic traits and their underlying genetic variation. The entropy, self transitioning probability, attractability and steady-state probability of the Markov Chain simulation of transitions between the attractors was compared with the experimentally observed phenotypic transformation of cells undergoing differentiation in vitro and in vivo. The model was able to rank attractors bearing markers of differentiation in a logical order. The reconstruction of the potential transition graph revealed cyclic patterns of recurring attractor states. This supports the hypothesis of an attractor of attractors: the Boolean version of canalization. The construction of a gene regulatory network for larval fat body remodeling shed light on components and combinations of components that instruct the system to maintain its inherit canalization.
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 2010-01-21 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.
Book Synopsis Discrete-Time and Discrete-Space Dynamical Systems by : Kuize Zhang
Download or read book Discrete-Time and Discrete-Space Dynamical Systems written by Kuize Zhang and published by Springer. This book was released on 2019-08-06 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discrete-Time and Discrete-Space Dynamical Systems provides a systematic characterization of the similarities and differences of several types of discrete-time and discrete-space dynamical systems, including: Boolean control networks; nondeterministic finite-transition systems; finite automata; labelled Petri nets; and cellular automata. The book's perspective is primarily based on topological properties though it also employs semitensor-product and graph-theoretic methods where appropriate. It presents a series of fundamental results: invertibility, observability, detectability, reversiblity, etc., with applications to systems biology. Academic researchers with backgrounds in applied mathematics, engineering or computer science and practising engineers working with discrete-time and discrete-space systems will find this book a helpful source of new understanding for this increasingly important class of systems. The basic results to be found within are of fundamental importance for further study of related problems such as automated synthesis and safety control in cyber-physical systems using formal methods.
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.
Book Synopsis Computational Systems Biology by : Andres Kriete
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. - Logical information flow aids understanding of basic building blocks of life through disease phenotypes - Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns - Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation - Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
Book Synopsis Computational and Statistical Approaches to Genomics by : Wei Zhang
Download or read book Computational and Statistical Approaches to Genomics written by Wei Zhang and published by Springer Science & Business Media. This book was released on 2007-12-26 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of this book adds eight new contributors to reflect a modern cutting edge approach to genomics. It contains the newest research results on genomic analysis and modeling using state-of-the-art methods from engineering, statistics, and genomics. These tools and models are then applied to real biological and clinical problems. The book’s original seventeen chapters are also updated to provide new initiatives and directions.
Book Synopsis Gene Regulation and Metabolism by : Julio Collado-Vides
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.
Book Synopsis Computational Systems Biology by : Joseph Xu Zhou
Download or read book Computational Systems Biology written by Joseph Xu Zhou and published by Elsevier Inc. Chapters. This book was released on 2013-11-26 with total page 59 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this chapter, we introduced the basic concepts of cell attractors and showed that Waddington’s metaphoric epigenetic landscape has a formal basis in the attractor landscape. This conceptual framework helps to understand core properties of cell differentiation and ultimately, multicellularity. Specifically, we developed the concept of relative stability of network states on the epigenetic landscape, thus providing the elevation in the landscape picture a formal, quantifiable basis. We proposed methods to quantify the relative stability of attractor states in discrete gene networks models. We show in two examples that even with incomplete information about network structures, the use of Boolean networks can capture the essential outlines of cell fate dynamics and more importantly, permit the estimation of relative stability and the attractor transition barriers. These measures hold great promise for the rational design of the perturbation protocols for cell reprogramming in regenerative medicine. As the knowledge of the structure of GRNs for the development of various tissues will undoubtedly increase in the next decade, the utilization of such network information for therapeutic reprogramming may benefit from the concepts developed here.
Book Synopsis Systems Genetics by : Florian Markowetz
Download or read book Systems Genetics written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.
Book Synopsis Artificial Life and Evolutionary Computation by : Stefano Cagnoni
Download or read book Artificial Life and Evolutionary Computation written by Stefano Cagnoni and published by Springer. This book was released on 2019-05-29 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the revised selected papers of the 13th Italian Workshop on Artificial Life and Evolutionary Computation, WIVACE 2018, held in Parma, Italy, in September 2018. The 12 full papers presented were thoroughly reviewed and selected from 30 submissions. They cover the following topics: Boolean networks and complex systems; economic, societal and technological applications; chemical, biological and medical applications. The chapter “Unveiling Latent Relations in the Photonics Techno-Economic Complex System” is open access under a CC BY 4.0 license at link.springer.com.
Book Synopsis Modeling Methods for Medical Systems Biology by : María Elena Álvarez-Buylla Roces
Download or read book Modeling Methods for Medical Systems Biology written by María Elena Álvarez-Buylla Roces and published by Springer. This book was released on 2018-08-03 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contributes to better understand how lifestyle modulations can effectively halt the emergence and progression of human diseases. The book will allow the reader to gain a better understanding of the mechanisms by which the environment interferes with the bio-molecular regulatory processes underlying the emergence and progression of complex diseases, such as cancer. Focusing on key and early cellular bio-molecular events giving rise to the emergence of degenerative chronic disease, it builds on previous experience on the development of multi-cellular organisms, to propose a mathematical and computer based framework that allows the reader to analyze the complex interplay between bio-molecular processes and the (micro)-environment from an integrative, mechanistic, quantitative and dynamical perspective. Taking the wealth of empirical evidence that exists it will show how to build and analyze models of core regulatory networks involved in the emergence and progression of chronic degenerative diseases, using a bottom-up approach.
Book Synopsis Dynamics and Complexity of Molecular Networks Controlling Cell Fate Decisions by : Chunhe Li
Download or read book Dynamics and Complexity of Molecular Networks Controlling Cell Fate Decisions written by Chunhe Li and published by Frontiers Media SA. This book was released on 2022-11-21 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Information Processing in Cells and Tissues by : Michael A. Lones
Download or read book Information Processing in Cells and Tissues written by Michael A. Lones and published by Springer. This book was released on 2012-03-22 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 9th International Conference on Information in Cells and Tissues, IPCAT 2012, held in Cambridge, UK, in March/April 2012. The 13 revised full papers presented together with 26 extended abstracts were carefully reviewed and selected from numerous submissions. The papers cover a wide range of topics in disciplines related to genetic and epigenetic networks, transcriptomics and gene regulation, signalling pathways and responses, protein structure and metabolic networks, patterning and rhythm generation, neural modelling and neural networks, biomedical modelling and signal processing, information processing and representation, and algorithmic approaches in computational biology.
Book Synopsis Systems Biology by : Robert A. Meyers
Download or read book Systems Biology written by Robert A. Meyers and published by John Wiley & Sons. This book was released on 2012-07-02 with total page 729 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is a relatively new biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. Systems biology is the study of the interconnected aspect of molecular, cellular, tissue, whole animal and ecological processes, and comprises mathematical and mechanistic studies of dynamical, mesoscopic, open, spatiotemporally defined, nonlinear, complex systems that are far from thermodynamic equilibrium.
Book Synopsis Computational Methods in Systems Biology by : Ion Petre
Download or read book Computational Methods in Systems Biology written by Ion Petre and published by Springer Nature. This book was released on 2022-08-18 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 20th International Conference on Computational Methods in Systems Biology, CMSB 2022, held in Bucharest, Romania, in September 2022. The 13 full papers and 4 tool papers were carefully reviewed and selected from 43 submissions. CMSB focuses on modeling, simulation, analysis, design and control of biological systems. The papers are arranged thematically as follows: Chemical reaction networks; Boolean networks; continuous and hybrid models; machine learning; software.
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 553 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
Book Synopsis Gene Network Inference by : Alberto Fuente
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.
