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Analysis Of Deterministic Cyclic Gene Regulatory Network Models With Delays
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Book Synopsis Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays by : Mehmet Eren Ahsen
Download or read book Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays written by Mehmet Eren Ahsen and published by Birkhäuser. This book was released on 2015-02-25 with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt: This brief examines a deterministic, ODE-based model for gene regulatory networks (GRN) that incorporates nonlinearities and time-delayed feedback. An introductory chapter provides some insights into molecular biology and GRNs. The mathematical tools necessary for studying the GRN model are then reviewed, in particular Hill functions and Schwarzian derivatives. One chapter is devoted to the analysis of GRNs under negative feedback with time delays and a special case of a homogenous GRN is considered. Asymptotic stability analysis of GRNs under positive feedback is then considered in a separate chapter, in which conditions leading to bi-stability are derived. Graduate and advanced undergraduate students and researchers in control engineering, applied mathematics, systems biology and synthetic biology will find this brief to be a clear and concise introduction to the modeling and analysis of GRNs.
Book Synopsis Time Delay Systems by : Tamás Insperger
Download or read book Time Delay Systems written by Tamás Insperger and published by Springer. This book was released on 2017-03-30 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume collects contributions related to selected presentations from the 12th IFAC Workshop on Time Delay Systems, Ann Arbor, June 28-30, 2015. The included papers present novel techniques and new results of delayed dynamical systems. The topical spectrum covers control theory, numerical analysis, engineering and biological applications as well as experiments and case studies. The target audience primarily comprises research experts in the field of time delay systems, but the book may also be beneficial for graduate students alike.
Book Synopsis Analysis and Design of Delayed Genetic Regulatory Networks by : Xian Zhang
Download or read book Analysis and Design of Delayed Genetic Regulatory Networks written by Xian Zhang and published by Springer. This book was released on 2019-04-11 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an essential introduction to the latest advances in delayed genetic regulatory networks (GRNs) and presents cutting-edge work on the analysis and design of delayed GRNs in which the system parameters are subject to uncertain, stochastic and/or parameter-varying changes. Specifically, the types examined include delayed switching GRNs, delayed stochastic GRNs, delayed reaction–diffusion GRNs, delayed discrete-time GRNs, etc. In addition, the solvability of stability analysis, control and estimation problems involving delayed GRNs are addressed in terms of linear matrix inequality or M-matrix tests. The book offers a comprehensive reference guide for researchers and practitioners working in system sciences and applied mathematics, and a valuable source of information for senior undergraduates and graduates in these areas. Further, it addresses a gap in the literature by providing a unified and concise framework for the analysis and design of delayed GRNs.
Book Synopsis Oscillations in Cyclic Gene Regulatory Networks with Time Delay by :
Download or read book Oscillations in Cyclic Gene Regulatory Networks with Time Delay written by and published by . This book was released on 2011 with total page 30 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Handbook of Research on Computational Methodologies in Gene Regulatory Networks by : Das, Sanjoy
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.
Book Synopsis Robust Stability Analysis for Cyclic Gene Regulatory Networks with Uncertainty by :
Download or read book Robust Stability Analysis for Cyclic Gene Regulatory Networks with Uncertainty written by and published by . This book was released on 2011 with total page 18 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Evolutionary Computation in Gene Regulatory Network Research by : Hitoshi Iba
Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Hitoshi Iba and published by John Wiley & Sons. This book was released on 2016-01-20 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.
Book Synopsis Emerging Research in the Analysis and Modeling of Gene Regulatory Networks by : Ivanov, Ivan V.
Download or read book Emerging Research in the Analysis and Modeling of Gene Regulatory Networks written by Ivanov, Ivan V. and published by IGI Global. This book was released on 2016-06-06 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: While technological advancements have been critical in allowing researchers to obtain more and better quality data about cellular processes and signals, the design and practical application of computational models of genomic regulation continues to be a challenge. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation. Exploring both theoretical and practical topics, this publication is an essential reference source for students, professionals, and researchers working in the fields of genomics, molecular biology, bioinformatics, and drug development.
Book Synopsis Oscillation Pattern Analysis for Gene Regulatory Networks with Negative Cyclic Feedback by :
Download or read book Oscillation Pattern Analysis for Gene Regulatory Networks with Negative Cyclic Feedback written by and published by . This book was released on 2010 with total page 22 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modelling and Control in Biomedical Systems 2006 by : David Dagan Feng
Download or read book Modelling and Control in Biomedical Systems 2006 written by David Dagan Feng and published by Elsevier. This book was released on 2006-09-19 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modelling and Control in Biomedical Systems (including Biological Systems) was held in Reims, France, 20-22 August 2006. This Symposium was organised by the University of Reims Champagne Ardenne and the Société de l’Electricité, de l’Electronique et des TIC (SEE). The Symposium attracted practitioners in engineering, information technology, mathematics, medicine and biology, and other related disciplines, with authors from 24 countries. Besides the abstracts of the four plenary lectures, this volume contains the 92 papers that were presented by their authors at the Symposium. The papers included two invited keynote presentations given by internationally prominent and well-recognised research leaders: Claudio Cobelli, whose talk is titled "Dynamic modelling in diabetes: from whole body to genes"; and Irving J. Bigio, whose talk is titled "Elastic scattering spectroscopy for non-invasive detection of cancer". Two prestigious industrial speakers were also invited to give keynote presentations: Terry O'Brien from LIDCO, whose talk is titled "LIDCO: From the laboratory to protocolized goal directed therapy"; and Lorenzo Quinzio of Philips, whose talk is titled "Clinical decision support in monitoring and information systems". A valuable source of information on the state-of- the-art in Modelling and Control in Biomedical Systems Including abstracts of four plenary lectures, and 92 papers presented by their authors
Book Synopsis Identification, Analysis and Control of Discrete and Continuous Models of Gene Regulation Networks by : Christian Breindl
Download or read book Identification, Analysis and Control of Discrete and Continuous Models of Gene Regulation Networks written by Christian Breindl and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: A systems biological approach towards cellular networks promises a better understanding of how these systems work. The development of mathematical models is however inherently complicated, as the involved molecules and their interactions are mostly difficult to measure. Focusing on gene regulation networks, this work therefore intends to provide systems theoretic tools that support the process of model development and analysis in presence of such incomplete knowledge. The contributions are threefold. First, the problem of identifying interconnections between genes from noisy data is addressed. Existing solutions formulated in a discrete framework are reviewed and simplified significantly with the help of tools from convex optimization theory. Second, a novel method for model verification and discrimination is introduced. It is based on concepts from robust control theory and allows to quantify the capability of a model to reproduce experimentally observed stationary behaviors. As the proposed formalism only requires a vague knowledge about the interactions between the molecules, the method is intended to test and compare early modeling hypotheses. Third, the problem of controlling gene regulation networks in presence of qualitative information only is studied. Methods from discrete event systems theory are adapted to obtain stimulation strategies that will steer the network toward a desired attractor. The benefits of all contributions are illustrated with examples in the individual chapters.
Book Synopsis MicroRNA Cancer Regulation by : Ulf Schmitz
Download or read book MicroRNA Cancer Regulation written by Ulf Schmitz and published by Springer Science & Business Media. This book was released on 2013-02-03 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited reflects the current state of knowledge about the role of microRNAs in the formation and progression of solid tumours. The main focus lies on computational methods and applications, together with cutting edge experimental techniques that are used to approach all aspects of microRNA regulation in cancer. We are sure that the emergence of high-throughput quantitative techniques will make this integrative approach absolutely necessary in the near future. This book will be a resource for researchers starting out with cancer microRNA research, but is also intended for the experienced researcher who wants to incorporate concepts and tools from systems biology and bioinformatics into his work. Bioinformaticians and modellers are provided with a general perspective on microRNA biology in cancer, and the state-of-the-art in computational microRNA biology.
Book Synopsis Modeling and Analysis of Bio-molecular Networks by : Jinhu Lü
Download or read book Modeling and Analysis of Bio-molecular Networks written by Jinhu Lü and published by Springer Nature. This book was released on 2020-12-06 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.
Book Synopsis Programming Logics by : Andrei Voronkov
Download or read book Programming Logics written by Andrei Voronkov and published by Springer. This book was released on 2013-04-05 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Festschrift volume, published in memory of Harald Ganzinger, contains 17 papers from colleagues all over the world and covers all the fields to which Harald Ganzinger dedicated his work during his academic career. The volume begins with a complete account of Harald Ganzinger's work and then turns its focus to the research of his former colleagues, students, and friends who pay tribute to him through their writing. Their individual papers span a broad range of topics, including programming language semantics, analysis and verification, first-order and higher-order theorem proving, unification theory, non-classical logics, reasoning modulo theories, and applications of automated reasoning in biology.
Book Synopsis Modeling Gene Regulatory Networks Using a State-space Model with Time Delays by :
Download or read book Modeling Gene Regulatory Networks Using a State-space Model with Time Delays written by and published by . This book was released on 2003 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Artificial Life IX by : Jordan B. Pollack
Download or read book Artificial Life IX written by Jordan B. Pollack and published by MIT Press. This book was released on 2004 with total page 612 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings from the ninth International Conference on Artificial Life; papers by scientists of many disciplines focusing on the principles of organization and applications of complex, life-like systems. Artificial Life is an interdisciplinary effort to investigate the fundamental properties of living systems through the simulation and synthesis of life-like processes. The young field brings a powerful set of tools to the study of how high-level behavior can arise in systems governed by simple rules of interaction. Some of the fundamental questions include: What are the principles of evolution, learning, and growth that can be understood well enough to simulate as an information process? Can robots be built faster and more cheaply by mimicking biology than by the product design process used for automobiles and airplanes? How can we unify theories from dynamical systems, game theory, evolution, computing, geophysics, and cognition? The field has contributed fundamentally to our understanding of life itself through computer models, and has led to novel solutions to complex real-world problems across high technology and human society. This elite biennial meeting has grown from a small workshop in Santa Fe to a major international conference. This ninth volume of the proceedings of the international A-life conference reflects the growing quality and impact of this interdisciplinary scientific community.
Book Synopsis On the Role of Delays in Biological Systems by : Marcella Mary Gomez
Download or read book On the Role of Delays in Biological Systems written by Marcella Mary Gomez and published by . This book was released on 2015 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system. Furthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.
