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 2019-06-25 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.
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.
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.
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.
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.
Download or read book Time delayed Models of Genetic Regulatory Networks written by Kiresh Parmar and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Design of Genetic Regulatory Networks written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Evolutionary Algorithms Swarm Dynamics and Complex Networks written by Ivan Zelinka and published by Springer. This book was released on 2017-11-25 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolutionary algorithms constitute a class of well-known algorithms, which are designed based on the Darwinian theory of evolution and Mendelian theory of heritage. They are partly based on random and partly based on deterministic principles. Due to this nature, it is challenging to predict and control its performance in solving complex nonlinear problems. Recently, the study of evolutionary dynamics is focused not only on the traditional investigations but also on the understanding and analyzing new principles, with the intention of controlling and utilizing their properties and performances toward more effective real-world applications. In this book, based on many years of intensive research of the authors, is proposing novel ideas about advancing evolutionary dynamics towards new phenomena including many new topics, even the dynamics of equivalent social networks. In fact, it includes more advanced complex networks and incorporates them with the CMLs (coupled map lattices), which are usually used for spatiotemporal complex systems simulation and analysis, based on the observation that chaos in CML can be controlled, so does evolution dynamics. All the chapter authors are, to the best of our knowledge, originators of the ideas mentioned above and researchers on evolutionary algorithms and chaotic dynamics as well as complex networks, who will provide benefits to the readers regarding modern scientific research on related subjects.
Download or read book Gene Regulatory Network Reconstruction Using Time delayed S system Model written by Ahsan Chowdhury and published by . This book was released on 2013 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advent of microarray technology and the availability of high-throughput timeseries gene expression data has gradually led to the emergence of system biologists' proficiency in determining cellular dynamics, thus enabling the reverse engineering of Gene Regulatory Networks (GRNs). However, the curse of dimensionality, i.e., very few observations available for a large number of genes, is still considered one of the key factors affecting the inferring of GRNs from time-series data. Amongst the available models to infer GRNs, S-system formalism is considered to be an excellent compromise between accuracy and mathematical flexibility. Although the S-system model has the ability to represent the regulations very accurately, due to the higher numberof parameters, it is currently limited to reconstructing small-and medium-scale GRNs. Evolutionary algorithms, a sub-field of computational intelligence, have been widely used for optimization in reverse engineering GRNs (and specifically with the S-system model) because of its computational simplicity and its capacity to cater difficult and intractable problems. As one of its objectives, this research aims to develop efficient evolutionary optimization techniques for S-system based GRN modeling.For implementing evolutionary optimization, Differential Evolution (DE) and its variants show promise in the complex multi-modal search landscape which exist during the process of reverse engineering GRNs. However, considering that for large-scale GRNs the performance of DE can deteriorate and cause the algorithm to frequently stall or become stuck in local minima, as the first step to achieve the objective of efficient algorithm design, we incorporate the domain knowledge in the initial population generation and a new mutation operation (Flip Operation or FO) in the optimization process. Incorporation of knowledge allows the population to commencewith good seeds, while the proposed FO allows the optimization to search for global solutions by not getting potentially trapped in local minima. A refinement algorithm is also included as a post-processing operation to eliminate possible false regulations from the near optimal candidate solutions.Further, domain knowledge is also incorporated to develop a novel cardinality based fitness criteria that is motivated with the biologically relevant power-law distribution of genes' in-degrees. The adaptive nature of the maximum and minimum in-degrees allows dynamic reduction of search space, thereby resulting in a skeletal structure of the network with accurate parameters values. In other words, the new approach improves the search technique and reaches the solution more quickly compared to the existing methods in the literature. The cardinality values are updated adaptively to further narrow down the search space to obtain superior results quickly.In addition, the method is further improvised so that it can cope with the absence of microRNA (miRNA) expression profiles during the inference process. A critical analysis is also presented on the influence of miRNAs regulations on the GRN, in spite of a lack of miRNA data.Since the traditional S-system models genetic interactions with non-time-delayed ordinary differential equations, all reverse engineering methods using the S-system model can only infer instantaneous regulations. Thus, time-delayed regulations, whose existence is obvious in the GRNs, are either missed completely or these are inferred with incorrect regulatory weight and/or direction by the existing methods. In this research, by including time-delays to be part of the S-system parameters, a novel time-delayed S-system (TDSS) model is proposed to overcome limitations of the existing S-system model. Moreover, we have further improved our inference method developed earlier to reconstruct the network by simultaneously inferring instantaneous andtime-delayed regulations present in the GRNs.Due to the large number of parameters to infer, the current state-of-the-art S-system modeling approaches are limited to reconstructing small-and medium-scale GNRs. Exploiting the biological interactions of a GRN and the knowledge about genes, we show that a GRN can be naturally decoupled and incorporated in our proposed time-delayed S-system modeling. In the process, the previous fitness function is also enhanced to work more effectively to infer model parameters (including time-delays) of very large-scale GRNs. We also demonstrate how a domain knowledgebasedclustering technique can be applied to develop a local search procedure that is very effective while inferring regulations of large-scale GRNs.
Download or read book Computational Modeling Of Gene Regulatory Networks A Primer written by Hamid Bolouri and published by World Scientific Publishing Company. This book was released on 2008-08-13 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./a
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.
Download or read book Fractional Dynamics and Control written by Dumitru Baleanu and published by Springer Science & Business Media. This book was released on 2011-11-19 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fractional Dynamics and Control provides a comprehensive overview of recent advances in the areas of nonlinear dynamics, vibration and control with analytical, numerical, and experimental results. This book provides an overview of recent discoveries in fractional control, delves into fractional variational principles and differential equations, and applies advanced techniques in fractional calculus to solving complicated mathematical and physical problems.Finally, this book also discusses the role that fractional order modeling can play in complex systems for engineering and science.
Download or read book Deterministic and Stochastic Analysis of Genetic Regulatory Networks written by Adiel Loinger and published by . This book was released on 2011 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Analysis and Synthesis of Switched Time Delay Systems The Average Dwell Time Approach written by Dan Zhang and published by Springer. This book was released on 2018-09-01 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, written by experts in the field, is based on the latest research on the analysis and synthesis of switched time-delay systems. It covers the stability, filtering, fault detection and control problems, which are studied using the average dwell time approach. It presents both the continuous-time and discrete-time systems and provides useful insights and methods, as well as practical algorithms that can be considered in other complex systems, such as neuron networks and genetic regulatory networks, making it a valuable resource for researchers, scientists and engineers in the field of system sciences and control communities.
Download or read book Advances in Swarm Intelligence written by Ying Tan and published by Springer Nature. This book was released on 2021-07-07 with total page 586 pages. Available in PDF, EPUB and Kindle. Book excerpt: his two-volume set LNCS 12689-12690 constitutes the refereed proceedings of the 12th International Conference on Advances in Swarm Intelligence, ICSI 2021, held in Qingdao, China, in July 2021. The 104 full papers presented in this volume were carefully reviewed and selected from 177 submissions. They cover topics such as: Swarm Intelligence and Nature-Inspired Computing; Swarm-based Computing Algorithms for Optimization; Particle Swarm Optimization; Ant Colony Optimization; Differential Evolution; Genetic Algorithm and Evolutionary Computation; Fireworks Algorithms; Brain Storm Optimization Algorithm; Bacterial Foraging Optimization Algorithm; DNA Computing Methods; Multi-Objective Optimization; Swarm Robotics and Multi-Agent System; UAV Cooperation and Control; Machine Learning; Data Mining; and Other Applications.
Download or read book Computational Representation and Analysis of Developmental Genetic Regulatory Networks written by James Brodie and published by . This book was released on 2007 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Alternative Frameworks for Analysis of Gene Regulatory Networks with Delay written by Irina Shlykova and published by . This book was released on 2010 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt:
