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Identification, Analysis and Control of Discrete and Continuous Models of Gene Regulation Networks

Identification, Analysis and Control of Discrete and Continuous Models of Gene Regulation Networks
Author: Christian Breindl
Publisher:
Total Pages: 0
Release: 2016
Genre: Gene regulatory networks
ISBN: 9783832542832
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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.

Emerging Research in the Analysis and Modeling of Gene Regulatory Networks

Emerging Research in the Analysis and Modeling of Gene Regulatory Networks
Author: Ivanov, Ivan V.
Publisher: IGI Global
Total Pages: 437
Release: 2016-06-06
Genre: Medical
ISBN: 1522503544
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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.

Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays

Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays
Author: Mehmet Eren Ahsen
Publisher: Birkhäuser
Total Pages: 104
Release: 2015-02-25
Genre: Science
ISBN: 3319156063
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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.

Analysis of Combinatorial Gene Regulation with Thermodynamic Models

Analysis of Combinatorial Gene Regulation with Thermodynamic Models
Author: Chieh-Chun Chen
Publisher:
Total Pages:
Release: 2010
Genre:
ISBN:
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Transcriptional control is a key regulatory mechanism for cells to direct their destinies. A large number of transcription factors (TFs) could simultaneously bind to a regulatory sequence. With the constellation of TFs bound, the expression level of a target gene is usually determined by the combinatorial control of a number of TFs. The interactions among regulatory proteins and their regulatory sequences collectively form a regulatory network. A major challenge in the study of gene regulation is to identify the interaction relationships within a regulatory network and further to reconstruct gene regulatory networks. In this thesis, we developed an analytical method, Interaction-Identifier, to identify a thermodynamic model that best describes the form of TF-TF interaction among a set of TFs for every target gene. Applying this approach to time-course microarray data in mouse embryonic stem cells, we have inferred five interaction patterns among three regulators: Oct4, Sox2 and Nanog on ten target genes. We further proposed a computational framework, Network-Identifier, utilizing Interaction-Identifier, to reconstruct gene regulatory networks. Applied to five datasets of differentiating embryonic stem cells, Network-Identifier identified a gene regulatory network among 87 transcription regulator genes. This network suggests that Oct4, Sox2 and Klf4 indirectly repress lineage specific differentiation genes by activating transcriptional repressors of Ctbp2, Rest and Mtf2.

Systems Biology in Practice

Systems Biology in Practice
Author: Edda Klipp
Publisher: John Wiley & Sons
Total Pages: 486
Release: 2008-07-15
Genre: Medical
ISBN: 352760488X
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Presenting the main concepts, this book leads students as well as advanced researchers from different disciplines to an understanding of current ideas in the complex field of comprehensive experimental investigation of biological objects, analysis of data, development of models, simulation, and hypothesis generation. It provides readers with guidance on how a specific complex biological question may be tackled: - How to formulate questions that can be answered - Which experiments to perform - Where to find information in databases and on the Internet - What kinds of models are appropriate - How to use simulation tools - What can be learned from the comparison of experimental data and modeling results - How to make testable predictions. The authors demonstrate how mathematical concepts can illuminate the principles underlying biology at a genetic, molecular, cellular and even organism level, and how to use mathematical tools for analysis and prediction.

Parallel Computing Technologies

Parallel Computing Technologies
Author: Victor Malyshkin
Publisher: Springer
Total Pages: 486
Release: 2009-09-01
Genre: Computers
ISBN: 3642032753
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The PaCT-2009 (Parallel Computing Technologies) conference was a four-day eventheld in Novosibirsk. This was the tenth internationalconference to be held in the PaCT series. The conferences are held in Russia every odd year. The ?rst conference, PaCT 1991, was held in Novosibirsk (Academgorodok), September 7–11, 1991. The next PaCT conferences were held in Obninsk (near Moscow), August 30 to September 4, 1993; in St. Petersburg, September 12–15, 1995; in Yaroslavl, September 9–12, 1997; in Pushkin (near St. Petersburg), September 6–10, 1999; in Academgorodok (Novosibirsk), September 3–7, 2001; in Nizhni Novgorod, September 15–19, 2003; in Krasnoyarsk, September 5–9, 2005; in Pereslavl-Zalessky, September 3–7, 2007. Since 1995 all the PaCT Proceedings have been published by Springer in the LNCS series. PaCT-2009 was jointly organized by the Institute of Computational Mathematics and Mathematical Geophysics of the Russian Academy of Sciences (RAS) and the State University of Novosibirsk. The purpose of the conference was to bring together scientists working on theory, architecture, software, hardware and the solution of lar- scale problems in order to provide integrated discussions on parallel computing technologies. The conference attracted about 100 participants from around the world. Authors from 17 countries submitted 72 papers. Of those submitted, 34 were selected for the conference as regular papers; there were also 2 invited - pers. In addition there were a number of posters presented. All the papers were internationallyreviewedby at leastthree referees. A demo sessionwasorganized for the participants.

Probabilistic Boolean Networks

Probabilistic Boolean Networks
Author: Ilya Shmulevich
Publisher: SIAM
Total Pages: 276
Release: 2010-01-21
Genre: Mathematics
ISBN: 0898716926
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The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.

A Mathematical Modeling and Approximation of Gene Expression Patterns by Linear and Quadratic Regulatory Relations and Analysis of Gene Networks

A Mathematical Modeling and Approximation of Gene Expression Patterns by Linear and Quadratic Regulatory Relations and Analysis of Gene Networks
Author:
Publisher:
Total Pages:
Release: 2004
Genre:
ISBN:
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This thesis mainly concerns modeling, approximation and inference of gene regulatory dynamics on the basis of gene expression patterns. The dynamical behavior of gene expressions is represented by a system of ordinary di erential equations. We introduce a gene-interaction matrix with some nonlinear entries, in particular, quadratic polynomials of the expression levels to keep the system solvable. The model parameters are determined by using optimization. Then, we provide the time-discrete approximation of our time-continuous model. We analyze the approximating model under the aspect of stability. Finally, from the considered models we derive gene regulatory networks, discuss their qualitative features of the networks and provide a basis for analyzing networks with nonlinear connections.