Identification Analysis And Control Of Discrete And Continuous Models Of Gene Regulation Networks

Author : Christian Breindl
Publisher : Unknown
Page : 0 pages
File Size : 44,6 Mb
Release : 2016
Category : Gene regulatory networks
ISBN : 3832542833

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Identification, Analysis and Control of Discrete and Continuous Models of Gene Regulation Networks by Christian Breindl Pdf

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.

Author : Mehmet Eren Ahsen,Hitay Özbay,Silviu-Iulian Niculescu
Publisher : Birkhäuser
Page : 104 pages
File Size : 43,9 Mb
Release : 2015-02-25
Category : Science
ISBN : 9783319156064

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Analysis of Deterministic Cyclic Gene Regulatory Network Models with Delays by Mehmet Eren Ahsen,Hitay Özbay,Silviu-Iulian Niculescu Pdf

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.

Author : Ivanov, Ivan V.,Qian, Xiaoning,Pal, Ranadip
Publisher : IGI Global
Page : 418 pages
File Size : 50,5 Mb
Release : 2016-06-06
Category : Medical
ISBN : 9781522503545

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Emerging Research in the Analysis and Modeling of Gene Regulatory Networks by Ivanov, Ivan V.,Qian, Xiaoning,Pal, Ranadip Pdf

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.

Author : Matthias Dehmer
Publisher : John Wiley & Sons
Page : 301 pages
File Size : 52,7 Mb
Release : 2012-11-28
Category : Medical
ISBN : 9783527665457

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Statistical Diagnostics for Cancer by Matthias Dehmer Pdf

This ready reference discusses different methods for statistically analyzing and validating data created with high-throughput methods. As opposed to other titles, this book focusses on systems approaches, meaning that no single gene or protein forms the basis of the analysis but rather a more or less complex biological network. From a methodological point of view, the well balanced contributions describe a variety of modern supervised and unsupervised statistical methods applied to various large-scale datasets from genomics and genetics experiments. Furthermore, since the availability of sufficient computer power in recent years has shifted attention from parametric to nonparametric methods, the methods presented here make use of such computer-intensive approaches as Bootstrap, Markov Chain Monte Carlo or general resampling methods. Finally, due to the large amount of information available in public databases, a chapter on Bayesian methods is included, which also provides a systematic means to integrate this information. A welcome guide for mathematicians and the medical and basic research communities.

Author : Fabricio Alves Barbosa da Silva,Nicolas Carels,Marcelo Trindade dos Santos,Francisco José Pereira Lopes
Publisher : Springer Nature
Page : 381 pages
File Size : 53,6 Mb
Release : 2020-10-03
Category : Computers
ISBN : 9783030518622

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Networks in Systems Biology by Fabricio Alves Barbosa da Silva,Nicolas Carels,Marcelo Trindade dos Santos,Francisco José Pereira Lopes Pdf

This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.

Author : Roger Sansom
Publisher : Life and Mind: Philosophical I
Page : 0 pages
File Size : 49,9 Mb
Release : 2011
Category : Science
ISBN : 026219581X

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Ingenious Genes by Roger Sansom Pdf

A proposal for a new model of the evolution of gene regulation networks and development that draws on work from artificial intelligence and philosophy of mind. Each of us is a collection of more than ten trillion cells, busy performing tasks crucial to our continued existence. Gene regulation networks, consisting of a subset of genes called transcription factors, control cellular activity, producing the right gene activities for the many situations that the multiplicity of cells in our bodies face. Genes working together make up a truly ingenious system. In this book, Roger Sansom investigates how gene regulation works and how such a refined but simple system evolved. Sansom describes in detail two frameworks for understanding gene regulation. The first, developed by the theoretical biologist Stuart Kauffman, holds that gene regulation networks are fundamentally systems that repeat patterns of gene expression. Sansom finds Kauffman's framework an inadequate explanation for how cells overcome the difficulty of development. Sansom proposes an alternative: the connectionist framework. Drawing on work from artificial intelligence and philosophy of mind, he argues that the key lies in how multiple transcription factors combine to regulate a single gene, acting in a way that is qualitatively consistent. This allows the expression of genes to be finely tuned to the variable microenvironments of cells. Because of the nature of both development and its evolution, we can gain insight into the developmental process when we identify gene regulation networks as the controllers of development. The ingenuity of genes is explained by how gene regulation networks evolve to control development.

Author : Aparna Das
Publisher : Unknown
Page : 121 pages
File Size : 45,7 Mb
Release : 2012
Category : Electronic
ISBN : OCLC:835285536

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Modeling the Dynamics of Gene Regulatory Networks by Aparna Das Pdf

In order to describe the dynamic behavior of gene regulatory networks different formalisms have been introduced. In this thesis, we describe first the discrete approach of René Thomas and piecewise linear differential equations approach. Then we proposed a correspondence result between the two approaches and based on it we proposed an automatic computational technique to understand the global behavior of such complex systems using MAPLE programming language. The proposed code provides a way to compute the trajectories of the discrete version of a gene regulatory network model given an initial condition, in the same way as usual numerical algorithms give the "true" solution of a differential model from an initial condition. Knowing a discrete trajectory is less precise than knowing a true trajectory but correspondence theorems shows the link between the two approaches. Hence, it is a mathematical tool for analysing gene regulatory networks models. Finally, we illustrate both discrete and piecewise linear approaches, theircorrespondence and the use of our Maple code on a specific example: a mathematical model of the circadian clock. Our first two presented 8 and 4 variables models are the simplification of a model proposed by Leloup and Goldbeter. We deliberately choose to push the simplicity of the model as far as possible, focusing only on a few biological behaviors of interest. The hope is to get nevertheless the essential abstract causalities that govern these behaviors.

Author : Matteo Barberis,Tomáš Helikar
Publisher : Frontiers Media SA
Page : 340 pages
File Size : 44,7 Mb
Release : 2019-08-16
Category : Electronic
ISBN : 9782889459834

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Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by Matteo Barberis,Tomáš Helikar Pdf

Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.

Author : Igor I. Goryanin,Andrew B. Goryachev
Publisher : Springer Science & Business Media
Page : 679 pages
File Size : 47,9 Mb
Release : 2011-12-09
Category : Science
ISBN : 9781441972101

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Advances in Systems Biology by Igor I. Goryanin,Andrew B. Goryachev Pdf

The International Society for Systems Biology (ISSB) is a society aimed at advancing world-wide systems biology research by providing a forum for scientific discussions and various academic services. The ISSB helps coordinate researchers to form alliances for meeting the unique needs of multidisciplinary and international systems biology research. The annual International Conference on Systems Biology (ICSB) serves as the main meeting for the society and is one of the largest academic and commercial gatherings under the broad heading of ‘Systems Biology’.

Author : Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach
Publisher : John Wiley & Sons
Page : 486 pages
File Size : 43,6 Mb
Release : 2008-07-15
Category : Medical
ISBN : 9783527604883

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Systems Biology in Practice by Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach Pdf

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.

Author : Manuel Seabra Pereira
Publisher : Springer Science & Business Media
Page : 605 pages
File Size : 50,5 Mb
Release : 2007-11-24
Category : Technology & Engineering
ISBN : 9781402056901

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A Portrait of State-of-the-Art Research at the Technical University of Lisbon by Manuel Seabra Pereira Pdf

This book celebrates the 75th anniversary of The Technical University of Lisbon (UTL). It provides a compelling picture of current state-of-art research at UTL. It contains the edited version of the invited lectures from a two day Symposium and brings together a comprehensive summary of high quality research contributions across basic and applied sciences. A broad spectrum of topics is covered reflecting UTL’s worldwide recognition.

Author : Terry Speed,Haiyan Huang
Publisher : Springer
Page : 565 pages
File Size : 55,8 Mb
Release : 2007-05-18
Category : Science
ISBN : 9783540716815

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Research in Computational Molecular Biology by Terry Speed,Haiyan Huang Pdf

This book constitutes the refereed proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007, held in Oakland, CA, USA in April 2007. The 37 revised full papers address all current issues in algorithmic, theoretical, and experimental bioinformatics.

Author : Andreas D. Baxevanis,Gary D. Bader,David S. Wishart
Publisher : John Wiley & Sons
Page : 648 pages
File Size : 41,6 Mb
Release : 2020-02-12
Category : Science
ISBN : 9781119335962

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Bioinformatics by Andreas D. Baxevanis,Gary D. Bader,David S. Wishart Pdf

Praise for the third edition of Bioinformatics “This book is a gem to read and use in practice.” —Briefings in Bioinformatics "This volume has a distinctive, special value as it offers an unrivalled level of details and unique expert insights from the leading computational biologists, including the very creators of popular bioinformatics tools." —ChemBioChem “A valuable survey of this fascinating field. . . I found it to be the most useful book on bioinformatics that I have seen and recommend it very highly.” —American Society for Microbiology News “This should be on the bookshelf of every molecular biologist.” —The Quarterly Review of Biology The field of bioinformatics is advancing at a remarkable rate. With the development of new analytical techniques that make use of the latest advances in machine learning and data science, today’s biologists are gaining fantastic new insights into the natural world’s most complex systems. These rapidly progressing innovations can, however, be difficult to keep pace with. The expanded fourth edition of the best-selling Bioinformatics aims to remedy this by providing students and professionals alike with a comprehensive survey of the current field. Revised to reflect recent advances in computational biology, it offers practical instruction on the gathering, analysis, and interpretation of data, as well as explanations of the most powerful algorithms presently used for biological discovery. Bioinformatics, Fourth Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists at all levels, covering both key concepts that have stood the test of time and the new and important developments driving this fast-moving discipline forwards. This new edition features: New chapters on metabolomics, population genetics, metagenomics and microbial community analysis, and translational bioinformatics A thorough treatment of statistical methods as applied to biological data Special topic boxes and appendices highlighting experimental strategies and advanced concepts Annotated reference lists, comprehensive lists of relevant web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics Bioinformatics is an indispensable companion for researchers, instructors, and students of all levels in molecular biology and computational biology, as well as investigators involved in genomics, clinical research, proteomics, and related fields.

Author : Jayajit Das,Ciriyam Jayaprakash
Publisher : CRC Press
Page : 405 pages
File Size : 41,6 Mb
Release : 2018-09-03
Category : Science
ISBN : 9781351646147

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Systems Immunology by Jayajit Das,Ciriyam Jayaprakash Pdf

"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.

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 55,7 Mb
Release : 2024-07-03
Category : Electronic
ISBN : 9789814478915

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Recent Advances in Artificial Life by Anonim Pdf