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.
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 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 418 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 Systems Biology in Practice written by Edda Klipp and published by John Wiley & Sons. This book was released on 2008-07-15 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Statistical Diagnostics for Cancer written by Matthias Dehmer and published by John Wiley & Sons. This book was released on 2012-11-28 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Modeling the Dynamics of Gene Regulatory Networks written by Aparna Das and published by . This book was released on 2012 with total page 121 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Gene Regulatory Networks written by Bart Deplancke and published by Humana Press. This book was released on 2011-09-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene regulatory networks play a vital role in organismal development and function by controlling gene expression. With the availability of complete genome sequences, several novel experimental and computational approaches have recently been developed which promise to significantly enhance our ability to comprehensively characterize these regulatory networks by enabling the identification of respectively their genomic or regulatory state components, or the interactions between these two in unprecedented detail. Divided into five convenient sections, Gene Regulatory Networks: Methods and Protocols details how each of these approaches contributes to a more thorough understanding of the composition and function of gene regulatory networks, while providing a comprehensive protocol on how to implement them in the laboratory. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Gene Regulatory Networks: Methods and Protocols aims to provide novices and experienced researchers alike with a comprehensive and timely toolkit to study gene regulatory networks from the point of data generation to processing, visualization, and modeling.
Download or read book Networks in Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer Nature. This book was released on 2020-10-03 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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.
Download or read book Ingenious Genes written by Roger Sansom and published by Life and Mind: Philosophical I. This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Logical Modeling of Cellular Processes From Software Development to Network Dynamics written by Matteo Barberis and published by Frontiers Media SA. This book was released on 2019-08-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Handbook of Computational Molecular Biology written by Srinivas Aluru and published by CRC Press. This book was released on 2005-12-21 with total page 1108 pages. Available in PDF, EPUB and Kindle. Book excerpt: The enormous complexity of biological systems at the molecular level must be answered with powerful computational methods. Computational biology is a young field, but has seen rapid growth and advancement over the past few decades. Surveying the progress made in this multidisciplinary field, the Handbook of Computational Molecular Biology of
Download or read book Advances in Systems Biology written by Igor I. Goryanin and published by Springer Science & Business Media. This book was released on 2011-12-09 with total page 679 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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’.
Download or read book A Portrait of State of the Art Research at the Technical University of Lisbon written by Manuel Seabra Pereira and published by Springer Science & Business Media. This book was released on 2007-11-24 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Research in Computational Molecular Biology written by Terry Speed and published by Springer. This book was released on 2007-05-18 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book In the Light of Evolution written by National Academy of Sciences and published by . This book was released on 2007 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, four or five such colloquia are scheduled, typically two days in length and international in scope. Colloquia are organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. Colloquia presentations are recorded and posted on the National Academy of Sciences Sackler colloquia website and published on CD-ROM. These Colloquia are made possible by a generous gift from Mrs. Jill Sackler, in memory of her husband, Arthur M. Sackler.
Download or read book Bioinformatics written by Andreas D. Baxevanis and published by John Wiley & Sons. This book was released on 2020-02-12 with total page 648 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
