[PDF] Computational Analysis And Simulation Of Bacterial Molecular Networks eBook

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File Size : 30,21 MB
Release : 2009
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The project examined a number of aspects of complex bacterial networks, their architecture, topology, dynamics and design principles.

Author : Saliha Durmuş
Publisher : Frontiers Media SA
Page : 200 pages
File Size : 43,56 MB
Release : 2016-05-30
Category : Microbiology
ISBN : 2889198219

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A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions: - Computational Inference of PHI Networks using Omics Data - Computational Prediction of PHIs - Text Mining of PHI Data from the Literature - Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data.

Author : Fabricio Alves Barbosa da Silva
Publisher : Springer
Page : 377 pages
File Size : 17,20 MB
Release : 2021-10-05
Category : Computers
ISBN : 9783030518646

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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.

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File Size : 49,6 MB
Release : 2003
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The objective of this research is to understand how genetic regulatory circuits function. The behavior of genetic regulatory networks in bacterial cells is analyzed using computer-based simulations of molecular-level models, positional information from observation of GFP-labeled regulatory molecules, and gene expression data from microarray assays of wild-type and mutant Caulobacter cells. A new view of the cell cycle as a sequence of modular functions controlled by a few networked master regulatory proteins challenges former paradigms for how the cell works and how to model cell function.

Author : Monika Heiner
Publisher : Springer
Page : 413 pages
File Size : 43,71 MB
Release : 2008-10-05
Category : Science
ISBN : 3540885625

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This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in Rostock, Germany, in September 2008. The 21 revised full papers presented together with the summaries of 5 invited papers were carefully reviewed and selected from more than 60 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

Author : Faouzi Zarai
Publisher : Morgan Kaufmann
Page : 965 pages
File Size : 49,6 MB
Release : 2015-04-21
Category : Computers
ISBN : 0128011580

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Modeling and Simulation of Computer Networks and Systems: Methodologies and Applications introduces you to a broad array of modeling and simulation issues related to computer networks and systems. It focuses on the theories, tools, applications and uses of modeling and simulation in order to effectively optimize networks. It describes methodologies for modeling and simulation of new generations of wireless and mobiles networks and cloud and grid computing systems. Drawing upon years of practical experience and using numerous examples and illustrative applications recognized experts in both academia and industry, discuss: Important and emerging topics in computer networks and systems including but not limited to; modeling, simulation, analysis and security of wireless and mobiles networks especially as they relate to next generation wireless networks Methodologies, strategies and tools, and strategies needed to build computer networks and systems modeling and simulation from the bottom up Different network performance metrics including, mobility, congestion, quality of service, security and more... Modeling and Simulation of Computer Networks and Systems is a must have resource for network architects, engineers and researchers who want to gain insight into optimizing network performance through the use of modeling and simulation. Discusses important and emerging topics in computer networks and Systems including but not limited to; modeling, simulation, analysis and security of wireless and mobiles networks especially as they relate to next generation wireless networks Provides the necessary methodologies, strategies and tools needed to build computer networks and systems modeling and simulation from the bottom up Includes comprehensive review and evaluation of simulation tools and methodologies and different network performance metrics including mobility, congestion, quality of service, security and more

Author : Francesco Masulli
Publisher : Springer Science & Business Media
Page : 331 pages
File Size : 14,86 MB
Release : 2010-08-11
Category : Science
ISBN : 3642145701

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This book constitutes the thoroughly refereed post-conference proceedings of the Sixth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2009, held in Genova, Italy, in October 2009. The revised 23 full papers presented were carefully reviewed and selected from 57 submissions. The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in tools for bioinformatics, gene expression analysis and new perspectives in bioinformatics together with 4 special sessions on using game-theoretical tools in bioinformatics, combining Bayesian and machine learning approaches in bioinformatics: state of the art and future perspectives, data clustering and bioinformatics (DCB 2009) and on intelligent systems for medical decisions support (ISMDS 2009).