Computational Systems Biology Of Pathogen Host Interactions

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Computational Systems Biology Of Pathogen Host Interactions

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Author : Saliha Durmuş
language : en
Publisher: Frontiers Media SA
Release Date : 2016-05-30

Computational Systems Biology Of Pathogen Host Interactions written by Saliha Durmuş and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-05-30 with Microbiology categories.

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.

Computational Systems Biology Of Pathogen Host Interactions

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Author :
language : en
Publisher:
Release Date : 2016

Computational Systems Biology Of Pathogen Host Interactions written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.

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. Acknowledgements: We, editors of this e-book, acknowledge Emrah Nikerel (Yeditepe University, Turkey) and Arzucan Özgür (Bogaaziçi University, Turkey) for their contributions during the initiation of the Research Topic.

Systems Biology Approaches For Host Pathogen Interaction Analysis

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Author : Mohd. Tashfeen Ashraf
language : en
Publisher: Elsevier
Release Date : 2024-02-16

Systems Biology Approaches For Host Pathogen Interaction Analysis written by Mohd. Tashfeen Ashraf and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-02-16 with Science categories.

System Biology Approaches for Microbial Pathogenesis Interaction Analysis aids biological researchers to expand their research scope using piled up data generated through recent technological advancement. In addition, it also opens avenues for bioinformatics and computer science researchers to utilize their expertise in biological meaningful ways. It also covers network biology approaches to decipher complex multiple host-pathogen interactions in addition to giving valuable coverage of artificial intelligence. The host-pathogen interactions are generally considered as highly specific interactions leading to a variety of consequences. The utilization of data science approaches has revolutionized scientific research including host-pathogen interaction analyses. Data science approaches coupled with network biology has taken host-pathogen interaction analysis from specific interaction to a new paradigm of understanding consequences of these interaction in the biological network. Unfortunately, basic biological researchers are mostly unaware of these advancements. In contrast, data scientists are not familiar with biological aspects of such data. System Biology Approaches for Microbial Pathogenesis Interaction Analysis will bridge these gaps through a new paradigm of understanding consequences of interaction in biological networks. - Cover approaches to decipher complex multiple host–pathogen interactions - Gives biological researcher an insight into the utilization of technological advancements in the field of host–pathogen interaction analyses in their work - Provides a new paradigm of understanding the consequences of host–pathogen interaction in biological systems

An Introduction To Computational Systems Biology

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Author : Karthik Raman
language : en
Publisher: CRC Press
Release Date : 2021-05-30

An Introduction To Computational Systems Biology written by Karthik Raman and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-30 with Computers categories.

This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling Covers a broad spectrum of modelling, from static networks to dynamic models and constraint-based models Thoughtful exercises to test and enable understanding of concepts State-of-the-art chapters on exciting new developments, like community modelling and biological circuit design Emphasis on coding and software tools for systems biology Companion website featuring lecture videos, figure slides, codes, supplementary exercises, further reading, and appendices: https://ramanlab.github.io/SysBioBook/ An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.

Metabolic Interaction In Infection

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Author : Ricardo Silvestre
language : en
Publisher: Springer
Release Date : 2018-04-06

Metabolic Interaction In Infection written by Ricardo Silvestre and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-04-06 with Science categories.

This book focuses on host–pathogen interactions at the metabolic level. It explores the metabolic requirements of the infectious agents, the microbial metabolic pathways that are dedicated to circumvent host immune mechanisms as well as the molecular mechanisms by which pathogens hijack host cell metabolism for their own benefit. Finally, it provides insights on the possible clinical and immunotherapeutic applications, as well as on the available experimental and analytical methods. The contributions break new ground in understanding the metabolic crosstalk between host and pathogen.

Microbial Interventions In Agriculture And Environment

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Author : Dhananjaya Pratap Singh
language : en
Publisher: Springer Nature
Release Date : 2019-11-09

Microbial Interventions In Agriculture And Environment written by Dhananjaya Pratap Singh and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-11-09 with Technology & Engineering categories.

Microbial communities and their multi-functionalities play a crucial role in the management of soil and plant health, and thus help in managing agro-ecology, the environment and agriculture. Microorganisms are key players in N-fixation, nutrient acquisition, carbon sequestration, plant growth promotion, pathogen suppression, induced systemic resistance and tolerance against stresses, and these parameters are used as indicators of improved crop productivity and sustainable soil health. Beneficial belowground microbial interactions in the rhizosphere help plants combat abiotic challenges in the unfavourable environmental conditions of native soils. These microorganisms and their products offer potential solutions for agriculture in problematic areas since they are able to degrade xenobiotic compounds, pesticides and toxic chemicals and help remediate heavy metals in the rhizosphere and so make deteriorated soils suitable for crop production. This book compiles the latest research on the role of microbes in the rhizosphere and agro-ecology, covering interaction mechanisms, microbe-mediated crop production, plant and soil health management, food and nutrition, nutrient recycling, land reclamation, clean water systems, agro-waste management, biodegradation, bioremediation, biomass and bioenergy, sanitation and rural livelihood security. It is a comprehensive reference resource for agricultural activists, policymakers, environmentalists and advisors working for governments, non-governmental organizations and industries, helping them update their knowledge of this important, but often neglected, research area.

Systems Biology Approaches Prevention Diagnosis And Understanding Mechanisms Of Complex Diseases

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Author : Sanket Joshi
language : en
Publisher: Springer Nature
Release Date : 2024-05-16

Systems Biology Approaches Prevention Diagnosis And Understanding Mechanisms Of Complex Diseases written by Sanket Joshi and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-05-16 with Science categories.

This book examines the development and applications of system biology approaches for the prevention, diagnosis, and understanding of disease mechanisms. It explores the applications of system biology in infectious diseases, including host-pathogen interaction, and the identification of targets for new therapeutics and intervention strategies. It covers the use of system biology for understanding and treating metabolic disorders towards personalized and precision medicine. The book further discusses the systems biology approaches for understanding the mechanisms of tumor progression and designing more effective cancer therapies. The chapter also reviews the current strategies in autoimmune disease treatment and highlights the opportunity that systems biology represents for the development of better and safer treatments. Importantly, the book discusses the current state of the systems-level understanding of diseases and both the therapeutic and adverse mechanisms of drug actions usingsystem biology approaches. Cutting across the disciplines, this book is a valuable source for researchers in genetics, molecular biology, cell biology, microbiology, and biomedical sciences. ​

Advances In Multi Omics Study Of Filamentous Plant Pathogens

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Author : Danyu Shen
language : en
Publisher: Frontiers Media SA
Release Date : 2022-09-22

Advances In Multi Omics Study Of Filamentous Plant Pathogens written by Danyu Shen and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-09-22 with Science categories.

Computational Methods In Drug Discovery And Repurposing For Cancer Therapy

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Author : Ganji Purnachandra Nagaraju
language : en
Publisher: Elsevier
Release Date : 2023-03-22

Computational Methods In Drug Discovery And Repurposing For Cancer Therapy written by Ganji Purnachandra Nagaraju and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-03-22 with Computers categories.

Computational Methods in Drug Discovery and Repurposing for Cancer Therapy provides knowledge about ongoing research as well as computational approaches for drug discovery and repurposing for cancer therapy. The book also provides detailed descriptions about target molecules, pathways, and their inhibitors for easy understanding and applicability. The book discusses tools and techniques such as integrated bioinformatics approaches, systems biology tools, molecular docking, computational chemistry, artificial intelligence, machine learning, structure-based virtual screening, biomarkers, and transcriptome; those are discussed in the context of different cancer types, such as colon, pancreatic, glioblastoma, endometrial, and retinoblastoma, among others. This book is a valuable resource for researchers, students, and members of the biomedical and medical fields who want to learn more about the use of computational modeling to better tailor the treatment for cancer patients. - Discusses in silico remodeling of effective phytochemical compounds for discovering improved anticancer agents for substantial/significant cancer therapy - Covers potential tools of bioinformatics that are applied toward discovering new targets by drug repurposing and strategies to cure different types of cancers - Demonstrates the significance of computational and artificial intelligence approaches in anticancer drug discovery - Explores how these various advances can be integrated into a precision and personalized medicine approach that can eventually enhance patient care

Genomics And Computational Science For Virus Research

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Author : Hironori Sato
language : en
Publisher: Frontiers E-books
Release Date :

Genomics And Computational Science For Virus Research written by Hironori Sato and has been published by Frontiers E-books this book supported file pdf, txt, epub, kindle and other format this book has been release on with categories.

A biologically striking and clinically important feature of viruses is their rapid evolutionary dynamics in nature. The continual interactions between viruses and host organisms promote quick changes in virus populations, eventually leading to co-evolution of viruses and hosts for their survival. The structural and functional information on the interactions between viruses and hosts should provide a molecular and biological basis to understand infection, replication, cell/host-tropism, immune escape, pathogenesis, and direction of evolution of viruses. The information is also essential to develop methods to control transmission and replication of pathogenic viruses. However, the integrated information on the structure, function, and evolution of viruses and hosts has remained poorly accumulated, partly due to the limitation of analytical methods. Recent progress in genome science and computational approach may open up a new avenue of research of the interactions between viruses and hosts by integrating information on the structures, functions, and evolution. In this Research Topic, we welcome papers concerning the computer-assisted structural and functional studies based on genomic information, with theoretical or in combination with experimental approaches, for understanding molecules, infection, replication, cell/host-tropism, immune escape, pathogenesis, and evolution of viruses in nature.