Computational Systems Biology of Pathogen-Host Interactions
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 mechanism...
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2021
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| author | Reinhard Guthke Saliha Durmus Tunahan Cak?r |
| author_browse | Reinhard Guthke Saliha Durmus Tunahan Cak?r |
| author_facet | Reinhard Guthke Saliha Durmus Tunahan Cak?r |
| author_sort | Reinhard Guthke |
| collection | Directory of Open Access Books |
| description | 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. |
| format | Online |
| id | doab-20.500.12854ir-43710 |
| institution | Directory of Open Access Books |
| language | eng |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media SA |
| publisherStr | Frontiers Media SA |
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| spelling | doab-20.500.12854ir-437102024-04-05T17:30:58Z Computational Systems Biology of Pathogen-Host Interactions Reinhard Guthke Saliha Durmus Tunahan Cak?r QR1-502 Q1-390 Image-based Systems Biology Network Inference OMICS data Computational Biology bioinformatics protein-protein interaction text mining Constraint-based modeling gene regulatory network pathogen-host interaction thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) 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. 2021-02-11T10:19:18Z 2021-02-11T10:19:18Z 2016-01-19 14:05:46 2016 book 18208 16648714 9782889198214 https://directory.doabooks.org/handle/20.500.12854/43710 eng Frontiers Research Topics image/jpeg Attribution 4.0 International http://www.frontiersin.org/books/Computational_Systems_Biology_of_Pathogen-Host_Interactions/888#nogo http://journal.frontiersin.org/researchtopic/2817/computational-systems-biology-of-pathogen-host-interactions Frontiers Media SA 10.3389/978-2-88919-821-4 10.3389/978-2-88919-821-4 bf5ce210-e72e-4860-ba9b-c305640ff3ae 9782889198214 198 open access |
| spellingShingle | QR1-502 Q1-390 Image-based Systems Biology Network Inference OMICS data Computational Biology bioinformatics protein-protein interaction text mining Constraint-based modeling gene regulatory network pathogen-host interaction thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) Reinhard Guthke Saliha Durmus Tunahan Cak?r Computational Systems Biology of Pathogen-Host Interactions |
| title | Computational Systems Biology of Pathogen-Host Interactions |
| title_full | Computational Systems Biology of Pathogen-Host Interactions |
| title_fullStr | Computational Systems Biology of Pathogen-Host Interactions |
| title_full_unstemmed | Computational Systems Biology of Pathogen-Host Interactions |
| title_short | Computational Systems Biology of Pathogen-Host Interactions |
| title_sort | computational systems biology of pathogen host interactions |
| topic | QR1-502 Q1-390 Image-based Systems Biology Network Inference OMICS data Computational Biology bioinformatics protein-protein interaction text mining Constraint-based modeling gene regulatory network pathogen-host interaction thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) |
| topic_facet | QR1-502 Q1-390 Image-based Systems Biology Network Inference OMICS data Computational Biology bioinformatics protein-protein interaction text mining Constraint-based modeling gene regulatory network pathogen-host interaction thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) |
| url | 18208 |
| work_keys_str_mv | AT reinhardguthke computationalsystemsbiologyofpathogenhostinteractions AT salihadurmus computationalsystemsbiologyofpathogenhostinteractions AT tunahancakr computationalsystemsbiologyofpathogenhostinteractions |