Systems Biology Approaches for Host-Pathogen Interaction Analysis

In: Developments in Microbiology Series

Abstract

Front Cover -- Systems Biology Approaches for Host-Pathogen Interaction Analyses -- Copyright Page -- Dedication -- Contents -- List of contributors -- Foreword -- Preface -- Acknowledgments -- 1 Host-pathogen interactions: a general introduction -- 1.1 Introduction -- 1.1.1 Role of pathogen -- 1.1.2 Host-pathogen relationship and mechanisms -- 1.1.3 Classification of host-pathogen interactions -- 1.1.3.1 Invasion of host through breach of primary barriers -- 1.1.3.2 Evasion of host defenses by pathogens -- 1.1.3.3 Pathogen replication in host -- 1.2 Methods for prediction of host-pathogen interactions -- 1.2.1 Ortholog-based protein interaction detection -- 1.2.2 Domain-based detection of protein interaction -- 1.2.3 Biological reasoning-based prediction of host-pathogen interactions -- 1.2.3.1 Homology-based predictions -- 1.2.3.2 Structure-based predictions -- 1.2.4 Domain/motif interaction-based predictions -- 1.2.5 Machine learning-based predictions of host-pathogen interactions -- 1.3 Online repositories for host-pathogen interactions -- 1.3.1 Database of fungal virulence factors -- 1.3.2 E-fungi -- 1.3.3 Fungi DB -- 1.3.4 Ensembl genomes -- 1.3.5 EuPathDB -- 1.3.6 HPIDB -- 1.3.6.1 Pathogen portal -- 1.3.7 PLEXdb -- 1.3.8 VFDB -- 1.4 Conclusion -- Acknowledgment -- References -- 2 Host-pathogen interactions: databases and approaches for data generation -- 2.1 Introduction -- 2.2 Databases for host-pathogen interactions -- 2.3 Bioinformatic methods to discover HPI networking -- 2.3.1 Biological methods -- 2.3.2 Computational methods -- 2.4 Microscopic imaging techniques as stage of the art -- 2.5 RNA-Seq profiling: tool for determining the HPI network -- 2.5.1 Bacteria-host interactions -- 2.5.2 Virus-host interactions -- 2.5.3 Fungus-host interaction and other pathogenic interactions -- 2.5.4 Technical approach of RNA-seq and data analysis.