Computational analysis of protein interaction networks for infectious diseases

Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies

(2015) Madhumita Bhattacharyya et al.   MALARIA JOURNAL

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

(2014) Hufeng Zhou et al.   Biology Direct

A review ofin silicoapproaches for analysis and prediction of HIV-1-human protein–protein interactions

(2014) Sanghamitra Bandyopadhyay et al.   BRIEFINGS IN BIOINFORMATICS

Unraveling novel broad-spectrum antibacterial targets in food and waterborne pathogens using comparative genomics and protein interaction network analysis

(2014) Ankush Jadhav et al.   INFECTION GENETICS AND EVOLUTION

Interactome analyses of Salmonella pathogenicity islands reveal SicA indispensable for virulence

(2014) Chandrajit Lahiri et al.   JOURNAL OF THEORETICAL BIOLOGY

Predicting protein–protein interactions between human and hepatitis C virus via an ensemble learning method

(2014) Abbasali Emamjomeh et al.   Molecular BioSystems

The Pathogen-Host Interactions database (PHI-base): additions and future developments

(2014) Martin Urban et al.   NUCLEIC ACIDS RESEARCH

VirusMentha: a new resource for virus-host protein interactions

(2014) Alberto Calderone et al.   NUCLEIC ACIDS RESEARCH

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

(2014) Thibaut Guirimand et al.   NUCLEIC ACIDS RESEARCH

PRIMOS: An Integrated Database of Reassessed Protein–Protein Interactions Providing Web-Based Access to In Silico Validation of Experimentally Derived Data

(2013) Raphaela Rid et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

FunCoup 3.0: database of genome-wide functional coupling networks

(2013) Thomas Schmitt et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Identification and Characterization of Potential Therapeutic Candidates in Emerging Human Pathogen Mycobacterium abscessus: A Novel Hierarchical In Silico Approach

(2013) Buvaneswari Shanmugham et al.   PLoS One

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

(2012) Karthik Raman et al.   BMC Systems Biology

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Insight into Bacterial Virulence Mechanisms against Host Immune Response via the Yersinia pestis-Human Protein-Protein Interaction Network

(2011) Huiying Yang et al.   INFECTION AND IMMUNITY

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Computational Prediction of Host-Parasite Protein Interactions between P. falciparum and H. sapiens

(2011) Stefan Wuchty   PLoS One

Path lengths in protein-protein interaction networks and biological complexity

(2011) Ke Xu et al.   PROTEOMICS

A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

(2011) A. Aderem et al.   mBio

HPIDB - a unified resource for host-pathogen interactions

(2010) Ranjit Kumar et al.   BMC BIOINFORMATICS

The biological context of HIV-1 host interactions reveals subtle insights into a system hijack

(2010) Jonathan E Dickerson et al.   BMC Systems Biology

Global Protein−Protein Interaction Network in the Human PathogenMycobacterium tuberculosisH37Rv

(2010) Yi Wang et al.   JOURNAL OF PROTEOME RESEARCH

Mapping the Protein Interaction Network in Methicillin-ResistantStaphylococcus aureus

(2010) Artem Cherkasov et al.   JOURNAL OF PROTEOME RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

(2010) Matthew D. Dyer et al.   PLoS One

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

Connecting viral with cellular interactomes

(2009) SM Bailer et al.   CURRENT OPINION IN MICROBIOLOGY

A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome

(2009) Stefan Wuchty et al.   PROTEOMICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Protein interaction network related to Helicobacter pylori infection response

(2009) Kyu Kwang Kim et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Precision and recall estimates for two-hybrid screens

(2008) Hailiang Huang et al.   BIOINFORMATICS

Identifying gene-disease associations using centrality on a literature mined gene-interaction network

(2008) A. Ozgur et al.   BIOINFORMATICS

Antimicrobial Resistance:Acinetobacter baumannii:Epidemiology, Antimicrobial Resistance, and Treatment Options

(2008) Lisa L. Maragakis et al.   CLINICAL INFECTIOUS DISEASES

Hepatitis C virus infection protein network

(2008) B de Chassey et al.   Molecular Systems Biology

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology

(2008) Chung-Yen Lin et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions

(2008) Xue-wen Chen et al.   PLoS One

The Binary Protein Interactome of Treponema pallidum – The Syphilis Spirochete

(2008) Björn Titz et al.   PLoS One