A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery

Benchmarking selected computational gene network growing tools in context of virus-host interactions

(2017) Biruhalem Taye et al.   Scientific Reports

Inferring gene targets of drugs and chemical compounds from gene expression profiles

(2016) Heeju Noh et al.   BIOINFORMATICS

Reconstructing the temporal progression of HIV-1 immune response pathways

(2016) Siddhartha Jain et al.   BIOINFORMATICS

Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection

(2016) Nicholas S. Heaton et al.   IMMUNITY

Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets

(2016) Arunachalam Vinayagam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family

(2016) Marina Uhart et al.   Scientific Reports

Input graph: the hidden geometry in controlling complex networks

(2016) Xizhe Zhang et al.   Scientific Reports

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Identifying problematic drugs based on the characteristics of their targets

(2015) Tiago J. S. Lopes et al.   Frontiers in Pharmacology

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

(2014) Mohammad Moni et al.   BMC BIOINFORMATICS

Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development

(2014) Tokiko Watanabe et al.   Cell Host & Microbe

Controllability in protein interaction networks

(2014) S. Wuchty   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influenza Viruses and mRNA Splicing: Doing More with Less

(2014) J. Dubois et al.   mBio

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Elucidating Novel Hepatitis C Virus–Host Interactions Using Combined Mass Spectrometry and Functional Genomics Approaches

(2013) Marie-Anne Germain et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrating protein-protein interaction networks with phenotypes reveals signs of interactions

(2013) Arunachalam Vinayagam et al.   NATURE METHODS

A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses

(2013) Hugh D. Mitchell et al.   PLoS One

Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer

(2013) Karina L. Mine et al.   Nature Communications

Emergence of bimodality in controlling complex networks

(2013) Tao Jia et al.   Nature Communications

Control Capacity and A Random Sampling Method in Exploring Controllability of Complex Networks

(2013) Tao Jia et al.   Scientific Reports

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

(2013) Martin H. Schaefer et al.   PLoS Computational Biology

Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors

(2013) Linhui Hao et al.   PLoS Computational Biology

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs

(2012) Jason E Shoemaker et al.   BMC Systems Biology

Tinkering with Translation: Protein Synthesis in Virus-Infected Cells

(2012) D. Walsh et al.   Cold Spring Harbor Perspectives in Biology

Chapter 5: Network Biology Approach to Complex Diseases

(2012) Dong-Yeon Cho et al.   PLoS Computational Biology

Viral Infections of the Lower Respiratory Tract: Old Viruses, New Viruses, and the Role of Diagnosis

(2011) A. T. Pavia   CLINICAL INFECTIOUS DISEASES

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

Trends in the exploitation of novel drug targets

(2011) Mathias Rask-Andersen et al.   NATURE REVIEWS DRUG DISCOVERY

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

Pattern Recognition Receptors and the Innate Immune Response to Viral Infection

(2011) Mikayla R. Thompson et al.   Viruses-Basel

Network-Based Prediction and Analysis of HIV Dependency Factors

(2011) T. M. Murali et al.   PLoS Computational Biology

Network Systems Biology for Drug Discovery

(2010) D K Arrell et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Role of Peroxiredoxin 1 and Peroxiredoxin 4 in Protection of Respiratory Syncytial Virus-Induced Cysteinyl Oxidation of Nuclear Cytoskeletal Proteins

(2010) M. Jamaluddin et al.   JOURNAL OF VIROLOGY

Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication

(2010) Alexander Karlas et al.   NATURE

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

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

(2009) Sagi D. Shapira et al.   CELL

The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus

(2009) Abraham L. Brass et al.   CELL

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

The analysis of the drug–targets based on the topological properties in the human protein–protein interaction network

(2009) Mingzhu Zhu et al.   JOURNAL OF DRUG TARGETING

Human host factors required for influenza virus replication

(2009) Renate König et al.   NATURE

Structure of Protein Interaction Networks and Their Implications on Drug Design

(2009) Takeshi Hase et al.   PLoS Computational Biology

Short Communication: Cataloguing the HIV Type 1 Human Protein Interaction Network

(2008) Roger G. Ptak et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Combining multiple positive training sets to generate confidence scores for protein–protein interactions

(2008) Jingkai Yu et al.   BIOINFORMATICS

Influenza viruses and the NF-κB signaling pathway – towards a novel concept of antiviral therapy

(2008) Stephan Ludwig et al.   BIOLOGICAL CHEMISTRY

Innate immune response to viral infection

(2008) Shohei Koyama et al.   CYTOKINE

NF- B Signaling Differentially Regulates Influenza Virus RNA Synthesis

(2008) N. Kumar et al.   JOURNAL OF VIROLOGY

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

(2008) Kartik M Mani et al.   Molecular Systems Biology

Hepatitis C virus infection protein network

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

Drosophila RNAi screen identifies host genes important for influenza virus replication

(2008) Linhui Hao et al.   NATURE

INTERFEROME: the database of interferon regulated genes

(2008) Shamith A. Samarajiwa et al.   NUCLEIC ACIDS RESEARCH