Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection

Correction for Malik-Soni and Frappier, Proteomic Profiling of EBNA1-Host Protein Interactions in Latent and Lytic Epstein-Barr Virus Infections

(2015) Natasha Malik-Soni et al.   JOURNAL OF VIROLOGY

Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression

(2015) Benjamin A. Diner et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Mapping of Herpesvirus-Host Protein Complexes Reveals a Transcription Strategy for Late Genes

(2015) Zoe H. Davis et al.   MOLECULAR CELL

Virology meets Proteomics

(2015) Ileana M. Cristea et al.   PROTEOMICS

Antiviral antibody profiling by high-density protein arrays

(2015) Xiaofang Bian et al.   PROTEOMICS

Quantitative Proteomics Identifies Serum Response Factor Binding Protein 1 as a Host Factor for Hepatitis C Virus Entry

(2015) Gisa Gerold et al.   Cell Reports

BRCA1 Regulates IFI16 Mediated Nuclear Innate Sensing of Herpes Viral DNA and Subsequent Induction of the Innate Inflammasome and Interferon-β Responses

(2015) Dipanjan Dutta et al.   PLoS Pathogens

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction

(2014) Michael P. Weekes et al.   CELL

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

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

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

(2014) Iakes Ezkurdia et al.   HUMAN MOLECULAR GENETICS

Elucidation of the Ebola Virus VP24 Cellular Interactome and Disruption of Virus Biology through Targeted Inhibition of Host-Cell Protein Function

(2014) Isabel García-Dorival et al.   JOURNAL OF PROTEOME RESEARCH

The Human Papillomavirus E7 Proteins Associate with p190RhoGAP and Alter Its Function

(2014) B. Todorovic et al.   JOURNAL OF VIROLOGY

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

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

How yeast can be used as a genetic platform to explore virus–host interactions: from ‘omics’ to functional studies

(2014) Peter D. Nagy et al.   TRENDS IN MICROBIOLOGY

Exploration of Panviral Proteome: High-Throughput Cloning and Functional Implications in Virus-host Interactions

(2014) Xiaobo Yu et al.   Theranostics

Virus-host interactomics: new insights and opportunities for antiviral drug discovery

(2014) Benoît de Chassey et al.   Genome Medicine

IFI16 Restricts HSV-1 Replication by Accumulating on the HSV-1 Genome, Repressing HSV-1 Gene Expression, and Directly or Indirectly Modulating Histone Modifications

(2014) Karen E. Johnson et al.   PLoS Pathogens

The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology

(2014) Todd M. Greco et al.   Annual Review of Virology

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

Human Cytomegalovirus Tegument Protein pUL83 Inhibits IFI16-Mediated DNA Sensing for Immune Evasion

(2013) Tuo Li et al.   Cell Host & Microbe

HRas Signal Transduction Promotes Hepatitis C Virus Cell Entry by Triggering Assembly of the Host Tetraspanin Receptor Complex

(2013) Laetitia Zona et al.   Cell Host & Microbe

The Viral Ubiquitin Ligase ICP0 Is neither Sufficient nor Necessary for Degradation of the Cellular DNA Sensor IFI16 during Herpes Simplex Virus 1 Infection

(2013) D. Cuchet-Lourenco et al.   JOURNAL OF VIROLOGY

Bovine Ephemeral Fever Rhabdovirus  1 Protein Has Viroporin-Like Properties and Binds Importin  1 and Importin 7

(2013) D. A. Joubert et al.   JOURNAL OF VIROLOGY

A Proteomic Perspective of Inbuilt Viral Protein Regulation: pUL46 Tegument Protein is Targeted for Degradation by ICP0 during Herpes Simplex Virus Type 1 Infection

(2013) Aaron E. Lin et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

The functional interactome landscape of the human histone deacetylase family

(2013) P. Joshi et al.   Molecular Systems Biology

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

(2013) N. Philippe et al.   SCIENCE

Proteomics-Based Methods for Discovery, Quantification, and Validation of Protein–Protein Interactions

(2012) Yana V. Miteva et al.   ANALYTICAL CHEMISTRY

Kinesin-3 Mediates Axonal Sorting and Directional Transport of Alphaherpesvirus Particles in Neurons

(2012) Tal Kramer et al.   Cell Host & Microbe

Cross-linking Measurements of the Potato leafroll virus Reveal Protein Interaction Topologies Required for Virion Stability, Aphid Transmission, and Virus–Plant Interactions

(2012) Juan D. Chavez et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive Analysis of Host Cellular Interactions with Human Papillomavirus E6 Proteins Identifies New E6 Binding Partners and Reflects Viral Diversity

(2012) E. A. White et al.   JOURNAL OF VIROLOGY

Functional Proteomics Establishes the Interaction of SIRT7 with Chromatin Remodeling Complexes and Expands Its Role in Regulation of RNA Polymerase I Transcription

(2012) Yuan-Chin Tsai et al.   MOLECULAR & CELLULAR PROTEOMICS

Viral immune modulators perturb the human molecular network by common and unique strategies

(2012) Andreas Pichlmair et al.   NATURE

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

(2012) Orit Rozenblatt-Rosen et al.   NATURE

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

(2012) Faviel F. Gonzalez-Galarza et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Cutaneous papillomavirus E6 oncoproteins associate with MAML1 to repress transactivation and NOTCH signaling

(2012) N Brimer et al.   ONCOGENE

Discovery and Targeted LC-MS/MS of Purified Polerovirus Reveals Differences in the Virus-Host Interactome Associated with Altered Aphid Transmission

(2012) Michelle Cilia et al.   PLoS One

Nuclear IFI16 induction of IRF-3 signaling during herpesviral infection and degradation of IFI16 by the viral ICP0 protein

(2012) M. H. Orzalli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cutaneous  -human papillomavirus E6 proteins bind Mastermind-like coactivators and repress Notch signaling

(2012) M. J. A. Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic identification of interactions between host cell proteins and E7 oncoproteins from diverse human papillomaviruses

(2012) E. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antiviral Inhibition Targeting the HCMV Kinase pUL97 Requires pUL27-Dependent Degradation of Tip60 Acetyltransferase and Cell-Cycle Arrest

(2011) Justin M. Reitsma et al.   Cell Host & Microbe

The antiviral protein viperin inhibits hepatitis C virus replication via interaction with nonstructural protein 5A

(2011) Karla J. Helbig et al.   HEPATOLOGY

Proteomic Profiling of the Human Cytomegalovirus UL35 Gene Products Reveals a Role for UL35 in the DNA Repair Response

(2011) J. Salsman et al.   JOURNAL OF VIROLOGY

A Physical Interaction Network of Dengue Virus and Human Proteins

(2011) Sudip Khadka et al.   MOLECULAR & CELLULAR PROTEOMICS

Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein

(2011) Kasia Hrecka et al.   NATURE

A roadmap to generate renewable protein binders to the human proteome

(2011) Karen Colwill et al.   NATURE METHODS

A proteomic study of TAR-RNA binding protein (TRBP)-associated factors

(2011) Ya-Hui Chi et al.   Cell and Bioscience

Chemical Cross-Linking and Mass Spectrometry As a Low-Resolution Protein Structure Determination Technique

(2010) Pragya Singh et al.   ANALYTICAL CHEMISTRY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Human Cytomegalovirus pUL83 Stimulates Activity of the Viral Immediate-Early Promoter through Its Interaction with the Cellular IFI16 Protein

(2010) I. M. Cristea et al.   JOURNAL OF VIROLOGY

Host Factors Associated with the Sindbis Virus RNA-Dependent RNA Polymerase: Role for G3BP1 and G3BP2 in Virus Replication

(2010) I. M. Cristea et al.   JOURNAL OF VIROLOGY

A Docking Model Based on Mass Spectrometric and Biochemical Data Describes Phage Packaging Motor Incorporation

(2010) Chi-yu Fu et al.   MOLECULAR & CELLULAR PROTEOMICS

A new cross-linking strategy: protein interaction reporter (PIR) technology for protein–protein interaction studies

(2010) Xiaoting Tang et al.   Molecular BioSystems

Systematic analysis of the IgG antibody immune response against varicella zoster virus (VZV) using a self-assembled protein microarray

(2010) Alessandro Ceroni et al.   Molecular BioSystems

Destabilization of TIP60 by Human Papillomavirus E6 Results in Attenuation of TIP60-Dependent Transcriptional Regulation and Apoptotic Pathway

(2010) Sudhakar Jha et al.   MOLECULAR CELL

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Cpr1 cyclophilin and Ess1 parvulin prolyl isomerases interact with the tombusvirus replication protein and inhibit viral replication in yeast model host

(2010) Venugopal Mendu et al.   VIROLOGY

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

(2009) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

The Human Immunodeficiency Virus Type 2 Vpx Protein Usurps the CUL4A-DDB1DCAF1 Ubiquitin Ligase To Overcome a Postentry Block in Macrophage Infection

(2009) A. Bergamaschi et al.   JOURNAL OF VIROLOGY

A Targeted Spatial-Temporal Proteomics Approach Implicates Multiple Cellular Trafficking Pathways in Human Cytomegalovirus Virion Maturation

(2009) Nathaniel J. Moorman et al.   MOLECULAR & CELLULAR PROTEOMICS

Ebola Virus Matrix Protein VP40 Uses the COPII Transport System for Its Intracellular Transport

(2008) Seiya Yamayoshi et al.   Cell Host & Microbe

Human Cytomegalovirus Protein UL38 Inhibits Host Cell Stress Responses by Antagonizing the Tuberous Sclerosis Protein Complex

(2008) Nathaniel J. Moorman et al.   Cell Host & Microbe

Utility of formaldehyde cross-linking and mass spectrometry in the study of protein–protein interactions

(2008) Brent W. Sutherland et al.   JOURNAL OF MASS SPECTROMETRY

Cdc34p Ubiquitin-Conjugating Enzyme Is a Component of the Tombusvirus Replicase Complex and Ubiquitinates p33 Replication Protein

(2008) Z. Li et al.   JOURNAL OF VIROLOGY

Tegument Proteins of Human Cytomegalovirus

(2008) R. F. Kalejta   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Hepatitis C virus infection protein network

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

Next-generation high-density self-assembling functional protein arrays

(2008) Niroshan Ramachandran et al.   NATURE METHODS

VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus–host interaction networks

(2008) Vincent Navratil et al.   NUCLEIC ACIDS RESEARCH

Biochemical approaches for discovering protein-protein interactions

(2008) Jan A. Miernyk et al.   PLANT JOURNAL

Lentiviral Vpx Accessory Factor Targets VprBP/DCAF1 Substrate Adaptor for Cullin 4 E3 Ubiquitin Ligase to Enable Macrophage Infection

(2008) Smita Srivastava et al.   PLoS Pathogens