Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size

(2011) Laure Sambourg et al.   BMC BIOINFORMATICS

Network-based methods for human disease gene prediction

(2011) X. Wang et al.   Briefings in Functional Genomics

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Using yeast as a model to study membrane proteins

(2011) Julia Petschnigg et al.   CURRENT OPINION IN NEPHROLOGY AND HYPERTENSION

Networks for systems biology: conceptual connection of data and function

(2011) F. Emmert-Streib et al.   IET Systems Biology

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

Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets

(2011) Xueping Yu et al.   MOLECULAR & CELLULAR PROTEOMICS

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS

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

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies

(2011) Nirmala Akula et al.   PLoS One

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Virus–host interactomes and global models of virus-infected cells

(2011) Caroline C. Friedel et al.   TRENDS IN MICROBIOLOGY

Towards Establishment of a Rice Stress Response Interactome

(2011) Young-Su Seo et al.   PLoS Genetics

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

Protein-protein interactions: Making sense of networks via graph-theoretic modeling

(2010) Nataša Pržulj   BIOESSAYS

dmGWAS: dense module searching for genome-wide association studies in protein–protein interaction networks

(2010) Peilin Jia et al.   BIOINFORMATICS

LEC–BiFC: a new method for rapid assay of protein interaction

(2010) J Lin et al.   BIOTECHNIC & HISTOCHEMISTRY

An improved bimolecular fluorescence complementation assay with a high signal-to-noise ratio

(2010) Yutaka Kodama* et al.   BIOTECHNIQUES

Proximity ligation assays: a recent addition to the proteomics toolbox

(2010) Irene Weibrecht et al.   Expert Review of Proteomics

Global approaches to study protein–protein interactions among viruses and hosts

(2010) Jorge Mendez-Rios et al.   Future Microbiology

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease

(2010) M. Soler-Lopez et al.   GENOME RESEARCH

Hub Promiscuity in Protein-Protein Interaction Networks

(2010) Ashwini Patil et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Yeast proteomics and protein microarrays

(2010) Rui Chen et al.   Journal of Proteomics

Dissecting spatio-temporal protein networks driving human heart development and related disorders

(2010) Kasper Lage et al.   Molecular Systems Biology

Exhaustive benchmarking of the yeast two-hybrid system

(2010) Yu-Chi Chen et al.   NATURE METHODS

Reply to "Exhaustive benchmarking of the yeast two-hybrid system"

(2010) Pascal Braun et al.   NATURE METHODS

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

Detecting interactions with membrane proteins using a membrane two-hybrid assay in yeast

(2010) Jamie Snider et al.   Nature Protocols

Quantifying protein–protein interactions in high throughput using protein domain microarrays

(2010) Alexis Kaushansky et al.   Nature Protocols

Network medicine: a network-based approach to human disease

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

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks

(2010) M. E. Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Next Generation Becomes the Now Generation

(2010) Diego A. Martinez et al.   PLoS Genetics

A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

(2010) Sylvie Lalonde   Frontiers in Physiology

Visualization of molecular interactions using bimolecular fluorescence complementation analysis: Characteristics of protein fragment complementation

(2009) Tom K. Kerppola   CHEMICAL SOCIETY REVIEWS

A network medicine approach to human disease

(2009) Andreas Zanzoni et al.   FEBS LETTERS

Shifted Transversal Design smart-pooling for high coverage interactome mapping

(2009) X. Xin et al.   GENOME RESEARCH

Pathway and network-based analysis of genome-wide association studies in multiple sclerosis

(2009) S. E. Baranzini et al.   HUMAN MOLECULAR GENETICS

Array MAPPIT: High-Throughput Interactome Analysis in Mammalian Cells

(2009) Sam Lievens et al.   JOURNAL OF PROTEOME RESEARCH

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

'Edgetic' perturbation of a C. elegans BCL2 ortholog

(2009) Matija Dreze et al.   NATURE METHODS

The Negatome database: a reference set of non-interacting protein pairs

(2009) Pawel Smialowski et al.   NUCLEIC ACIDS RESEARCH

Network Properties of Complex Human Disease Genes Identified through Genome-Wide Association Studies

(2009) Fredrik Barrenas et al.   PLoS One

Structural domain-domain interactions: Assessment and comparison with protein-protein interaction data to improve the interactome

(2009) C. Prieto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Understanding Modularity in Molecular Networks Requires Dynamics

(2009) R. P. Alexander et al.   Science Signaling

Mammalian two-hybrids come of age

(2009) Sam Lievens et al.   TRENDS IN BIOCHEMICAL SCIENCES

Evolutionarily Conserved Herpesviral Protein Interaction Networks

(2009) Even Fossum et al.   PLoS Pathogens

Analyzing Protein Interaction Networks Using Structural Information

(2008) Christina Kiel et al.   Annual Review of Biochemistry

Bimolecular Fluorescence Complementation (BiFC) Analysis as a Probe of Protein Interactions in Living Cells

(2008) Tom K. Kerppola   Annual Review of Biophysics

Precision and recall estimates for two-hybrid screens

(2008) Hailiang Huang et al.   BIOINFORMATICS

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

(2008) Mike Boxem et al.   CELL

System-wide Investigation of ErbB4 Reveals 19 Sites of Tyr Phosphorylation that Are Unusually Selective in Their Recruitment Properties

(2008) Alexis Kaushansky et al.   CHEMISTRY & BIOLOGY

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R

(2008) Alexis Kaushansky et al.   Molecular BioSystems

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

(2008) Arun K Ramani et al.   Molecular Systems Biology

Hepatitis C virus infection protein network

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

Cost-effective strategies for completing the interactome

(2008) Ariel S Schwartz et al.   NATURE METHODS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

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

(2008) Niroshan Ramachandran et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

VirusMINT: a viral protein interaction database

(2008) A. Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

The Binary Protein Interactome of Treponema pallidum – The Syphilis Spirochete

(2008) Björn Titz et al.   PLoS One

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

BIOCHEMISTRY: Not Comparable, But Complementary

(2008) L. J. Jensen et al.   SCIENCE

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE

Protein interactions in human genetic diseases

(2008) Benjamin Schuster-Böckler et al.   GENOME BIOLOGY

Study and selection of in vivo protein interactions by coupling bimolecular fluorescence complementation and flow cytometry

(2007) Montse Morell et al.   Nature Protocols