HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks

Integration of multiple biological features yields high confidence human protein interactome

(2016) Kubra Karagoz et al.   JOURNAL OF THEORETICAL BIOLOGY

Cytoscape.js: a graph theory library for visualisation and analysis

(2015) Max Franz et al.   BIOINFORMATICS

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

(2015) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

Integrated interactions database: tissue-specific view of the human and model organism interactomes

(2015) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 10: expanded protein families and functions, and analysis tools

(2015) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

Correcting for the study bias associated with protein–protein interaction measurements reveals differences between protein degree distributions from different cancer types

(2015) Martin H. Schaefer et al.   Frontiers in Genetics

Predicting disease associations via biological network analysis

(2014) Kai Sun et al.   BMC BIOINFORMATICS

Bias tradeoffs in the creation and analysis of protein–protein interaction networks

(2014) Jesse Gillis et al.   Journal of Proteomics

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways

(2014) Martin H. Schaefer et al.   PLoS Computational Biology

Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen

(2014) Apichat Suratanee et al.   PLoS Computational Biology

Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases

(2014) Ruth Barshir et al.   PLoS Computational Biology

A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks

(2013) Alexander Lan et al.   BIOINFORMATICS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

A new reference implementation of the PSICQUIC web service

(2013) Noemi del-Toro et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Integration of Protein Abundance and Structure Data Reveals Competition in the ErbB Signaling Network

(2013) C. Kiel et al.   Science Signaling

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

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

The TissueNet database of human tissue protein–protein interactions

(2012) Ruth Barshir et al.   NUCLEIC ACIDS RESEARCH

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways

(2012) N. Tuncbag et al.   NUCLEIC ACIDS RESEARCH

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

(2012) Oded Magger et al.   PLoS Computational Biology

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

(2011) Tiago J. S. Lopes et al.   BIOINFORMATICS

Network-based functional enrichment

(2011) Christopher L Poirel et al.   BMC BIOINFORMATICS

Removing bias against membrane proteins in interaction networks

(2011) Glauber C Brito et al.   BMC Systems Biology

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

(2011) Bruno Aranda 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

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

The Biomolecular Interaction Network Database in PSI-MI 2.5

(2011) Ruth Isserlin et al.   Database-The Journal of Biological Databases and Curation

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Human Protein Reference Database--2009 update

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

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA