Assessment of network module identification across complex diseases

Chromatin three-dimensional interactions mediate genetic effects on gene expression

(2019) O. Delaneau et al.   SCIENCE

GeNets: a unified web platform for network-based genomic analyses

(2018) Taibo Li et al.   NATURE METHODS

Rare and low-frequency coding variants alter human adult height

(2017) Eirini Marouli et al.   NATURE

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

(2017) Rebecca Sims et al.   NATURE GENETICS

Current and emerging therapeutic targets for IBD

(2017) Markus F. Neurath   Nature Reviews Gastroenterology & Hepatology

Disease variants alter transcription factor levels and methylation of their binding sites

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Inferring causal molecular networks: empirical assessment through a community-based effort

(2016) Steven M Hill et al.   NATURE METHODS

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

(2016) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

Community detection in networks: A user guide

(2016) Santo Fortunato et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

(2016) David Lamparter et al.   PLoS Computational Biology

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

Biological interpretation of genome-wide association studies using predicted gene functions

(2015) Tune H. Pers et al.   Nature Communications

Identifying communities from multiplex biological networks

(2015) Gilles Didier et al.   PeerJ

New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence

(2014) Mengfei Cao et al.   BIOINFORMATICS

Expansion of Biological Pathways Based on Evolutionary Inference

(2014) Yang Li et al.   CELL

Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens

(2014) Krzysztof Kiryluk et al.   NATURE GENETICS

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

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Ranking and combining multiple predictors without labeled data

(2014) F. Parisi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets

(2014) Kimberly Glass et al.   Scientific Reports

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data

(2013) Andrew Gallant et al.   BMC BIOINFORMATICS

Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks

(2013) Mengfei Cao et al.   PLoS One

Developing predictive molecular maps of human disease through community-based modeling

(2012) Jonathan M J Derry et al.   NATURE GENETICS

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Consensus clustering in complex networks

(2012) Andrea Lancichinetti et al.   Scientific Reports

SPICi: a fast clustering algorithm for large biological networks

(2010) Peng Jiang et al.   BIOINFORMATICS

The map equation

(2010) M. Rosvall et al.   European Physical Journal-Special Topics

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Analysis of the structure of complex networks at different resolution levels

(2008) A Arenas et al.   NEW JOURNAL OF PHYSICS