Integration of molecular network data reconstructs Gene Ontology

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression

(2014) Yiyi Liu et al.   BMC BIOINFORMATICS

Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization

(2013) Hua Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Network Topology Reveals Key Cardiovascular Disease Genes

(2013) Anida Sarajlić et al.   PLoS One

Discovering disease-disease associations by fusing systems-level molecular data

(2013) Marinka Žitnik et al.   Scientific Reports

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

Co-clustering phenome–genome for phenotype classification and disease gene discovery

(2012) TaeHyun Hwang et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

Fast integration of heterogeneous data sources for predicting gene function with limited annotation

(2010) Sara Mostafavi et al.   BIOINFORMATICS

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data

(2009) T. Milenkovic et al.   Journal of the Royal Society Interface

Protein function annotation by homology-based inference

(2009) Yaniv Loewenstein et al.   GENOME BIOLOGY

Position-dependent motif characterization using non-negative matrix factorization

(2008) Lucie N. Hutchins et al.   BIOINFORMATICS

Implementation of GenePattern within the Stanford Microarray Database

(2008) J. Hubble et al.   NUCLEIC ACIDS RESEARCH

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY