ROMA: Representation and Quantification of Module Activity from Target Expression Data

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Detection of miRNA regulatory effect on triple negative breast cancer transcriptome

(2015) Loredana Martignetti et al.   BMC GENOMICS

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

(2015) I Kuperstein et al.   Oncogenesis

Signaling pathways activation profiles make better markers of cancer than expression of individual genes

(2015) Nikolay M. Borisov et al.   Oncotarget

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

(2014) Maia Chanrion et al.   Nature Communications

Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes

(2014) Anne Biton et al.   Cell Reports

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis

(2013) Gautier Stoll et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind source separation methods for deconvolution of complex signals in cancer biology

(2012) Andrei Zinovyev et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

COMPADRE: an R and web resource for pathway activity analysis by component decompositions

(2012) Roberto-Rafael Ramos-Rodriguez et al.   BIOINFORMATICS

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Mechanism and relevance of EWS/FLI-mediated transcriptional repression in Ewing sarcoma

(2012) S Sankar et al.   ONCOGENE

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Combined Gene Expression and Genomic Profiling Define Two Intrinsic Molecular Subtypes of Urothelial Carcinoma and Gene Signatures for Molecular Grading and Outcome

(2010) David Lindgren et al.   CANCER RESEARCH

A transcriptional profiling meta-analysis reveals a core EWS-FLI gene expression signature

(2010) Jeffrey D. Hancock et al.   CELL CYCLE

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Next-generation genomics: an integrative approach

(2010) R. David Hawkins et al.   NATURE REVIEWS GENETICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE