CLEAN: CLustering Enrichment ANalysis. - Johannes M. Freudenberg; Vineet K. Joshi; Zhen Hu; Mario Medvedovic (BMC Bioinform., 2009)

A semi-parametric Bayesian model for unsupervised differential co-expression analysis. - Johannes M. Freudenberg; Siva Sivaganesan; Michael Wagner 010; Mario Medvedovic (BMC Bioinform., 2010)

Generalized random set framework for functional enrichment analysis using primary genomics datasets. - Johannes M. Freudenberg; Siva Sivaganesan; Mukta Phatak; Kaustubh Shinde; Mario Medvedovic (Bioinform., 2011)

WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results. - Vineet K. Joshi; Johannes M. Freudenberg; Zhen Hu; Mario Medvedovic (Source Code Biol. Medicine, 2011)

Evaluation of Analytical Methods for Connectivity Map Data. - Jie Cheng; Qing Xie 007; Vinod Kumar; Mark Hurle; Johannes M. Freudenberg; Lun Yang; Pankaj Agarwal (Pacific Symposium on Biocomputing, 2013)

Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules. - Jing Chen 021; Zhen Hu; Mukta Phatak; John Reichard; Johannes M. Freudenberg; Siva Sivaganesan; Mario Medvedovic (PLoS Comput. Biol., 2013)

Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands. - Johannes M. Freudenberg; Ian Dunham; Philippe Sanseau; Deepak K. Rajpal (BMC Bioinform., 2018)