Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. - Ricardo de Matos Simoes; Shailesh Tripathi; Frank Emmert-Streib (BMC Syst. Biol., 2012)

Functional and genetic analysis of the colon cancer network. - Frank Emmert-Streib; Ricardo de Matos Simoes; Galina V. Glazko; Simon S. McDade; Benjamin Haibe-Kains; Andreas Holzinger; Matthias Dehmer; Frederick Campbell (BMC Bioinform., 2014)

Network signatures based on gene pair expression ratios improve classification and the analysis of muscle-invasive urothelial cancer. - Ricardo de Matos Simoes; Constantine Mitsiades; Kate E. Williamson; Frank Emmert-Streib (BIBM, 2015)

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. - Ricardo de Matos Simoes; Sabine Dalleau; Kate E. Williamson; Frank Emmert-Streib (BMC Syst. Biol., 2015)

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. - Alexey Stupnikov; Shailesh Tripathi; Ricardo de Matos Simoes; Darragh G. McArt; Manuel Salto-Tellez; Galina V. Glazko; Matthias Dehmer; Frank Emmert-Streib (Bioinform., 2016)