pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression. - Simona Cristea; Jack Kuipers; Niko Beerenwinkel (RECOMB, 2016)

pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. - Simona Cristea; Jack Kuipers; Niko Beerenwinkel (J. Comput. Biol., 2017)

ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. - Dana Silverbush; Simona Cristea; Gali Yanovich; Tamar Geiger; Niko Beerenwinkel; Roded Sharan (RECOMB, 2018)