ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster. - Gernot Stocker; Dietmar Rieder; Zlatko Trajanoski (Bioinform., 2004)

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. - Gernot Stocker; Maria Fischer; Dietmar Rieder; Gabriela Bindea; Simon Kainz; Michael Oberstolz; James G. McNally; Zlatko Trajanoski (BMC Bioinform., 2009)

meRanTK: methylated RNA analysis ToolKit. - Dietmar Rieder; Thomas Amort; Elisabeth Kugler; Alexandra Lusser; Zlatko Trajanoski (Bioinform., 2016)

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. - Elias Tappeiner; Francesca Finotello; Pornpimol Charoentong; Clemens Mayer; Dietmar Rieder; Zlatko Trajanoski (Bioinform., 2017)

NeoFuse: predicting fusion neoantigens from RNA sequencing data. - Georgios Fotakis; Dietmar Rieder; Marlene Haider; Zlatko Trajanoski; Francesca Finotello (Bioinform., 2020)

Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. - Gregor Sturm; Tamás Szabó; Georgios Fotakis; Marlene Haider; Dietmar Rieder; Zlatko Trajanoski; Francesca Finotello (Bioinform., 2020)

MIO: microRNA target analysis system for immuno-oncology. - Pablo Monfort-Lanzas; Raphael Gronauer; Leonie Madersbacher; Christoph Schatz; Dietmar Rieder; Hubert Hackl (Bioinform., 2022)

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction. - Dietmar Rieder; Georgios Fotakis; Markus Ausserhofer; Rene Geyeregger; Wolfgang Paster; Zlatko Trajanoski; Francesca Finotello (Bioinform., 2022)