Software validation with CASE-TOOLS. - Johannes Rainer (SAFECOMP, 1993)

Client-Server environment for high-performance gene expression data analysis. - Alexander Sturn; Bernhard Mlecnik; Roland Pieler; Johannes Rainer; Thomas Truskaller; Zlatko Trajanoski (Bioinform., 2003)

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. - Johannes Rainer; Fátima Sánchez-Cabo; Gernot Stocker; Alexander Sturn; Zlatko Trajanoski (Nucleic Acids Res., 2006)

FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees. - Johannes Rainer; Daniel Taliun; Yuri D'Elia; Cristian Pattaro; Francisco S. Domingues; Christian X. Weichenberger (Bioinform., 2016)

ensembldb: an R package to create and use Ensembl-based annotation resources. - Johannes Rainer; Laurent Gatto; Christian X. Weichenberger (Bioinform., 2019)

Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees. - Christian X. Weichenberger; Johannes Rainer; Cristian Pattaro; Peter P. Pramstaller; Francisco S. Domingues (Bioinform., 2019)

MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. - Thomas Naake; Johannes Rainer; Wolfgang Huber (Bioinform., 2023)

Eleven quick tips for writing a Bioconductor package. - Charlotte Soneson; Lori A. Shepherd; Marcel Ramos; Kevin C. Rue-Albrecht; Johannes Rainer; Hervé Pagès; Vincent J. Carey (PLoS Comput. Biol., 2025)

SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python. - Marilyn De Graeve; Wout Bittremieux; Thomas Naake; Carolin Huber; Matthias Anagho-Mattanovich; Nils Hoffmann; Pierre Marchal; Victor Chrone; Philippine Louail; Helge Hecht; Michael Witting; Johannes Rainer (J. Open Source Softw., 2025)