Web-TCGA: an online platform for integrated analysis of molecular cancer data sets. - Mario Deng; Johannes Brägelmann; Joachim L. Schultze; Sven Perner (BMC Bioinform., 2016)

FirebrowseR: an R client to the Broad Institute's Firehose Pipeline. - Mario Deng; Johannes Brägelmann; Ivan Kryukov; Nuno Saraiva-Agostinho; Sven Perner (Database J. Biol. Databases Curation, 2017)

A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets. - Johannes Brägelmann; Justo Lorenzo Bermejo (Briefings Bioinform., 2019)

Histo-Miner: Deep Learning based Tissue Features Extraction Pipeline from H&E Whole Slide Images of Cutaneous Squamous Cell Carcinoma. - Lucas Sancere; Carina Lorenz; Doris Helbig; Oana-Diana Persa; Sonja Dengler; Alexander Kreuter; Martim Laimer; Anne Fröhlich; Jennifer Landsberg; Johannes Brägelmann; Katarzyna Bozek (CoRR, 2025)