NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing. - Lennart F. Johansson; Hendrik A. de Weerd; Eddy N. de Boer; Freerk van Dijk; Gerard J. te Meerman; Rolf Sijmons; Birgit Sikkema-Raddatz; Morris A. Swertz (BMC Bioinform., 2018)

miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer. - Emmy Borgmästars; Hendrik A. de Weerd; Zelmina Lubovac-Pilav; Malin Sund (BMC Bioinform., 2019)

MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks. - Hendrik A. de Weerd; Tejaswi V. S. Badam; David Martínez-Enguita; Julia Åkesson; Daniel Muthas; Mika Gustafsson; Zelmina Lubovac-Pilav (Bioinform., 2020)

Novel methods and software for disease module inference. - Hendrik A. de Weerd (2023)

Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules. - Hendrik A. de Weerd; Dimitri Guala; Mika Gustafsson; Jane Synnergren; Jesper Tegnér; Zelmina Lubovac-Pilav; Rasmus Magnusson (Patterns, 2024)