Transcription factor site dependencies in human, mouse and rat genomes. - Andrija Tomovic; Michael B. Stadler; Edward J. Oakeley (BMC Bioinform., 2009)

DNA-binding factors shape the mouse methylome at distal regulatory regions. - Michael B. Stadler; Rabih Murr; Lukas Burger; Robert Ivanek; Florian Lienert; Anne Schöler; Christiane Wirbelauer; Edward J. Oakeley; Dimos Gaidatzis; Vijay K. Tiwari; Dirk Schübeler (Nat., 2011)

Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions. - Michael B. Stadler; Rabih Murr; Lukas Burger; Robert Ivanek; Florian Lienert; Anne Schöler; Erik van Nimwegen; Christiane Wirbelauer; Edward J. Oakeley; Dimos Gaidatzis; Vijay K. Tiwari; Dirk Schübeler (Nat., 2012)

QuasR: quantification and annotation of short reads in R. - Dimos Gaidatzis; Anita Lerch; Florian Hahne; Michael B. Stadler (Bioinform., 2015)

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. - Charlotte Soneson; Avi Srivastava; Rob Patro; Michael B. Stadler (PLoS Comput. Biol., 2021)

monaLisa: an R/Bioconductor package for identifying regulatory motifs. - Dania Machlab; Lukas Burger; Charlotte Soneson; Filippo M. Rijli; Dirk Schübeler; Michael B. Stadler (Bioinform., 2022)

einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data. - Charlotte Soneson; Vytautas Iesmantavicius; Daniel Hess; Michael B. Stadler; Jan Seebacher (J. Open Source Softw., 2023)

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. - Silvia Barbiero; Charlotte Soneson; Prisca Liberali; Michael B. Stadler (J. Open Source Softw., 2025)