Parallel algorithms for slicing based final placement - Henning Spruth; Georg Sigl; Frank Johannes (Forschungsberichte, TU Munich, 1992)

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. - Frank Johannes; René Wardenaar; Maria Colomé-Tatché; Florence Mousson; Petra de Graaf; Michal Mokry; Victor Guryev; H. Th. Marc Timmers; Edwin Cuppen; Ritsert C. Jansen (Bioinform., 2010)

MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. - Michael Seifert; Sandra Cortijo; Maria Colomé-Tatché; Frank Johannes; François Roudier; Vincent Colot (Bioinform., 2012)

histoneHMM: Differential analysis of histone modifications with broad genomic footprints. - Matthias Heinig; Maria Colomé-Tatché; Aaron Taudt; Carola Rintisch; Sebastian Schafer; Michal Pravenec; Norbert Hübner; Martin Vingron; Frank Johannes (BMC Bioinform., 2015)

Computational tools for plant small RNA detection and categorization. - Lionel Morgado; Frank Johannes (Briefings Bioinform., 2019)

Recursive Convolutional Neural Networks for Epigenomics. - Aikaterini Symeonidi; Anguelos Nicolaou; Frank Johannes; Vincent Christlein (ICPR, 2020)