CausalTrail: Testing hypothesis using causal Bayesian networks. - Daniel Stöckel; Florian Schmidt 003; Patrick Trampert; Hans-Peter Lenhof (F1000Research, 2015)

RegulatorTrail: a web service for the identification of key transcriptional regulators. - Tim Kehl; Lara Schneider; Florian Schmidt 003; Daniel Stöckel; Nico Gerstner; Christina Backes; Eckart Meese; Andreas Keller; Marcel H. Schulz; Hans-Peter Lenhof (Nucleic Acids Res., 2017)

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. - Florian Schmidt 003; Markus List; Engin Cukuroglu; Sebastian Köhler 001; Jonathan Göke; Marcel H. Schulz (Bioinform., 2018)

Predicting transcription factor binding using ensemble random forest models. - Fatemeh Behjati-Ardakani; Florian Schmidt 003; Marcel H. Schulz (F1000Research, 2018)

TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis. - Florian Schmidt 003; Fabian Kern; Peter Ebert; Nina Baumgarten; Marcel H. Schulz (Bioinform., 2019)

On the problem of confounders in modeling gene expression. - Florian Schmidt 003; Marcel H. Schulz (Bioinform., 2019)

Applications, challenges and new perspectives on the analysis of transcriptional regulation using ep. - Florian Schmidt 003 (2019)

Improved linking of motifs to their TFs using domain information. - Nina Baumgarten; Florian Schmidt 003; Marcel H. Schulz (Bioinform., 2020)

EpiRegio: analysis and retrieval of regulatory elements linked to genes. - Nina Baumgarten; Dennis Hecker; Sivarajan Karunanithi; Florian Schmidt 003; Markus List; Marcel H. Schulz (Nucleic Acids Res., 2020)

Machine learning for deciphering cell heterogeneity and gene regulation. - Michael Scherer; Florian Schmidt 003; Olga Lazareva; Jörn Walter; Jan Baumbach; Marcel H. Schulz; Markus List (Nat. Comput. Sci., 2021)