Selection of organisms for the co-evolution-based study of protein interactions. - Dorota Herman; David Ochoa; David de Juan; Daniel Lopez; Alfonso Valencia; Florencio Pazos (BMC Bioinform., 2011)

Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration. - Dorota Herman; Christopher M. Thomas; Dov J. Stekel (BMC Syst. Biol., 2011)

Balancing Imbalanced Toxicity Models: Using MolBERT with Focal Loss. - Muhammad Arslan Masood; Samuel Kaski; Hugo Ceulemans; Dorota Herman; Markus Heinonen (AIDD@ICANN, 2024)

VitroBert: modeling DILI by pretraining BERT on in vitro data. - Muhammad Arslan Masood; Anamya Ajjolli Nagaraja; Katia Belaid; Natalie Mesens; Hugo Ceulemans; Samuel Kaski; Dorota Herman; Markus Heinonen (J. Cheminformatics, 2025)

Improving route development using convergent retrosynthesis planning. - Paula Torren-Peraire; Jonas Verhoeven; Dorota Herman; Hugo Ceulemans; Igor V. Tetko; Jörg K. Wegner (J. Cheminformatics, 2025)