Program Partitioning Using Dynamic Trust Models. - Dan Søndergaard; Christian W. Probst; Christian Damsgaard Jensen; René Rydhof Hansen (Formal Aspects in Security and Trust, 2006)

Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. - Michael Knudsen; Dan Søndergaard; Claus Tofting-Olesen; Frederik T. Hansen; Ditlev Egeskov Brodersen; Christian N. S. Pedersen (Bioinform., 2016)

Prediction of Primary Tumors in Cancers of Unknown Primary. - Dan Søndergaard; Svend V. Nielsen; Christian N. S. Pedersen; Søren Besenbacher (J. Integr. Bioinform., 2017)

Recommendations for the packaging and containerizing of bioinformatics software. - Björn A. Grüning; Olivier Sallou; Pablo A. Moreno; Felipe da Veiga Leprevost; Hervé Ménager; Dan Søndergaard; Hannes L. Röst; Timo Sachsenberg; Brian O'Connor; Fábio Madeira; Victoria Dominguez Del Angel; Michael R. Crusoe; et al. (F1000Research, 2018)