| 2024 | FUSION | Reproducible Mapping of Tabular Data into Semantic Knowledge Graphs with OntoWeaver and BioCypher. | Johann Dro, Claire Laudy, Sebastian Lobentanzer, Marko Baric, Ekaterina Gaydukova, Benno Schwikowski |
| 2004 | ISMB | Predicting protein-peptide interactions via a network-based motif sampler. | David J. Reiss, Benno Schwikowski |
| 2003 | RECOMB | Towards optimally multiplexed applications of universal DNA tag systems. | Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini |
| 2002 | GI | Algorithmic Challenges in Mass Spectrometry and Systems Biology. | Benno Schwikowski |
| 2002 | ISMB | Discovering regulatory and signalling circuits in molecular interaction networks. | Trey Ideker, Owen Ozier, Benno Schwikowski, Andrew F. Siegel |
| 2002 | RECOMB | The restriction scaffold problem. | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir |
| 2000 | ISMB | An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. | Mathieu Blanchette, Benno Schwikowski, Martin Tompa |
| 2000 | RECOMB | Universal DNA tag systems: a combinatorial design scheme. | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini |
| 1997 | RECOMB | The deferred path heuristic for the generalized tree alignment problem. | Benno Schwikowski, Martin Vingron |