| 2025 | WABI | DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. | Ali Ghaffaari, Alexander Schnhuth, Tobias Marschall |
| 2022 | WABI | Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. | Konstantinn Bonnet, Tobias Marschall, Daniel Doerr |
| 2018 | RECOMB | Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. | Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz |
| 2017 | CiE | A Guided Tour to Computational Haplotyping. | Gunnar W. Klau, Tobias Marschall |
| 2015 | BTW | Genome sequence analysis with monetdb: a case study on ebola virus diversity. | Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schnhuth, Tobias Marschall, Ying Zhang |
| 2014 | RECOMB | WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. | Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schnhuth |
| 2014 | RECOMB | Viral Quasispecies Assembly via Maximal Clique Enumeration. | Armin Tpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schnhuth, Niko Beerenwinkel |
| 2012 | ALENEX | Solving the Minimum String Cover Problem. | Stefan Canzar, Tobias Marschall, Sven Rahmann, Chris Schwiegelshohn |
| 2010 | LATA | Exact Analysis of Horspool's and Sunday's Pattern Matching Algorithms with Probabilistic Arithmetic Automata. | Tobias Marschall, Sven Rahmann |
| 2010 | WABI | Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size. | Tobias Marschall, Sven Rahmann |
| 2009 | GECCO | Modeling evolutionary fitness for DNA motif discovery. | Sven Rahmann, Tobias Marschall, Frank Behler, Oliver Kramer |
| 2008 | CPM | Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics. | Tobias Marschall, Sven Rahmann |
| 2006 | ICPR | Automatic Detection of Song Changes in Music Mixes Using Stochastic Models. | Thomas Pltz, Gernot A. Fink, Peter Husemann, Sven Kanies, Kai Lienemann, Tobias Marschall, Marcel Martin, Lars Schillingmann, Matthias Steinrcken, Henner Sudek |