| 2026 | ALENEX | Smaller and More Flexible Cuckoo Filters. | Johanna Elena Schmitz, Jens Zentgraf, Sven Rahmann |
| 2026 | WABI | Designing Exact Spaced Seed Filters Based on Combined Hit and Coverage Information. | Moein Karami, Jens Zentgraf, Sven Rahmann |
| 2026 | WABI | DivQuant: Estimation of Species Richness and Entropy from Small Samples. | Johanna Elena Schmitz, Sven Rahmann |
| 2025 | WABI | Design of Worst-Case-Optimal Spaced Seeds. | Jens Zentgraf, Sven Rahmann |
| 2024 | RECOMB | Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. | Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier |
| 2024 | WABI | Swiftly Identifying Strongly Unique k-Mers. | Jens Zentgraf, Sven Rahmann |
| 2022 | WABI | Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables. | Jens Zentgraf, Sven Rahmann |
| 2020 | ALENEX | Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables. | Jens Zentgraf, Henning Timm, Sven Rahmann |
| 2020 | WABI | Fast Lightweight Accurate Xenograft Sorting. | Jens Zentgraf, Sven Rahmann |
| 2019 | SISAP | Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. | Bianca K. Stcker, Till Schfer, Petra Mutzel, Johannes Kster, Nils M. Kriege, Sven Rahmann |
| 2018 | WABI | Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts. | Till Hartmann, Sven Rahmann |
| 2017 | WABI | Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping. | Jens Quedenfeld, Sven Rahmann |
| 2016 | WABI | A Hybrid Parameter Estimation Algorithm for Beta Mixtures and Applications to Methylation State Classification. | Christopher Schrder, Sven Rahmann |
| 2014 | WABI | An Online Peak Extraction Algorithm for Ion Mobility Spectrometry Data. | Dominik Kopczynski, Sven Rahmann |
| 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 | COCOON | Structural Identifiability in Low-Rank Matrix Factorization. | Epameinondas Fritzilas, Yasmn . Ros-Sols, Sven Rahmann |
| 2008 | CPM | Probabilistic Arithmetic Automata and Their Application to Pattern Matching Statistics. | Tobias Marschall, Sven Rahmann |
| 2008 | WABI | Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata. | Inke Herms, Sven Rahmann |
| 2006 | CPM | Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms. | Sven Rahmann |
| 2006 | ISMB | Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. | Alexander Schliep, Sven Rahmann |
| 2006 | RECOMB | Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. | Hans-Michael Kaltenbach, Sebastian Bcker, Sven Rahmann |
| 2006 | WABI | Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning. | Srgio A. de Carvalho, Sven Rahmann |
| 2006 | WABI | Integer Linear Programs for Discovering Approximate Gene Clusters. | Sven Rahmann, Gunnar W. Klau |
| 2005 | SAC | Editorial message: special track on bioinformatics. | Mathew J. Palakal, Sven Rahmann, Birong Liao |
| 2004 | ISMB | Functional inference from non-random distributions of conserved predicted transcription factor binding sites. | Christoph Dieterich, Sven Rahmann, Martin Vingron |
| 2004 | ISMB | Optimal robust non-unique probe selection using Integer Linear Programming. | Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert |
| 2003 | ECCB | The shortest common supersequence problem in a microarray production setting. | Sven Rahmann |
| 2003 | WABI | Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology. | Sven Rahmann |
| 2002 | WABI | Rapid Large-Scale Oligonucleotide Selection for Microarrays. | Sven Rahmann |
| 2001 | ICALP | Combinatorics of Periods in Strings. | Eric Rivals, Sven Rahmann |
| 2001 | ISMB | Non-symmetric score matrices and the detection of homologous transmembrane proteins. | Tobias Mller, Sven Rahmann, Marc Rehmsmeier |
| 2000 | CPM | Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. | Sven Rahmann, Eric Rivals |