| 2026 | WABI | PRISM: Partition-Function Decomposition into Structural Classes for Hierarchically Constrained RNA Pseudoknot Ensembles. | Mateo Gray, Sebastian Will, Hosna Jabbari |
| 2025 | SLE | A Model-Driven Approach to Design, Generation, and Deployment of GUI Component Libraries. | Arkadii Gerasimov, Nico Jansen, Judith Michael, Bernhard Rumpe, Sebastian Will |
| 2025 | WABI | Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. | Mateo Gray, Sebastian Will, Hosna Jabbari |
| 2024 | GECCO | Hot off the Press: Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. | Matthieu Dinot, Benjamin Doerr, Ulysse Hennebelle, Sebastian Will |
| 2024 | WABI | RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. | Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty |
| 2023 | IJCAI | Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. | Matthieu Dinot, Benjamin Doerr, Ulysse Hennebelle, Sebastian Will |
| 2023 | WABI | SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. | Mateo Gray, Sebastian Will, Hosna Jabbari |
| 2022 | WABI | Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. | Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty |
| 2019 | WABI | Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. | Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen |
| 2018 | RECOMB | Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. | Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will |
| 2017 | WABI | Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. | Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will |
| 2015 | WABI | Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction. | Sebastian Will, Hosna Jabbari |
| 2014 | WABI | A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. | Sebastian Will, Peter F. Stadler |
| 2013 | RECOMB | SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. | Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Mhl, Rolf Backofen |
| 2012 | CPM | Local Exact Pattern Matching for Non-fixed RNA Structures. | Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Mhl, Christina Schmiedl, Sebastian Will |
| 2012 | RECOMB | Exact Pattern Matching for RNA Structure Ensembles. | Christina Schmiedl, Mathias Mhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen |
| 2012 | RECOMB | Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. | Sebastian Will, Michael Yu, Bonnie Berger |
| 2010 | CP | A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies. | Alessandro Dal Pal, Mathias Mhl, Sebastian Will |
| 2010 | ICLP | Alignnment of RNA with Structures of Unlimited Complexity. | Alessandro Dal Pal, Mathias Mhl, Sebastian Will |
| 2010 | RECOMB | Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. | Raheleh Salari, Mathias Mhl, Sebastian Will, Sleyman Cenk Sahinalp, Rolf Backofen |
| 2010 | WABI | Sparsification of RNA Structure Prediction Including Pseudoknots. | Mathias Mhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Sleyman Cenk Sahinalp |
| 2009 | RECOMB | Lifting Prediction to Alignment of RNA Pseudoknots. | Mathias Mhl, Sebastian Will, Rolf Backofen |
| 2009 | RECOMB | Simultaneous Alignment and Folding of Protein Sequences. | Jrme Waldisphl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger |
| 2008 | CPM | Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. | Mathias Mhl, Sebastian Will, Rolf Backofen |
| 2003 | ICLP | A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods. | Rolf Backofen, Sebastian Will |
| 2002 | PSB | Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice. | Sebastian Will |
| 2001 | CP | Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. | Rolf Backofen, Sebastian Will |
| 2001 | CPM | Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC. | Rolf Backofen, Sebastian Will |
| 1999 | CP | Excluding Symmetries in Constraint-Based Search. | Rolf Backofen, Sebastian Will |