| 2019 | ESANN | Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings. | Stefan Mautner, Rolf Backofen, Fabrizio Costa |
| 2019 | WABI | Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. | Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen |
| 2016 | RECOMB | AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. | Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka |
| 2014 | ECCB | Scalable structural clustering of local RNA secondary structures. | Fabrizio Costa, Steffen Heyne, Dominic Rose, Rolf Backofen |
| 2013 | CP | Atom Mapping with Constraint Programming. | Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm |
| 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 |
| 2013 | WABI | Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. | Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler |
| 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 | CPM | Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. | Saad Sheikh, Rolf Backofen, Yann Ponty |
| 2012 | RECOMB | Exact Pattern Matching for RNA Structure Ensembles. | Christina Schmiedl, Mathias Mhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen |
| 2010 | PSB | Session Introduction. | Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Sleyman Cenk Sahinalp, Peter F. Stadler |
| 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 | CPM | Fast RNA Structure Alignment for Crossing Input Structures. | Rolf Backofen, Gad M. Landau, Mathias Mhl, Dekel Tsur, Oren Weimann |
| 2009 | CPM | Sparse RNA Folding: Time and Space Efficient Algorithms. | Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson |
| 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 |
| 2009 | WABI | biRNA: Fast RNA-RNA Binding Sites Prediction. | Hamidreza Chitsaz, Rolf Backofen, Sleyman Cenk Sahinalp |
| 2009 | WABI | Fast Prediction of RNA-RNA Interaction. | Raheleh Salari, Rolf Backofen, Sleyman Cenk Sahinalp |
| 2008 | CPM | Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. | Mathias Mhl, Sebastian Will, Rolf Backofen |
| 2006 | CPM | Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. | Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann |
| 2005 | CIBCB | A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction. | Sven Siebert, Rolf Backofen |
| 2005 | SPIRE | Normalized Similarity of RNA Sequences. | Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann |
| 2004 | CPM | Computational Design of New and Recombinant Selenoproteins. | Rolf Backofen, Anke Busch |
| 2004 | SPIRE | Fast Detection of Common Sequence Structure Patterns in RNAs. | Rolf Backofen, Sven Siebert |
| 2003 | ICLP | A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods. | Rolf Backofen, Sebastian Will |
| 2002 | STACS | On the Complexity of Protein Similarity Search under mRNA Structure Constraints. | Rolf Backofen, N. S. Narayanaswamy, Firas Swidan |
| 2001 | ACL | Introduction to Bioinformatics. | Rolf Backofen |
| 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 |
| 2001 | IDA | RNA-Sequence-Structure Properties and Selenocysteine Insertion. | Rolf Backofen |
| 2000 | CPM | An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC). | Rolf Backofen |
| 1999 | CP | Excluding Symmetries in Constraint-Based Search. | Rolf Backofen, Sebastian Will |
| 1998 | CP | Constraint Techniques for Solving the Protein Structure Prediction Problem. | Rolf Backofen |
| 1997 | CSL | Evolution as a Computational Engine. | Rolf Backofen, Peter Clote |
| 1996 | ECAI | Controlling Functional Uncertainty. | Rolf Backofen |
| 1994 | COLING | DISCO-An HPSG-based NLP System and its Application for Appointment Scheduling Project Note. | Hans Uszkoreit, Rolf Backofen, Stephan Busemann, Abdel Kader Diagne, Elizabeth A. Hinkelman, Walter Kasper, Bernd Kiefer, Hans-Ulrich Krieger, Klaus Netter, Gnter Neumann, Stephan Oepen, Stephen P. Spackman |
| 1993 | ACL | On the Decidability of Functional Uncertainty. | Rolf Backofen |
| 1993 | ACL | A Complete and Recursive Feature Theory. | Rolf Backofen, Gert Smolka |
| 1991 | WI | Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends. | Rolf Backofen, Harald Trost, Hans Uszkoreit |
| 1990 | KI | Towards the Integration of Functions, Relations and Types in an AI Programming Language. | Rolf Backofen, Lutz Euler, Gnther Grz |