Structure prediction in an HP-type lattice with an extended alphabet. - Rolf Backofen; Sebastian Will (German Conference on Bioinformatics, 1998)

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. - Rolf Backofen; Sebastian Will; Peter Clote (German Conference on Bioinformatics, 1999)

Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. - Rolf Backofen; Sebastian Will; Erich Bornberg-Bauer (Bioinform., 1999)

Classroom Assignment Using Constraint Logic Programming. - Slim Abdennadher; Matthias Saft; Sebastian Will (PACPL, 2000)

Constraintbasierte Raumplanung für Universitäten. - Slim Abdennadher; Matthias Saft; Sebastian Will (WLP, 2000)

Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. - Rolf Backofen; Sebastian Will (CP, 2001)

Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC. - Rolf Backofen; Sebastian Will (CPM, 2001)

Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice. - Sebastian Will (Pacific Symposium on Biocomputing, 2002)

Excluding Symmetries in Constraint-Based Search. - Rolf Backofen; Sebastian Will (Constraints An Int. J., 2002)

A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods. - Rolf Backofen; Sebastian Will (ICLP, 2003)

Local Sequence-structure Motifs in Rna. - Rolf Backofen; Sebastian Will (J. Bioinform. Comput. Biol., 2004)

SECISDesign: a server to design SECIS-elements within the coding sequence. - Anke Busch; Sebastian Will; Rolf Backofen (Bioinform., 2005)

A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models. - Rolf Backofen; Sebastian Will (Constraints An Int. J., 2006)

Decomposition During Search for Propagation-Based Constraint Solvers - Martin Mann; Guido Tack; Sebastian Will (CoRR, 2007)

Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. - Sebastian Will; Kristin Reiche; Ivo L. Hofacker; Peter F. Stadler; Rolf Backofen (PLoS Comput. Biol., 2007)

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. - Mathias Möhl; Sebastian Will; Rolf Backofen (CPM, 2008)

Structural Local Multiple Alignment of RNA. - Wolfgang Otto 001; Sebastian Will; Rolf Backofen (German Conference on Bioinformatics, 2008)

RNAalifold: improved consensus structure prediction for RNA alignments. - Stephan H. Bernhart; Ivo L. Hofacker; Sebastian Will; Andreas R. Gruber; Peter F. Stadler (BMC Bioinform., 2008)

CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies. - Martin Mann; Sebastian Will; Rolf Backofen (BMC Bioinform., 2008)

Introduction to the Special Issue on Bioinformatics and Constraints. - Alessandro Dal Palù; Agostino Dovier; Sebastian Will (Constraints An Int. J., 2008)

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination. - Sebastian Will; Anke Busch; Rolf Backofen (Constraints An Int. J., 2008)

Lightweight comparison of RNAs based on exact sequence-structure matches. - Steffen Heyne; Sebastian Will; Michael Beckstette; Rolf Backofen (Bioinform., 2009)

CPSP-web-tools: a server for 3D lattice protein studies. - Martin Mann; Cameron Smith; Mohamad Rabbath; Marlien Edwards; Sebastian Will; Rolf Backofen (Bioinform., 2009)

Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains - Martin Mann; Rolf Backofen; Sebastian Will (CoRR, 2009)

A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies. - Alessandro Dal Palù; Mathias Möhl; Sebastian Will (CP, 2010)

Alignnment of RNA with Structures of Unlimited Complexity. - Alessandro Dal Palù; Mathias Möhl; Sebastian Will (WCB@ICLP, 2010)

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. - Raheleh Salari; Mathias Möhl; Sebastian Will; Süleyman Cenk Sahinalp; Rolf Backofen (RECOMB, 2010)

Sparsification of RNA structure prediction including pseudoknots. - Mathias Möhl; Raheleh Salari; Sebastian Will; Rolf Backofen; Süleyman Cenk Sahinalp (Algorithms Mol. Biol., 2010)

Lifting Prediction to Alignment of RNA Pseudoknots. - Mathias Möhl; Sebastian Will; Rolf Backofen (J. Comput. Biol., 2010)

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. - Cameron Smith; Steffen Heyne; Andreas S. Richter; Sebastian Will; Rolf Backofen (Nucleic Acids Res., 2010)

Structator: fast index-based search for RNA sequence-structure patterns. - Fernando Meyer; Stefan Kurtz; Rolf Backofen; Sebastian Will; Michael Beckstette (BMC Bioinform., 2011)

Local Exact Pattern Matching for Non-fixed RNA Structures. - Mika Amit; Rolf Backofen; Steffen Heyne; Gad M. Landau; Mathias Möhl; Christina Schmiedl; Sebastian Will (CPM, 2012)

Exact Pattern Matching for RNA Structure Ensembles. - Christina Schmiedl; Mathias Möhl; Steffen Heyne; Mika Amit; Gad M. Landau; Sebastian Will; Rolf Backofen (RECOMB, 2012)

Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. - Sebastian Will; Michael Yu; Bonnie Berger (RECOMB, 2012)

CARNA - alignment of RNA structure ensembles. - Dragos Alexandru Sorescu; Mathias Möhl; Martin Mann; Rolf Backofen; Sebastian Will (Nucleic Acids Res., 2012)

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. - Sebastian Will; Christina Schmiedl; Milad Miladi; Mathias Möhl; Rolf Backofen (RECOMB, 2013)

The Trouble with Long-Range Base Pairs in RNA Folding. - Fabian Amman; Stephan H. Bernhart; Gero Doose; Ivo L. Hofacker; Jing Qin 006; Peter F. Stadler; Sebastian Will (BSB, 2013)

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. - Sebastian Will; Michael F. Siebauer; Steffen Heyne; Jan Engelhardt; Peter F. Stadler; Kristin Reiche; Rolf Backofen (Algorithms Mol. Biol., 2013)

Comparative Detection of Processed Small RNAs in Archaea. - Christian Höner zu Siederdissen; Sarah Berkemer; Fabian Amman; Axel Wintsche; Sebastian Will; Sonja J. Prohaska; Peter F. Stadler (IWBBIO, 2014)

A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. - Sebastian Will; Peter F. Stadler (WABI, 2014)

Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115. - Hugo W. Schneider; Sebastian Bartschat; Gero Doose; Lucas Maciel 001; Erick Pizani; Marcelo Bassani; Fernando Araripe Torres; Sebastian Will; Tainá Raiol; Marcelo M. Brigido; Maria Emília Telles Walter; Peter F. Stadler (BSB, 2014)

ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. - Christina Otto; Mathias Möhl; Steffen Heyne; Mika Amit; Gad M. Landau; Rolf Backofen; Sebastian Will (BMC Bioinform., 2014)

Simultaneous Alignment and Folding of Protein Sequences. - Jérôme Waldispühl; Charles W. O'Donnell; Sebastian Will; Srinivas Devadas; Rolf Backofen; Bonnie Berger (J. Comput. Biol., 2014)

Local Exact Pattern Matching for Non-FixedRNA Structures. - Mika Amit; Rolf Backofen; Steffen Heyne; Gad M. Landau; Mathias Möhl; Christina Otto; Sebastian Will (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction. - Sebastian Will; Hosna Jabbari (WABI, 2015)

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. - Sebastian Will; Christina Otto; Milad Miladi; Mathias Möhl; Rolf Backofen (Bioinform., 2015)

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction. - Sebastian Will; Hosna Jabbari (Algorithms Mol. Biol., 2016)

Impacts of an Intersection Assistance System: Social Interaction between Drivers and Motorcyclists. - Michael Walz; Christian Lehsing; Klaus Bengler; Sebastian Will; Magdalena Sich (ICCAE, 2017)

Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. - Hosna Jabbari; Ian Wark; Carlo Montemagno; Sebastian Will (WABI, 2017)

Tractable RNA-ligand interaction kinetics. - Felix Kühnl; Peter F. Stadler; Sebastian Will (BMC Bioinform., 2017)

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. - Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben; Florian Eggenhofer; Torsten Houwaart; Bérénice Batut; Pavankumar Videm; Andrea Bagnacani; Markus Wolfien; Steffen Lott; et al. (Nucleic Acids Res., 2017)

Design of Artificial Riboswitches as Biosensors. - Sven Findeiß; Maja Etzel; Sebastian Will; Mario Mörl; Peter F. Stadler (Sensors, 2017)

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. - Hosna Jabbari; Ian Wark; Carlo Montemagno; Sebastian Will (Bioinform., 2018)

Freiburg RNA tools: a central online resource for RNA-focused research and teaching. - Martin Raden; Syed M. Ali; Omer S. Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A. Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; et al. (Nucleic Acids Res., 2018)

Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction. - Rick Gelhausen; Sebastian Will; Ivo L. Hofacker; Rolf Backofen; Martin Raden (BIOINFORMATICS, 2019)

Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. - Maria Waldl; Sebastian Will; Michael T. Wolfinger; Ivo L. Hofacker; Peter F. Stadler (CIBB, 2019)

Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. - Milad Miladi; Martin Raden; Sebastian Will; Rolf Backofen (WABI, 2019)

Fixed-parameter tractable sampling for RNA design with multiple target structures. - Stefan Hammer; Wei Wang 263; Sebastian Will; Yann Ponty (BMC Bioinform., 2019)

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. - Rick Gelhausen; Sebastian Will; Ivo L. Hofacker; Rolf Backofen; Martin Raden (J. Bioinform. Comput. Biol., 2019)

Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. - Milad Miladi; Martin Raden; Sebastian Will; Rolf Backofen (Algorithms Mol. Biol., 2020)

The locality dilemma of Sankoff-like RNA alignments. - Teresa Müller; Milad Miladi; Frank Hutter; Ivo L. Hofacker; Sebastian Will; Rolf Backofen (Bioinform., 2020)

Bi-alignments with affine gaps costs. - Peter F. Stadler; Sebastian Will (Algorithms Mol. Biol., 2022)

Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. - Matthieu Dinot; Benjamin Doerr; Ulysse Hennebelle; Sebastian Will (IJCAI, 2023)

SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. - Mateo Gray; Sebastian Will; Hosna Jabbari (WABI, 2023)

Automated design of dynamic programming schemes for RNA folding with pseudoknots. - Bertrand Marchand; Sebastian Will; Sarah J. Berkemer; Yann Ponty; Laurent Bulteau (Algorithms Mol. Biol., 2023)

Hot off the Press: Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. - Matthieu Dinot; Benjamin Doerr; Ulysse Hennebelle; Sebastian Will (GECCO Companion, 2024)

RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. - Kimon Boehmer; Sarah J. Berkemer; Sebastian Will; Yann Ponty (WABI, 2024)

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration. - Mateo Gray; Sebastian Will; Hosna Jabbari (Algorithms Mol. Biol., 2024)

Infrared: a declarative tree decomposition-powered framework for bioinformatics. - Hua-Ting Yao; Bertrand Marchand; Sarah J. Berkemer; Yann Ponty; Sebastian Will (Algorithms Mol. Biol., 2024)

A Model-Driven Approach to Design, Generation, and Deployment of GUI Component Libraries. - Arkadii Gerasimov; Nico Jansen; Judith Michael; Bernhard Rumpe; Sebastian Will (SLE, 2025)

Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. - Mateo Gray; Sebastian Will; Hosna Jabbari (WABI, 2025)