Sebastian Will

83 papers A* 1A 3B 12C 9Misc 1Journal 42Unranked 14

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	RNA triplet repeats: improved algorithms for structure prediction and interactions. Algorithms Mol. Biol. Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty
2025	J	`jnl`	<tt>CREMSA</tt>: compressed indexing of (ultra) large multiple sequence alignments. Bioinform. Mikaël Salson, Arthur Boddaert, Awa Bousso Gueye, Laurent Bulteau, Yohan Hernandez-Courbevoie, Camille Marchet, Nan Pan, Sebastian Will, Yann Ponty
2025	B	`conf`	A Model-Driven Approach to Design, Generation, and Deployment of GUI Component Libraries. SLE Arkadii Gerasimov, Nico Jansen, Judith Michael, Bernhard Rumpe, Sebastian Will
2025	J	`jnl`	CParty: hierarchically constrained partition function of RNA pseudoknots. Bioinform. Mateo Gray, Luke Trinity, Ulrike Stege, Yann Ponty, Sebastian Will, Hosna Jabbari
2025	C	`conf`	Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. WABI Mateo Gray, Sebastian Will, Hosna Jabbari
2024	—	`conf`	Hot off the Press: Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. GECCO Companion Matthieu Dinot, Benjamin Doerr, Ulysse Hennebelle, Sebastian Will
2024	J	`jnl`	Infrared: a declarative tree decomposition-powered framework for bioinformatics. Algorithms Mol. Biol. Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, Sebastian Will
2024	C	`conf`	RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. WABI Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty
2024	J	`jnl`	SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration. Algorithms Mol. Biol. Mateo Gray, Sebastian Will, Hosna Jabbari
2023	J	`jnl`	Automated design of dynamic programming schemes for RNA folding with pseudoknots. Algorithms Mol. Biol. Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty, Laurent Bulteau
2023	A*	`conf`	Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. IJCAI Matthieu Dinot, Benjamin Doerr, Ulysse Hennebelle, Sebastian Will
2023	J	`jnl`	Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise. CoRR Matthieu Dinot, Benjamin Doerr, Ulysse Hennebelle, Sebastian Will
2023	C	`conf`	SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. WABI Mateo Gray, Sebastian Will, Hosna Jabbari
2022	C	`conf`	Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. WABI Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty
2022	J	`jnl`	Bi-alignments with affine gaps costs. Algorithms Mol. Biol. Peter F. Stadler, Sebastian Will
2020	J	`jnl`	Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms Mol. Biol. Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen
2020	J	`jnl`	The locality dilemma of Sankoff-like RNA alignments. Bioinform. Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen
2019	—	`conf`	Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. CIBB Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler
2019	—	`conf`	Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction. BIOINFORMATICS Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
2019	C	`conf`	Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. WABI Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen
2019	J	`jnl`	Fixed-parameter tractable sampling for RNA design with multiple target structures. BMC Bioinform. Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty
2019	J	`jnl`	IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. J. Bioinform. Comput. Biol. Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
2018	B	`conf`	Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will
2018	J	`jnl`	Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res. 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, Robert Kleinkauf, Steffen Lott, Mostafa M. Mohamed, Alexander Mattheis, Milad Miladi, Andreas S. Richter, Sebastian Will, Joachim Wolff, Patrick R. Wright, Rolf Backofen
2018	J	`jnl`	Knotty: efficient and accurate prediction of complex RNA pseudoknot structures. Bioinform. Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will
2017	J	`jnl`	Design of Artificial Riboswitches as Biosensors. Sensors Sven Findeiß, Maja Etzel, Sebastian Will, Mario Mörl, Peter F. Stadler
2017	—	`conf`	Impacts of an Intersection Assistance System: Social Interaction between Drivers and Motorcyclists. ICCAE Michael Walz, Christian Lehsing, Klaus Bengler, Sebastian Will, Magdalena Sich
2017	C	`conf`	Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice. WABI Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will
2017	J	`jnl`	The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 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, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen
2017	J	`jnl`	Tractable RNA-ligand interaction kinetics. BMC Bioinform. Felix Kühnl, Peter F. Stadler, Sebastian Will
2016	J	`jnl`	Sparse RNA folding revisited: space-efficient minimum free energy structure prediction. Algorithms Mol. Biol. Sebastian Will, Hosna Jabbari
2015	J	`jnl`	SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinform. Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, Rolf Backofen
2015	C	`conf`	Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction. WABI Sebastian Will, Hosna Jabbari
2014	C	`conf`	A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. WABI Sebastian Will, Peter F. Stadler
2014	—	`conf`	Comparative Detection of Processed Small RNAs in Archaea. IWBBIO Christian Höner zu Siederdissen, Sarah Berkemer, Fabian Amman, Axel Wintsche, Sebastian Will, Sonja J. Prohaska, Peter F. Stadler
2014	J	`jnl`	ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinform. Christina Otto, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, Sebastian Will
2014	—	`conf`	Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115. BSB Hugo W. Schneider, Sebastian Bartschat, Gero Doose, Lucas Maciel, Erick Pizani, Marcelo Bassani, Fernando Araripe Torres, Sebastian Will, Tainá Raiol, Marcelo M. Brigido, Maria Emília Telles Walter, Peter F. Stadler
2014	J	`jnl`	Local Exact Pattern Matching for Non-FixedRNA Structures. IEEE ACM Trans. Comput. Biol. Bioinform. Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, Sebastian Will
2014	J	`jnl`	Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2013	J	`jnl`	LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol. Biol. Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen
2013	B	`conf`	SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. RECOMB Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen
2013	—	`conf`	The Trouble with Long-Range Base Pairs in RNA Folding. BSB Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, Sebastian Will
2012	J	`jnl`	CARNA - alignment of RNA structure ensembles. Nucleic Acids Res. Dragos Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, Sebastian Will
2012	B	`conf`	Exact Pattern Matching for RNA Structure Ensembles. RECOMB Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen
2012	B	`conf`	Local Exact Pattern Matching for Non-fixed RNA Structures. CPM Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl, Sebastian Will
2012	B	`conf`	Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. RECOMB Sebastian Will, Michael Yu, Bonnie Berger
2012	—	`ed.`	Workshop on Constraint Based Methods for Bioinformatics, WCB10, Edinburgh, UK, July 21, 2010 WCB@ICLP Agostino Dovier, Alessandro Dal Palù, Sebastian Will
2011	J	`jnl`	Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinform. Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette
2010	A	`conf`	A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies. CP Alessandro Dal Palù, Mathias Möhl, Sebastian Will
2010	—	`conf`	Alignnment of RNA with Structures of Unlimited Complexity. WCB@ICLP Alessandro Dal Palù, Mathias Möhl, Sebastian Will
2010	J	`jnl`	Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acids Res. Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen
2010	J	`jnl`	Lifting Prediction to Alignment of RNA Pseudoknots. J. Comput. Biol. Mathias Möhl, Sebastian Will, Rolf Backofen
2010	C	`conf`	Sparsification of RNA Structure Prediction Including Pseudoknots. WABI Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
2010	J	`jnl`	Sparsification of RNA structure prediction including pseudoknots. Algorithms Mol. Biol. Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
2010	B	`conf`	Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen
2009	J	`jnl`	CPSP-web-tools: a server for 3D lattice protein studies. Bioinform. Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen
2009	J	`jnl`	Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains CoRR Martin Mann, Rolf Backofen, Sebastian Will
2009	B	`conf`	Lifting Prediction to Alignment of RNA Pseudoknots. RECOMB Mathias Möhl, Sebastian Will, Rolf Backofen
2009	J	`jnl`	Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinform. Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen
2009	B	`conf`	Simultaneous Alignment and Folding of Protein Sequences. RECOMB Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2008	J	`jnl`	CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies. BMC Bioinform. Martin Mann, Sebastian Will, Rolf Backofen
2008	J	`jnl`	Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination. Constraints An Int. J. Sebastian Will, Anke Busch, Rolf Backofen
2008	B	`conf`	Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. CPM Mathias Möhl, Sebastian Will, Rolf Backofen
2008	J	`jnl`	Introduction to the Special Issue on Bioinformatics and Constraints. Constraints An Int. J. Alessandro Dal Palù, Agostino Dovier, Sebastian Will
2008	—	`conf`	Lightweight Comparison of RNAs based on Exact Sequence-structure Matches. German Conference on Bioinformatics Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen
2008	J	`jnl`	RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinform. Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler
2008	—	`conf`	Structural Local Multiple Alignment of RNA. German Conference on Bioinformatics Wolfgang Otto, Sebastian Will, Rolf Backofen
2007	J	`jnl`	Decomposition During Search for Propagation-Based Constraint Solvers CoRR Martin Mann, Guido Tack, Sebastian Will
2007	J	`jnl`	Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
2006	J	`jnl`	A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models. Constraints An Int. J. Rolf Backofen, Sebastian Will
2005	J	`jnl`	SECISDesign: a server to design SECIS-elements within the coding sequence. Bioinform. Anke Busch, Sebastian Will, Rolf Backofen
2004	J	`jnl`	Local Sequence-structure Motifs in Rna. J. Bioinform. Comput. Biol. Rolf Backofen, Sebastian Will
2003	B	`conf`	A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods. ICLP Rolf Backofen, Sebastian Will
2002	Misc	`conf`	Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice. Pacific Symposium on Biocomputing Sebastian Will
2002	J	`jnl`	Excluding Symmetries in Constraint-Based Search. Constraints An Int. J. Rolf Backofen, Sebastian Will
2001	A	`conf`	Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. CP Rolf Backofen, Sebastian Will
2001	B	`conf`	Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC. CPM Rolf Backofen, Sebastian Will
2000	—	`conf`	Classroom Assignment Using Constraint Logic Programming. PACPL Slim Abdennadher, Matthias Saft, Sebastian Will
2000	—	`conf`	Constraintbasierte Raumplanung für Universitäten. WLP Slim Abdennadher, Matthias Saft, Sebastian Will
1999	—	`conf`	Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. German Conference on Bioinformatics Rolf Backofen, Sebastian Will, Peter Clote
1999	J	`jnl`	Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. Bioinform. Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer
1999	A	`conf`	Excluding Symmetries in Constraint-Based Search. CP Rolf Backofen, Sebastian Will
1998	—	`conf`	Structure prediction in an HP-type lattice with an extended alphabet. German Conference on Bioinformatics Rolf Backofen, Sebastian Will