Sebastian Will

Orcid: 0000-0002-2376-9205

Affiliations:
  • University Vienna, Department Theoretical Chemistry, Austria
  • University of Leipzig, Department of Computer Science, Germany


According to our database1, Sebastian Will authored at least 69 papers between 1998 and 2024.

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Bibliography

2024
Infrared: a declarative tree decomposition-powered framework for bioinformatics.
Algorithms Mol. Biol., December, 2024

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.
Algorithms Mol. Biol., December, 2024

RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions.
Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

Hot off the Press: Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise.
Proceedings of the Genetic and Evolutionary Computation Conference Companion, 2024

2023
Automated design of dynamic programming schemes for RNA folding with pseudoknots.
Algorithms Mol. Biol., December, 2023

SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles.
Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

Runtime Analyses of Multi-Objective Evolutionary Algorithms in the Presence of Noise.
Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence, 2023

2022
Bi-alignments with affine gaps costs.
Algorithms Mol. Biol., 2022

2020
The locality dilemma of Sankoff-like RNA alignments.
Bioinform., 2020

Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.
Algorithms Mol. Biol., 2020

2019
IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.
J. Bioinform. Comput. Biol., 2019

Fixed-parameter tractable sampling for RNA design with multiple target structures.
BMC Bioinform., 2019

Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs.
Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2019

Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction.
Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019), 2019

2018
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
Nucleic Acids Res., 2018

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures.
Bioinform., 2018

2017
Design of Artificial Riboswitches as Biosensors.
Sensors, 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Nucleic Acids Res., 2017

Tractable RNA-ligand interaction kinetics.
BMC Bioinform., 2017

Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice.
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Impacts of an Intersection Assistance System: Social Interaction between Drivers and Motorcyclists.
Proceedings of the 9th International Conference on Computer and Automation Engineering, 2017

2016
Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.
Algorithms Mol. Biol., 2016

2015
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.
Bioinform., 2015

Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014
Local Exact Pattern Matching for Non-FixedRNA Structures.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Simultaneous Alignment and Folding of Protein Sequences.
J. Comput. Biol., 2014

ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs.
BMC Bioinform., 2014

Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2014

A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems.
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Comparative Detection of Processed Small RNAs in Archaea.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

2013
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Algorithms Mol. Biol., 2013

The Trouble with Long-Range Base Pairs in RNA Folding.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics.
Proceedings of the Research in Computational Molecular Biology, 2013

2012
CARNA - alignment of RNA structure ensembles.
Nucleic Acids Res., 2012

Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs.
Proceedings of the Research in Computational Molecular Biology, 2012

Exact Pattern Matching for RNA Structure Ensembles.
Proceedings of the Research in Computational Molecular Biology, 2012

Local Exact Pattern Matching for Non-fixed RNA Structures.
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

2011
Structator: fast index-based search for RNA sequence-structure patterns.
BMC Bioinform., 2011

2010
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA.
Nucleic Acids Res., 2010

Lifting Prediction to Alignment of RNA Pseudoknots.
J. Comput. Biol., 2010

Sparsification of RNA structure prediction including pseudoknots.
Algorithms Mol. Biol., 2010

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding.
Proceedings of the Research in Computational Molecular Biology, 2010

Alignnment of RNA with Structures of Unlimited Complexity.
Proceedings of the Workshop on Constraint Based Methods for Bioinformatics, 2010

A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies.
Proceedings of the Principles and Practice of Constraint Programming - CP 2010, 2010

2009
Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains
CoRR, 2009

CPSP-web-tools: a server for 3D lattice protein studies.
Bioinform., 2009

Lightweight comparison of RNAs based on exact sequence-structure matches.
Bioinform., 2009

2008
Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination.
Constraints An Int. J., 2008

Introduction to the Special Issue on Bioinformatics and Constraints.
Constraints An Int. J., 2008

CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies.
BMC Bioinform., 2008

RNAalifold: improved consensus structure prediction for RNA alignments.
BMC Bioinform., 2008

Structural Local Multiple Alignment of RNA.
Proceedings of the German Conference on Bioinformatics, 2008

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots.
Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering.
PLoS Comput. Biol., 2007

Decomposition During Search for Propagation-Based Constraint Solvers
CoRR, 2007

2006
A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models.
Constraints An Int. J., 2006

2005
SECISDesign: a server to design SECIS-elements within the coding sequence.
Bioinform., 2005

2004
Local Sequence-structure Motifs in Rna.
J. Bioinform. Comput. Biol., 2004

2003
A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods.
Proceedings of the Logic Programming, 19th International Conference, 2003

2002
Excluding Symmetries in Constraint-Based Search.
Constraints An Int. J., 2002

Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC.
Proceedings of the Combinatorial Pattern Matching, 12th Annual Symposium, 2001

Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores.
Proceedings of the Principles and Practice of Constraint Programming, 2001

2000
Constraintbasierte Raumplanung für Universitäten.
Proceedings of the 14. Workshop Logische Programmierung, 2000

Classroom Assignment Using Constraint Logic Programming.
Proceedings of the Second International Conference on the Practical Application of Constraint Technologies and Logic Programming, 2000

1999
Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets.
Bioinform., 1999

Algorithmic approach to quantifying the hydrophobic force contribution in protein folding.
Proceedings of the German Conference on Bioinformatics, 1999

1998
Structure prediction in an HP-type lattice with an extended alphabet.
Proceedings of the German Conference on Bioinformatics, 1998


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