Rolf Backofen
Orcid: 0000-0001-8231-3323Affiliations:
- University of Freiburg, Germany
- Saarland University, Saarbrücken, Germany
According to our database1,
Rolf Backofen
authored at least 156 papers
between 1990 and 2023.
Collaborative distances:
Collaborative distances:
Timeline
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Bibliography
2023
BMC Bioinform., December, 2023
Bioinform., October, 2023
Proceedings of the 1st Conference on Research Data Infrastructure - Connecting Communities, 2023
2022
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease.
J. Cheminformatics, 2022
Bioinform., 2022
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria.
Briefings Bioinform., 2022
2021
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.
Bioinform., November, 2021
Nucleic Acids Res., 2021
Bioinform., 2021
Bioinform., 2021
2020
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.
Nucleic Acids Res., 2020
Nucleic Acids Res., 2020
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.
BMC Bioinform., 2020
Heterogeneous networks integration for disease-gene prioritization with node kernels.
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
Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342).
Dagstuhl Reports, 2019
Integration of accessibility data from structure probing into RNA-RNA interaction prediction.
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
Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings.
Proceedings of the 27th European Symposium on Artificial Neural Networks, 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
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.
Nucleic Acids Res., 2018
Nucleic Acids Res., 2018
Bioinform., 2018
Bioinform., 2018
2017
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.
PLoS Comput. Biol., 2017
DHX9 suppresses RNA processing defects originating from the <i>Alu</i> invasion of the human genome.
Nat., 2017
Nucleic Acids Res., 2017
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Nucleic Acids Res., 2017
Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252).
Dagstuhl Reports, 2017
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.
Bioinform., 2017
2016
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.
BMC Bioinform., 2016
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016
2015
antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization.
BMC Bioinform., 2015
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.
Bioinform., 2015
2014
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.
Nucleic Acids Res., 2014
BMC Bioinform., 2014
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
Bioinform., 2014
MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions.
Bioinform., 2014
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci.
Bioinform., 2014
Algorithms Mol. Biol., 2014
Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), 2014
2013
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.
J. Biomed. Semant., 2013
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains.
Bioinform., 2013
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Algorithms Mol. Biol., 2013
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013
SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics.
Proceedings of the Research in Computational Molecular Biology, 2013
Proceedings of the Principles and Practice of Constraint Programming, 2013
2012
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.
Bioinform., 2012
Bioinform., 2012
Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains.
Adv. Bioinformatics, 2012
Proceedings of the Research in Computational Molecular Biology, 2012
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012
2011
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.
Nucleic Acids Res., 2011
J. Discrete Algorithms, 2011
J. Discrete Algorithms, 2011
BMC Bioinform., 2011
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
Bioinform., 2011
Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Bioinform., 2011
2010
Nucleic Acids Res., 2010
BMC Bioinform., 2010
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1.
Bioinform., 2010
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.
Algorithms Mol. Biol., 2010
Algorithms Mol. Biol., 2010
Proceedings of the Research in Computational Molecular Biology, 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Proceedings of the German Conference on Bioinformatics 2010, 2010
2009
Int. J. Pattern Recognit. Artif. Intell., 2009
Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains
CoRR, 2009
CoRR, 2009
Bioinform., 2009
Bioinform., 2009
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009
2008
Constraints An Int. J., 2008
BMC Bioinform., 2008
CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies.
BMC Bioinform., 2008
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.
Bioinform., 2008
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
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data.
Nucleic Acids Res., 2007
Nucleic Acids Res., 2007
J. Discrete Algorithms, 2007
J. Comput. Biol., 2007
2006
Proceedings of the Handbook of Constraint Programming, 2006
A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative.
Prax. Inf.verarb. Kommun., 2006
A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models.
Constraints An Int. J., 2006
Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006
2005
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.
Bioinform., 2005
A multiple-feature framework for modelling and predicting transcription factor binding sites.
Bioinform., 2005
Bioinform., 2005
Proceedings of the String Processing and Information Retrieval, 2005
A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction.
Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005
Computational molecular biology - an introduction.
Wiley series in mathematical and computational biology, Wiley-VCH, ISBN: 978-0-471-87252-8, 2005
2004
A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC).
J. Discrete Algorithms, 2004
Silico Biol., 2004
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004
Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 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
MARNA: A server for multiple alignment of RNAs.
Proceedings of the German Conference on Bioinformatics, 2003
2002
Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation.
Silico Biol., 2002
Proceedings of the STACS 2002, 19th Annual Symposium on Theoretical Aspects of Computer Science, Antibes, 2002
2001
The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound.
Constraints An Int. J., 2001
Proceedings of the Advances in Intelligent Data Analysis, 4th International Conference, 2001
Proceedings of the Combinatorial Pattern Matching, 12th Annual Symposium, 2001
Proceedings of the Principles and Practice of Constraint Programming, 2001
Introduction to Bioinformatics.
Proceedings of the Association for Computational Linguistic, 2001
2000
An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC).
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000
Proceedings of the Seventh Workshop on Automated Reasoning, 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
Proceedings of the Principles and Practice of Constraint Programming, 1998
1997
Using constraint programming for lattice protein folding.
Proceedings of the German Conference on Bioinformatics, 1997
Proceedings of the Computer Science Logic, 11th International Workshop, 1997
Proceedings of the 5th Applied Natural Language Processing Conference, 1997
1996
Controlling Functional Uncertainty.
Proceedings of the 12th European Conference on Artificial Intelligence, 1996
1995
J. Log. Program., 1995
1994
PhD thesis, 1994
DISCO-An HPSG-based NLP System and its Application for Appointment Scheduling Project Note.
Proceedings of the 15th International Conference on Computational Linguistics, 1994
1993
Proceedings of the Rewriting Techniques and Applications, 5th International Conference, 1993
Proceedings of the 31st Annual Meeting of the Association for Computational Linguistics, 1993
1991
Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends.
Proceedings of the Verteilte Künstliche Intelligenz und kooperatives Arbeiten, 1991
Proceedings of the Processing Declarative Knowledge, 1991
1990
Towards the Integration of Functions, Relations and Types in an AI Programming Language.
Proceedings of the GWAI-90, 1990