Rolf Backofen

According to our database1, Rolf Backofen authored at least 134 papers between 1990 and 2020.

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Bibliography

2020
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.
BMC Bioinformatics, 2020

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.
Bioinformatics, 2019

ShaKer: RNA SHAPE prediction using graph kernel.
Bioinformatics, 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

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 Research, 2018

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

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.
Bioinformatics, 2018

CMV: visualization for RNA and protein family models and their comparisons.
Bioinformatics, 2018

2017
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.
PLoS Computational Biology, 2017

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions.
Nucleic Acids Research, 2017

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

2016
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.
BMC Bioinformatics, 2016

Characterizing leader sequences of CRISPR loci.
Bioinformatics, 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 Bioinformatics, 2015

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

antaRNA: ant colony-based RNA sequence design.
Bioinformatics, 2015

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

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.
Nucleic Acids Research, 2014

Simultaneous Alignment and Folding of Protein Sequences.
Journal of Computational Biology, 2014

Cluster based prediction of PDZ-peptide interactions.
BMC Genomics, 2014

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

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
Bioinformatics, 2014

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions.
Bioinformatics, 2014

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci.
Bioinformatics, 2014

Exact methods for lattice protein models.
Bio-Algorithms and Med-Systems, 2014

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.
Algorithms for Molecular Biology, 2014

Atom mapping with constraint programming.
Algorithms for Molecular Biology, 2014

Scalable structural clustering of local RNA secondary structures.
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. Biomedical Semantics, 2013

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains.
Bioinformatics, 2013

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Algorithms for Molecular Biology, 2013

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures.
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

Atom Mapping with Constraint Programming.
Proceedings of the Principles and Practice of Constraint Programming, 2013

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

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.
Bioinformatics, 2012

GraphClust: alignment-free structural clustering of local RNA secondary structures.
Bioinformatics, 2012

Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains.
Adv. Bioinformatics, 2012

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

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots.
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

Local Exact Pattern Matching for Non-fixed RNA Structures.
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 Research, 2011

Sparse RNA folding: Time and space efficient algorithms.
J. Discrete Algorithms, 2011

Fast RNA structure alignment for crossing input structures.
J. Discrete Algorithms, 2011

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

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
Bioinformatics, 2011

Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Bioinformatics, 2011

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

Lifting Prediction to Alignment of RNA Pseudoknots.
Journal of Computational Biology, 2010

TassDB2 - A comprehensive database of subtle alternative splicing events.
BMC Bioinformatics, 2010

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1.
Bioinformatics, 2010

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.
Algorithms for Molecular Biology, 2010

Fast prediction of RNA-RNA interaction.
Algorithms for Molecular Biology, 2010

Sparsification of RNA structure prediction including pseudoknots.
Algorithms for Molecular Biology, 2010

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

Session Introduction.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Shape-based Barrier Estimation for RNAs.
Proceedings of the German Conference on Bioinformatics 2010, 2010

2009
Fast Feature Subset Selection in Biological Sequence Analysis.
IJPRAI, 2009

Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains
CoRR, 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.
Bioinformatics, 2009

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

A partition function algorithm for interacting nucleic acid strands.
Bioinformatics, 2009

biRNA: Fast RNA-RNA Binding Sites Prediction.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

2008
Decomposition Techniques for Subgraph Matching
CoRR, 2008

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

Improved identification of conserved cassette exons using Bayesian networks.
BMC Bioinformatics, 2008

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

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions.
Bioinformatics, 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 Computational Biology, 2007

BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data.
Nucleic Acids Research, 2007

TassDB: a database of alternative tandem splice sites.
Nucleic Acids Research, 2007

INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints.
Nucleic Acids Research, 2007

Fast detection of common sequence structure patterns in RNAs.
J. Discrete Algorithms, 2007

A Dynamic Programming Approach for Finding Common Patterns in RNAs.
Journal of Computational Biology, 2007

Locality and Gaps in RNA Comparison.
Journal of Computational Biology, 2007

2006
Bioinformatics and Constraints.
Proceedings of the Handbook of Constraint Programming, 2006

A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative.
Praxis der Informationsverarbeitung und Kommunikation, 2006

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

INFO-RNA - a fast approach to inverse RNA folding.
Bioinformatics, 2006

Local Alignment of RNA Sequences with Arbitrary Scoring Schemes.
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.
Bioinformatics, 2005

A multiple-feature framework for modelling and predicting transcription factor binding sites.
Bioinformatics, 2005

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

Normalized Similarity of RNA Sequences.
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

Local Sequence-structure Motifs in Rna.
J. Bioinformatics and Computational Biology, 2004

Efficient prediction of alternative splice forms using protein domain homology.
In Silico Biology, 2004

Feature Based Representation and Detection of Transcription Factor Binding Sites.
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

Computational Design of New and Recombinant Selenoproteins.
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.
In Silico Biology, 2002

Excluding Symmetries in Constraint-Based Search.
Constraints, 2002

On the Complexity of Protein Similarity Search under mRNA Structure Constraints.
Proceedings of the STACS 2002, 19th Annual Symposium on Theoretical Aspects of Computer Science, Antibes, 2002

2001
Introduction to the Special Issue on Bioinformatics.
Constraints, 2001

Bioinformatics and Constraints.
Constraints, 2001

The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound.
Constraints, 2001

RNA-Sequence-Structure Properties and Selenocysteine Insertion.
Proceedings of the Advances in Intelligent Data Analysis, 4th International Conference, 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

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

Exclusion of Symmetries in Search - A Spin-off from Bioinformatics Research.
Proceedings of the Seventh Workshop on Automated Reasoning, 2000

1999
Bioinformatik - Aktuelles Schlagwort.
Informatik Spektrum, 1999

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

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

1998
How to Win a Game with Features.
Inf. Comput., 1998

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

Constraint Techniques for Solving the Protein Structure Prediction Problem.
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

Evolution as a Computational Engine.
Proceedings of the Computer Science Logic, 11th International Workshop, 1997

An Information Extraction Core System for Real World German Text Processing.
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
A Complete and Recursive Feature Theory.
Theor. Comput. Sci., 1995

A First-Order Axiomatization of the Theory of Finite Trees.
Journal of Logic, Language and Information, 1995

A Complete Axiomatization of a Theory with Feature and Arity Constraints.
J. Log. Program., 1995

1994
Expressivity and decidability of first-order languages over feature trees.
PhD thesis, 1994

Regular Path Expressions in Feature Logic.
J. Symb. Comput., 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
Regular Path Expression in Feature Logic.
Proceedings of the Rewriting Techniques and Applications, 5th International Conference, 1993

On the Decidability of Functional Uncertainty.
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

Distributed Disjunctions for LIFE.
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


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