Towards the Integration of Functions, Relations and Types in an AI Programming Language. - Rolf Backofen; Lutz Euler; Günther Görz (GWAI, 1990)

Distributed Disjunctions for LIFE. - Rolf Backofen; Lutz Euler; Günther Görz (PDK, 1991)

Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends. - Rolf Backofen; Harald Trost; Hans Uszkoreit (Wissensbasierte Systeme, 1991)

On the Decidability of Functional Uncertainty. - Rolf Backofen (ACL, 1993)

Regular Path Expression in Feature Logic. - Rolf Backofen (RTA, 1993)

DISCO-An HPSG-based NLP System and its Application for Appointment Scheduling Project Note. - Hans Uszkoreit; Rolf Backofen; Stephan Busemann; Abdel Kader Diagne; Elizabeth A. Hinkelman; Walter Kasper; Bernd Kiefer; Hans-Ulrich Krieger; Klaus Netter; Günter Neumann; Stephan Oepen; Stephen P. Spackman (COLING, 1994)

Regular Path Expressions in Feature Logic. - Rolf Backofen (J. Symb. Comput., 1994)

Expressivity and decidability of first-order languages over feature trees. - Rolf Backofen (1994)

A Complete Axiomatization of a Theory with Feature and Arity Constraints. - Rolf Backofen (J. Log. Program., 1995)

A First-Order Axiomatization of the Theory of Finite Trees. - Rolf Backofen; James Rogers; K. Vijay-Shanker (J. Log. Lang. Inf., 1995)

A Complete and Recursive Feature Theory. - Rolf Backofen; Gert Smolka (Theor. Comput. Sci., 1995)

Controlling Functional Uncertainty. - Rolf Backofen (ECAI, 1996)

An Information Extraction Core System for Real World German Text Processing. - Günter Neumann; Rolf Backofen; Judith Baur; Markus Becker 002; Christian Braun 003 (ANLP, 1997)

Evolution as a Computational Engine. - Rolf Backofen; Peter Clote (CSL, 1997)

Using constraint programming for lattice protein folding. - Rolf Backofen (German Conference on Bioinformatics, 1997)

Constraint Techniques for Solving the Protein Structure Prediction Problem. - Rolf Backofen (CP, 1998)

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

How to Win a Game with Features. - Rolf Backofen; Ralf Treinen (Inf. Comput., 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)

Bioinformatik - Aktuelles Schlagwort. - Rolf Backofen; François Bry; Peter Clote; Hans-Peter Kriegel; Thomas Seidl 001; Klaus U. Schulz (Inform. Spektrum, 1999)

Exclusion of Symmetries in Search - A Spin-off from Bioinformatics Research. - Rolf Backofen (ARW, 2000)

An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC). - Rolf Backofen (CPM, 2000)

Introduction to Bioinformatics. - Rolf Backofen (ACL (Companion Volume), 2001)

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)

RNA-Sequence-Structure Properties and Selenocysteine Insertion. - Rolf Backofen (IDA, 2001)

The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound. - Rolf Backofen (Constraints An Int. J., 2001)

Bioinformatics and Constraints. - Rolf Backofen; David R. Gilbert (Constraints An Int. J., 2001)

Introduction to the Special Issue on Bioinformatics. - David R. Gilbert; Rolf Backofen; Roland H. C. Yap (Constraints An Int. J., 2001)

On the Complexity of Protein Similarity Search under mRNA Structure Constraints. - Rolf Backofen; N. S. Narayanaswamy; Firas Swidan (STACS, 2002)

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

Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. - Rolf Backofen; N. S. Narayanaswamy; Firas Swidan (Silico Biol., 2002)

MARNA: A server for multiple alignment of RNAs. - Sven Siebert; Rolf Backofen (German Conference on Bioinformatics, 2003)

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

Computational Design of New and Recombinant Selenoproteins. - Rolf Backofen; Anke Busch (CPM, 2004)

Feature Based Representation and Detection of Transcription Factor Binding Sites. - Rainer Pudimat; Ernst Günter Schukat-Talamazzini; Rolf Backofen (German Conference on Bioinformatics, 2004)

Efficient prediction of alternative splice forms using protein domain homology. - Michael Hiller; Rolf Backofen; Stephan Heymann; Anke Busch; Timo Mika Gläßer; Johann Christoph Freytag (Silico Biol., 2004)

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

A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC). - Rolf Backofen (J. Discrete Algorithms, 2004)

Computational molecular biology - an introduction. - Peter Clote; Rolf Backofen (Wiley-VCH, 2005)

A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction. - Sven Siebert; Rolf Backofen (CIBCB, 2005)

Normalized Similarity of RNA Sequences. - Rolf Backofen; Danny Hermelin; Gad M. Landau; Oren Weimann (SPIRE, 2005)

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

A multiple-feature framework for modelling and predicting transcription factor binding sites. - Rainer Pudimat; Ernst Günter Schukat-Talamazzini; Rolf Backofen (Bioinform., 2005)

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. - Sven Siebert; Rolf Backofen (Bioinform., 2005)

Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. - Rolf Backofen; Danny Hermelin; Gad M. Landau; Oren Weimann (CPM, 2006)

INFO-RNA - a fast approach to inverse RNA folding. - Anke Busch; Rolf Backofen (Bioinform., 2006)

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

A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative. - Rolf Backofen; Hans-Gunther Borrmann; Werner Deck; Andreas Dedner; Luc De Raedt; Klaus Desch; Markus Diesmann; Martin Geier; Andreas Greiner; Wolfgang R. Hess; Josef Honerkamp; Stefan Jankowski; et al. (Prax. Inf.verarb. Kommun., 2006)

Bioinformatics and Constraints. - Rolf Backofen; David R. Gilbert (Handbook of Constraint Programming, 2006)

Locality and Gaps in RNA Comparison. - Rolf Backofen; Shihyen Chen; Danny Hermelin; Gad M. Landau; Mikhail A. Roytberg; Oren Weimann; Kaizhong Zhang (J. Comput. Biol., 2007)

A Dynamic Programming Approach for Finding Common Patterns in RNAs. - Sven Siebert; Rolf Backofen (J. Comput. Biol., 2007)

Fast detection of common sequence structure patterns in RNAs. - Rolf Backofen; Sven Siebert (J. Discrete Algorithms, 2007)

INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints. - Anke Busch; Rolf Backofen (Nucleic Acids Res., 2007)

TassDB: a database of alternative tandem splice sites. - Michael Hiller; Swetlana Nikolajewa; Klaus Huse; Karol Szafranski; Philip Rosenstiel; Stefan Schuster; Rolf Backofen; Matthias Platzer (Nucleic Acids Res., 2007)

BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. - Swetlana Nikolajewa; Rainer Pudimat; Michael Hiller; Matthias Platzer; Rolf Backofen (Nucleic Acids Res., 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)

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. - Anke Busch; Andreas S. Richter; Rolf Backofen (Bioinform., 2008)

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

Improved identification of conserved cassette exons using Bayesian networks. - Rileen Sinha; Michael Hiller; Rainer Pudimat; Ulrike Gausmann; Matthias Platzer; Rolf Backofen (BMC Bioinform., 2008)

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

Decomposition Techniques for Subgraph Matching - Stéphane Zampelli; Martin Mann; Yves Deville; Rolf Backofen (CoRR, 2008)

biRNA: Fast RNA-RNA Binding Sites Prediction. - Hamidreza Chitsaz; Rolf Backofen; Süleyman Cenk Sahinalp (WABI, 2009)

A partition function algorithm for interacting nucleic acid strands. - Hamidreza Chitsaz; Raheleh Salari; Süleyman Cenk Sahinalp; Rolf Backofen (Bioinform., 2009)

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)

Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains - Martin Mann; Mohamed Abou Hamra; Kathleen Steinhöfel; Rolf Backofen (CoRR, 2009)

Fast Feature Subset Selection in Biological Sequence Analysis. - Rainer Pudimat; Rolf Backofen; Ernst Günter Schukat-Talamazzini (Int. J. Pattern Recognit. Artif. Intell., 2009)

Shape-based Barrier Estimation for RNAs. - Sergiy Bogomolov; Martin Mann; Björn Voß; Andreas Podelski; Rolf Backofen (GCB, 2010)

Session Introduction. - Rolf Backofen; Hamidreza Chitsaz; Ivo L. Hofacker; Süleyman Cenk Sahinalp; Peter F. Stadler (Pacific Symposium on Biocomputing, 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)

Fast prediction of RNA-RNA interaction. - Raheleh Salari; Rolf Backofen; Süleyman Cenk Sahinalp (Algorithms Mol. Biol., 2010)

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. - Stefan E. Seemann; Andreas S. Richter; Jan Gorodkin; Rolf Backofen (Algorithms Mol. Biol., 2010)

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. - Andreas S. Richter; Christian Schleberger; Rolf Backofen; Claudia Steglich (Bioinform., 2010)

TassDB2 - A comprehensive database of subtle alternative splicing events. - Rileen Sinha; Thorsten Lenser; Niels Jahn; Ulrike Gausmann; Swetlana Friedel; Karol Szafranski; Klaus Huse; Philip Rosenstiel; Jochen Hampe; Stefan Schuster; Michael Hiller; Rolf Backofen; et al. (BMC Bioinform., 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)

Computational discovery of human coding and non-coding transcripts with conserved splice sites. - Dominic Rose; Michael Hiller; Katharina Schutt; Jörg Hackermüller; Rolf Backofen; Peter F. Stadler (Bioinform., 2011)

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. - Stefan E. Seemann; Andreas S. Richter; Tanja Gesell; Rolf Backofen; Jan Gorodkin (Bioinform., 2011)

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

Fast RNA structure alignment for crossing input structures. - Rolf Backofen; Gad M. Landau; Mathias Möhl; Dekel Tsur; Oren Weimann (J. Discrete Algorithms, 2011)

Sparse RNA folding: Time and space efficient algorithms. - Rolf Backofen; Dekel Tsur; Shay Zakov; Michal Ziv-Ukelson (J. Discrete Algorithms, 2011)

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. - Stefan E. Seemann; Peter Menzel; Rolf Backofen; Jan Gorodkin (Nucleic Acids Res., 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)

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. - Saad Sheikh; Rolf Backofen; Yann Ponty (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)

Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. - Martin Mann; Rhodri Saunders; Cameron Smith; Rolf Backofen; Charlotte M. Deane (Adv. Bioinformatics, 2012)

GraphClust: alignment-free structural clustering of local RNA secondary structures. - Steffen Heyne; Fabrizio Costa; Dominic Rose; Rolf Backofen (Bioinform., 2012)

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. - Nuno D. Mendes; Steffen Heyne; Ana T. Freitas; Marie-France Sagot; Rolf Backofen (Bioinform., 2012)

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

Atom Mapping with Constraint Programming. - Martin Mann; Feras Nahar; Heinz Ekker; Rolf Backofen; Peter F. Stadler; Christoph Flamm (CP, 2013)

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)

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. - Rolf Backofen; Markus Fricke; Manja Marz; Jing Qin 006; Peter F. Stadler (WABI, 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)

A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. - Kousik Kundu; Fabrizio Costa; Rolf Backofen (Bioinform., 2013)

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. - Dietrich Rebholz-Schuhmann; Senay Kafkas; Jee-Hyub Kim; Chen Li 011; Antonio Jimeno-Yepes; Robert Hoehndorf; Rolf Backofen; Ian Lewin (J. Biomed. Semant., 2013)

Scalable structural clustering of local RNA secondary structures. - Fabrizio Costa; Steffen Heyne; Dominic Rose; Rolf Backofen (CMSR@ECCB, 2014)

Atom mapping with constraint programming. - Martin Mann; Feras Nahar; Norah Schnorr; Rolf Backofen; Peter F. Stadler; Christoph Flamm (Algorithms Mol. Biol., 2014)

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. - Jing Qin 006; Markus Fricke; Manja Marz; Peter F. Stadler; Rolf Backofen (Algorithms Mol. Biol., 2014)

Exact methods for lattice protein models. - Martin Mann; Rolf Backofen (Bio Algorithms Med Syst., 2014)

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. - Omer S. Alkhnbashi; Fabrizio Costa; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Rolf Backofen (Bioinform., 2014)

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. - Kousik Kundu; Martin Mann; Fabrizio Costa; Rolf Backofen (Bioinform., 2014)

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. - Pavankumar Videm; Dominic Rose; Fabrizio Costa; Rolf Backofen (Bioinform., 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)

Cluster based prediction of PDZ-peptide interactions. - Kousik Kundu; Rolf Backofen (BMC Genom., 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)

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. - Patrick R. Wright; Jens Georg; Martin Mann; Dragos Alexandru Sorescu; Andreas S. Richter; Steffen Lott; Robert Kleinkauf; Wolfgang R. Hess; Rolf Backofen (Nucleic Acids Res., 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)

antaRNA: ant colony-based RNA sequence design. - Robert Kleinkauf; Martin Mann; Rolf Backofen (Bioinform., 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)

antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. - Robert Kleinkauf; Torsten Houwaart; Rolf Backofen; Martin Mann (BMC Bioinform., 2015)

AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. - Phuong Dao; Jan Hoinka; Yijie Wang 004; Mayumi Takahashi; Jiehua Zhou; Fabrizio Costa; John Rossi; John Burnett; Rolf Backofen; Teresa M. Przytycka (RECOMB, 2016)

Characterizing leader sequences of CRISPR loci. - Omer S. Alkhnbashi; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Fabrizio Costa; Rolf Backofen (Bioinform., 2016)

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. - João Victor de Araújo Oliveira; Fabrizio Costa; Rolf Backofen; Peter F. Stadler; Maria Emília Telles Walter; Jana Hertel (BMC Bioinform., 2016)

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. - Milad Miladi; Alexander Junge; Fabrizio Costa; Stefan E. Seemann; Jakob Hull Havgaard; Jan Gorodkin; Rolf Backofen (Bioinform., 2017)

Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252). - Rolf Backofen; Yael Mandel-Gutfreund; Uwe Ohler; Gabriele Varani (Dagstuhl Reports, 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)

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. - Martin Mann; Patrick R. Wright; Rolf Backofen (Nucleic Acids Res., 2017)

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. - Tugçe Aktas; Ibrahim Avsar Ilik; Daniel Maticzka; Vivek Bhardwaj 002; Cecilia Pessoa Rodrigues; Gerhard Mittler; Thomas Manke; Rolf Backofen; Asifa Akhtar (Nat., 2017)

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. - Björn A. Grüning; Eric Rasche; Boris Rebolledo-Jaramillo; Carl Eberhard; Torsten Houwaart; John Chilton; Nate Coraor; Rolf Backofen; James Taylor 001; Anton Nekrutenko (PLoS Comput. Biol., 2017)

CMV: visualization for RNA and protein family models and their comparisons. - Florian Eggenhofer; Ivo L. Hofacker; Rolf Backofen; Christian Höner zu Siederdissen (Bioinform., 2018)

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. - Alexander Gawronski; Michael Uhl; Yajia Zhang; Yen-Yi Lin; Yashar S. Niknafs; Varune R. Ramnarine; Rohit Malik; Felix Feng; Arul M. Chinnaiyan; Colin C. Collins; Süleyman Cenk Sahinalp; Rolf Backofen (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)

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. - Joachim Wolff; Vivek Bhardwaj 002; Stephan Nothjunge; Gautier Richard; Gina Renschler; Ralf Gilsbach; Thomas Manke; Rolf Backofen; Fidel Ramírez; Björn A. Grüning (Nucleic Acids Res., 2018)

MICA: Multiple interval-based curve alignment. - Martin Mann; Hans-Peter Kahle; Matthias Beck; Bela Johannes Bender; Heinrich Spiecker; Rolf Backofen (SoftwareX, 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)

Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings. - Stefan Mautner; Rolf Backofen; Fabrizio Costa (ESANN, 2019)

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

ShaKer: RNA SHAPE prediction using graph kernel. - Stefan Mautner; Soheila Montaseri; Milad Miladi; Martin Raden; Fabrizio Costa; Rolf Backofen (Bioinform., 2019)

Integration of accessibility data from structure probing into RNA-RNA interaction prediction. - Milad Miladi; Soheila Montaseri; Rolf Backofen; Martin Raden (Bioinform., 2019)

Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342). - Rolf Backofen; Yael Mandel-Gutfreund; Uwe Ohler; Gabriele Varani (Dagstuhl Reports, 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)

The RNA workbench 2.0: next generation RNA data analysis. - Jörg Fallmann; Pavankumar Videm; Andrea Bagnacani; Bérénice Batut; Maria A. Doyle; Tomas Klingström; Florian Eggenhofer; Peter F. Stadler; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 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)

Heterogeneous networks integration for disease-gene prioritization with node kernels. - Dinh Van Tran; Alessandro Sperduti; Rolf Backofen; Fabrizio Costa (Bioinform., 2020)

The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment. - Martin Raden; Teresa Müller; Stefan Mautner; Rick Gelhausen; Rolf Backofen (BMC Bioinform., 2020)

MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. - Milad Miladi; Martin Raden; Sven Diederichs; Rolf Backofen (Nucleic Acids Res., 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. - Joachim Wolff; Leily Rabbani; Ralf Gilsbach; Gautier Richard; Thomas Manke; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 2020)

pyGenomeTracks: reproducible plots for multivariate genomic datasets. - Lucille Lopez-Delisle; Leily Rabbani; Joachim Wolff; Vivek Bhardwaj 002; Rolf Backofen; Björn A. Grüning; Fidel Ramírez; Thomas Manke (Bioinform., 2021)

Casboundary: automated definition of integral Cas cassettes. - Victor Alexandre Padilha; Omer S. Alkhnbashi; Van Dinh Tran; Shiraz A. Shah; André C. P. L. F. de Carvalho; Rolf Backofen (Bioinform., 2021)

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. - Miguel Roncoroni; Bert Droesbeke; Ignacio Eguinoa; Kim De Ruyck; Flora D'anna; Dilmurat Yusuf; Björn A. Grüning; Rolf Backofen; Frederik Coppens (Bioinform., 2021)

Scool: a new data storage format for single-cell Hi-C data. - Joachim Wolff; Nezar Abdennur; Rolf Backofen; Björn A. Grüning (Bioinform., 2021)

CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. - Omer S. Alkhnbashi; Alexander Mitrofanov; Robson Bonidia; Martin Raden; Van Dinh Tran; Florian Eggenhofer; Shiraz A. Shah; Ekrem Öztürk; Victor Alexandre Padilha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho; Rolf Backofen (Nucleic Acids Res., 2021)

Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. - Joachim Wolff; Rolf Backofen; Björn A. Grüning (Bioinform., 2021)

RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. - Rick Gelhausen; Teresa Müller; Sarah L. Svensson; Omer S. Alkhnbashi; Cynthia M. Sharma; Florian Eggenhofer; Rolf Backofen (Briefings Bioinform., 2022)

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection. - Alexander Mitrofanov; Marcus Ziemann; Omer S. Alkhnbashi; Wolfgang R. Hess; Rolf Backofen (Bioinform., 2022)

Peakhood: individual site context extraction for CLIP-seq peak regions. - Michael Uhl; Dominik Rabsch; Florian Eggenhofer; Rolf Backofen (Bioinform., 2022)

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. - Simon Bray; Tim Dudgeon; Rachael Skyner; Rolf Backofen; Björn A. Grüning; Frank von Delft (J. Cheminformatics, 2022)

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. - Nils Hoffmann; Irena Maus; Sebastian Beier; Peter Belmann; Jan Krüger; Andreas Tauch; Alexander Goesmann; Roland Eils; Peer Bork; Oliver Kohlbacher; Ursula Kummer; Rolf Backofen; et al. (CoRDI, 2023)

RNA interaction format: a general data format for RNA interactions. - Richard A. Schäfer; Dominik Rabsch; Guillaume E. Scholz; Peter F. Stadler; Wolfgang R. Hess; Rolf Backofen; Jörg Fallmann; Björn Voß (Bioinform., 2023)

Transformer-based tool recommendation system in Galaxy. - Anup Kumar; Björn A. Grüning; Rolf Backofen (BMC Bioinform., 2023)

CRISPert: A Transformer-Based Model for CRISPR-Cas Off-Target Prediction. - William Jobson Pargeter; Rolf Backofen; Van Dinh Tran (ECML/PKDD (7), 2024)

Partial RNA design. - Frederic Runge; Jörg K. H. Franke; Daniel Fertmann; Rolf Backofen; Frank Hutter (Bioinform., 2024)

Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data. - Maren Hackenberg; Laia Canal Guitart; Rolf Backofen; Harald Binder (Briefings Bioinform., 2025)

Learning to generate feasible graphs using graph grammars. - Stefan Mautner; Rolf Backofen; Fabrizio Costa (CoRR, 2025)

Small Data Explainer - The impact of small data methods in everyday life. - Maren Hackenberg; Sophia G. Connor; Fabian Kabus; June Brawner; Ella Markham; Mahi Hardalupas; Areeq Chowdhury; Rolf Backofen; Anna Köttgen; Angelika Rohde; Nadine Felizitas Binder; Harald Binder (CoRR, 2025)