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ORCIDRolf Backofen
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- affiliation: University of Freiburg, Germany
- affiliation: Saarland University, Saarbrücken, Germany
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2020 – today
- 2024
[c59]William Jobson Pargeter, Rolf Backofen, Van Dinh Tran:
CRISPert: A Transformer-Based Model for CRISPR-Cas Off-Target Prediction. ECML/PKDD (7) 2024: 92-104- 2023
- [j103]Richard A. Schäfer
, Dominik Rabsch, Guillaume E. Scholz, Peter F. Stadler, Wolfgang R. Hess, Rolf Backofen, Jörg Fallmann, Björn Voß:
RNA interaction format: a general data format for RNA interactions. Bioinform. 39(10) (2023) - [j102]Anup Kumar, Björn A. Grüning, Rolf Backofen:
Transformer-based tool recommendation system in Galaxy. BMC Bioinform. 24(1): 446 (2023) - [c58]Nils Hoffmann, Irena Maus, Sebastian Beier, Peter Belmann, Jan Krüger, Andreas Tauch, Alexander Goesmann, Roland Eils, Peer Bork, Oliver Kohlbacher, Ursula Kummer, Rolf Backofen, Ivo Buchhalter, Alexander Sczyrba:
Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. CoRDI 2023 - 2022
- [j101]Rick Gelhausen, Teresa Müller, Sarah L. Svensson, Omer S. Alkhnbashi, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen:
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. Briefings Bioinform. 23(2) (2022) - [j100]Michael Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen:
Peakhood: individual site context extraction for CLIP-seq peak regions. Bioinform. 38(4): 1139-1140 (2022) - [j99]Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn A. Grüning, Frank von Delft:
Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. J. Cheminformatics 14(1): 22 (2022) - 2021
- [j98]Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn A. Grüning, Fidel Ramírez, Thomas Manke:
pyGenomeTracks: reproducible plots for multivariate genomic datasets. Bioinform. 37(3): 422-423 (2021) - [j97]Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning:
Scool: a new data storage format for single-cell Hi-C data. Bioinform. 37(9): 1337 (2021) - [j96]Victor Alexandre Padilha, Omer S. Alkhnbashi, Van Dinh Tran, Shiraz A. Shah, André C. P. L. F. de Carvalho, Rolf Backofen:
Casboundary: automated definition of integral Cas cassettes. Bioinform. 37(10): 1352-1359 (2021) - [j95]Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'anna, Dilmurat Yusuf, Björn A. Grüning, Rolf Backofen, Frederik Coppens:
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinform. 37(21): 3983-3985 (2021) - [j94]Joachim Wolff, Rolf Backofen, Björn A. Grüning:
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. Bioinform. 37(22): 4006-4013 (2021) - [j93]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:
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. Nucleic Acids Res. 49(Webserver-Issue): 125-130 (2021) - 2020
- [j92]Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen:
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms Mol. Biol. 15(1): 19 (2020) - [j91]Dinh Van Tran, Alessandro Sperduti, Rolf Backofen, Fabrizio Costa:
Heterogeneous networks integration for disease-gene prioritization with node kernels. Bioinform. 36(9): 2649-2656 (2020) - [j90]Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen:
The locality dilemma of Sankoff-like RNA alignments. Bioinform. 36(Supplement-1): i242-i250 (2020) - [j89]Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen, Rolf Backofen:
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment. BMC Bioinform. 21(1): 15 (2020) - [j88]Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A. Grüning:
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. 48(Webserver-Issue): W177-W184 (2020) - [j87]Milad Miladi, Martin Raden, Sven Diederichs, Rolf Backofen:
MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. Nucleic Acids Res. 48(Webserver-Issue): W287-W291 (2020)
2010 – 2019
- 2019
- [j86]Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa, Rolf Backofen:
ShaKer: RNA SHAPE prediction using graph kernel. Bioinform. 35(14): i354-i359 (2019) - [j85]Milad Miladi, Soheila Montaseri, Rolf Backofen, Martin Raden:
Integration of accessibility data from structure probing into RNA-RNA interaction prediction. Bioinform. 35(16): 2862-2864 (2019) - [j84]Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden:
IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. J. Bioinform. Comput. Biol. 17(5): 1940009:1-1940009:16 (2019) - [j83]Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning:
The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Res. 47(Webserver-Issue): W511-W515 (2019) - [c57]Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden:
Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction. BIOINFORMATICS 2019: 131-140 - [c56]Stefan Mautner, Rolf Backofen, Fabrizio Costa:
Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings. ESANN 2019 - [c55]Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen:
Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. WABI 2019: 14:1-14:13 - [i10]Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani:
Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342). Dagstuhl Reports 9(8): 49-69 (2019) - 2018
- [j82]Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen, Christian Höner zu Siederdissen:
CMV: visualization for RNA and protein family models and their comparisons. Bioinform. 34(15): 2676-2678 (2018) - [j81]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:
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Bioinform. 34(18): 3101-3110 (2018) - [j80]Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A. Grüning:
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res. 46(Webserver-Issue): W11-W16 (2018) - [j79]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:
Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res. 46(Webserver-Issue): W25-W29 (2018) - [j78]Martin Mann, Hans-Peter Kahle, Matthias Beck, Bela Johannes Bender, Heinrich Spiecker, Rolf Backofen:
MICA: Multiple interval-based curve alignment. SoftwareX 7: 53-58 (2018) - 2017
- [j77]Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen:
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. Bioinform. 33(14): 2089-2096 (2017) - [j76]Martin Mann, Patrick R. Wright, Rolf Backofen:
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res. 45(Webserver-Issue): W435-W439 (2017) - [j75]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:
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 45(Webserver-Issue): W560-W566 (2017) - [j74]Tugçe Aktas, Ibrahim Avsar Ilik, Daniel Maticzka, Vivek Bhardwaj, Cecilia Pessoa Rodrigues, Gerhard Mittler, Thomas Manke, Rolf Backofen, Asifa Akhtar:
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. Nat. 544(7648): 115-119 (2017) - [j73]Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko:
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PLoS Comput. Biol. 13(5) (2017) - [i9]Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani:
Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252). Dagstuhl Reports 7(6): 86-108 (2017) - 2016
- [j72]Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa, Rolf Backofen:
Characterizing leader sequences of CRISPR loci. Bioinform. 32(17): 576-585 (2016) - [j71]João Victor de Araújo Oliveira, Fabrizio Costa, Rolf Backofen, Peter F. Stadler, Maria Emília Telles Walter, Jana Hertel:
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. BMC Bioinform. 17(S-18): 73-86 (2016) - [c54]Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka:
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. RECOMB 2016: 261-262 - [i8]Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka:
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. CoRR abs/1604.03081 (2016) - 2015
- [j70]Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, Rolf Backofen:
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinform. 31(15): 2489-2496 (2015) - [j69]Robert Kleinkauf, Martin Mann, Rolf Backofen:
antaRNA: ant colony-based RNA sequence design. Bioinform. 31(19): 3114-3121 (2015) - [j68]Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, Martin Mann:
antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. BMC Bioinform. 16: 389:1-389:7 (2015) - 2014
- [j67]Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler, Rolf Backofen:
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. Algorithms Mol. Biol. 9: 19 (2014) - [j66]Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm:
Atom mapping with constraint programming. Algorithms Mol. Biol. 9: 23 (2014) - [j65]Martin Mann, Rolf Backofen:
Exact methods for lattice protein models. Bio Algorithms Med Syst. 10(4): 213-225 (2014) - [j64]Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen:
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. Bioinform. 30(12): 274-282 (2014) - [j63]Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen:
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinform. 30(17): 489-496 (2014) - [j62]Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen:
MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. Bioinform. 30(18): 2668-2669 (2014) - [j61]Christina Otto, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, Sebastian Will:
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinform. 15: 6602 (2014) - [j60]Kousik Kundu, Rolf Backofen:
Cluster based prediction of PDZ-peptide interactions. BMC Genom. 15(S-1): S5 (2014) - [j59]Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. 21(7): 477-491 (2014) - [j58]Patrick R. Wright, Jens Georg, Martin Mann, Dragos Alexandru Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, Rolf Backofen:
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res. 42(Webserver-Issue): 119-123 (2014) - [j57]Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, Sebastian Will:
Local Exact Pattern Matching for Non-FixedRNA Structures. IEEE ACM Trans. Comput. Biol. Bioinform. 11(1): 219-230 (2014) - [c53]Fabrizio Costa, Steffen Heyne, Dominic Rose, Rolf Backofen:
Scalable structural clustering of local RNA secondary structures. CMSR@ECCB 2014: 59-61 - [c52]Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen:
Blockclust: efficient clustering and classification of non-coding rnas from short Read RNA-seq profiles. GCB 2014: 12-22 - 2013
- [j56]Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen:
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol. Biol. 8: 14 (2013) - [j55]Kousik Kundu, Fabrizio Costa, Rolf Backofen:
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. Bioinform. 29(13): 335-343 (2013) - [j54]Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin:
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. 4: 28 (2013) - [c51]Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm:
Atom Mapping with Constraint Programming. CP 2013: 805-822 - [c50]Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen:
SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. RECOMB 2013: 289-290 - [c49]Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler:
Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. WABI 2013: 112-125 - 2012
- [j53]Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane:
Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. Adv. Bioinformatics 2012: 148045:1-148045:6 (2012) - [j52]Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen:
GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinform. 28(12): 224-232 (2012) - [j51]Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen:
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinform. 28(23): 3034-3041 (2012) - [j50]Dragos Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, Sebastian Will:
CARNA - alignment of RNA structure ensembles. Nucleic Acids Res. 40(Web-Server-Issue): 49-53 (2012) - [c48]Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl, Sebastian Will:
Local Exact Pattern Matching for Non-fixed RNA Structures. CPM 2012: 306-320 - [c47]Saad Sheikh, Rolf Backofen, Yann Ponty:
Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. CPM 2012: 321-333 - [c46]Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen:
Exact Pattern Matching for RNA Structure Ensembles. RECOMB 2012: 245-260 - 2011
- [j49]Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin:
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinform. 27(2): 211-219 (2011) - [j48]Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler:
Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinform. 27(14): 1894-1900 (2011) - [j47]Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette:
Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinform. 12: 214 (2011) - [j46]Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann:
Fast RNA structure alignment for crossing input structures. J. Discrete Algorithms 9(1): 2-11 (2011) - [j45]Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson:
Sparse RNA folding: Time and space efficient algorithms. J. Discrete Algorithms 9(1): 12-31 (2011) - [j44]Stefan E. Seemann, Peter Menzel, Rolf Backofen, Jan Gorodkin:
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. Nucleic Acids Res. 39(Web-Server-Issue): 107-111 (2011) - 2010
- [j43]Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp:
Fast prediction of RNA-RNA interaction. Algorithms Mol. Biol. 5: 5 (2010) - [j42]Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen:
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms Mol. Biol. 5: 22 (2010) - [j41]Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp:
Sparsification of RNA structure prediction including pseudoknots. Algorithms Mol. Biol. 5: 39 (2010) - [j40]Andreas S. Richter, Christian Schleberger, Rolf Backofen, Claudia Steglich:
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinform. 26(1): 1-5 (2010) - [j39]Rileen Sinha, Thorsten Lenser, Niels Jahn, Ulrike Gausmann, Swetlana Friedel, Karol Szafranski, Klaus Huse, Philip Rosenstiel, Jochen Hampe, Stefan Schuster, Michael Hiller, Rolf Backofen, Matthias Platzer:
TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinform. 11: 216 (2010) - [j38]Mathias Möhl, Sebastian Will, Rolf Backofen:
Lifting Prediction to Alignment of RNA Pseudoknots. J. Comput. Biol. 17(3): 429-442 (2010) - [j37]Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen:
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acids Res. 38(Web-Server-Issue): 373-377 (2010) - [c45]Sergiy Bogomolov, Martin Mann, Björn Voß, Andreas Podelski, Rolf Backofen:
Shape-based Barrier Estimation for RNAs. GCB 2010: 41-50 - [c44]Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler:
Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56 - [c43]Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen:
Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB 2010: 473-490 - [c42]Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp:
Sparsification of RNA Structure Prediction Including Pseudoknots. WABI 2010: 40-51
2000 – 2009
- 2009
- [j36]Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen:
CPSP-web-tools: a server for 3D lattice protein studies. Bioinform. 25(5): 676-677 (2009) - [j35]Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen:
A partition function algorithm for interacting nucleic acid strands. Bioinform. 25(12) (2009) - [j34]Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen:
Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinform. 25(16): 2095-2102 (2009) - [j33]Rainer Pudimat, Rolf Backofen, Ernst Günter Schukat-Talamazzini:
Fast Feature Subset Selection in Biological Sequence Analysis. Int. J. Pattern Recognit. Artif. Intell. 23(2): 191-207 (2009) - [c41]Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann:
Fast RNA Structure Alignment for Crossing Input Structures. CPM 2009: 236-248 - [c40]Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson:
Sparse RNA Folding: Time and Space Efficient Algorithms. CPM 2009: 249-262 - [c39]Mathias Möhl, Sebastian Will, Rolf Backofen:
Lifting Prediction to Alignment of RNA Pseudoknots. RECOMB 2009: 285-301 - [c38]Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
Simultaneous Alignment and Folding of Protein Sequences. RECOMB 2009: 339-355 - [c37]Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp:
biRNA: Fast RNA-RNA Binding Sites Prediction. WABI 2009: 25-36 - [c36]Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp:
Fast Prediction of RNA-RNA Interaction. WABI 2009: 261-272 - [i7]Martin Mann, Rolf Backofen, Sebastian Will:
Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains. CoRR abs/0910.3848 (2009) - [i6]Martin Mann, Mohamed Abou Hamra, Kathleen Steinhöfel, Rolf Backofen:
Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains. CoRR abs/0910.3880 (2009) - 2008
- [j32]Anke Busch, Andreas S. Richter, Rolf Backofen:
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinform. 24(24): 2849-2856 (2008) - [j31]Martin Mann, Sebastian Will, Rolf Backofen:
CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies. BMC Bioinform. 9 (2008) - [j30]Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, Rolf Backofen:
Improved identification of conserved cassette exons using Bayesian networks. BMC Bioinform. 9 (2008) - [j29]Sebastian Will, Anke Busch, Rolf Backofen:
Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination. Constraints An Int. J. 13(1-2): 110-129 (2008) - [c35]Mathias Möhl, Sebastian Will, Rolf Backofen:
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. CPM 2008: 69-81 - [c34]Wolfgang Otto, Sebastian Will, Rolf Backofen:
Structural Local Multiple Alignment of RNA. German Conference on Bioinformatics 2008: 178-188 - [c33]Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen:
Lightweight Comparison of RNAs based on Exact Sequence-structure Matches. German Conference on Bioinformatics 2008: 189-199 - [i5]Stéphane Zampelli, Martin Mann, Yves Deville, Rolf Backofen:
Decomposition Techniques for Subgraph Matching. CoRR abs/0805.1030 (2008) - 2007
- [j28]Sven Siebert, Rolf Backofen:
A Dynamic Programming Approach for Finding Common Patterns in RNAs. J. Comput. Biol. 14(1): 33-44 (2007) - [j27]Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang:
Locality and Gaps in RNA Comparison. J. Comput. Biol. 14(8): 1074-1087 (2007) - [j26]Rolf Backofen, Sven Siebert:
Fast detection of common sequence structure patterns in RNAs. J. Discrete Algorithms 5(2): 212-228 (2007) - [j25]Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer:
TassDB: a database of alternative tandem splice sites. Nucleic Acids Res. 35(Database-Issue): 188-192 (2007) - [j24]Anke Busch, Rolf Backofen:
INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints. Nucleic Acids Res. 35(Web-Server-Issue): 310-313 (2007) - [j23]Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen:
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. Nucleic Acids Res. 35(Web-Server-Issue): 688-693 (2007) - [j22]Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen:
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. 3(4) (2007) - 2006
- [j21]Anke Busch, Rolf Backofen:
INFO-RNA - a fast approach to inverse RNA folding. Bioinform. 22(15): 1823-1831 (2006) - [j20]Rolf Backofen, Sebastian Will:
A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models. Constraints An Int. J. 11(1): 5-30 (2006) - [j19]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, Ingo Krossing, Andreas W. Liehr, Andreas Karwath, Robert Klöfkorn, Raphaël Pesché, Tobias C. Potjans, Michael C. Röttger, Lars Schmidt-Thieme, Gerhard Schneider, Björn Voß, Bernd Wiebelt, Peter Wienemann, Volker-Henning Winterer:
A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative. Prax. Inf.verarb. Kommun. 29(2): 81-87 (2006) - [c32]Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann:
Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. CPM 2006: 246-257 - [r1]Rolf Backofen, David R. Gilbert:
Bioinformatics and Constraints. Handbook of Constraint Programming 2006: 905-944 - 2005
- [b2]Peter Clote, Rolf Backofen:
Computational molecular biology - an introduction. Wiley series in mathematical and computational biology, Wiley-VCH 2005, ISBN 978-0-471-87252-8, pp. I-IX, 1-286 - [j18]Rainer Pudimat, Ernst Günter Schukat-Talamazzini, Rolf Backofen:
A multiple-feature framework for modelling and predicting transcription factor binding sites. Bioinform. 21(14): 3082-3088 (2005) - [j17]Anke Busch, Sebastian Will, Rolf Backofen:
SECISDesign: a server to design SECIS-elements within the coding sequence. Bioinform. 21(15): 3312-3313 (2005) - [j16]Sven Siebert, Rolf Backofen:
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinform. 21(16): 3352-3359 (2005) - [c31]Sven Siebert, Rolf Backofen:
A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction. CIBCB 2005: 150-157 - [c30]Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann:
Normalized Similarity of RNA Sequences. SPIRE 2005: 360-369 - 2004
- [j15]Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Gläßer, Johann Christoph Freytag:
Efficient prediction of alternative splice forms using protein domain homology. Silico Biol. 4(2): 195-208 (2004) - [j14]Rolf Backofen, Sebastian Will:
Local Sequence-structure Motifs in Rna. J. Bioinform. Comput. Biol. 2(4): 681-698 (2004) - [j13]Rolf Backofen:
A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC). J. Discrete Algorithms 2(2): 161-206 (2004) - [c29]Rolf Backofen, Anke Busch:
Computational Design of New and Recombinant Selenoproteins. CPM 2004: 270-284 - [c28]Rainer Pudimat, Ernst Günter Schukat-Talamazzini, Rolf Backofen:
Feature Based Representation and Detection of Transcription Factor Binding Sites. German Conference on Bioinformatics 2004: 43-52 - [c27]Rolf Backofen, Sven Siebert:
Fast Detection of Common Sequence Structure Patterns in RNAs. SPIRE 2004: 79-92 - 2003
- [c26]Sven Siebert, Rolf Backofen:
MARNA: A server for multiple alignment of RNAs. German Conference on Bioinformatics 2003: 135-140 - [c25]Rolf Backofen, Sebastian Will:
A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods. ICLP 2003: 49-71 - 2002
- [j12]Rolf Backofen, Sebastian Will:
Excluding Symmetries in Constraint-Based Search. Constraints An Int. J. 7(3-4): 333-349 (2002) - [j11]Rolf Backofen, N. S. Narayanaswamy, Firas Swidan:
Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. Silico Biol. 2(3): 275-290 (2002) - [c24]Rolf Backofen, N. S. Narayanaswamy, Firas Swidan:
On the Complexity of Protein Similarity Search under mRNA Structure Constraints. STACS 2002: 274-286 - 2001
- [j10]David R. Gilbert, Rolf Backofen, Roland H. C. Yap:
Introduction to the Special Issue on Bioinformatics. Constraints An Int. J. 6(2/3): 139 (2001) - [j9]Rolf Backofen, David R. Gilbert:
Bioinformatics and Constraints. Constraints An Int. J. 6(2/3): 141-156 (2001) - [j8]Rolf Backofen:
The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound. Constraints An Int. J. 6(2/3): 223-255 (2001) - [c23]Rolf Backofen:
Introduction to Bioinformatics. ACL (Companion Volume) 2001: 4 - [c22]Rolf Backofen, Sebastian Will:
Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. CP 2001: 494-508 - [c21]Rolf Backofen, Sebastian Will:
Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC. CPM 2001: 257-272 - [c20]Rolf Backofen, N. S. Narayanaswamy, Firas Swidan:
Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. German Conference on Bioinformatics 2001: 135-140 - [c19]Rolf Backofen:
RNA-Sequence-Structure Properties and Selenocysteine Insertion. IDA 2001: 187-197 - 2000
- [c18]Rolf Backofen:
Exclusion of Symmetries in Search - A Spin-off from Bioinformatics Research. ARW 2000 - [c17]Rolf Backofen:
An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC). CPM 2000: 277-292
1990 – 1999
- 1999
- [j7]Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer:
Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. Bioinform. 15(3): 234-242 (1999) - [j6]Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz:
Bioinformatik - Aktuelles Schlagwort. Inform. Spektrum 22(5): 376-378 (1999) - [c16]Rolf Backofen, Sebastian Will:
Excluding Symmetries in Constraint-Based Search. CP 1999: 73-87 - [c15]Rolf Backofen, Sebastian Will, Peter Clote:
Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. German Conference on Bioinformatics 1999: 93-106 - 1998
- [j5]Rolf Backofen, Ralf Treinen:
How to Win a Game with Features. Inf. Comput. 142(1): 76-101 (1998) - [c14]Rolf Backofen:
Constraint Techniques for Solving the Protein Structure Prediction Problem. CP 1998: 72-86 - [c13]Rolf Backofen, Sebastian Will:
Structure prediction in an HP-type lattice with an extended alphabet. German Conference on Bioinformatics 1998 - 1997
- [c12]Günter Neumann, Rolf Backofen, Judith Baur, Markus Becker, Christian Braun:
An Information Extraction Core System for Real World German Text Processing. ANLP 1997: 209-216 - [c11]Rolf Backofen, Peter Clote:
Evolution as a Computational Engine. CSL 1997: 35-55 - [c10]Rolf Backofen:
Using constraint programming for lattice protein folding. German Conference on Bioinformatics 1997: 123 - [i4]Günter Neumann, Rolf Backofen, Judith Baur, Markus Becker, Christian Braun:
An Information Extraction Core System for Real World German Text Processing. CoRR cmp-lg/9706023 (1997) - 1996
- [c9]Rolf Backofen:
Controlling Functional Uncertainty. ECAI 1996: 557-561 - [i3]Rolf Backofen:
Controlling Functional Uncertainty. CoRR cmp-lg/9608002 (1996) - 1995
- [j4]Rolf Backofen:
A Complete Axiomatization of a Theory with Feature and Arity Constraints. J. Log. Program. 24(1&2): 37-71 (1995) - [j3]Rolf Backofen, James Rogers, K. Vijay-Shanker:
A First-Order Axiomatization of the Theory of Finite Trees. J. Log. Lang. Inf. 4(1): 5-39 (1995) - [j2]Rolf Backofen, Gert Smolka:
A Complete and Recursive Feature Theory. Theor. Comput. Sci. 146(1&2): 243-268 (1995) - 1994
- [b1]Rolf Backofen:
Expressivity and decidability of first-order languages over feature trees. Saarland University, Saarbrücken, Germany, 1994, pp. 1-170 - [j1]Rolf Backofen:
Regular Path Expressions in Feature Logic. J. Symb. Comput. 17(5): 421-455 (1994) - [c8]Rolf Backofen, Ralf Treinen:
How to Win a Game with Features. CCL 1994: 320-335 - [c7]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:
DISCO-An HPSG-based NLP System and its Application for Appointment Scheduling Project Note. COLING 1994: 436-440 - [i2]Rolf Backofen, Gert Smolka:
A Complete and Recursive Feature Theory. CoRR abs/cmp-lg/9406019 (1994) - [i1]Hans Uszkoreit, Rolf Backofen, Stephan Busemann, Abdel Kader Diagne, Elizabeth A. Hinkelman, Walter Kasper, Bernd Kiefer, Hans-Ulrich Krieger, Klaus Netter, Guenter Neumann, Stephan Oepen, Stephen P. Spackman:
DISCO - An HPSG-based NLP System and its Application for Appointment Scheduling (Project Note). CoRR abs/cmp-lg/9406035 (1994) - 1993
- [c6]Rolf Backofen, Gert Smolka:
A Complete and Recursive Feature Theory. ACL 1993: 193-200 - [c5]Rolf Backofen:
On the Decidability of Functional Uncertainty. ACL 1993: 201-208 - [c4]Rolf Backofen:
Regular Path Expression in Feature Logic. RTA 1993: 121-135 - 1991
- [c3]Rolf Backofen, Lutz Euler, Günther Görz:
Distributed Disjunctions for LIFE. PDK 1991: 161-170 - [c2]Rolf Backofen, Harald Trost, Hans Uszkoreit:
Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends. Wissensbasierte Systeme 1991: 375-383 - 1990
- [c1]Rolf Backofen, Lutz Euler, Günther Görz:
Towards the Integration of Functions, Relations and Types in an AI Programming Language. GWAI 1990: 297-306
Coauthor Index
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