Rolf Backofen - RankMe

183 papers A* 2A 6B 20C 8Misc 1Journal 121Unranked 22

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	An evolutionary approach to predict the orientation of CRISPR arrays. PLoS Comput. Biol. Axel Fehrenbach, Alexander Mitrofanov, Omer S. Alkhnbashi, Rolf Backofen, Franz Baumdicker
2025	J	`jnl`	Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data. Briefings Bioinform. Maren Hackenberg, Laia Canal Guitart, Rolf Backofen, Harald Binder
2025	J	`jnl`	Learning to generate feasible graphs using graph grammars. CoRR Stefan Mautner, Rolf Backofen, Fabrizio Costa
2025	J	`jnl`	Small Data Explainer - The impact of small data methods in everyday life. CoRR 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
2024	—	`conf`	CRISPert: A Transformer-Based Model for CRISPR-Cas Off-Target Prediction. ECML/PKDD (7) William Jobson Pargeter, Rolf Backofen, Van Dinh Tran
2024	J	`jnl`	Partial RNA design. Bioinform. Frederic Runge, Jörg K. H. Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter
2023	—	`conf`	Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. CoRDI 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
2023	J	`jnl`	RNA interaction format: a general data format for RNA interactions. Bioinform. Richard A. Schäfer, Dominik Rabsch, Guillaume E. Scholz, Peter F. Stadler, Wolfgang R. Hess, Rolf Backofen, Jörg Fallmann, Björn Voß
2023	J	`jnl`	Transformer-based tool recommendation system in Galaxy. BMC Bioinform. Anup Kumar, Björn A. Grüning, Rolf Backofen
2022	J	`jnl`	CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection. Bioinform. Alexander Mitrofanov, Marcus Ziemann, Omer S. Alkhnbashi, Wolfgang R. Hess, Rolf Backofen
2022	J	`jnl`	Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. J. Cheminformatics Simon Bray, Tim Dudgeon, Rachael Skyner, Rolf Backofen, Björn A. Grüning, Frank von Delft
2022	J	`jnl`	Peakhood: individual site context extraction for CLIP-seq peak regions. Bioinform. Michael Uhl, Dominik Rabsch, Florian Eggenhofer, Rolf Backofen
2022	J	`jnl`	RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. Briefings Bioinform. Rick Gelhausen, Teresa Müller, Sarah L. Svensson, Omer S. Alkhnbashi, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen
2021	J	`jnl`	<tt>CRISPRloci: </tt> comprehensive and accurate annotation of CRISPR-Cas systems. Nucleic Acids Res. 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
2021	J	`jnl`	A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinform. Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'anna, Dilmurat Yusuf, Björn A. Grüning, Rolf Backofen, Frederik Coppens
2021	J	`jnl`	Casboundary: automated definition of integral Cas cassettes. Bioinform. Victor Alexandre Padilha, Omer S. Alkhnbashi, Van Dinh Tran, Shiraz A. Shah, André C. P. L. F. de Carvalho, Rolf Backofen
2021	J	`jnl`	HRIBO: high-throughput analysis of bacterial ribosome profiling data. Bioinform. Rick Gelhausen, Sarah L. Svensson, Kathrin Froschauer, Florian Heyl, Lydia Hadjeras, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen
2021	J	`jnl`	Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. Bioinform. Joachim Wolff, Rolf Backofen, Björn A. Grüning
2021	J	`jnl`	Scool: a new data storage format for single-cell Hi-C data. Bioinform. Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning
2021	J	`jnl`	Scool: a new data storage format for single-cell Hi-C data. Bioinform. Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning
2021	J	`jnl`	pyGenomeTracks: reproducible plots for multivariate genomic datasets. Bioinform. Lucille Lopez-Delisle, Leily Rabbani, Joachim Wolff, Vivek Bhardwaj, Rolf Backofen, Björn A. Grüning, Fidel Ramírez, Thomas Manke
2020	J	`jnl`	Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. Algorithms Mol. Biol. Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen
2020	J	`jnl`	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. Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A. Grüning
2020	J	`jnl`	Heterogeneous networks integration for disease-gene prioritization with node kernels. Bioinform. Dinh Van Tran, Alessandro Sperduti, Rolf Backofen, Fabrizio Costa
2020	J	`jnl`	MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. Nucleic Acids Res. Milad Miladi, Martin Raden, Sven Diederichs, Rolf Backofen
2020	J	`jnl`	The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment. BMC Bioinform. Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen, Rolf Backofen
2020	J	`jnl`	The locality dilemma of Sankoff-like RNA alignments. Bioinform. Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen
2019	J	`jnl`	Advances and Challenges in Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 19342). Dagstuhl Reports Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani
2019	—	`conf`	Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction. BIOINFORMATICS Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
2019	C	`conf`	Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. WABI Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen
2019	J	`jnl`	IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. J. Bioinform. Comput. Biol. Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
2019	J	`jnl`	Integration of accessibility data from structure probing into RNA-RNA interaction prediction. Bioinform. Milad Miladi, Soheila Montaseri, Rolf Backofen, Martin Raden
2019	B	`conf`	Progress Towards Graph Optimization: Efficient Learning of Vector to Graph Space Mappings. ESANN Stefan Mautner, Rolf Backofen, Fabrizio Costa
2019	J	`jnl`	ShaKer: RNA SHAPE prediction using graph kernel. Bioinform. Stefan Mautner, Soheila Montaseri, Milad Miladi, Martin Raden, Fabrizio Costa, Rolf Backofen
2019	J	`jnl`	The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Res. Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning
2018	J	`jnl`	CMV: visualization for RNA and protein family models and their comparisons. Bioinform. Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen, Christian Höner zu Siederdissen
2018	J	`jnl`	Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res. 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
2018	J	`jnl`	Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res. Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A. Grüning
2018	J	`jnl`	MICA: Multiple interval-based curve alignment. SoftwareX Martin Mann, Hans-Peter Kahle, Matthias Beck, Bela Johannes Bender, Heinrich Spiecker, Rolf Backofen
2018	J	`jnl`	MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Bioinform. 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
2017	J	`jnl`	Computational Challenges in RNA-Based Gene Regulation: Protein-RNA Recognition, Regulation and Prediction (Dagstuhl Seminar 17252). Dagstuhl Reports Rolf Backofen, Yael Mandel-Gutfreund, Uwe Ohler, Gabriele Varani
2017	J	`jnl`	DHX9 suppresses RNA processing defects originating from the Nat. Tugçe Aktas, Ibrahim Avsar Ilik, Daniel Maticzka, Vivek Bhardwaj, Cecilia Pessoa Rodrigues, Gerhard Mittler, Thomas Manke, Rolf Backofen, Asifa Akhtar
2017	J	`jnl`	IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. Nucleic Acids Res. Martin Mann, Patrick R. Wright, Rolf Backofen
2017	J	`jnl`	Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PLoS Comput. Biol. Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
2017	J	`jnl`	RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. Bioinform. Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen
2017	J	`jnl`	The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 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
2016	B	`conf`	AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. RECOMB Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka
2016	J	`jnl`	AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. CoRR Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen, Teresa M. Przytycka
2016	J	`jnl`	Characterizing leader sequences of CRISPR loci. Bioinform. Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa, Rolf Backofen
2016	J	`jnl`	SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. BMC Bioinform. João Victor de Araújo Oliveira, Fabrizio Costa, Rolf Backofen, Peter F. Stadler, Maria Emília Telles Walter, Jana Hertel
2015	J	`jnl`	SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinform. Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, Rolf Backofen
2015	J	`jnl`	antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. BMC Bioinform. Robert Kleinkauf, Torsten Houwaart, Rolf Backofen, Martin Mann
2015	J	`jnl`	antaRNA: ant colony-based RNA sequence design. Bioinform. Robert Kleinkauf, Martin Mann, Rolf Backofen
2014	J	`jnl`	Atom mapping with constraint programming. Algorithms Mol. Biol. Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm
2014	J	`jnl`	BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. Bioinform. Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen
2014	—	`conf`	Blockclust: efficient clustering and classification of non-coding rnas from short Read RNA-seq profiles. GCB Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen
2014	J	`jnl`	CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinform. Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen
2014	J	`jnl`	Cluster based prediction of PDZ-peptide interactions. BMC Genom. Kousik Kundu, Rolf Backofen
2014	J	`jnl`	CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res. Patrick R. Wright, Jens Georg, Martin Mann, Dragos Alexandru Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, Rolf Backofen
2014	J	`jnl`	Exact methods for lattice protein models. Bio Algorithms Med Syst. Martin Mann, Rolf Backofen
2014	J	`jnl`	ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinform. Christina Otto, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Rolf Backofen, Sebastian Will
2014	J	`jnl`	Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. Algorithms Mol. Biol. Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler, Rolf Backofen
2014	J	`jnl`	Local Exact Pattern Matching for Non-FixedRNA Structures. IEEE ACM Trans. Comput. Biol. Bioinform. Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Otto, Sebastian Will
2014	J	`jnl`	MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. Bioinform. Kousik Kundu, Martin Mann, Fabrizio Costa, Rolf Backofen
2014	—	`conf`	Scalable structural clustering of local RNA secondary structures. CMSR@ECCB Fabrizio Costa, Steffen Heyne, Dominic Rose, Rolf Backofen
2014	J	`jnl`	Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2013	J	`jnl`	A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. Bioinform. Kousik Kundu, Fabrizio Costa, Rolf Backofen
2013	A	`conf`	Atom Mapping with Constraint Programming. CP Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm
2013	C	`conf`	Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. WABI Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler
2013	J	`jnl`	Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J. Biomed. Semant. Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno-Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin
2013	J	`jnl`	LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol. Biol. Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen
2013	B	`conf`	SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. RECOMB Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen
2012	J	`jnl`	CARNA - alignment of RNA structure ensembles. Nucleic Acids Res. Dragos Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, Sebastian Will
2012	B	`conf`	Exact Pattern Matching for RNA Structure Ensembles. RECOMB Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen
2012	J	`jnl`	GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinform. Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen
2012	B	`conf`	Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. CPM Saad Sheikh, Rolf Backofen, Yann Ponty
2012	B	`conf`	Local Exact Pattern Matching for Non-fixed RNA Structures. CPM Mika Amit, Rolf Backofen, Steffen Heyne, Gad M. Landau, Mathias Möhl, Christina Schmiedl, Sebastian Will
2012	J	`jnl`	Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinform. Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen
2012	J	`jnl`	Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. Adv. Bioinformatics Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane
2011	J	`jnl`	Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinform. Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler
2011	J	`jnl`	Fast RNA structure alignment for crossing input structures. J. Discrete Algorithms Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann
2011	J	`jnl`	PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinform. Stefan E. Seemann, Andreas S. Richter, Tanja Gesell, Rolf Backofen, Jan Gorodkin
2011	J	`jnl`	Sparse RNA folding: Time and space efficient algorithms. J. Discrete Algorithms Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
2011	J	`jnl`	Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinform. Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette
2011	J	`jnl`	The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. Nucleic Acids Res. Stefan E. Seemann, Peter Menzel, Rolf Backofen, Jan Gorodkin
2010	J	`jnl`	Fast prediction of RNA-RNA interaction. Algorithms Mol. Biol. Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
2010	J	`jnl`	Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. Nucleic Acids Res. Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen
2010	J	`jnl`	Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms Mol. Biol. Stefan E. Seemann, Andreas S. Richter, Jan Gorodkin, Rolf Backofen
2010	J	`jnl`	Lifting Prediction to Alignment of RNA Pseudoknots. J. Comput. Biol. Mathias Möhl, Sebastian Will, Rolf Backofen
2010	J	`jnl`	Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinform. Andreas S. Richter, Christian Schleberger, Rolf Backofen, Claudia Steglich
2010	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
2010	—	`conf`	Shape-based Barrier Estimation for RNAs. GCB Sergiy Bogomolov, Martin Mann, Björn Voß, Andreas Podelski, Rolf Backofen
2010	C	`conf`	Sparsification of RNA Structure Prediction Including Pseudoknots. WABI Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
2010	J	`jnl`	Sparsification of RNA structure prediction including pseudoknots. Algorithms Mol. Biol. Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp
2010	J	`jnl`	TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinform. 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
2010	B	`conf`	Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. RECOMB Raheleh Salari, Mathias Möhl, Sebastian Will, Süleyman Cenk Sahinalp, Rolf Backofen
2009	J	`jnl`	A partition function algorithm for interacting nucleic acid strands. Bioinform. Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen
2009	J	`jnl`	CPSP-web-tools: a server for 3D lattice protein studies. Bioinform. Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen
2009	J	`jnl`	Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains CoRR Martin Mann, Mohamed Abou Hamra, Kathleen Steinhöfel, Rolf Backofen
2009	J	`jnl`	Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains CoRR Martin Mann, Rolf Backofen, Sebastian Will
2009	J	`jnl`	Fast Feature Subset Selection in Biological Sequence Analysis. Int. J. Pattern Recognit. Artif. Intell. Rainer Pudimat, Rolf Backofen, Ernst Günter Schukat-Talamazzini
2009	C	`conf`	Fast Prediction of RNA-RNA Interaction. WABI Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
2009	B	`conf`	Fast RNA Structure Alignment for Crossing Input Structures. CPM Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann
2009	B	`conf`	Lifting Prediction to Alignment of RNA Pseudoknots. RECOMB Mathias Möhl, Sebastian Will, Rolf Backofen
2009	J	`jnl`	Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinform. Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen
2009	B	`conf`	Simultaneous Alignment and Folding of Protein Sequences. RECOMB Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2009	B	`conf`	Sparse RNA Folding: Time and Space Efficient Algorithms. CPM Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson
2009	C	`conf`	biRNA: Fast RNA-RNA Binding Sites Prediction. WABI Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp
2008	J	`jnl`	CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies. BMC Bioinform. Martin Mann, Sebastian Will, Rolf Backofen
2008	J	`jnl`	Decomposition Techniques for Subgraph Matching CoRR Stéphane Zampelli, Martin Mann, Yves Deville, Rolf Backofen
2008	J	`jnl`	Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination. Constraints An Int. J. Sebastian Will, Anke Busch, Rolf Backofen
2008	B	`conf`	Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. CPM Mathias Möhl, Sebastian Will, Rolf Backofen
2008	J	`jnl`	Improved identification of conserved cassette exons using Bayesian networks. BMC Bioinform. Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, Rolf Backofen
2008	J	`jnl`	IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinform. Anke Busch, Andreas S. Richter, Rolf Backofen
2008	—	`conf`	Lightweight Comparison of RNAs based on Exact Sequence-structure Matches. German Conference on Bioinformatics Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen
2008	—	`conf`	Structural Local Multiple Alignment of RNA. German Conference on Bioinformatics Wolfgang Otto, Sebastian Will, Rolf Backofen
2007	J	`jnl`	A Dynamic Programming Approach for Finding Common Patterns in RNAs. J. Comput. Biol. Sven Siebert, Rolf Backofen
2007	J	`jnl`	BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. Nucleic Acids Res. Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen
2007	J	`jnl`	Fast detection of common sequence structure patterns in RNAs. J. Discrete Algorithms Rolf Backofen, Sven Siebert
2007	J	`jnl`	INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints. Nucleic Acids Res. Anke Busch, Rolf Backofen
2007	J	`jnl`	Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
2007	J	`jnl`	Locality and Gaps in RNA Comparison. J. Comput. Biol. Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang
2007	J	`jnl`	TassDB: a database of alternative tandem splice sites. Nucleic Acids Res. Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, Matthias Platzer
2006	J	`jnl`	A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative. Prax. Inf.verarb. Kommun. 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
2006	J	`jnl`	A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models. Constraints An Int. J. Rolf Backofen, Sebastian Will
2006	—	`ch.`	Bioinformatics and Constraints. Handbook of Constraint Programming Rolf Backofen, David R. Gilbert
2006	J	`jnl`	INFO-RNA - a fast approach to inverse RNA folding. Bioinform. Anke Busch, Rolf Backofen
2006	B	`conf`	Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. CPM Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann
2005	C	`conf`	A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction. CIBCB Sven Siebert, Rolf Backofen
2005	J	`jnl`	A multiple-feature framework for modelling and predicting transcription factor binding sites. Bioinform. Rainer Pudimat, Ernst Günter Schukat-Talamazzini, Rolf Backofen
2005	—	`book`	Computational molecular biology - an introduction. Peter Clote, Rolf Backofen
2005	J	`jnl`	MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinform. Sven Siebert, Rolf Backofen
2005	C	`conf`	Normalized Similarity of RNA Sequences. SPIRE Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann
2005	J	`jnl`	SECISDesign: a server to design SECIS-elements within the coding sequence. Bioinform. Anke Busch, Sebastian Will, Rolf Backofen
2004	J	`jnl`	A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC). J. Discrete Algorithms Rolf Backofen
2004	B	`conf`	Computational Design of New and Recombinant Selenoproteins. CPM Rolf Backofen, Anke Busch
2004	J	`jnl`	Efficient prediction of alternative splice forms using protein domain homology. Silico Biol. Michael Hiller, Rolf Backofen, Stephan Heymann, Anke Busch, Timo Mika Gläßer, Johann Christoph Freytag
2004	C	`conf`	Fast Detection of Common Sequence Structure Patterns in RNAs. SPIRE Rolf Backofen, Sven Siebert
2004	—	`conf`	Feature Based Representation and Detection of Transcription Factor Binding Sites. German Conference on Bioinformatics Rainer Pudimat, Ernst Günter Schukat-Talamazzini, Rolf Backofen
2004	J	`jnl`	Local Sequence-structure Motifs in Rna. J. Bioinform. Comput. Biol. Rolf Backofen, Sebastian Will
2003	B	`conf`	A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods. ICLP Rolf Backofen, Sebastian Will
2003	—	`conf`	MARNA: A server for multiple alignment of RNAs. German Conference on Bioinformatics Sven Siebert, Rolf Backofen
2002	J	`jnl`	Excluding Symmetries in Constraint-Based Search. Constraints An Int. J. Rolf Backofen, Sebastian Will
2002	A	`conf`	On the Complexity of Protein Similarity Search under mRNA Structure Constraints. STACS Rolf Backofen, N. S. Narayanaswamy, Firas Swidan
2002	J	`jnl`	Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. Silico Biol. Rolf Backofen, N. S. Narayanaswamy, Firas Swidan
2001	J	`jnl`	Bioinformatics and Constraints. Constraints An Int. J. Rolf Backofen, David R. Gilbert
2001	A	`conf`	Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. CP Rolf Backofen, Sebastian Will
2001	—	`conf`	Introduction to Bioinformatics. ACL (Companion Volume) Rolf Backofen
2001	J	`jnl`	Introduction to the Special Issue on Bioinformatics. Constraints An Int. J. David R. Gilbert, Rolf Backofen, Roland H. C. Yap
2001	B	`conf`	Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC. CPM Rolf Backofen, Sebastian Will
2001	—	`conf`	Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation. German Conference on Bioinformatics Rolf Backofen, N. S. Narayanaswamy, Firas Swidan
2001	B	`conf`	RNA-Sequence-Structure Properties and Selenocysteine Insertion. IDA Rolf Backofen
2001	J	`jnl`	The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound. Constraints An Int. J. Rolf Backofen
2000	B	`conf`	An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC). CPM Rolf Backofen
2000	—	`conf`	Exclusion of Symmetries in Search - A Spin-off from Bioinformatics Research. ARW Rolf Backofen
1999	—	`conf`	Algorithmic approach to quantifying the hydrophobic force contribution in protein folding. German Conference on Bioinformatics Rolf Backofen, Sebastian Will, Peter Clote
1999	J	`jnl`	Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. Bioinform. Rolf Backofen, Sebastian Will, Erich Bornberg-Bauer
1999	J	`jnl`	Bioinformatik - Aktuelles Schlagwort. Inform. Spektrum Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz
1999	A	`conf`	Excluding Symmetries in Constraint-Based Search. CP Rolf Backofen, Sebastian Will
1998	A	`conf`	Constraint Techniques for Solving the Protein Structure Prediction Problem. CP Rolf Backofen
1998	J	`jnl`	How to Win a Game with Features. Inf. Comput. Rolf Backofen, Ralf Treinen
1998	—	`conf`	Structure prediction in an HP-type lattice with an extended alphabet. German Conference on Bioinformatics Rolf Backofen, Sebastian Will
1997	J	`jnl`	An Information Extraction Core System for Real World German Text Processing CoRR Günter Neumann, Rolf Backofen, Judith Baur, Markus Becker, Christian Braun
1997	—	`conf`	An Information Extraction Core System for Real World German Text Processing. ANLP Günter Neumann, Rolf Backofen, Judith Baur, Markus Becker, Christian Braun
1997	B	`conf`	Evolution as a Computational Engine. CSL Rolf Backofen, Peter Clote
1997	—	`conf`	Using constraint programming for lattice protein folding. German Conference on Bioinformatics Rolf Backofen
1996	J	`jnl`	Controlling Functional Uncertainty CoRR Rolf Backofen
1996	A	`conf`	Controlling Functional Uncertainty. ECAI Rolf Backofen
1995	J	`jnl`	A Complete Axiomatization of a Theory with Feature and Arity Constraints. J. Log. Program. Rolf Backofen
1995	J	`jnl`	A Complete and Recursive Feature Theory. Theor. Comput. Sci. Rolf Backofen, Gert Smolka
1995	J	`jnl`	A First-Order Axiomatization of the Theory of Finite Trees. J. Log. Lang. Inf. Rolf Backofen, James Rogers, K. Vijay-Shanker
1994	J	`jnl`	A Complete and Recursive Feature Theory. CoRR Rolf Backofen, Gert Smolka
1994	J	`jnl`	DISCO - An HPSG-based NLP System and its Application for Appointment Scheduling (Project Note). CoRR 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
1994	B	`conf`	DISCO-An HPSG-based NLP System and its Application for Appointment Scheduling Project Note. COLING 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
1994	—	`—`	Expressivity and decidability of first-order languages over feature trees. Rolf Backofen
1994	—	`conf`	How to Win a Game with Features. CCL Rolf Backofen, Ralf Treinen
1994	J	`jnl`	Regular Path Expressions in Feature Logic. J. Symb. Comput. Rolf Backofen
1993	A*	`conf`	A Complete and Recursive Feature Theory. ACL Rolf Backofen, Gert Smolka
1993	A*	`conf`	On the Decidability of Functional Uncertainty. ACL Rolf Backofen
1993	—	`conf`	Regular Path Expression in Feature Logic. RTA Rolf Backofen
1991	—	`conf`	Distributed Disjunctions for LIFE. PDK Rolf Backofen, Lutz Euler, Günther Görz
1991	—	`conf`	Linking Typed Feature Formalisms and Terminological Knowledge Representation Languages in Natural Language Front-Ends. Wissensbasierte Systeme Rolf Backofen, Harald Trost, Hans Uszkoreit
1990	—	`conf`	Towards the Integration of Functions, Relations and Types in an AI Programming Language. GWAI Rolf Backofen, Lutz Euler, Günther Görz