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Rolf Backofen
2010 – today
- 2013
[j54]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 for Molecular Biology 8: 14 (2013)- [c48]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
- 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 (2012)
- [j52]Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen: GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics 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. Bioinformatics 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 Research 40(Web-Server-Issue): 49-53 (2012)
- [c47]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
- [c46]Saad Sheikh, Rolf Backofen, Yann Ponty: Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. CPM 2012: 321-333
- [c45]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. Bioinformatics 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. Bioinformatics 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 Bioinformatics 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 Research 39(Web-Server-Issue): 107-111 (2011)
- 2010
- [j43]Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp: Fast prediction of RNA-RNA interaction. Algorithms for Molecular Biology 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 for Molecular Biology 5: 22 (2010)
- [j41]Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, Süleyman Cenk Sahinalp: Sparsification of RNA structure prediction including pseudoknots. Algorithms for Molecular Biology 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. Bioinformatics 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 Bioinformatics 11: 216 (2010)
- [j38]Mathias Möhl, Sebastian Will, Rolf Backofen: Lifting Prediction to Alignment of RNA Pseudoknots. Journal of Computational Biology 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 Research 38(Web-Server-Issue): 373-377 (2010)
- [c44]Sergiy Bogomolov, Martin Mann, Björn Voß, Andreas Podelski, Rolf Backofen: Shape-based Barrier Estimation for RNAs. GCB 2010: 41-50
- [c43]Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler: Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56
- [c42]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
- [c41]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. Bioinformatics 25(5): 676-677 (2009)
- [j35]Hamidreza Chitsaz, Raheleh Salari, Süleyman Cenk Sahinalp, Rolf Backofen: A partition function algorithm for interacting nucleic acid strands. Bioinformatics 25(12) (2009)
- [j34]Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen: Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics 25(16): 2095-2102 (2009)
- [j33]Rainer Pudimat, Rolf Backofen, Ernst Günter Schukat-Talamazzini: Fast Feature Subset Selection in Biological Sequence Analysis. IJPRAI 23(2): 191-207 (2009)
- [c40]Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann: Fast RNA Structure Alignment for Crossing Input Structures. CPM 2009: 236-248
- [c39]Rolf Backofen, Dekel Tsur, Shay Zakov, Michal Ziv-Ukelson: Sparse RNA Folding: Time and Space Efficient Algorithms. CPM 2009: 249-262
- [c38]Mathias Möhl, Sebastian Will, Rolf Backofen: Lifting Prediction to Alignment of RNA Pseudoknots. RECOMB 2009: 285-301
- [c37]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
- [c36]Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp: biRNA: Fast RNA-RNA Binding Sites Prediction. WABI 2009: 25-36
- [c35]Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp: Fast Prediction of RNA-RNA Interaction. WABI 2009: 261-272
- [i5]Martin Mann, Rolf Backofen, Sebastian Will: Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains. CoRR abs/0910.3848 (2009)
- [i4]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. Bioinformatics 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 Bioinformatics 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 Bioinformatics 9 (2008)
- [j29]Sebastian Will, Anke Busch, Rolf Backofen: Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination. Constraints 13(1-2): 110-129 (2008)
- [c34]Mathias Möhl, Sebastian Will, Rolf Backofen: Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. CPM 2008: 69-81
- [c33]Wolfgang Otto, Sebastian Will, Rolf Backofen: Structural Local Multiple Alignment of RNA. German Conference on Bioinformatics 2008: 178-177
- [c32]Steffen Heyne, Sebastian Will, Michael Beckstette, Rolf Backofen: Lightweight Comparison of RNAs based on Exact Sequence-structure Matches. German Conference on Bioinformatics 2008: 189-
- [i3]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. Journal of Computational Biology 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. Journal of Computational Biology 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 Research 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 Research 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 Research 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 Computational Biology 3(4) (2007)
- 2006
- [j21]Anke Busch, Rolf Backofen: INFO-RNA - a fast approach to inverse RNA folding. Bioinformatics 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 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. Praxis der Informationsverarbeitung und Kommunikation 29(2): 81-87 (2006)
- [c31]Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann: Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. CPM 2006: 246-257
- 2005
- [j18]Rainer Pudimat, Ernst Günter Schukat-Talamazzini, Rolf Backofen: A multiple-feature framework for modelling and predicting transcription factor binding sites. Bioinformatics 21(14): 3082-3088 (2005)
- [j17]Anke Busch, Sebastian Will, Rolf Backofen: SECISDesign: a server to design SECIS-elements within the coding sequence. Bioinformatics 21(15): 3312-3313 (2005)
- [j16]Sven Siebert, Rolf Backofen: MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 21(16): 3352-3359 (2005)
- [c30]Sven Siebert, Rolf Backofen: A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction. CIBCB 2005: 150-157
- [c29]Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann: Normalized Similarity of RNA Sequences. SPIRE 2005: 360-369
- 2004
- [b1]Rolf Backofen: Expressivity and decidability of first-order languages over feature trees. Saarland University 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. In Silico Biology 4 (2004)
- [j14]Rolf Backofen, Sebastian Will: Local Sequence-structure Motifs in Rna. J. Bioinformatics and Computational Biology 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)
- [c28]Rolf Backofen, Anke Busch: Computational Design of New and Recombinant Selenoproteins. CPM 2004: 270-284
- [c27]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
- [c26]Rolf Backofen, Sven Siebert: Fast Detection of Common Sequence Structure Patterns in RNAs. SPIRE 2004: 79-92
- 2003
- [c25]Sven Siebert, Rolf Backofen: MARNA: A server for multiple alignment of RNAs. German Conference on Bioinformatics 2003: 135-140
- [c24]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 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. In Silico Biology 2: 26 (2002)
- [c23]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 Gilbert, Rolf Backofen, Roland H. C. Yap: Introduction to the Special Issue on Bioinformatics. Constraints 6(2/3): 139 (2001)
- [j9]
- [j8]Rolf Backofen: The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound. Constraints 6(2/3): 223-255 (2001)
- [c22]
- [c21]Rolf Backofen, Sebastian Will: Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores. CP 2001: 494-508
- [c20]Rolf Backofen, Sebastian Will: Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC. CPM 2001: 257-272
- [c19]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
- [c18]
- 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. Bioinformatics 15(3): 234-242 (1999)
- [j6]Rolf Backofen, François Bry, Peter Clote, Hans-Peter Kriegel, Thomas Seidl, Klaus U. Schulz: Bioinformatik - Aktuelles Schlagwort. Informatik Spektrum 22(5): 376-378 (1999)
- [c16]
- [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]
- [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]
- [c10]Rolf Backofen: Using constraint programming for lattice protein folding. German Conference on Bioinformatics 1997: 123
- [i2]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]
- [i1]
- 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. Journal of Logic, Language and Information 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
- [j1]
- [c8]
- [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
- 1993
- [c6]
- [c5]
- [c4]
- 1991
- [c3]
- [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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last updated on 2013-05-13 21:38 CEST by the dblp team