 | 2009 |
|---|
| 79 |       | Rolf Backofen,
Gad M. Landau,
Mathias Möhl,
Dekel Tsur,
Oren Weimann:
Fast RNA Structure Alignment for Crossing Input Structures.
CPM 2009: 236-248 |
| 78 | | Rolf Backofen,
Dekel Tsur,
Shay Zakov,
Michal Ziv-Ukelson:
Sparse RNA Folding: Time and Space Efficient Algorithms.
CPM 2009: 249-262 |
| 77 | | Mathias Möhl,
Sebastian Will,
Rolf Backofen:
Lifting Prediction to Alignment of RNA Pseudoknots.
RECOMB 2009: 285-301 |
| 76 | | 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 |
| 75 | | Hamidreza Chitsaz,
Rolf Backofen,
Süleyman Cenk Sahinalp:
biRNA: Fast RNA-RNA Binding Sites Prediction.
WABI 2009: 25-36 |
| 74 | | Raheleh Salari,
Rolf Backofen,
Süleyman Cenk Sahinalp:
Fast Prediction of RNA-RNA Interaction.
WABI 2009: 261-272 |
| 73 | | Hamidreza Chitsaz,
Raheleh Salari,
Süleyman Cenk Sahinalp,
Rolf Backofen:
A partition function algorithm for interacting nucleic acid strands.
Bioinformatics 25(12): (2009) |
| 72 | | Steffen Heyne,
Sebastian Will,
Michael Beckstette,
Rolf Backofen:
Lightweight comparison of RNAs based on exact sequence-structure matches.
Bioinformatics 25(16): 2095-2102 (2009) |
| 71 | | 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) |
| 70 | | Martin Mann,
Rolf Backofen,
Sebastian Will:
Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains
CoRR abs/0910.3848: (2009) |
| 69 | | 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) |
| 68 | | Rainer Pudimat,
Rolf Backofen,
Ernst Günter Schukat-Talamazzini:
Fast Feature Subset Selection in Biological Sequence Analysis.
IJPRAI 23(2): 191-207 (2009) |
| 2008 |
|---|
| 67 | | Mathias Möhl,
Sebastian Will,
Rolf Backofen:
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots.
CPM 2008: 69-81 |
| 66 |  | Wolfgang Otto,
Sebastian Will,
Rolf Backofen:
Structural Local Multiple Alignment of RNA.
German Conference on Bioinformatics 2008: 178-177 |
| 65 | | Steffen Heyne,
Sebastian Will,
Michael Beckstette,
Rolf Backofen:
Lightweight Comparison of RNAs based on Exact Sequence-structure Matches.
German Conference on Bioinformatics 2008: 189- |
| 64 | | Martin Mann,
Sebastian Will,
Rolf Backofen:
CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies.
BMC Bioinformatics 9: (2008) |
| 63 | | 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) |
| 62 | | 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) |
| 61 | | Stéphane Zampelli,
Martin Mann,
Yves Deville,
Rolf Backofen:
Decomposition Techniques for Subgraph Matching
CoRR abs/0805.1030: (2008) |
| 60 | | Sebastian Will,
Anke Busch,
Rolf Backofen:
Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination.
Constraints 13(1-2): 110-129 (2008) |
| 2007 |
|---|
| 59 | | Rolf Backofen,
Sven Siebert:
Fast detection of common sequence structure patterns in RNAs.
J. Discrete Algorithms 5(2): 212-228 (2007) |
| 58 | | Sven Siebert,
Rolf Backofen:
A Dynamic Programming Approach for Finding Common Patterns in RNAs.
Journal of Computational Biology 14(1): 33-44 (2007) |
| 57 | | 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) |
| 56 | | 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) |
| 55 | | 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) |
| 54 | | 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) |
| 2006 |
|---|
| 53 | | Rolf Backofen,
Danny Hermelin,
Gad M. Landau,
Oren Weimann:
Local Alignment of RNA Sequences with Arbitrary Scoring Schemes.
CPM 2006: 246-257 |
| 52 | | Anke Busch,
Rolf Backofen:
INFO-RNA - a fast approach to inverse RNA folding.
Bioinformatics 22(15): 1823-1831 (2006) |
| 51 | | 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) |
| 2005 |
|---|
| 50 | | Sven Siebert,
Rolf Backofen:
A New Distance Measure of RNA Ensembles and Its Application to Phylogenetic Tree Construction.
CIBCB 2005: 150-157 |
| 49 | | Rolf Backofen,
Danny Hermelin,
Gad M. Landau,
Oren Weimann:
Normalized Similarity of RNA Sequences.
SPIRE 2005: 360-369 |
| 48 | | 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) |
| 47 | | Anke Busch,
Sebastian Will,
Rolf Backofen:
SECISDesign: a server to design SECIS-elements within the coding sequence.
Bioinformatics 21(15): 3312-3313 (2005) |
| 46 | | Sven Siebert,
Rolf Backofen:
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.
Bioinformatics 21(16): 3352-3359 (2005) |
| 2004 |
|---|
| 45 | | Rolf Backofen,
Anke Busch:
Computational Design of New and Recombinant Selenoproteins.
CPM 2004: 270-284 |
| 44 | | 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 |
| 43 | | Rolf Backofen,
Sven Siebert:
Fast Detection of Common Sequence Structure Patterns in RNAs.
SPIRE 2004: 79-92 |
| 42 | | 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) |
| 41 | | Rolf Backofen,
Sebastian Will:
Local Sequence-structure Motifs in Rna.
J. Bioinformatics and Computational Biology 2(4): 681-698 (2004) |
| 40 | | 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) |
| 2003 |
|---|
| 39 | | Sven Siebert,
Rolf Backofen:
MARNA: A server for multiple alignment of RNAs.
German Conference on Bioinformatics 2003: 135-140 |
| 38 | | 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 |
|---|
| 37 | | Rolf Backofen,
N. S. Narayanaswamy,
Firas Swidan:
On the Complexity of Protein Similarity Search under mRNA Structure Constraints.
STACS 2002: 274-286 |
| 36 | | Rolf Backofen,
Sebastian Will:
Excluding Symmetries in Constraint-Based Search.
Constraints 7(3-4): 333-349 (2002) |
| 35 | | Rolf Backofen,
N. S. Narayanaswamy,
Firas Swidan:
Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation.
In Silico Biology 2: 26 (2002) |
| 2001 |
|---|
| 34 | | Rolf Backofen:
Introduction to Bioinformatics.
ACL (Companion Volume) 2001: 4 |
| 33 | | Rolf Backofen,
Sebastian Will:
Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores.
CP 2001: 494-508 |
| 32 | | Rolf Backofen,
Sebastian Will:
Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC.
CPM 2001: 257-272 |
| 31 | | 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 |
| 30 | | Rolf Backofen:
RNA-Sequence-Structure Properties and Selenocysteine Insertion.
IDA 2001: 187-197 |
| 29 | | David Gilbert,
Rolf Backofen,
Roland H. C. Yap:
Introduction to the Special Issue on Bioinformatics.
Constraints 6(2/3): 139 (2001) |
| 28 | | Rolf Backofen,
David Gilbert:
Bioinformatics and Constraints.
Constraints 6(2/3): 141-156 (2001) |
| 27 | | Rolf Backofen:
The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound.
Constraints 6(2/3): 223-255 (2001) |
| 2000 |
|---|
| 26 | | Rolf Backofen:
An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC).
CPM 2000: 277-292 |
| 1999 |
|---|
| 25 | | Rolf Backofen,
Sebastian Will:
Excluding Symmetries in Constraint-Based Search.
CP 1999: 73-87 |
| 24 | | Rolf Backofen,
Sebastian Will,
Peter Clote:
Algorithmic approach to quantifying the hydrophobic force contribution in protein folding.
German Conference on Bioinformatics 1999: 93-106 |
| 23 | | 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) |
| 22 | | Rolf Backofen,
François Bry,
Peter Clote,
Hans-Peter Kriegel,
Thomas Seidl,
Klaus U. Schulz:
Bioinformatik - Aktuelles Schlagwort.
Informatik Spektrum 22(5): 376-378 (1999) |
| 1998 |
|---|
| 21 | | Rolf Backofen:
Constraint Techniques for Solving the Protein Structure Prediction Problem.
CP 1998: 72-86 |
| 20 | | Rolf Backofen,
Sebastian Will:
Structure prediction in an HP-type lattice with an extended alphabet.
German Conference on Bioinformatics 1998 |
| 19 | | Rolf Backofen,
Ralf Treinen:
How to Win a Game with Features.
Inf. Comput. 142(1): 76-101 (1998) |
| 1997 |
|---|
| 18 | | 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 |
| 17 | | Rolf Backofen,
Peter Clote:
Evolution as a Computational Engine.
CSL 1997: 35-55 |
| 16 | | Rolf Backofen:
Using constraint programming for lattice protein folding.
German Conference on Bioinformatics 1997: 123 |
| 15 | | 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 |
|---|
| 14 | | Rolf Backofen:
Controlling Functional Uncertainty.
ECAI 1996: 557-561 |
| 13 | | Rolf Backofen:
Controlling Functional Uncertainty
CoRR cmp-lg/9608002: (1996) |
| 1995 |
|---|
| 12 | | Rolf Backofen:
A Complete Axiomatization of a Theory with Feature and Arity Constraints.
J. Log. Program. 24(1&2): 37-71 (1995) |
| 11 | | 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) |
| 10 | | Rolf Backofen,
Gert Smolka:
A Complete and Recursive Feature Theory.
Theor. Comput. Sci. 146(1&2): 243-268 (1995) |
| 1994 |
|---|
| 9 | | Rolf Backofen,
Ralf Treinen:
How to Win a Game with Features.
CCL 1994: 320-335 |
| 8 | | 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 |
| 7 | | Rolf Backofen:
Regular Path Expressions in Feature Logic.
J. Symb. Comput. 17(5): 421-455 (1994) |
| 1993 |
|---|
| 6 | | Rolf Backofen,
Gert Smolka:
A Complete and Recursive Feature Theory.
ACL 1993: 193-200 |
| 5 | | Rolf Backofen:
On the Decidability of Functional Uncertainty.
ACL 1993: 201-208 |
| 4 | | Rolf Backofen:
Regular Path Expression in Feature Logic.
RTA 1993: 121-135 |
| 1991 |
|---|
| 3 | | Rolf Backofen,
Lutz Euler,
Günther Görz:
Distributed Disjunctions for LIFE.
PDK 1991: 161-170 |
| 2 | | 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 |
|---|
| 1 | | Rolf Backofen,
Lutz Euler,
Günther Görz:
Towards the Integration of Functions, Relations and Types in an AI Programming Language.
GWAI 1990: 297-306 |
