2008 | ||
---|---|---|
58 | EE | Ulrike Mückstein, Hakim Tafer, Stephan H. F. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker: Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. BIRD 2008: 114-127 |
57 | EE | Andreas Heffel, Peter F. Stadler, Sonja J. Prohaska, Gerhard Kauer, Jens-Peer Kuska: Process flow for classification and clustering of fruit fly gene expression patterns. ICIP 2008: 721-724 |
56 | EE | Jana Hertel, Ivo L. Hofacker, Peter F. Stadler: SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24(2): 158-164 (2008) |
2007 | ||
55 | Christopher R. Stephens, Marc Toussaint, L. Darrell Whitley, Peter F. Stadler: Foundations of Genetic Algorithms, 9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers Springer 2007 | |
54 | EE | Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler: Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA 2007: 194-212 |
53 | Axel Mosig, Peter Menzel, Peter F. Stadler: Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. German Conference on Bioinformatics 2007: 68-77 | |
52 | EE | Axel Mosig, Julian J.-L. Chen, Peter F. Stadler: Homology Search with Fragmented Nucleic Acid Sequence Patterns. WABI 2007: 335-345 |
51 | EE | Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf: CREx: inferring genomic rearrangements based on common intervals. Bioinformatics 23(21): 2957-2958 (2007) |
50 | EE | Manja Marz, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler: U7 snRNAs: A Computational Survey. Genomics, Proteomics & Bioinformatics 5(3-4): 187-195 (2007) |
2006 | ||
49 | EE | Jana Hertel, Peter F. Stadler: Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. ISMB (Supplement of Bioinformatics) 2006: 197-202 |
48 | EE | Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm: Visualization of Lattice-Based Protein Folding Simulations. IV 2006: 89-94 |
47 | EE | Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler: Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 7: 67 (2006) |
46 | EE | Ivo L. Hofacker, Peter F. Stadler: Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22(10): 1172-1176 (2006) |
45 | EE | Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: Thermodynamics of RNA-RNA binding. Bioinformatics 22(10): 1177-1182 (2006) |
44 | EE | Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler: Local RNA base pairing probabilities in large sequences. Bioinformatics 22(5): 614-615 (2006) |
43 | EE | Axel Mosig, Katrin Sameith, Peter F. Stadler: Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences. Genomics, Proteomics & Bioinformatics 4(1): 56-60 (2006) |
42 | EE | Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler: Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12(5): 781-788 (2006) |
41 | EE | Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker: miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Research 34(Database-Issue): 135-139 (2006) |
2005 | ||
40 | EE | Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm: CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL 2005: 500-509 |
39 | EE | Gil Benkö, Christoph Flamm, Peter F. Stadler: Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL 2005: 725-733 |
38 | EE | Kristin Missal, Dominic Rose, Peter F. Stadler: Non-coding RNAs in Ciona intestinalis. ECCB/JBI 2005: 78 |
37 | Ivo L. Hofacker, Peter F. Stadler: Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics 2005: 15-25 | |
36 | Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: Thermodynamics of RNA-RNA Binding. German Conference on Bioinformatics 2005: 3-13 | |
35 | EE | Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler: Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinformatics 6: 160 (2005) |
34 | EE | Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff: Multiple sequence alignment with user-defined constraints at GOBICS. Bioinformatics 21(7): 1271-1273 (2005) |
33 | EE | Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Minimum path bases and relevant paths. Networks 46(3): 119-123 (2005) |
2004 | ||
32 | C. Thurner, Ivo L. Hofacker, Peter F. Stadler: Conserved RNA Pseudoknots. German Conference on Bioinformatics 2004: 207-216 | |
31 | Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler: Multiple sequence alignment with user-defined constraints. German Conference on Bioinformatics 2004: 25-36 | |
30 | EE | Ivo L. Hofacker, Peter F. Stadler: The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science 2004: 728-735 |
29 | EE | Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits: Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics 20(10): 1495-1499 (2004) |
28 | EE | Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler: Alignment of RNA base pairing probability matrices. Bioinformatics 20(14): 2222-2227 (2004) |
27 | EE | Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler: Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20(2): 186-190 (2004) |
26 | EE | Christina Witwer, Ivo L. Hofacker, Peter F. Stadler: Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE/ACM Trans. Comput. Biology Bioinform. 1(2): 66-77 (2004) |
25 | EE | Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Counterexamples in Chemical Ring Perception. Journal of Chemical Information and Modeling 44(2): 323-331 (2004) |
24 | EE | Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler: The Footprint Sorting Problem. Journal of Chemical Information and Modeling 44(2): 332-338 (2004) |
2003 | ||
23 | EE | Gil Benkö, Christoph Flamm, Peter F. Stadler: Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL 2003: 10-19 |
22 | Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler: Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics 2003: 1-7 | |
21 | Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits: Conserved RNA secondary structures in viral genomes: A survey. German Conference on Bioinformatics 2003: 57-62 | |
20 | Peter F. Stadler, Christoph Flamm: Barrier Trees on Poset-Valued Landscapes. Genetic Programming and Evolvable Machines 4(1): 7-20 (2003) | |
19 | EE | Gil Benkö, Christoph Flamm, Peter F. Stadler: A Graph-Based Toy Model of Chemistry. Journal of Chemical Information and Computer Sciences 43(4): 1085-1093 (2003) |
2002 | ||
18 | Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler: Stochastic pairwise alignments. ECCB 2002: 153-160 | |
17 | EE | Bärbel M. R. Stadler, Peter F. Stadler: Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry. Journal of Chemical Information and Computer Sciences 42(3): 577-585 (2002) |
2000 | ||
16 | Jan Cupal, Stephan Kopp, Peter F. Stadler: RNA Shape Space Topology. Artificial Life 6(1): 3-23 (2000) | |
15 | EE | Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Interchangeability of Relevant Cycles in Graphs. Electr. J. Comb. 7: (2000) |
14 | Martin Fekete, Ivo L. Hofacker, Peter F. Stadler: Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. Journal of Computational Biology 7(1-2): 171-182 (2000) | |
1999 | ||
13 | G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler: An efficient potential for protein sequence design. German Conference on Bioinformatics 1999: 107-112 | |
12 | Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler: Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics 1999: 73-79 | |
11 | EE | Ivo L. Hofacker, Peter F. Stadler: Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Computers & Chemistry 23(3-4): 401-414 (1999) |
1998 | ||
10 | EE | Ivo L. Hofacker, Peter Schuster, Peter F. Stadler: Combinatorics of RNA Secondary Structures. Discrete Applied Mathematics 88(1-3): 207-237 (1998) |
9 | EE | Josef Leydold, Peter F. Stadler: Minimal Cycle Bases of Outerplanar Graphs. Electr. J. Comb. 5: (1998) |
1997 | ||
8 | Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler: Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. ISMB 1997: 88-91 | |
7 | Peter F. Stadler, Günter P. Wagner: Algebraic Theory of Recombination Spaces. Evolutionary Computation 5(3): 241-275 (1997) | |
1996 | ||
6 | Jan Cupal, Ivo L. Hofacker, Peter F. Stadler: Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. German Conference on Bioinformatics 1996: 184-186 | |
5 | Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz: Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. KDD 1996: 20-25 | |
4 | EE | Christian Reidys, Peter F. Stadler: Bio-molecular Shapes and Algebraic Structures. Computers & Chemistry 20(1): 85-94 (1996) |
3 | Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler: Base Pairing Probabilities in a Complete HIV-1 RNA. Journal of Computational Biology 3(2): 253-274 (1996) | |
1995 | ||
2 | EE | Peter F. Stadler: Random walks and orthogonal functions associated with highly symmetric graphs. Discrete Mathematics 145(1-3): 229-237 (1995) |
1994 | ||
1 | EE | Peter Schuster, Peter F. Stadler: Landscapes: Complex Optimization Problems and Biopolymer Structures. Computers & Chemistry 18(3): 295-324 (1994) |