| * | 2009 |
|---|
| 77 | EE | Andreas Heffel,
Sonja J. Prohaska,
Peter F. Stadler,
Gerhard Kauer,
Jens-Peer Kuska:
Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns.
Bildverarbeitung für die Medizin 2009: 415-419 |
| 76 | EE | Markus Riester,
Peter F. Stadler,
Konstantin Klemm:
FRANz: reconstruction of wild multi-generation pedigrees.
Bioinformatics 25(16): 2134-2139 (2009) |
| 75 | EE | David Langenberger,
Clara Bermudez-Santana,
Jana Hertel,
Steve Hoffmann,
Philipp Khaitovich,
Peter F. Stadler:
Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Bioinformatics 25(18): 2298-2301 (2009) |
| 74 | EE | Fenix W. D. Huang,
Jing Qin,
Christian M. Reidys,
Peter F. Stadler:
Partition function and base pairing probabilities for RNA-RNA interaction prediction.
Bioinformatics 25(20): 2646-2654 (2009) |
| 73 | EE | Bogumil Kaczkowski,
Elfar Torarinsson,
Kristin Reiche,
Jakob Hull Havgaard,
Peter F. Stadler,
Jan Gorodkin:
Structural profiles of human miRNA families from pairwise clustering.
Bioinformatics 25(3): 291-294 (2009) |
| 72 | EE | Andreas W. M. Dress,
Bülent Karasözen,
Peter F. Stadler,
Gerhard-Wilhelm Weber:
Preface.
Discrete Applied Mathematics 157(10): 2217-2220 (2009) |
| 71 | EE | Konstantin Klemm,
Peter F. Stadler:
A note on fundamental, non-fundamental, and robust cycle bases.
Discrete Applied Mathematics 157(10): 2432-2438 (2009) |
| 70 | EE | Axel Mosig,
Türker Bíyíkoglu,
Sonja J. Prohaska,
Peter F. Stadler:
Discovering cis-regulatory modules by optimizing barbecues.
Discrete Applied Mathematics 157(10): 2458-2468 (2009) |
| 69 | EE | Frank Jühling,
Mario Mörl,
Roland K. Hartmann,
Mathias Sprinzl,
Peter F. Stadler,
Joern Pütz:
tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Nucleic Acids Research 37(Database-Issue): 159-162 (2009) |
| 2008 |
|---|
| 68 | 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 |
| 67 | | Markus Riester,
Peter F. Stadler,
Konstantin Klemm:
FRANz: Fast Reconstruction of Wild Pedigrees.
German Conference on Bioinformatics 2008: 168-177 |
| 66 | 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 |
| 65 | EE | Andreas W. M. Dress,
Christoph Flamm,
Guido Fritzsch,
Stefan Grünewald,
Matthias Kruspe,
Sonja J. Prohaska,
Peter F. Stadler:
Noisy: Identification of problematic columns in multiple sequence alignments.
Algorithms for Molecular Biology 3: (2008) |
| 64 | EE | Stephan H. F. Bernhart,
Ivo L. Hofacker,
Sebastian Will,
Andreas R. Gruber,
Peter F. Stadler:
RNAalifold: improved consensus structure prediction for RNA alignments.
BMC Bioinformatics 9: (2008) |
| 63 | EE | Jörg Lehmann,
Peter F. Stadler,
Sonja J. Prohaska:
SynBlast: Assisting the analysis of conserved synteny information.
BMC Bioinformatics 9: (2008) |
| 62 | EE | Jana Hertel,
Ivo L. Hofacker,
Peter F. Stadler:
SnoReport: computational identification of snoRNAs with unknown targets.
Bioinformatics 24(2): 158-164 (2008) |
| 61 | EE | Dominic Rose,
Julian Jöris,
Jörg Hackermüller,
Kristin Reiche,
Qiang Li,
Peter F. Stadler:
Duplicated RNA genes in teleost Fish genomes.
J. Bioinformatics and Computational Biology 6(6): 1157-1175 (2008) |
| 2007 |
|---|
| 60 | | 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 |
| 59 | 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 |
| 58 | | Axel Mosig,
Peter Menzel,
Peter F. Stadler:
Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores.
German Conference on Bioinformatics 2007: 68-77 |
| 57 | EE | Axel Mosig,
Julian J.-L. Chen,
Peter F. Stadler:
Homology Search with Fragmented Nucleic Acid Sequence Patterns.
WABI 2007: 335-345 |
| 56 | EE | Kristin Reiche,
Peter F. Stadler:
RNAstrand: reading direction of structured RNAs in multiple sequence alignments.
Algorithms for Molecular Biology 2: (2007) |
| 55 | EE | Matthias Kruspe,
Peter F. Stadler:
Progressive multiple sequence alignments from triplets.
BMC Bioinformatics 8: (2007) |
| 54 | 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) |
| 53 | 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 |
|---|
| 52 | EE | Jana Hertel,
Peter F. Stadler:
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.
ISMB (Supplement of Bioinformatics) 2006: 197-202 |
| 51 | EE | Sebastian Potzsch,
Gerik Scheuermann,
Peter F. Stadler,
Michael T. Wolfinger,
Christoph Flamm:
Visualization of Lattice-Based Protein Folding Simulations.
IV 2006: 89-94 |
| 50 | EE | Burkhard Morgenstern,
Sonja J. Prohaska,
Dirk Pöhler,
Peter F. Stadler:
Multiple sequence alignment with user-defined anchor points.
Algorithms for Molecular Biology 1: (2006) |
| 49 | EE | Burkhard Morgenstern,
Peter F. Stadler:
New journal: Algorithms for Molecular Biology.
Algorithms for Molecular Biology 1: (2006) |
| 48 | EE | Stephan H. F. Bernhart,
Hakim Tafer,
Ulrike Mückstein,
Christoph Flamm,
Peter F. Stadler,
Ivo L. Hofacker:
Partition function and base pairing probabilities of RNA heterodimers.
Algorithms for Molecular Biology 1: (2006) |
| 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 M. 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) |
