Peter F. Stadler

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)

Marcus Lechner, Manja Marz, Christian Ihling, Andrea Sinz, Peter F. Stadler, Veiko Krauss: The correlation of genome size and DNA methylation rate in metazoans. Theory in Biosciences 132(1): 47-60 (2013)

Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler: Square Property, Equitable Partitions, and Product-like Graphs. CoRR abs/1301.6898 (2013)

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler: Generic Strategies for Chemical Space Exploration. CoRR abs/1302.4006 (2013)

David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin: deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics 28(1): 17-24 (2012)

Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel: Addendum: topology and prediction of RNA pseudoknots. Bioinformatics 28(2): 300 (2012)

Christian Otto, Peter F. Stadler, Steve Hoffmann: Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics 28(13): 1698-1704 (2012)

Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler: From event-labeled gene trees to species trees. BMC Bioinformatics 13(S-19): S6 (2012)

Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler: Diagonalized Cartesian products of s-prime graphs are s-prime. Discrete Mathematics 312(1): 74-80 (2012)

Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler: Symmetric circular matchings and RNA folding. Discrete Mathematics 312(1): 100-112 (2012)

Lydia Ostermeier, Marc Hellmuth, Peter F. Stadler: The Cartesian product of hypergraphs. Journal of Graph Theory 70(2): 180-196 (2012)

Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler: A Survey on Hypergraph Products. Mathematics in Computer Science 6(1): 1-32 (2012)

Jan Engelhardt, Peter F. Stadler: Hidden treasures in unspliced EST data. Theory in Biosciences 131(1): 49-57 (2012)

Markus Rohrschneider, Peter F. Stadler, Gerik Scheuermann: A Visual Cross-Database Comparison of Metabolic Networks. ISVC (2) 2012: 678-687

Ronny Lorenz, Stephan H. F. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler: RNA Folding Algorithms with G-Quadruplexes. BSB 2012: 49-60

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler: Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars. CoRR abs/1208.3153 (2012)

Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, Christoph Flamm: In Silico Evolution of Early Metabolism. Artificial Life 17(2): 87-108 (2011)

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler: Fast local fragment chaining using sum-of-pair gap costs. Algorithms for Molecular Biology 6: 4 (2011)

Ronny Lorenz, Stephan H. F. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker: ViennaRNA Package 2.0. Algorithms for Molecular Biology 6: 26 (2011)

Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, Hakim Tafer: PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics 27(2): 279-280 (2011)

Peter Menzel, Peter F. Stadler, Jan Gorodkin: maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinformatics 27(3): 317-325 (2011)

Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel: Topology and prediction of RNA pseudoknots. Bioinformatics 27(8): 1076-1085 (2011)

Christian Höner zu Siederdissen, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: A folding algorithm for extended RNA secondary structures. Bioinformatics [ISMB/ECCB] 27(13): 129-136 (2011)

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)

Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker: Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics 27(14): 1934-1940 (2011)

Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F. Stadler, Sonja J. Prohaska: Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinformatics 12: 124 (2011)

Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, Steve Hoffmann: DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Research 39(Web-Server-Issue): 112-117 (2011)

Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker: RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Research 39(Web-Server-Issue): 149-154 (2011)

Wolfgang Otto, Peter F. Stadler, Sonja J. Prohaska: Phylogenetic Footprinting and Consistent Sets of Local Aligments. CPM 2011: 118-131

David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, Peter F. Stadler: MicroRNA or Not MicroRNA? BSB 2011: 1-9

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler: Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete. CoRR abs/1110.6051 (2011)

Christian Arnold, Peter F. Stadler: Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Algorithms for Molecular Biology 5: 25 (2010)

Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler: Target prediction and a statistical sampling algorithm for RNA-RNA interaction. Bioinformatics 26(2): 175-181 (2010)

Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler: RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics 26(5): 610-616 (2010)

Mario Fasold, Peter F. Stadler, Hans Binder: G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinformatics 11: 207 (2010)

Manja Marz, Nathalie Vanzo, Peter F. Stadler: Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History. J. Bioinformatics and Computational Biology 8(1): 1-17 (2010)

Stefan Jänicke, Christian Heine, Marc Hellmuth, Peter F. Stadler, Gerik Scheuermann: Visualization of Graph Products. IEEE Trans. Vis. Comput. Graph. 16(6): 1082-1089 (2010)

Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska: Quantitative Comparison of Genomic-Wide Protein Domain Distributions. GCB 2010: 93-102

Markus Rohrschneider, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, Gerik Scheuermann: Visual Network Analysis of Dynamic Metabolic Pathways. ISVC (1) 2010: 316-327

Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler: Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56

Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler: RNAz 2.0: Improved Noncoding RNA Detection. Pacific Symposium on Biocomputing 2010: 69-79

David Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann: Identification and Classification of Small RNAs in Transcriptome Sequence Data. Pacific Symposium on Biocomputing 2010: 80-87

Peter F. Stadler: Evolution of the Long Non-coding RNAs MALAT1 and MENbeta/epsilon. BSB 2010: 1-12

Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska: Detection of Protein Domains in Eukaryotic Genome Sequences. BSB 2010: 71-74

Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler (Eds.): Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings. Lecture Notes in Computer Science 6268, Springer 2010, isbn 978-3-642-15059-3

Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler: A Topological Approach to Chemical Organizations. Artificial Life 15(1): 71-88 (2009)

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)

Markus Riester, Peter F. Stadler, Konstantin Klemm: FRANz: reconstruction of wild multi-generation pedigrees. Bioinformatics 25(16): 2134-2139 (2009)

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)

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)

K. Scheibye-Alsing, Steve Hoffmann, A. Frankel, Peter Jensen, Peter F. Stadler, Y. Mang, N. Tommerup, M. J. Gilchrist, A.-B. Nygård, Susanna Cirera, Claus B. Jørgensen, Merete Fredholm, Jan Gorodkin: Sequence assembly. Computational Biology and Chemistry 33(2): 121-136 (2009)

Andreas W. M. Dress, Bülent Karasözen, Peter F. Stadler, Gerhard-Wilhelm Weber: Preface. Discrete Applied Mathematics 157(10): 2217-2220 (2009)

Konstantin Klemm, Peter F. Stadler: A note on fundamental, non-fundamental, and robust cycle bases. Discrete Applied Mathematics 157(10): 2432-2438 (2009)

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)

Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler: Approximate graph products. Eur. J. Comb. 30(5): 1119-1133 (2009)

Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler: Local Algorithms for the Prime Factorization of Strong Product Graphs. Mathematics in Computer Science 2(4): 653-682 (2009)

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)

Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller: Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Computational Biology 5(9) (2009)

Karen E. Chambers, Ryan McDaniell, Jeremy D. Raincrow, Maya Deshmukh, Peter F. Stadler, Chi-hua Chiu: Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory in Biosciences 128(2): 109-120 (2009)

Peter F. Stadler, Sonja J. Prohaska, Christian V. Forst, David C. Krakauer: Defining genes: a computational framework. Theory in Biosciences 128(3): 165-170 (2009)

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

Peter Menzel, Jan Gorodkin, Peter F. Stadler: Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. GCB 2009: 211-220

Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, Peter F. Stadler (Eds.): German Conference on Bioinformatics 2009, 28th to 30th September 2009, Martin Luther University Halle-Wittenberg, Germany. LNI 157, GI 2009, isbn 978-3-88579-251-2

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)

Jana Hertel, Ivo L. Hofacker, Peter F. Stadler: SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24(2): 158-164 (2008)

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)

Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska: SynBlast: Assisting the analysis of conserved synteny information. BMC Bioinformatics 9 (2008)

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)

Sonja J. Prohaska, Peter F. Stadler: "Genes". Theory in Biosciences 127(3): 215-221 (2008)

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

Markus Riester, Peter F. Stadler, Konstantin Klemm: FRANz: Fast Reconstruction of Wild Pedigrees. German Conference on Bioinformatics 2008: 168-177

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

Kristin Reiche, Peter F. Stadler: RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms for Molecular Biology 2 (2007)

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)

Matthias Kruspe, Peter F. Stadler: Progressive multiple sequence alignments from triplets. BMC Bioinformatics 8 (2007)

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)

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)

Olaf Breidbach, Jürgen Jost, Peter F. Stadler: Towards theoretical formalisms. Theory in Biosciences 126(1): 1-2 (2007)

Axel Mosig, Guofeng Meng, Bärbel M. R. Stadler, Peter F. Stadler: Evolution of the vertebrate Y RNA cluster. Theory in Biosciences 126(1): 9-14 (2007)

Marleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelsson, Detlef Bernhard, Martin Schlegel: The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. Theory in Biosciences 126(1): 35-42 (2007)

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

Axel Mosig, Peter Menzel, Peter F. Stadler: Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. German Conference on Bioinformatics 2007: 68-77

Axel Mosig, Julian J.-L. Chen, Peter F. Stadler: Homology Search with Fragmented Nucleic Acid Sequence Patterns. WABI 2007: 335-345

Christopher R. Stephens, Marc Toussaint, L. Darrell Whitley, Peter F. Stadler (Eds.): Foundations of Genetic Algorithms, 9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers. Lecture Notes in Computer Science 4436, Springer 2007, isbn 978-3-540-73479-6

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)

Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler: Multiple sequence alignment with user-defined anchor points. Algorithms for Molecular Biology 1 (2006)

Burkhard Morgenstern, Peter F. Stadler: New journal: Algorithms for Molecular Biology. Algorithms for Molecular Biology 1 (2006)

Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler: Local RNA base pairing probabilities in large sequences. Bioinformatics 22(5): 614-615 (2006)

Ivo L. Hofacker, Peter F. Stadler: Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22(10): 1172-1176 (2006)

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)

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)

Wilfried Imrich, Peter F. Stadler: A prime factor theorem for a generalized direct product. Discussiones Mathematicae Graph Theory 26(1): 135-140 (2006)

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)

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)

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)

Axel Mosig, Ivo L. Hofacker, Peter F. Stadler: Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. German Conference on Bioinformatics 2006: 93-102

Jana Hertel, Peter F. Stadler: Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. ISMB (Supplement of Bioinformatics) 2006: 197-202

Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm: Visualization of Lattice-Based Protein Folding Simulations. IV 2006: 89-94

Camille Stephan-Otto Attolini, Peter F. Stadler: Neutral Networks of Interacting RNA Secondary Structures. Advances in Complex Systems 8(2-3): 275-283 (2005)

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)

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)

Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Minimum path bases and relevant paths. Networks 46(3): 119-123 (2005)

Ante Graovac, Peter F. Stadler: MATH/CHEM/COMP 2004 Contributions. Theory in Biosciences 123(4): 263-264 (2005)

Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer: Evolutionary patterns of non-coding RNAs. Theory in Biosciences 123(4): 301-369 (2005)

Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson: Erratum to "Aggregation of variables and system decomposability: Applications to fitness landscape analysis. Theory in Biosciences 124(1): 87-88 (2005)

Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm: CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL 2005: 500-509

Gil Benkö, Christoph Flamm, Peter F. Stadler: Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL 2005: 725-733

Kristin Missal, Dominic Rose, Peter F. Stadler: Non-coding RNAs in Ciona intestinalis. ECCB/JBI 2005: 78

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

Ivo L. Hofacker, Peter F. Stadler: Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics 2005: 15-25

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)

Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits: Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics 20(10): 1495-1499 (2004)

Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler: Alignment of RNA base pairing probability matrices. Bioinformatics 20(14): 2222-2227 (2004)

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)

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)

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)

Olaf Breidbach, Jürgen Jost, Peter F. Stadler, Michael S. Weingarten: Editorial. Theory in Biosciences 123(1): 1-2 (2004)

Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson: Aggregation of variables and system decomposition: Applications to fitness landscape analysis. Theory in Biosciences 123(1): 33-68 (2004)

Sonja J. Prohaska, Peter F. Stadler: The duplication of the Hox gene clusters in teleost fishes. Theory in Biosciences 123(1): 89-110 (2004)

Max Shpak, Peter F. Stadler, Günter P. Wagner, Lee Altenberg: Simon-Ando decomposability and fitness landscapes. Theory in Biosciences 123(2): 139-180 (2004)

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

C. Thurner, Ivo L. Hofacker, Peter F. Stadler: Conserved RNA Pseudoknots. German Conference on Bioinformatics 2004: 207-216

Ivo L. Hofacker, Peter F. Stadler: The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science 2004: 728-735

Bärbel M. R. Stadler, Peter F. Stadler: Molecular Replicator Dynamics. Advances in Complex Systems 6(1): 47-78 (2003)

Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Circuit bases of strongly connected digraphs. Discussiones Mathematicae Graph Theory 23(2): 241-260 (2003)

Peter F. Stadler, Christoph Flamm: Barrier Trees on Poset-Valued Landscapes. Genetic Programming and Evolvable Machines 4(1): 7-20 (2003)

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)

Peter F. Stadler: Minimum cycle bases of Halin graphs. Journal of Graph Theory 43(2): 150-155 (2003)

Gil Benkö, Christoph Flamm, Peter F. Stadler: Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL 2003: 10-19

Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler: Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics 2003: 1-7

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

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)

Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler: Stochastic pairwise alignments. ECCB 2002: 153-160

Jan Cupal, Stephan Kopp, Peter F. Stadler: RNA Shape Space Topology. Artificial Life 6(1): 3-23 (2000)

Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Interchangeability of Relevant Cycles in Graphs. Electr. J. Comb. 7 (2000)

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)

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)

Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler: Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics 1999: 73-79

G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler: An efficient potential for protein sequence design. German Conference on Bioinformatics 1999: 107-112

Josef Leydold, Peter F. Stadler: Minimal Cycle Bases of Outerplanar Graphs. Electr. J. Comb. 5 (1998)

Ivo L. Hofacker, Peter Schuster, Peter F. Stadler: Combinatorics of RNA Secondary Structures. Discrete Applied Mathematics 88(1-3): 207-237 (1998)

Peter F. Stadler, Günter P. Wagner: Algebraic Theory of Recombination Spaces. Evolutionary Computation 5(3): 241-275 (1997)

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

Christian M. Reidys, Peter F. Stadler: Bio-molecular Shapes and Algebraic Structures. Computers & Chemistry 20(1): 85-94 (1996)

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)

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

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

Peter F. Stadler: Random walks and orthogonal functions associated with highly symmetric graphs. Discrete Mathematics 145(1-3): 229-237 (1995)

Peter Schuster, Peter F. Stadler: Landscapes: Complex Optimization Problems and Biopolymer Structures. Computers & Chemistry 18(3): 295-324 (1994)