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Peter F. Stadler: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
    CelloS: A Multi-level Approach to Evolutionary Dynamics. [Citation Graph (0, 0)][DBLP]
    ECAL, 2005, pp:500-509 [Conf]
  2. Gil Benkö, Christoph Flamm, Peter F. Stadler
    Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. [Citation Graph (0, 0)][DBLP]
    ECAL, 2003, pp:10-19 [Conf]
  3. Gil Benkö, Christoph Flamm, Peter F. Stadler
    Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. [Citation Graph (0, 0)][DBLP]
    ECAL, 2005, pp:725-733 [Conf]
  4. Kristin Missal, Dominic Rose, Peter F. Stadler
    Non-coding RNAs in Ciona intestinalis. [Citation Graph (0, 0)][DBLP]
    ECCB/JBI, 2005, pp:78- [Conf]
  5. Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler
    Stochastic pairwise alignments. [Citation Graph (0, 0)][DBLP]
    ECCB, 2002, pp:153-160 [Conf]
  6. Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler
    Design of multi-stable nucleid acid sequences. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2003, pp:1-7 [Conf]
  7. Jan Cupal, Ivo L. Hofacker, Peter F. Stadler
    Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1996, pp:184-186 [Conf]
  8. Ivo L. Hofacker, Peter F. Stadler
    Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2005, pp:15-25 [Conf]
  9. Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
    Conserved RNA secondary structures in viral genomes: A survey. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2003, pp:57-62 [Conf]
  10. 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. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2004, pp:25-36 [Conf]
  11. Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker
    Thermodynamics of RNA-RNA Binding. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2005, pp:3-13 [Conf]
  12. Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler
    Conserved secondary structures in hepatitis B virus DNA. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1999, pp:73-79 [Conf]
  13. C. Thurner, Ivo L. Hofacker, Peter F. Stadler
    Conserved RNA Pseudoknots. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2004, pp:207-216 [Conf]
  14. G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
    An efficient potential for protein sequence design. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1999, pp:107-112 [Conf]
  15. Ivo L. Hofacker, Peter F. Stadler
    The Partition Function Variant of Sankoff's Algorithm. [Citation Graph (0, 0)][DBLP]
    International Conference on Computational Science, 2004, pp:728-735 [Conf]
  16. 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. [Citation Graph (0, 0)][DBLP]
    ISMB, 1997, pp:88-91 [Conf]
  17. Jana Hertel, Peter F. Stadler
    Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2006, pp:197-202 [Conf]
  18. Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm
    Visualization of Lattice-Based Protein Folding Simulations. [Citation Graph (0, 0)][DBLP]
    IV, 2006, pp:89-94 [Conf]
  19. Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
    Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. [Citation Graph (0, 0)][DBLP]
    KDD, 1996, pp:20-25 [Conf]
  20. Jan Cupal, Stephan Kopp, Peter F. Stadler
    RNA Shape Space Topology. [Citation Graph (0, 0)][DBLP]
    Artificial Life, 2000, v:6, n:1, pp:3-23 [Journal]
  21. Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler
    Local RNA base pairing probabilities in large sequences. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:5, pp:614-615 [Journal]
  22. Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler
    Alignment of RNA base pairing probability matrices. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:14, pp:2222-2227 [Journal]
  23. Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
    Prediction of locally stable RNA secondary structures for genome-wide surveys. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:2, pp:186-190 [Journal]
  24. Ivo L. Hofacker, Peter F. Stadler
    Memory efficient folding algorithms for circular RNA secondary structures. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:10, pp:1172-1176 [Journal]
  25. Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
    Conserved RNA secondary structures in viral genomes: a survey. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:10, pp:1495-1499 [Journal]
  26. 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. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:7, pp:1271-1273 [Journal]
  27. Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker
    Thermodynamics of RNA-RNA binding. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:10, pp:1177-1182 [Journal]
  28. Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2006, v:7, n:, pp:67- [Journal]
  29. Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
    Multiple sequence alignments of partially coding nucleic acid sequences. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2005, v:6, n:, pp:160- [Journal]
  30. Ivo L. Hofacker, Peter F. Stadler
    Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. [Citation Graph (0, 0)][DBLP]
    Computers & Chemistry, 1999, v:23, n:3-4, pp:401-414 [Journal]
  31. Christian Reidys, Peter F. Stadler
    Bio-molecular Shapes and Algebraic Structures. [Citation Graph (0, 0)][DBLP]
    Computers & Chemistry, 1996, v:20, n:1, pp:85-94 [Journal]
  32. Peter Schuster, Peter F. Stadler
    Landscapes: Complex Optimization Problems and Biopolymer Structures. [Citation Graph (0, 0)][DBLP]
    Computers & Chemistry, 1994, v:18, n:3, pp:295-324 [Journal]
  33. Petra M. Gleiss, Josef Leydold, Peter F. Stadler
    Interchangeability of Relevant Cycles in Graphs. [Citation Graph (0, 0)][DBLP]
    Electr. J. Comb., 2000, v:7, n:, pp:- [Journal]
  34. Josef Leydold, Peter F. Stadler
    Minimal Cycle Bases of Outerplanar Graphs. [Citation Graph (0, 0)][DBLP]
    Electr. J. Comb., 1998, v:5, n:, pp:- [Journal]
  35. Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
    Combinatorics of RNA Secondary Structures. [Citation Graph (0, 0)][DBLP]
    Discrete Applied Mathematics, 1998, v:88, n:1-3, pp:207-237 [Journal]
  36. Peter F. Stadler, Günter P. Wagner
    Algebraic Theory of Recombination Spaces. [Citation Graph (0, 0)][DBLP]
    Evolutionary Computation, 1997, v:5, n:3, pp:241-275 [Journal]
  37. Peter F. Stadler, Christoph Flamm
    Barrier Trees on Poset-Valued Landscapes. [Citation Graph (0, 0)][DBLP]
    Genetic Programming and Evolvable Machines, 2003, v:4, n:1, pp:7-20 [Journal]
  38. Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
    Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2000, v:7, n:1-2, pp:171-182 [Journal]
  39. Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler
    Base Pairing Probabilities in a Complete HIV-1 RNA. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1996, v:3, n:2, pp:253-274 [Journal]
  40. Gil Benkö, Christoph Flamm, Peter F. Stadler
    A Graph-Based Toy Model of Chemistry. [Citation Graph (0, 0)][DBLP]
    Journal of Chemical Information and Computer Sciences, 2003, v:43, n:4, pp:1085-1093 [Journal]
  41. Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler
    Counterexamples in Chemical Ring Perception. [Citation Graph (0, 0)][DBLP]
    Journal of Chemical Information and Modeling, 2004, v:44, n:2, pp:323-331 [Journal]
  42. Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler
    The Footprint Sorting Problem. [Citation Graph (0, 0)][DBLP]
    Journal of Chemical Information and Modeling, 2004, v:44, n:2, pp:332-338 [Journal]
  43. Bärbel M. R. Stadler, Peter F. Stadler
    Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry. [Citation Graph (0, 0)][DBLP]
    Journal of Chemical Information and Computer Sciences, 2002, v:42, n:3, pp:577-585 [Journal]
  44. Paul W. C. 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. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Database-Issue, pp:135-139 [Journal]
  45. Petra M. Gleiss, Josef Leydold, Peter F. Stadler
    Minimum path bases and relevant paths. [Citation Graph (0, 0)][DBLP]
    Networks, 2005, v:46, n:3, pp:119-123 [Journal]
  46. Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
    Prediction of Consensus RNA Secondary Structures Including Pseudoknots. [Citation Graph (0, 0)][DBLP]
    IEEE/ACM Trans. Comput. Biology Bioinform., 2004, v:1, n:2, pp:66-77 [Journal]
  47. Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    Visualization of Barrier Tree Sequences. [Citation Graph (0, 0)][DBLP]
    IEEE Trans. Vis. Comput. Graph., 2006, v:12, n:5, pp:781-788 [Journal]
  48. Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler
    Saddles and Barrier in Landscapes of Generalized Search Operators. [Citation Graph (0, 0)][DBLP]
    FOGA, 2007, pp:194-212 [Conf]
  49. Axel Mosig, Julian J.-L. Chen, Peter F. Stadler
    Homology Search with Fragmented Nucleic Acid Sequence Patterns. [Citation Graph (0, 0)][DBLP]
    WABI, 2007, pp:335-345 [Conf]
  50. Peter F. Stadler
    Random walks and orthogonal functions associated with highly symmetric graphs. [Citation Graph (0, 0)][DBLP]
    Discrete Mathematics, 1995, v:145, n:1-3, pp:229-237 [Journal]

  51. Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns. [Citation Graph (, )][DBLP]


  52. Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. [Citation Graph (, )][DBLP]


  53. FRANz: Fast Reconstruction of Wild Pedigrees. [Citation Graph (, )][DBLP]


  54. Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. [Citation Graph (, )][DBLP]


  55. Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. [Citation Graph (, )][DBLP]


  56. Process flow for classification and clustering of fruit fly gene expression patterns. [Citation Graph (, )][DBLP]


  57. Evolution of the Long Non-coding RNAs MALAT1 and MENbeta/epsilon. [Citation Graph (, )][DBLP]


  58. Detection of Protein Domains in Eukaryotic Genome Sequences. [Citation Graph (, )][DBLP]


  59. Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. [Citation Graph (, )][DBLP]


  60. A Topological Approach to Chemical Organizations. [Citation Graph (, )][DBLP]


  61. CREx: inferring genomic rearrangements based on common intervals. [Citation Graph (, )][DBLP]


  62. SnoReport: computational identification of snoRNAs with unknown targets. [Citation Graph (, )][DBLP]


  63. Structural profiles of human miRNA families from pairwise clustering. [Citation Graph (, )][DBLP]


  64. FRANz: reconstruction of wild multi-generation pedigrees. [Citation Graph (, )][DBLP]


  65. Evidence for human microRNA-offset RNAs in small RNA sequencing data. [Citation Graph (, )][DBLP]


  66. Partition function and base pairing probabilities for RNA-RNA interaction prediction. [Citation Graph (, )][DBLP]


  67. RNAsnoop: efficient target prediction for H/ACA snoRNAs. [Citation Graph (, )][DBLP]


  68. Target prediction and a statistical sampling algorithm for RNA-RNA interaction. [Citation Graph (, )][DBLP]


  69. Progressive multiple sequence alignments from triplets. [Citation Graph (, )][DBLP]


  70. RNAalifold: improved consensus structure prediction for RNA alignments. [Citation Graph (, )][DBLP]


  71. SynBlast: Assisting the analysis of conserved synteny information. [Citation Graph (, )][DBLP]


  72. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. [Citation Graph (, )][DBLP]


  73. Sequence assembly. [Citation Graph (, )][DBLP]


  74. Discovering cis-regulatory modules by optimizing barbecues. [Citation Graph (, )][DBLP]


  75. Preface. [Citation Graph (, )][DBLP]


  76. A note on fundamental, non-fundamental, and robust cycle bases. [Citation Graph (, )][DBLP]


  77. Approximate graph products. [Citation Graph (, )][DBLP]


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