List of Publications

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    pre-published



    2010


    [317]BIOINF 10-001 [Abstract]
    Stephan A. Müller, Tibor Kohajda, Sven Findeiß, Peter F. Stadler, Stefan Washietl, Manolis Kellis, Martin von Bergen, Stefan Kalkhof
    Optimization of parameters for coverage of low molecular weight proteins.
    Anal. Bioanal. Chem. 398: 2867-2881 (2010)
    [316]BIOINF 10-010 [Abstract] [PDF]
    Markus Rohrschneider, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, and Gerik Scheuermann
    Visual Network Analysis of Dynamic Metabolic Pathways
    In: Advances in Visual Computing (ISVC 2010), G. Bebis et al. (eds)., Springer, Berlin
    Lect. Notes Comp. Sci. 6453: 316-327 (2010)
    [315]BIOINF 10-019 [Abstract] [PDF]
    Stefan Jänicke, Christian Heine, Marc Hellmuth, Peter F. Stadler, Gerik Scheuermann
    Visualization of graph products.
    IEEE Trans. Vis. Comput. Graph., 16:1082–1089, 2010.
    [314]BIOINF 10-003 [Abstract] [PDF]
    Bärbel M. R. Stadler and Peter F. Stadler.
    Combinatorial vector fields and the valley structure of fitness landscapes.
    J. Math. Biol., 61: 877-898 (2010).
    [313]BIOINF 10-016 [Abstract] [PDF]
    Alexander Ullrich, Peter F. Stadler, Markus Rohrschneider, Peter F. Stadler
    In silico evolution of early metabolism
    In: Harold Fellermann, Mark Dörr, Martin M. Hanczyc, Lone Ladegaard Laursen, Sarah Maurer, Daniel Merkle, Pierre-Alain Monnard, Kasper Stoy, Steen Rasmussen (eds.),
    Artificial Life XII: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, pp. 57–64, Cambridge, MA, MIT Press, 2010.
    [312]BIOINF-10-034 [Abstract] [PDF]
    Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
    Quantitative Comparison of Genomic-Wide Protein Domain Distributions
    In: D. Schomburg, A. Grote (eds.), German Conference on Bioinformatics 2010,
    Gesellschaft f. Informatik, Bonn, 2010. Lecture Notes in Informatics, vol. P-173, pp. 93–102.
    Extended Abstract
    Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
    Detection of Protein Domains in Eukaryotic Genome Sequences
    In: Advances in Bioinformatics and Computational Biology,
    Carlos E. Ferreira, Satoru Miyano, Peter F. Stadler (eds.),
    Springer, Heidelberg, Lect. Notes Comp. Sci. 6268 (2010), pp.71-74
    5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010.

    [311]BIOINF-09-037 [Abstract] [PDF]
    Rami A Dalloul, Julie A Long, Aleksey V Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W Burt, Oswald Crasta, Richard P M A Crooijmans, Kristal Cooper, Roger A Coulombe, Supriyo De, Mary E Delany, Jerry B Dodgson, Jennifer J Dong, Clive Evans, Karin M Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A M Groenen, Tim T Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R Paton, William S Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L Salzberg, Michael C Schatz, Chantel Scheuring, Carl J Schmidt, Steven Schroeder, Stephen M J Searle, Edward J Smith, Jacqueline Smith, Tad S Sonstegard, Peter F Stadler, Hakim Tafer, Zhijian (Jake) Tu, Curtis P Van Tassell, Albert J Vilella, Kelly P Williams, James A Yorke, Liqing Zhang, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M Reed
    Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
    PLoS Biology 8: e1000475 (2010).
    [310]BIOINF PREPRINT 10-033 [Abstract] [PDF]
    Peter F. Stadler
    Evolution of the Long Non-coding RNAs MALAT1 and MEN{beta}/{epsilon}
    In: Advances in Bioinformatics and Computational Biology,
    Carlos E. Ferreira, Satoru Miyano, Peter F. Stadler (eds.),
    Springer, Heidelberg, Lect. Notes Comp. Sci. 6268 (2010), pp.1-12
    5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010.
    [309]BIOINF PREPRINT 10-014 [Abstract] [PDF]
    Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider,Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker, Peter F. Stadler
    Evolution of Metabolic Networks: A Computational Framework.
    J.Syst.Chem 1: 4 (2010).
    [308]BIOINF PREPRINT 10-022 [Abstract] [PDF]
    Christian Arnold and Peter F. Stadler
    Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees.
    Alg. Mol. Biol. 5: 25 (2010).
    [307]BIOINF PREPRINT 10-008 [Abstract] [PDF]
    Markus Riester, Peter F. Stadler, Konstantin Klemm
    Reconstruction of pedigrees in clonal plant populations.
    Theor. Popul. Biol. 78:109-117 (2010).
    [306]BIOINF PREPRINT 10-024 [Abstract] [PDF]
    YDilmurat Yusuf, Manja Marz, Peter F. Stadler, and Ivo L. Hofacker
    bcheck: a wrapper tool for detecting RNase P RNA genes
    BMC Bioinformatics 11: 432 (2010).
    [305]BIOINF 09-036 [Abstract] [PDF
    Jörg Lehmann, Carina Eisenhardt, Peter F. Stadler, Veiko Krauss
    Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication
    BMC Evol Biol. 10:156 (2010).
    [304] BIOINF 09-050 [Abstract] [PDF]
    Clara Bermudez-Santana, Camille Stephan-Otto Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J. Prohaska, Stephan Steigele, Peter F. Stadler
    Genomic organization of eukaryotic tRNAs.
    BMC Genomics, 11:270 (2010).
    [303] BIOINF 10-007 [Abstract] [PDF]
    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).
    [302]BIOINF 09-048 [Abstract] [PDF]
    Ivo L. Hofacker, Christoph Flamm, Christian Heine, Michael T. Wolfinger, Gerik Scheuermann, and Peter F. Stadler.
    BarMap: RNA folding on dynamics energy landscapes.
    RNA 16: 1308-1316 (2010).
    [301]BIOINF 09-049 [Abstract] [PDF]
    Marleen Perseke, Detlef Bernhard, Guido Fritzsch, Franz Brümmer, Peter F. Stadler, and Martin Schlegel.
    Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata.
    Mol. Phylog. Evol. 56: 201-211 (2010).
    [300]BIOINF 09-041 [Abstract] [PDF]
    Sven Findeiß, Cornelius Schubert, Peter F. Stadler, Ulla Bonas
    A novel family of plasmid-transferred anti-sense ncRNAs.
    RNA Biology, 7: 120-124 (2010)
    [299]BIOINF 09-020 [Abstract] [PDF]
    Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan Bernhart, Ronny Lorenze, Michael M. Mueller, Ivo L. Hofacker, and Peter F. Stadler.
    Nematode sbRNAs: homologs of vertebrate Y RNAs.
    J. Mol. Evol. 70: 346-358 (2010)
    [298]BIOINF 08-017 [Abstract] [PDF]
    Andrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler
    Evolutionary Genomics of MicroRNAs and Their Relatives
    In Evolutionary Genomics and Systems Biology, Gustavo Caetano-Anolles, Gustavo (ed.),
    Wiley-Blackwell, Hoboken NJ, 2010, pp. 295-327.
    [297]BIOINF 08-018 [Abstract] [PDF]
    Alexander Donath, Sven Findeiß, Jana Hertel, Manja Marz, Wolfgang Otto, Christine Schulz, Peter F. Stadler, Stefan Wirth
    Non-Coding RNAs
    In Evolutionary Genomics and Systems Biology, Gustavo Caetano-Anolles, Gustavo (ed.),
    Wiley-Blackwell, Hoboken NJ, 2010, pp. 251-293.
    [296]BIOINF 10-002 [Abstract] [PDF]
    Sonja J Prohaska, Peter F. Stadler, and David C. Krakauer
    Innovation in gene regulation: The case of chromatin computation.
    J. Theor. Biol. 265: 27-44 (2010)
    [295]BIOINF 10-006 [Abstract]
    Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jéréemy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler, Jörg Vogel.
    The primary transcriptome of the major human pathogen Helicobacter pylori.
    Nature 464: 250-255 (2010).
    [294]BIOINF 09-025 [Abstract] [PDF]
    Hakim Tafer, Stephanie Kehr, Jana Hertel, and Peter F. Stadler.
    RNAsnoop: Efficient target prediction for box H/ACA snoRNAs.
    Bioinformatics 26: 610-616 (2010)
    [293]BIOINF 09-002 [Abstract] [PDF]
    Chris T. Amemiya, Thomas P. Powers, Sonja J. Prohaska, Jane Grimwood, Jeremy Schmutz, Mark Dickson, Tsutomu Miyake, Michael A. Schoenborn, Richard M. Myers, Francis H. Ruddle, and Peter F. Stadler
    Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome.
    Proc. Natl. Acad. Sci. 23:3622-3627 (2010)
    [292]BIOINF 09-009 [Abstract] [PDF]
    Manja Marz, Nathalie Vanzo, and Peter F. Stadler.
    Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history.
    J. Bioinf. Comp. Biol. 8: 1-17 (2010).
    [291]BIOINF 09-026 [Abstract] [PDF]
    Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, and Peter F. Stadler.
    RNAz 2.0: improved noncoding RNA detection.
    Pac. Symp. Biocomput. 15: 69-79 (2010).
    [290]BIOINF 09-034 [Abstract] [PDF]
    David Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann
    Identification and classification of small RNAs in transcriptome sequence data.
    Pac. Symp. Biocomput. 15: 80-87 (2010)
    [289]BIOINF 09-032 [Abstract] [PDF]
    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: 175-181 (2010)

    2009


    [288]BIOINF 09-018 [Abstract] [PDF]
    Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler
    Local algorithms for the prime factorization of strong product graphs.
    Math. Comp. Sci. 2: 653-682 (2009).
    [287]BIOINF 09-021 [Abstract] [PDF]
    Manja Marz and Peter F. Stadler.
    Comparative analysis of eukaryotic U3 snoRNAs.
    RNA Biol., 6:503-507, 2009.
    [286]BIOINF 09-005 [Abstract] [PDF]
    Jens-Philipp Ostermeier, Marc Helmuth, Konstantin Klemm, Josef Leydold, and Peter F. Stadler
    A note on quasi-robust cycle bases.
    Acta Math. Contemp. 2:231-240 (2009).
    [285]BIOINF 08-025 [Abstract] [PDF]
    Peter Menzel, Jan Gorodkin, and Peter F. Stadler
    The tedious task of finding homologous non-coding RNA genes.
    RNA 15:2075-2082 (2009).
    [284]BIOINF 09-008 [Abstract] [PDF]
    Fenix W. D. Huang, Jing Qin, Christian M. Reidys, and Peter F. Stadler.
    Partition function and base pairing probabilities for RNA-RNA interaction prediction.
    Bioinformatics 25: 2646-2654 (2009).
    [283]BIOINF 09-042 [Abstract] [PDF]
    Peter F. Stadler, Sonja J. Prohaska, Christian V. Forst, and David C. Krakauer.
    Defining genes: A computational framework.
    Th. Biosci. 128:165-170 (2009).
    [282]BIOINF 09-006 [Abstract] [PDF]
    Roman R. Stocsits, Harald Letsch, Jana Hertel, Berhard Misof, and Peter F. Stadler.
    Accurate and efficient reconstruction of deep phylogenies from structured RNA.
    Nucleic Acids Res. 37: 6184-6193 (2009).
    [281]BIOINF 09-014 [Abstract] [PDF]
    Claudia C. Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J. Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan-Otto Attolini, and Peter F. Stadler.
    Non-coding RNA annotation of the Schistosoma mansoni genome.
    BMC Genomics 10:464 (2009).
    [280]BIOINF 09-010 [Abstract] [PDF]
    Manja Marz, Alexander Donath, Nina Verstaete, Van Trung Nguyen, Peter F. Stadler, and Olivier Bensaude.
    Evolution of 7SK RNA and its protein partners in metazoa.
    Mol. Biol. Evol. 26:2821-2830 (2009).
    [279]BIOINF 09-012 [Abstract] [PDF]
    Axel Mosig, Liang Zhu, and Peter F. Stadler.
    Customized strategies for discovering distant ncRNA homologs
    Brief. Funct. Genomics Proteomics 8:451-460 (2009).
    [278]BIOINF 09-046
    Peter Menzel, Jan Gorodkin, and Peter F. Stadler. Maximum likelihood estimation of weight matrices for targeted homology search.
    In: Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter F. Stadler, editors, German Conference on Bioinformatics 2009, volume 157 of Lecture Notes in Informatics, pages 211-220, Bonn, 2009. Gesellschaft f. Informatik
    [277]BIOINF 09-045 [Abstract] [PDF]
    Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia Sharma, Philipp Khaitovich, Peter F. Stadler, and Jörg Hackermüller
    Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
    PLoS Comp. Biol. 5:e1000502 (2009).
    [276]BIOINF 09-003 [Abstract] [PDF]
    Andreea Munteanu and Peter F. Stadler
    Mutate now, die later: Evolutionary dynamics with delayed selection.
    J.Theor.Biol. 260:412-421 (2009).
    [275]BIOINF 09-015 [Abstract] [PDF]
    David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Steve Khaitovich, and Peter F. Stadler. Evidence for human microRNA-offset RNAs in small RNA sequencing data.
    Bioinformatics 25:2298-2301 (2009)
    [274]BIOINF 08-022 [Abstract] [PDF]
    Peter F. Stadler, Julian J.-L. Chen, Jörg Hackermüller, Steve Hoffmann, Friedemann Horn, Phillip Khaitovich, Antje K. Kretzschmar, Axel Mosig, Sonja J. Prohaska, Xiaodong Qi, Katharina Schutt, and Kerstin Ullmann.
    Evolution of vault RNAs.
    Mol. Biol. Evol. 26:1975-1991, 2009.
    [273] BIOINF 08-011 [Abstract] [PDF]
    Markus Riester, Peter F. Stadler, and Konstantin Klemm.
    FRANz: Fast reconstruction of wild pedigrees
    Bioinformatics, 25:2134-2139 (2009).

    [272]BIOINF 08-021 [Abstract] [PDF]
    Michael Hiller, Sven Findeiß, Sandro Lein, Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter, and Peter F. Stadler.
    Conserved introns reveal novel transcripts in Drosophila melanogaster.
    Genome Res. 19:1289-1300 (2009).
    [271]BIOINF 09-097 [Abstract]
    Wolfang Otto, Peter F. Stadler, Francesc L&oacut;pez-Giald&eacut;z, Jeffrey P. Townsend, Vincent J. Lynch, and Günter P. Wagner.
    Measuring transcription factor binding site turnover: A maximum likelihood approach using phylogenies.
    Genome Biol. Evol., 1:85-98, 2009.
    [270] BIOINF 04-020 [Abstract] [PDF]
    Discovering cis-regulatory modules by optimizing Barbeques
    Axel Mosig, Türker Biyikoglu, Sonja J. Prohaska, Peter F. Stadler
    Discr. Appl. Math. 157: 2458-2468 (2009).
    DOI: doi:10.1016/j.dam.2008.06.042
    [269] BIOINF 07-005 [Abstract] [PDF]
    A Note on Fundamental, Non-fundamental, and Robust Cycle Bases
    Konstantin Klemm, Peter F. Stadler
    Discr. Appl. Math. 157: 2432-2438 (2009)
    DOI: doi:10.1016/j.dam.2008.06.047
    [268] BIOINF 09-016
    Solvent exposure imparts similar selective pressures across a range of yeast proteins
    Gavin C. Conant, Peter F. Stadler
    Mol. Biol. Evol. 26: 1155-1161 (2009)
    publisher
    [267] BIOINF 08-029 [PDF]
    Hox cluster duplications in the basal teleost Hiodon alosoides (Osteoglossomorpha)
    Karen E. Chambers, Ryan McDaniell, Jeremy F. Raincrow, Maya Deshmukh, Peter F Stadler, Chi-hua Chiu
    Th. Biosci 128: 109-120 (2009)
    [266] BIOINF 08-020 [PDF]
    Approximate Graph Products Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler
    Eur.J.Comb. 30: 1119-1133 (2009).
    [265]
    Andreas Heffel, Sonja J. Prohaska, Peter F. Stadler, Gerhard Kauer, and Jens-Peer Kuska.
    Automatic classification of embryonic fruit fly gene expression patterns.
    In: H.-P. Meinzer, Th. M. Deserno, H. Handels, and Th. Tolxdorff, editors, Bildverarbeitung für die Medizin 2009: Algorithmen - Systeme - Anwendungen, pp.415¿419, Heidelberg, 2009. Springer.
    [264]
    Karsten Scheibye-Alsing, Steve Hoffmann, Annett M. Frankel, Peter Jensen, Peter F. Stadler, Yuan Mang, Niels Tommerup, Mike J Gilchrist, Ann-Britt N. Hillig, Susanna Cirera, Claus B Jørgensen, Merete Fredholm, and Jan Gorodkin.
    Sequence assembly.
    Comp. Biol. Chem. 33: 121¿136 (2009).
    [263] BIOINF 08-024 [PDF]
    Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens
    Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler
    Nucleic Acids Res. 37: 1602-1615 (2009)
    [262] BIOINF 08-026 [PDF]
    Structural profiles of human miRNA families from pairwise clustering
    Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin
    Bioinformatics 25: 291-294 (2009).
    doi: 10.1093/bioinformatics/btn628 (2008).
    [261] BIOINF 09-001
    A survey of nematode SmY RNAs
    Thomas A. Jones, Wolfgang Otto, Manja Marz, Sean R. Eddy, Peter F. Stadler
    RNA Biology 6: 5-8 (2009)
    [260] BIOINF 08-023
    tRNAdb 2009: compilation of tRNA sequences and tRNA genes
    Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz
    Nucleic. Acids Research, 37: D159-D162 (2009). DOI: doi:10.1093/nar/gkn772
    [259] BIOINF 06-011 [Abstract] [PDF]
    A Topological Approach to Chemical Organization
    Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler
    Alife 15: 71-88 (2009)
    doi: 10.1162/artl.2009.15.1.15105

    2008


    [258] BIOINF 08-001 [PDF]
    Evolution of Spliceosomal snRNA Genes in Metazoan Animals
    Manuela Marz, Toralf Kirsten, Peter F. Stadler
    J.Mol.Evol. 67: 594-607 (2008) DOI: doi:10.1007/s00239-008-9149-6
    [257] BIOINF 08-010 [PDF] -->
    RNAalifold: improved consensus structure prediction for RNA alignments
    Stephan H Bernhart, Ivo L Hofacker, Sebastian Will Andreas R Gruber, and Stadler, Peter F
    BMC Bioinformatics 9: 474 (2008)
    DOI: doi:10.1186/1471-2105-9-474
    [256] BIOINF 07-024 [PDF]
    Duplicated RNA Genes in Teleost Fish Genomes
    Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang LI, Peter F. Stadlera
    J Bioinform Comput Biol. 6: 1157-1175 (2008).
    [255] BIOINF 08-027
    Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns
    Andrea Heffel, Peter F. Stadler, Sonja J. Prohaska, Gerhard Kauer, Jens-Peer Kuska
    In: Proceedings of the 15'th IEEE International Conference on Image Processing, ICIP 2008. IEEE CD Proceedings ICIP'08, pp. 721-724 (2008).
    [254]
    Replicator Dynamics in Protocells
    Peter F. Stadler and Bärbel M. R. Stadler
    In: Protocells: Bridging Nonliving and Living Matter, Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard, Peter F. Stadler (eds.), MIT Press, Cambridge MA, pp. 317-336 (2008).
    [253]
    Detection of small non-coding RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatics tools
    Elisabeth Sonnleitner, Theresa Sorger-Domenigg, Monika J. Madej, Sven Findeiß, Jörg Hackermüller, Alexander Hüttenhofer, Peter F. Stadler, Udo Bläsi and Isabella Moll
    Microbiology 154: 3175-3187 (2008)
    [252]
    Nature and Evolution of Early Replicons
    Peter Schuster, Peter F. Stadler In: Domingo, E. and Parrish, C. R. and Holland, J.
    Nature and Evolution of Early Replicons
    Academic Press, London, UK 2008, pp. 1-41.
    [251] BIOINF 08-005 [PDF]
    Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics
    Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker
    In: Bioinformatics Research and Development (BIRD 2008 Vienna, Austria, July 7-9, 2008 Proceedings);
    M. Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, C. Toma (eds), Springer Verlag, Heidelberg.
    CICS Vol 13, pp.114-127 (2008)
    [250] BIOINF 08-002 [PDF]
    SynBlast: Assisting the Analysis of Conserved Synteny Information
    Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska
    BMC Bioinformatics 9: 351 (2008)
    [249] BIOINF 08-008 [PDF]
    Arthropod 7SK RNA
    Andreas R. Gruber, Carsten Kilgus, Axel Mosig, Ivo L. Hofacker, Wolfgang Hennig, Peter F. Stadler
    Mol.Biol.Evol. 25: 1923-1930 (2008).
    [248] BIOINF 08-016
    HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis
    Steve Hoffmann, Sabine Cepok, Verena Grummel, Klaus Lehmann-Horn, Jörg Hackermüller, Peter F. Stadler, Hans-Peter Hartung, Achim Berthele, Florian Deisenhammer, Ralf Wasmuth, Bernhard Hemmer
    Am J Hum Genet. 83:219-227 (2008)
    [247] BIOINF 08-004 [PDF]
    ``Genes''
    Sonja J. Prohaska, Peter F. Stadler
    Theory Biosci . 127: 215-221 (2008)
    [246] BIOINF 07-030 [PDF]
    A Story of Growing Confusion: Genes and Their Regulation
    Sonja J. Prohaska, Peter F. Stadler
    In: Rubem P. Mondaini, Rui Dilão Biomat 2007 - International Symposium on Mathematical and Computational Biology , World Scientific, Singapore 2008, pp.325-345
    [245] BIOINF 08-012 [PDF]
    Noisy: identification of problematic columns in multiple sequence alignments
    Andreas W.M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
    Alg. Mol. Biol. 3: 7 (2008)
    Extended abstract presented at ICMSB 2008, Diliman, Phillipes
    [244] BIOINF 07-013 [PDF]
    Funnels in Energy Landscapes
    Konstantin Klemm, Christoph Flamm, Peter F. Stadler
    Eur.J.Phys.B 63: 387-391
    [243] BIOINF 07-013 [PDF]
    NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
    Dominic Rose, Jana Hertel, Kristin Reiche, Jörg Hackermüller, Peter F. Stadler
    Genomics 92: 65-74 (2008).
    [242] BIOINF 07-029 [PDF]
    The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and Evolution
    Chris T. Amemiya, Sonja J. Prohaska, Alicia Hill-Force, April Cooke, Jessica Wasserscheid, David E. K. Ferrier, Juan Pacual Anaya, Jordi Garcia-Fernàndez, Ken Dewar, Peter F. Stadler
    J.Exp.Zool.MDE 310B: 465-477 (2008).
    [241] BIOINF 08-006 [PDF]
    Rate Variations, Phylogenetics, and Partial Orders
    Sonja J. Prohaska, Guido Fritzsch, Peter F. Stadler
    In: Fifth Workshop on Computational System Biology, WCSB 2008, (M. Ahdesmäki, K. Strimmer, N. Radde, J. Rahnenführer, K. Klemm, H. Lähdesmäki, O. Yli-Harja, eds.), TU Tampere, 2008.
    [240] BIOINF 07-028 [PDF]
    Folding Kinetics of Large RNAs
    Michael Geis, Christoph Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker Martin Middendorf, Christian Mandl, Peter F. Stadler, Caroline Thurner
    J.Mol.Biol. 379: 160-173 (2008)
    [239] BIOINF 08-003 [PDF] [Supplement PDF]
    Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein-synthesis
    Christoph Jöchl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, Alexander Hüttenhofer
    Nucleic Acids Res. 36: 2677-2689 (2008)
    [238] BIOINF 07-017 [PDF] [Supplement]
    Evolution of Mitochondrial Gene Orders in Echinoderms
    Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter Stadler, Martin Schlegel
    Mol.Phylog.Evol. 47: 855-864 (2008).
    [237] BIOINF 07-022 [PDF]
    Near intron positions are reliable phylogenetic markers: An application to Holometabolous Insects
    Veiko Krauss, Christian Thümmler, Franziska Georgi, Jörg Lehmann, Peter F. Stadler, Carina Eisenhardt
    Mol.Biol.Evol. 25: 821-830 (2008)
    [236] BIOINf 07-012 [PDF]
    A PCR Survey of Xenoturbella bocki
    Guido Fritzsch, Manja U. Böhme, Mike Thorndyke, Hiroaki Nakano, Olle Israelsson, Thomas Stach, Martin Schlegel, Thomas Hankeln, Peter F. Stadler
    J.Exp.Zool.B: Mol.Dev.Evol., 310B: 278-284 (2008)
    [235] BIOINF 07-021 [PDF] [Supplement]
    Invertebrate 7SK snRNAs
    Andreas R. Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo L.Hofacker, Peter F. Stadler, Bernd-Joachim Benecke
    J.Mol.Evol. 66:107-115 (2008).
    [234] BIOINF 07-025 [Abstract] [PDF]
    Size Variation and Structural Conservation of Vertebrate Telomerase RNA
    Mingyi Xie, Axel Mosig, Xiaodong Qi, Yang Li, Peter F. Stadler, Julian J.-L. Chen
    J.Biol.Chem. 283: 2049-2059 (2008).
    [233] BIOINF 07-015 [PDF] [Supplement] [Software]
    Earlier version: BIOINF 07-003 [PDF] [Supplemental Material]
    snoReport: Computational identification of snoRNAs with unknown targets
    Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
    Bioinformatics, 24: 158-164 (2008)
    [232] BIOINF 06-014 [PDF]
    Variations on RNA Folding and Alignment: Lessons from Benasque
    Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Berhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will
    J.Math.Biol. 56:119-144 (2008).

    2007


    [231]
    Visualization of Barrier Tree Sequences Revisited
    Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo Hofacker, Peter F. Stadler
    In: L. Linsen, H. Hagen, B. Hamann: Visualization in Medicine and Life Sciences, Springer, Berlin, Heidelberg, pp. 275-290 (2007)
    [230] BIOINF 07-010 [Abstract] [PDF] [Supplemental Material]
    U7 snRNAs: A Computational Survey
    Manja Lindemeyer, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler
    Geno.Prot.Bioinf. 5: 187-195 (2007)
    [229] BIOINF 07-001 [Abstract] [PDF] [Supplemental Matrial]
    Computational RNomics of Drosophilids
    Dominic Rose, Jörg Hackermüller, Stefan Washietl, Sven Findeiß, Kristin Reiche, Jana Hertel, Peter F. Stadler, Sonja J. Prohaska
    BMC Genomics 8:406 (2007).
    [228] BIOINF 07-018 [Abstract] [PDF]
    CREx: inferring genomic rearrangements based on common intervals
    Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf
    Bioinformatics 23: 2957-2958 (2007)
    [227] BIOINF 07-014 [open access]
    Detection of RNA structures in porcine EST data and related mammals
    Stefan E. Seemann, Michael J. Gilchrist, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
    BMC Genomics 8:316 (2007)
    [226] BIOINF 07-016
    Tanimoto's Best Barbecue:
    Discovering Regulatory Modules using Tanimoto Scores
    Peter Menzel, Peter F. Stadler, Axel Mosig
    German Conference on Bioinformatics (GCB 2007)
    C.Falter, A.Schliep, J.Selbig, M.Vingron, D.Walther (eds)
    Gesellschaft f. Informatik, Bonn; Lecture Notes in Informatics 155: 68-77 (2007)
    [225] [PDF]
    Regulatory Signals in Genomic Sequences
    Sonja J. Prohaska, Axel Mosig, Peter F. Stadler
    In: Networks: From Biology to Theory
    Jianfeng Feng, Jürgen Jost, Minping Qian (Eds.)
    Springer, New York 2007, pp. 191-220.
    [224] BIOINF 07-011 [Abstract] [PDF] [Supplemental Material]
    Homology Search with Fragmented Nucleic Acid Sequence Patterns
    Axel Mosig, Julian L. Chen, Peter F. Stadler
    In: Algorithms in Bioinformatics (WABI 2007), Raffaele Giancarlo and Sridhar Hannenhalli (Eds),
    Springer Verlag, Berlin, Lect. Notes Comp. Sci. 4645, pp. 335-345 (2006).
    [223]
    Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example
    Peter Schuster, Peter F. Stadler
    In: Structural Approaches to Sequence Evolution: Molecules, Networks, Populations
    Bastolla, Ugo and Porto, Markus and Roman, H. Eduardo and Vendruscolo, Michele (Eds.)
    Springer Verlag, Berlin Heidelberg, pp. 3-36 (2007)
    [222] BIOINF 06-015 [Abstract] [PDF]
    Saddles and Barrier in Landscapes of Generalized Search Operators
    Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler
    In: Foundations of Genetic Algortithms IX
    Stephens, C. R., Toussaint, M., Whitley, D. and Stadler, P. F. (eds.)
    Lecture Notes Comp. Sci. 4436: 194-212 (2007)
    Springer Verlag, Berlin, Heidelberg.
    [221] BIOINF 06-016 [PDF] [Software]
    Progressive sequence alignments from Triplets
    Matthias Kruspe, Peter F. Stadler
    BMC Bioinformatics 8: 254 (2007)
    [220]
    Interleukin-6âdependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer
    Dennis Löffler, Katja Brocke-Heidrich, Gabriele Pfeifer, Claudia Stocsits, Jörg Hackermüller, Antje Kretzschmar, Renate Burger, Martin Gramatzki, Conny Blumert, Kay Bauer, Helena Cvijic, Kerstin Ullmann, Peter F. Stadler, Friedemann Horn
    Blood 110: 1330-1333 (2007)
    [219] BIOINF 06-017 [PDF] [Supplemental Material]
    Comparative Analysis of Structured RNAs in S. cerevisiae Indicates a Multitude of Different Functions
    Stephan Steigele, Wolfgang Huber, Claudia Stocsits, Peter F. Stadler, Kay Nieselt
    BMC Biology, 5:25 in press (2007).
    [218] BIOINF 07-006 [Abstract] [PDF]
    The transient probability distribution of M/M/&infty: a stochastic model for transcription factor binding site evolution
    Günter P. Wagner, Wolfgang Otto, Vincent Lynch, Peter F. Stadler
    J.Theor.Biol. 247:544-553 (2007)
    [217] BIOINF 06-009 [Full Text]
    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    The ENCODE Project Consortium
    Nature 447: 799-816 (2007)
    [216] BIOINF 06-010 [Abstract] [PDF]
    Structured RNAs in the ENCODE Selected Regions of the Human Genome
    Stefan Washietl, Jakob S. Pedersen, Jan O. Korbel, Andreas R. Gruber, Jöorg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Reiche, Claudia Stocsits, Andrea Tanzer, Catherine Ucla, Carine Wyss, Stylianos E. Antonarakis, France Denoeud, Julien Lagarde, Jorg Drenkow, Philipp Kapranov, Thomas R. Gingeras, Roderic Guigo, Michael Snyder, Mark B. Gerstein, Alexandre Reymond, Ivo L. Hofacker, Peter F. Stadler
    Genome Res., 17:852-864 (2007).
    [215] BIOINF 06-006 [Abstract] [PDF]
    RNAstrand: Reading Direction of Structured RNAs in Multiple Sequence Alignments
    Kristin Reiche, Peter F. Stadler
    Alg.Mol.Biol. 2:6 (2007)
    [214] [Publisher's Page][Supplemental Material]
    RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.
    Science 316: 1484-1488 (2007).
    [213] BIOINF 07-009 [Abstract] [PDF] [Supplemental Material]
    The Mitochondrial DNA of Xenoturbella bocki: Genomic Architecture and Phylogenetic Analysis
    Marleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelson, Detlef Bernhard, Martin Schlegel
    Th Biosci. 126: 35-42 (2007)
    [212] BIOINF 07-004 [Abstract] [PDF] [Supplemental Material]
    Evolution of the Vertebrate Y-RNA Cluster
    Axel Mosig, Meng Guofeng, Bärbel M. R. Stadler, Peter F. Stadler
    Th.Biosci., 126: 9-14 (2007).
    [211] BIOINF 06-007 [Abstract] [Abstract]
    PCR Survey of Hox Genes in the Goldfish Carassius auratus auratus
    Jing Luo, Peter F. Stadler, Shunping He, Axel Meyer
    J.Exp.Zool.B: Mol.Dev.Evol, 308B: 250-258 (2007)
    [210] BIOINF 06-012 [Abstract] [PDF] [Supplemental Material]
    Inferring Non-Coding RNA Families and Classes by Means of Structure-Based Clustering
    Sebastian Will, Kristin Missal, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
    PLoS Comp. Biol., 3: e65 (2007)
    [Full Text at Publisher's Page]
    [209] BIOINF 06-003 [Abstract] [PDF]
    RNase MRP and the RNA Processing Cascade in the Eukaryotic Ancestor
    Michael D. Woodhams, Peter F. Stadler, David Penny, Lesley J. Collins
    BMC Evol. Biol. 7(Suppl 1): S13
    [208]
    Ivo L. Hofacker, Peter F. Stadler
    RNA Secondary Structure
    In: Bioinformatics: From Genomes to Therapies,
    T. Lengauer (ed), Wiley-VCH, Weinheim, Germany, 2007, pp.439-489.
    [207] BIOINF 06-005 [Abstract] [PDF]
    RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
    The Athanasius F. Bompfünewerer, Consortium: Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will
    J.Exp.Zool.(Mol.Dev.Evol.) 308B: 1-25 (2007).
    [206] 05-011 [Abstract]
    Modeling amino acid substitution patterns in orthologous and paralogous genes
    Gavin C. Conant, Günter P. Wagner, Peter F. Stadler
    Mol. Phylog. Evol. 42: 298-307 (2007).

    2006


    [205]
    Evolutionary Genomics of Hox Gene Clusters Sonja J. Prohaska, Peter F. Stadler, Günter P. Wagner
    In: HOX Gene Expression, S. Papageorgiou (ed), Landes Bioscience & Springer, 2006, pp.***-***.
    [204] 02-pfs-002 [Abstract] [Postscript] [PDF]
    Genotype-Phenotype Maps
    Peter F. Stadler, Bärbel M. R. Stadler
    Biological Theory 3: 268-279 (2006).
    [203] BIOINF 06-008 [Abstract] [PDF] [Software]
    Comparative Analysis of Cyclic Sequences:
    Viroids and other Small Circular RNAs
    Axel Mosig, Ivo L. Hofacker, Peter F. Stadler
    In: Proceedings GCB 2006, R. Giegerich & Stoye, J. (eds),
    Lecture Notes in Informatics, P-83: 93-102 (2006)
    [202] BIOINF 06-004 [Abstract]
    Visualization of Lattice-Based Protein Folding Simulations
    Sebastian Pötzsch, Gerik Scheuermann, Michael T. Wolfinger, Christoph Flamm, Peter F. Stadler
    Tenth International Conference on Information Visualization (IV'06), 89-94. (2006). [IEEE Computer Science Press, Los Alamitos, CA]
    [201]
    Visualization of Barrier Tree Sequences
    Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    IEEE Trans. Vis. Comp. Graphics 12: 781-788 (2006).
    [200] BIOINF 05-007 [Abstract] [Postscript] [PDF]
    [Supplementary Material]
    Evolution of the Vertebrate Parahox Clusters
    Sonja J. Prohaska, Peter F. Stadler
    J.Exp.Zool B(Mol.Dev.Evol.) 306B: 481-487 (2006)
    [199]
    Evolution of MicroRNAs
    Andrea Tanzer, Peter F. Stadler
    In: MicroRNA Protocols, YS Ying (ed.),
    Methods in Molecular Biolog 342: 335-350 (2006)
    Humana Press, Totowa, NJ
    [198] BIOINF 06-002 [Abstract] [PDF] [Software]
    Hairpins in a Haystack: Recognizing microRNA Precursors in Comparative Genomics Data
    Jana Hertel, Peter F. Stadler
    Bioinformatics 22: e197-e202 (2006).
    ISMB contribution
    [197] BIOINF 05-023 [Abstract] [PS] [PDF] [Supplemental Material]
    Prediction of Structured Non-Coding RNAs in the Genomes
    of the Nematodes Caenorhabditis elegans and Caenorhabditis briggsae
    Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbø, Runsheng Chen, Peter F. Stadler
    J.Exp.Zool.(Mol.Dev.Evol.) 306B: 379-392 (2006).
    [196] BIOINF 04-012 [Abstract] [Postscript] [PDF]
    Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution
    Camille Stephan-Otto Attolini, Peter F. Stadler
    Physica D, 217: 143-141 (2006).
    [195] BIOINF 04-015 [Abstract] [Postscript] [PDF] [Supplement]
    Alignments of Mitochondrial Genome Arrangements:
    Applications to Metazoan Phylogeny
    Guido Fritzsch, Martin Schlegel, Peter F. Stadler
    J.Theor.Biol., 240: 511-520 (2006)
    [194] BIOINF 05-026 [Abstract] [PS] [PDF]
    Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
    Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler
    Europhys. Lett. 74: 726-732 (2006).
    [193] update of [156] Multiple sequence alignment with user-defined anchor points
    Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pohler, Peter F. Stadler
    Alg.Mol.Biol. 1:6 (2006).
    [192] BIOINF 04-019 [Abstract] [PDF]
    fragrep: Efficient Search for Fragmented Patterns in Genomic Sequences
    Axel Mosig, Katrin Sameith, Peter F. Stadler
    Geno. Prot. Bioinfo. 4: 56-60 (2006).
    [191] BIOINF 03-013 [Abstract] [PostScript] [PDF]
    Modeling RNA Folding
    Ivo L. Hofacker, Peter F. Stadler
    In: Complex Systems Science in BioMedicine, pp. 227-245, edited by Thomas S Deisboeck, J. Yasha Kresh. Springer Verlag, New York, NY, 2006.

    [190] BIOINF 05-025 [Abstract] [PS] [PDF]
    Software [Vienna RNA Package]
    Partition Function and Base Pairing Probabilities of RNA Heterodimers
    Stephan Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
    Alg.Mol.Biol. 1:3 (2006).
    [189] BIOINF 05-010 [Abstract] [Postscript] [PDF]
    A Prime Factor Theorem for a Generalized Direct Product
    Wilfried Imrich, Peter F. Stadler
    Disc. Math. Graph Theory, 26: 135-140 (2006).
    [188] BIOINF 05-024 [Abstract] [PS] [PDF]
    [Software]
    Local Base Pairing Probabilities in Large RNAs
    Stephan Bernhart, Ivo L. Hofacker, Peter F. Stadler Bioinformatics 22: 614-615 (2006).
    [187] BIOINF 05-020 [Abstract] [PS] [PDF] [cond-mat/0506493]
    Statistics of cycles in large networks
    Konstantin Klemm, Peter F. Stadler

    Phy.Rev.E, 73: 025101 (2006).
    [186] BIOINF 05-017 [Abstract] [PS] [PDF]
    Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation
    Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    BMC Bioinformatics, 7: 67 (2006).
    [185] BIOINF 05-021 [Abstract] [PS] [PDF]
    [Supplementary Material]
    The Expansion of the Metazoan MicroRNA Repertoire
    Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried,
    Andrea Tanzer, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler,
    and The Students of Bioinformatics Computer Labs 2004 and 2005:
    Sten Heinze, Alexander ''muppet'' Donath, Sven Findeß, Stephanie Keller, Kevin Peter,
    Julian Jöris, Jokab Mühmel, Marco Dienelt (in Leipzig),
    Martina Hödl, Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits,
    Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor Neumayr,
    Reinhard Wohlfart (in Vienna).

    BMC Genomics, 7: 15 (2006).
    [184] BIOINF 05-027 [Abstract] [PDF]
    miRNAMap: Genomic Maps of MicroRNA Genes and Their Target Genes in Mammalian Genomes
    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
    Nucleic Acids Res. 34: D135-D139 (2006).
    [183] BIOINF 05-006 [Abstract] [PDF]
    The fish specific Hox cluster duplication is coincident with the origin of teleosts
    Karen D. Crow, Peter F. Stadler, Vincent J. Lynch, Chris T. Amemiya, Günter P. Wagner
    Mol.Biol.Evol. 23: 121-136 (2006).

    2005


    [182] BIOINF 05-016 [Abstract] [PS] [PDF]
    Neutral Networks of Interacting RNA Secondary Structures
    Camille Stephan-Otto Attolini, Peter F. Stadler
    Adv. Complex Syst, 8: 275-284 (2005)

    [181] BIOINF 05-022 [Abstract] [PS] [PDF]
    Nodal Domain Theorems and Bipartite Subgraphs
    Türker Biyikoglu, Josef Leydold, Peter F. Stadler
    Elec.J.Lin.Alg. 13: 344-351 (2005).
    [180] BIOINF 05-005 [Abstract] [Postscript] [PDF]
    [Supplemental Material]
    Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
    Stefan Washietl, Ivo L. Hofacker, Melanie Lukasser, Alexander Hüttenhofer, Peter F. Stadler
    Nature Biotech. 23: 1383-1390 (2005).
    [179] BIOINF 05-008 [Abstract] [Postscript] [PDF]
    [Supplementary Material]
    Non-coding RNAs in Ciona intestinalis
    Kristin Missal, Dominic Rose, Peter F. Stadler
    Bioinformatics, 21(S2): i77-i78 (2005)
    ECCB/JBI'05, Madrid
    [178] BIOINF 05-018 [Abstract] [PS] [PDF]
    Memory Efficient Folding Algorithms for Circular RNA Secondary Structures
    Ivo L. Hofacker, Peter F. Stadler
    Bioinformatics 22: 1172-1176 (2006)
    Earlier version:
    In: German Conference on Bioinformatics 2005, pp. 15-25
    A. Torda, S. Kurtz, M. Rarey (eds.), LNI P-71
    Gesellschaft f. Informatik, Bonn, 2005.

    [177] BIOINF 05-019 [Abstract] [PS] [PDF]
    Thermodynamics of RNA-RNA Binding
    Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler, Ivo L. Hofacker
    Bioinformatics 22: 1177-1182 (2006)
    Earlier Version:
    In: German Conference on Bioinformatics 2005, pp. 3-13
    A. Torda, S. Kurtz, M. Rarey (eds.), LNI P-71
    Gesellschaft f. Informatik, Bonn, 2005.

    [176] RNA Secondary Structures
    I.L. Hofacker, P.F. Stadler
    In: Encyclopedia of Molecular Cell Biology and Molecular Medicine (2nd ed.) Vol.12, pp. 581-603
    Robert A. Meyers (Ed.)
    Wiley-VCH Weinheim, (2005).

    [175] BIOINF 05-015 [Abstract] [PS] [PDF]
    Explicit Collision Simulation of Chemical Reactions in a Graph Based Artifical Chemistry
    Gil Benkö, Christoph Flamm, Peter F. Stadler
    In: LNCS 3630: 725-733 (2005)
    Advances in Artificial Life: 8th European Conference, ECAL 2005.
    Mathieu S. Capcarrere, Alex A. Freitas, Peter J. Bentley, Colin G. Johnson, Jon Timmis (eds)
    Canterbury, UK, September 5-9, 2005

    [174] BIOINF 05-012 [Abstract] [PostScript] [PDF]
    CelloS: A Multi-level Approach to Evolutionary Dynamics
    Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
    In: LNCS 3630: 500-509 (2005)
    Advances in Artificial Life: 8th European Conference, ECAL 2005.
    Mathieu S. Capcarrere, Alex A. Freitas, Peter J. Bentley, Colin G. Johnson, Jon Timmis (eds)
    Canterbury, UK, September 5-9, 2005

    [173] 01-pfs-014 [Abstract] [Postscript] [PDF]
    [Software]
    Minimum Path Bases and Relevant Paths
    Petra M. Gleiss, Josef Leydold, Peter F. Stadler
    Networks, 46: 119-12346: 119-12346: 119-12346: 119-123 (2005).
    Older version:
    A note On Minimum Path Bases
    [Postscript] [PDF] Presented at the conference Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms, Bled (Slovenia) Sep 24-27 2001.


    [172] BIOINF 05-004
    [Abstract] [Postscript] [PDF]
    [Software]
    Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
    Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
    BMC Bioinformatics 6:160 [pub] (2005)
    [171] BIOINF 05-013 [Abstract] [PDF]
    Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate
    Gudrun Böhmdorfer, Ivo L. Hofacker, Karin Garber, Srecko Jelenic, Viktoria Nizhynska, Hirohiko Hirochika, Peter F. Stadler, Andreas Bachmair
    RNA, 11: 1181-1191 (2005).
    [170] BIOINF 04-014 [Abstract] [PDF] [Supplement]
    Molecular Evolution of Duplicated Ray Finned Fisch HoxA Clusters:
    Increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.
    Günter P. Wagner, Kazuhiko Takahashi, Vincent Lynch, Sonja J. Prohaska, Claudia Fried, Peter F. Stadler, Chris T. Amemiya
    J.Mol.Evol. 60: 665-676 (2005).
    [169] BIOINF 05-001 [Abstract] [Postscript] [PDF]
    [Supplemental Material]
    Evolutionary Patterns of Non-Coding RNAs
    A.F. Bompfünewerer, Ch. Flamm, C. Fried, G. Fritzsch, I.L. Hofacker, J. Lehmann, K. Missal, A. Mosig, B. Müller, S.J. Prohaska, B.M.R. Stadler, P.F. Stadler, A. Tanzer, S. Washietl, Ch. Witwer
    Th.Biosci. 123: 301-369 (2005).
    [168] BIOINF 04-017
    [Abstract] [PDF] Comparative promoter region analysis powered by CORG
    Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Ropcke, Peter F Arndt, Peter F Stadler, Martin Vingron
    BMC Genomics, 6: 24 [10 pages] (2005).
    [167] BIOINF 04-018 [Abstract] [PDF]
    Multiple sequence alignment with user-defined constraints@ GOBICS
    Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff
    Bioinformatics 21: 1271-1273 (2005).
    [166] BIOINF 05-003 [Abstract] [Postscript] [PDF]
    [Supplementary Material]
    Fast and reliable prediction of noncoding RNAs
    Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
    Proc.Natl.Acad.Sci.USA 102: 2454-2459 (2005).
    [165] BIOINF 04-015 [Abstract] [Postscript] [PDF]
    The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA Mechanism: A Quantitative Model
    Jörg Hackermüller, Nicole-Claudia Meisner, Manfred Auer, Markus Jaritz, Peter F. Stadler Gene 345: 3-12 (2005).
    [164] BIOINF 04-013 [Abstract] [Postscript] [PDF] [Supplement]
    Evolution of MicroRNAs Located Within Hox Gene Clusters
    Andrea Tanzer, Chris T. Amemiya, Chang-Bae Kim, Peter F. Stadler
    J.Exp.Zool.(Mol.Dev.Evol.) 304B: 75-85 (2005).

    2004


    [163] 99-NN-004 [Abstract] [Postscript] [PDF]
    Discrete Models of Biopolymers
    Peter Schuster, Peter F. Stadler
    In: Handbook of Computational Chemistry and Biology;
    J. Crabbe, A. Konopka, and M. Drew, eds. Marcel Dekker, Inc., pp. 187-221 (2004).
    [162]

    Comparative genomics, cis-regulatory elements, and gene duplication
    A. Force, C. Shashikant, P.F. Stadler, C.T. Amemiya
    In: Detrich~III, H., Zon, L., and Westerfield, M. (eds),
    The Zebrafish, Vol.2 (Methods in Cell Biology, Vol.77)
    Elsevier, New York, 2004, pp. 545-561.
    [161] BIOINF 04-004 [Abstract] [full text not available]
    Interactions in Oligonucleotide Hybrid Duplexes on microarrays
    Hans Binder, Toralf Kirsten, Ivo L. Hofacker, Peter F. Stadler, Markus Loeffler
    J.Phys.Chem.B 108: 18015-18025 (2004).
    [160] BIOINF 04-003 [Abstract] [full text not available]
    Sensitivity of Microarray Oligonucleotide Probes: Variability and Effect of Base Composition
    Hans Binder, Toralf Kirsten, Markus Loeffler, Peter F. Stadler
    J.Phys.Chem.B 108: 18003-18014 (2004).
    [159] BIOINF 04-001 [Abstract] [Postscript] [PDF]
    Prediction of Consensus RNA Secondary Structures Including Pseudoknots
    Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
    IEEE/ACM Trans.Comp.Biol.Bioinf., 1: 66-77 (2004).

    [158] BIOINF 04-007 [Abstract] [Postscript] [PDF] [Supplement]
    Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests
    Günter P. Wagner, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
    Mol.Biol.Evol. 21: 2116-2121 (2004)

    [157] BIOINF 04-010 [Abstract] [Postscript] [PDF]
    Conserved RNA Pseudoknots
    Caroline Thurner, Ivo L. Hofacker, Peter F. Stadler
    In: Robert Giegerich and Jens Stoye (eds), German Conference on Bioinformatics 2004, pp.207-216 (2004)
    [GI-Edition; Lecture Notes in Informatics Vol. P-53].
    [156] BIOINF 04-011 [Abstract] [Postscript] [PDF]
    Multiple sequence alignment with user-defined constraints
    Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler
    In: Robert Giegerich and Jens Stoye (eds), German Conference on Bioinformatics 2004, pp.25-36 (2004)
    [GI-Edition; Lecture Notes in Informatics Vol. P-53].
    [155]BIOINF 03-026 [Abstract] [PostScript] [PDF]
    Alignment of RNA Base Pairing Probability Matrices
    Ivo L. Hofacker, Stephan H.F. Bernhart, Peter F. Stadler
    Bioinformatics, 20: 2222-2227 (2004).
    [154] BIOINF 02-002 [Abstract] [Postscript] [PDF]
    Graph Laplacians, Nodal Domains, and Hyperplane Arrangements
    T Biyikoglu, W Hordijk, J Leydold, T Pisanski, P F Stadler
    Lin.Alg.Appl. 390: 155-174 (2004)
    [153] BIOINF 04-009 [Abstract] [Postscript] [PDF]
    Gene Phylogenies and Protein-Protein Interactions:
    Possible Artifacts Resulting From Shared Protein Interaction Partners
    Paulo R. A. Campos, Viviane M. de Olivera, Günter P. Wagner, Peter F. Stadler
    J.Theor.Biol 231: 197-202 (2004).
    [152] BIOINF 04-008 [Abstract] [PDF]
    Simon Ando Decomposability and Fitness Landscapes
    Max Shpak, Peter F. Stadler, Günter P. Wagner, Lee Altenberg
    Th. Biosci., 123: 139-180 (2004).

    [151] BIOINF 03-028 [Abstract] [PostScript] [PDF]
    Computational Chemistry with RNA Secondary Structures
    Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    Kemija u indistriji 53: 315-322 (2004).
    [150] BIOINF 03-024 [Abstract] [PostScript] [PDF] [Supplemental Material]
    Evidence for independent Hox ene duplications in the hagfish lineage: A PCR-based gene inventory of Eptatretus stoutii
    Peter F. Stadler, Claudia Fried, Sonja J. Prohaska, Wendy J. Bailey, Bernhard Y. Misof, Frank H. Ruddle, Günter P. Wagner
    Mol.Phylog.Evol., 32: 686-694 (2004)
    [149] BIOINF 04-006 [Abstract] [Postscript] [PDF]
    [Supplement]
    The Duplication of the Hox Gene Clusters in Teleost Fishes
    Sonja J. Prohaska, Peter F. Stadler
    Th. Biosci., 123: 89-110 (2004)

    [148] BIOINF 03-008 [Abstract] [PDF]
    Aggregation of Variables and System Decomposition:
    Applications to Fitness Landscape Analysis
    Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson
    Th. Biosci. 123: 33-68 (2004)
    [147] BIOINF 03-003 [Abstract] [Postscript] [PDF]
    The Topology of Evolutionary Biology
    Bärbel M.R. Stadler and Peter F. Stadler
    G.Ciobanu, G. Rozenberg (Eds.): Modeling in Molecular Biology,
    Springer Verlag, Natural Computing Series 2004; pp. 267-286

    [146]
    RNA Folding in silico
    Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    In: Evolutionary Methods in Biotechnology
    Susanne Brakmann, Andreas Schwienhost (eds.)
    Wiley-VCH, Weinheim, Germany, 2004; pp. 177-190.

    [145] BIOINF 03-030 [Abstract] [PostScript] [PDF]
    The Partition Function Variant of Sankoff's Algorithm
    Ivo L. Hofacker, Peter F. Stadler
    In: Marian Bubak, Geert Dick van Albada, Peter M. A. Sloot, and Jack J. Dongarra (Eds.): Computational Science - ICCS 2004, Part IV, Lecture Notes in Computer Science LNCS 3039, Springer Verlag, Heidelberg, 2004, pp 728-735.
    Presented at ICCS 2004, Kraków, Jun 6-9 2004

    [144] BIOINF 04-002 [Abstract] [Postscript] [PDF]
    [Supplemental Material]
    Molecular Evolution of a MicroRNA Cluster
    Andrea Tanzer, Peter F. Stadler
    J.Mol.Biol. 339: 327-335 (2004).

    [143] BIOINF 03-015 [Abstract] [PostScript] [PDF]
    Conserved RNA Secondary Structures in Flaviviridae Genomes
    Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
    J. Gen. Virol. 85: 1113-1124. (2004).

    [142] BIOINF 03-029 [Abstract] [PostScript] [PDF]
    Multi-Phase Artificial Chemistry
    Gil Benkö, Christoph Flamm, Peter F. Stadler
    H Schaub, F. Detje, U. Brüggemann (eds.) The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, IOS Press, Akademische Verlagsgesellschaft, Berlin, pp. 16-22 (2004)
    (Proceedings of GWAL 2004, Bamberg, 14-16 April 2004)
    [141] BIOINF 04-005 [Abstract] [Postscript] [PDF]
    Graph Grammars as Models for the Evolution of Developmental Pathways
    Martin Beck, Gil Benkö, Gunther J. Eble, Christoph Flamm Stefan Müller, Peter F. Stadler
    H Schaub, F. Detje, U. Brüggemann (eds.) The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, IOS Press, Akademische Verlagsgesellschaft, Berlin, pp. 8-15 (2004)
    (Proceedings of GWAL 2004, Bamberg, 14-16 April 2004)
    [140] BIOINF 03-027 [Abstract] [PostScript] [PDF]
    Exact Folding Dynamics of RNA Secondary Structures
    Michael T. Wolfinger, W. Andreas Svrcek-Seiler Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
    J.Phys.A: Math.Gen. 37: 4731-4741 (2004).

    [139] BIOINF 03-002 [Abstract] [Postscript] [PDF] [PDF with pixelgraphics]
    [Supplemental Material]
    Surveying Phylogenetic Footprints in Large Gene Clusters:
    Applications to Hox Cluster Duplications
    Sonja Prohaska, Claudia Fried, Christoph Flamm, Günter P. Wagner, Peter F. Stadler
    Mol.Evol.Phylog. 31: 581-604 (2004).

    [138] BIOINF 03-025 [Abstract] [PostScript] [PDF]
    Exclusion of Repetitive DNA Elements from Gnathostome Hox Clusters
    Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
    J.Exp.Zool. Mol.Devel.Evol. 302B: 165-173 (2004)

    [137] BIOINF 03-021 [Abstract]
    The Footprint Sorting Problem
    Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler
    J.Chem.Inf.Comput.Sci 44: 332-338 (2004).

    [136] BIOINF 03-012 [Abstract]
    Counterexamples in Chemical Ring Perception
    Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler
    J.Chem.Inf.Comput.Sci 44: 323-331 (2004).

    [135] BIOINF 03-023 [Abstract]
    [Supplemental Material]
    Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon
    Claudia S. Copeland, Oliver Heyers, Bernd H. Kalinna, Andreas Bachmair, Peter F. Stadler, Ivo L. Hofacker, Paul J. Brindley
    Gene 329: 103-114 (2004)

    [134] BIOINF 03-010 [Abstract] [PostScript] [PDF]
    [Supplemental Material]
    The Shark HoxN cluster is homologous to the Human HoxD cluster
    Sonja J. Prohaska, Claudia Fried, Chris T. Amemiya, Frank H. Ruddle, Günter P. Wagner, Peter F. Stadler
    J.Mol.Evol. 58: 212-217 (2004).
    [133] [Publisher's Page] [Full Text]
    Transitions from Nonliving to Living Matter
    Steen Rasmussen, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard, Peter F. Stadler, and Mark A. Bedau
    Science 303: 963-965 (2004) [Perspectives]

    [132] BIOINF 03-009 [Abstract] [PostScript] [PDF]
    Prediction of Locally Stable RNA Secondary Structures for Genome-Wide Surveys
    Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
    Bioinformatics 20: 191-198 (2004).
    [131] BIOINF 02-005 [Abstract] [Postscript] [PDF]
    Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism
    Steen Rasmussen, Liaohai Chen, Bärbel M.R. Stadler, Peter F. Stadler
    Orig. Life Evol. Biosph. 34: 171-180 (2004).

    [130] BIOINF 03-007 [text not yet available]
    Bichir HoxA cluster sequence reveals surprising trends in rayfinned fish genomic evolution
    Chi-Hua Chiu, Ken Dewar, Günter P. Wagner, Kazuhiko Takahashi, Frank Ruddle, Christina Ledje, Peter Bartsch, Jean-Luc Scemama, Edmund Stellwag, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler, Chris T. Amemiya
    Genome Res. 14: 11-17 (2004)

    2003


    [129] 01-pfs-017 [Abstract] [Postscript] [PDF]
    Higher Separation Axioms in Generalized Closure Spaces
    Bärbel M. R. Stadler, Peter F. Stadler
    Commentationes Mathematicae Warszawa, Ser. I, 43: 257-273 (2003)

    [128] BIOINF 03-014 [Abstract] [PostScript] [PDF]
    litsift: Automated Text Categorization in Bibliographic Search
    Lukas C. Faulstich, Peter F. Stadler, Caroline Thurner, Christina Witwer
    In: Data Mining and Text Mining for Bioinformatics [Proceedings of the European Workshop Held in Conjunction with ECML / PKDD- 2003 in Dubrovnik, Croatia 22 September, 2003] , Tobias Scheffer Ulf Leser (eds.), Humboldt Univ., Berlin, 2003, pp. 20-25.

    [127] BIOINF 03-020 [Abstract] [PostScript] [PDF]
    Conserved RNA Secondary Structures in Viral Genomes: A Survey
    Ivo L. Hofacker, Peter F. Stadler, Roman Stocsits
    Bioinformatics 20: 1495-1499 (2004)
    and
    Proceedings of the German Conference on Bioinformatics. Volume I. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer (Eds.), belleville Verlag Michael Farin, Müünchen, 2003, p.57-62. submitted to GCB 2003.

    [126] BIOINF 03-018 [Abstract] [PostScript] [PDF]
    Design of Multi-Stable Nucleic Acid Sequences
    Ingrid Abfalter, Christoph Flamm, Peter F. Stadler
    Proceedings of the German Conference on Bioinformatics. Volume I. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer (Eds.), belleville Verlag Michael Farin, Müünchen, 2003, p.1-7. submitted to GCB 2003.

    [125] BIOINF 03-011 [Abstract] [PostScript] [PDF]
    Independent Hox-Cluster Duplications in Lampreys
    Claudia Fried, Sonja J. Prohaska,, Peter F. Stadler
    J.Exp.Zool., Mol. Dev. Evol 299B: 18-25 (2003).
    [124] BIOINF 03-006 [Abstract] [Postscript] [PDF]

    Generic Properties of Chemical Networks:
    Artificial Chemistry Based on Graph Rewriting
    Gil Benkö, Christoph Flamm, Peter F. Stadler
    In: Artificial Chemistry Based on Graph Rewriting.
    Banzhaf, W., Christaller, T., Dittrich, P., Kim, J.T., and Ziegler, J. (Eds.), Springer-Verlag (Heidelberg), 2003, pp.10-20.
    7th European Conference, ECAL 2003, Dortmund, Germany, September 14-17, 2003, Proceedings

    [123] 02-08-034 [Abstract] [Postscript] [PDF]
    On the Evolution of Primitive Genetic Codes
    G. Weberndorfer, I.L. Hofacker, P.F. Stadler

    Origins Life Evol. Biosph., 33: 491-514 (2003)

    [122] BIOINF 02-006 [Abstract] [Postscript] [PDF]
    Landscapes and Effective Fitness
    Peter F. Stadler, Christopher R. Stephens
    Comments Theor. Biol. 8: 389 - 431 (2003).
    [121] BIOINF 02-001 [Abstract] [Postscript] [PDF]
    A Graph-Based Toy Model of Chemistry
    G Benkö, C Flamm PF Stadler
    J. Chem. Inf. Comput. Sci. 43: 1085-1093 (2003).
    [120] 01-10-056 [Abstract] [Postscript] [PDF]
    Circuit Bases of Strongly Connected Digraphs
    Petra M. Gleiss, Josef Leydold, Peter F. Stadler
    Discussiones Math. Graph Th.23: 241-260 (2003).
    Presented at the conference Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms, Bled (Slovenia) Sep 24-27 2001.

    [119] BIOINF 02-003 [Abstract] [Postscript] [PDF]
    Molecular Replicator Dynamics
    B.M.R. Stadler and P.F. Stadler
    Adv. Complex Systems 6: 47-77 (2003)
    presented at Emergence in Chemical Systems, University of Alaska Anchorage, June 20-23 2002
    [118] BIOINF 02-004 [Abstract] [Postscript] [PDF]
    Centers of Complex Networks
    S.Wuchty and P.F. Stadler
    J.Theor.Biol. 223: 45-53 (2003)

    [117] BIOINF 03-001 [Abstract] [Postscript] [PDF]
    Phase transition and landscape statistics of the number partitioning problem
    Peter F. Stadler, Wim Hordijk, José F. Fontanari
    Phys.Rev.E 67: 056701 (2003)

    [116] 00-pfs-003 [Abstract] [Postscript]
    Minimum Cycle Bases of Halin Graphs
    Peter F. Stadler
    J. Graph Th. 43: 150-155 (2003).

    [115] BIOINF 02-007 [Abstract] [Postscript] [PDF]
    Shapes of tree representations of spin-glass landscapes
    Wim Hordijk, José F. Fontanari, Peter F. Stadler
    J.Phys.A:Math.Gen. 36: 3671-3681 (2003).

    [114] 02-04-015 [Abstract] [Postscript] [PDF]
    Quasi-Independence, Homology and the Unity of Type:
    A Topological Theory of Characters
    G.P. Wagner, P.F. Stadler

    J. Theor. Biol. 220: 505-527 (2003).
    [113] 02-pfs-003 [Abstract] [Postscript] [PDF]
    Barrier Trees on Poset-Valued Landscapes
    P.F. Stadler, Ch. Flamm

    Genet. Prog. Evolv. Mach., 4: 7-20 (2003)

    2002


    [112] 02-pks-003 [Abstract] [Postscript] [PDF]
    Networks in Molecular Evolution
    P. Schuster, P.F. Stadler

    Complexity, 8:34-42 (2002)

    [111] 99-NN-001 [Abstract] [Postscript] [PDF]
    Spectral Landscape Theory
    Peter F. Stadler
    In: J.P. Crutchfield and P. Schuster (eds.)
    Evolutionary Dynamics - Exploring the Interplay of Selection, Neutrality, Accident, and Function
    Oxford University Press, 2002 p.231-272
    [110] 02-03-012 [Abstract] [Postscript] [PDF]
    [Software]
    Stochastic Pairwise Alignments
    U. Mückstein, I.L. Hofacker, P.F. Stadler

    Bioinformatics 18 (Supplement 2), S153-S160 (2002)

    [109] 01-08-044 [Abstract] [Postscript] [PDF]
    Minimum Cycle Bases of Product Graphs
    W. Imrich, P.F. Stadler
    Australasian J. Comb. 26: 233-244 (2002).

    [108] 01-01-006 [Abstract] [Postscript] [PDF]
    Landscapes on Spaces of Trees
    Oliver Bastert, Dan Rockmore, Peter F. Stadler, Gottfried Tinhofer
    Appl.Math.Comput 131: 439-459 (2002).
    [107] 01-11-067 [Abstract] [Postscript] [PDF]
    Secondary Structure Prediction for Aligned RNA Sequences
    Ivo L. Hofacker, Martin Fekete, Peter F. Stadler
    J.Mol.Biol. 319: 1059-1066 (2002)

    [106] 01-pfs-004 [Abstract] [Postscript] [PDF]
    Fitness Landscapes
    Peter F. Stadler
    In: M. Lässig and A. Valleriani (eds.):
    Biological Evolution and Statistical Physics
    Springer-Verlag, Berlin, 2002, pp. 187-207.

    [105] 01-pfs-007 [Abstract] [Postscript] [PDF]
    Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry
    B.M.R. Stadler, P.F. Stadler
    J.Chem.Inf.Comput.Sci. 42: 577-585 (2002).
    [ASAP Article 10.1021/ci0100898 S0095-2338(01)00089-0
    Web Release Date: January 29, 2002]

    Supplemental Material:
    Basic Properties of Filter Convergence Spaces [Postscript] [PDF]
    Basic Properties of Closure Spaces [Postscript] [PDF]

    [104] 01-03-14 [Abstract] [Postscript] [PDF]
    Combinatorial Landscapes
    Christian M. Reidys Peter F. Stadler
    SIAM Review 44: 3-54 (2002)

    [103] 01-06-034 [Abstract] [Postscript] [PDF] [cond-mat/0106366]
    Fractal geometry of spin-glass models
    J.F. Fontanari, P.F. Stadler
    J.Phys.A:Math.Gen. 35: 1509-1516 (2002).

    [102] 01-02-011 [Abstract] [Postscript] [PDF]
    Recombination Spaces, Metrics, and Pretopologies
    Bärbel M.R. Stadler, Peter F. Stadler, Max Shpak, Günter P. Wagner
    Z.Phys.Chem. 216: 217-234 (2002).
    [101] 01-09-053 [Abstract] [Postscript] [PDF]
    Barrier Trees of Degenerate Landscapes
    Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
    Z.Phys.Chem. 216: 155-173 (2002)

    [100] 01-09-052 [Abstract] [Postscript] [PDF]
    Evolution in Systems of Ligation-Based Replicators
    Bärbel M. R. Stadler, Peter F. Stadler, Peter R. Wills
    Z.Phys.Chem., 216: 21-33 (2002).

    [99] 99-10-068 [Abstract] [Postscript] [PDF]
    Fast Fourier Transform for Fitness Landscapes
    Dan Rockmore, Peter Kostelec, Wim Hordijk, Peter F. Stadler
    Appl.Comput.Harm.Anal., 12: 57-76 (2002).

    2001


    [98] 01-pfs-015 [Abstract] [Postscript] [PDF] [cond-mat/0110472]
    Glassy states in a shaken sandbox
    Peter F. Stadler, Anita Mehta, Jean-Marc Luck
    Adv. Complex Syst. 4: 429-439 (2001).
    Presented at the research workshop on Challenges in Granular Physics, ICTP Trieste, Italy, Aug 07-11 2001.

    [97] 01-03-013 [Abstract] [Postscript] [PDF] [cond-mat/0103076]
    Shaking a Box of Sand
    Peter F. Stadler, Anita Mehta, Jean-Marc Luck
    Europhys.Lett. 57: 46-52 (2001).
    [96] 01-08-040 [Abstract] [Postscript] [PDF]
    Conserved RNA Secondary Structures in Picornaviridae Genomes
    C. Witwer, S. Rauscher, I.L. Hofacker, P.F. Stadler
    Nucleic Acids Res. 29: 5079-5089 (2001).

    [95] 00-12-070 [Abstract] [Postscript]
    The topology of the possible: Formal spaces underlying patterns of evolutionary change
    B. M. R. Stadler, P. F. Stadler, G. Wagner and W. Fontana
    J.Theor.Biol. 213: 241-274 (2001).
    [94] 01-pfs-005 [Abstract] [Postscript] [PDF]
    Relevant Cycles in Chemical Reaction Network
    Petra M. Gleiss, P.F. Stadler, A. Wagner, D.A. Fell
    Adv.Complex Syst. 4:207-226 (2001).

    [93] 00-09-001 [Abstract] [Postscript] [PDF] [ PS Preprint version at the ESI]
    Discrete Nodal Domain Theorems
    E. Brian Davies, Graham M. L. Gladwell Josef Leydold, Peter F. Stadler
    Lin.Alg.Appl. 336: 51-60 (2001).
    Earlier Version: [math/0009120]

    [92] 98-11-103 [Abstract] [Postscript]
    Exploring Protein Sequence Space Using Knowledge Based Potentials
    A. Babajide, R. Farber, I.L. Hofacker, J. Inman, A.S. Lapedes, P.F. Stadler
    J.Theor.Biol. 212: 35-46 (2001).
    [91] 00-05-027 [Abstract] [Postscript]
    Design of Multi-Stable RNA Molecules
    Christoph Flamm, Ivo L. Hofacker, Sebastian Maurer-Stroh, Peter F. Stadler, Martin Zehl
    RNA 7: 254-265 (2001).
    [90] 98-10-089 [Abstract] [Postscript]
    Neutrality in Fitness Landscapes
    Christian M. Reidys, Peter F. Stadler
    Appl. Math. & Comput. 117: 321-350 (2001).

    2000


    [89] 00-07-033 [Abstract] [Postscript]
    Landscape statistics of the low autocorrelated binary string problem
    Fernando F. Ferreira, José F. Fontanari, Peter F Stadler
    J.Phys.A:Math.Gen 33: 8635-8647 (2000).

    [88] 99-09-065 [Abstract] [Postscript]
    Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions
    Bärbel M.R. Stadler, Peter F. Stadler, Peter Schuster
    Bull.Math.Biol. 62: 1061-1086 (2000).
    [87] 99-03-022 [Abstract] [Postscript]
    RNA Shape Space Topology
    Jan Cupal, Stefan Kopp, Peter F. Stadler
    Alife 6: 3-23 (2000).
    [86] 98-06-009 [Abstract] [Postscript] (SFI 98-06-57)
    Prediction of RNA base pairing probabilities using massively parallel computers
    Martin Fekete, Ivo L. Hofacker, and Peter F. Stadler
    J.Comp.Biol. 7: 171-182(2000)

    [85] 99-01-001 [Abstract] [Postscript]
    Population Dependent Fourier Decomposition of Fitness Landscapes over Recombination Spaces: Evolvability of Complex Characters:
    P.F.Stadler, R.Seitz, G.P.Wagner
    Bull.Math.Biol. 62: 399-428 (2000).

    [84] 00-pfs-001 [Abstract] [Postscript] [PDF]
    Three Different Premature Stop Codons Lead to Skipping of Exon 7 in Neurofibromatosis Type I Patients
    Katharina Wimmer, Markus Eckart, Peter F. Stadler, Helga Rehder, Christa Fonatsch
    Human Mutation, Mutation in Brief #341 (2000) [Online]

    [83] 99-07-046 [Abstract] [Postscript] [Erratum]
    Interchangeability of Relevant Cycles in Graphs
    Petra M. Gleiss, Josef Leydold, Peter F. Stadler.
    Electronic J. Combinatorics 7:R16, 16 pages (2000).
    [82] 99-09-063 [Abstract] [Postscript] [xxx.lanl.gov]
    Error Propagation in the Hypercycle
    Paulo R.A. Campos, J. Fernando Fontanari, Peter F. Stadler
    Phys.Rev.E 61: 2996-3002 (2000).

    1999


    [81] 99-09-062 [Abstract] [Postscript] [xxx.lanl.gov]
    Metastable States in High Order Short-Range Spin Glasses
    Viviane M. de Oliveira, J.F. Fontanari, Peter F. Stadler
    J.Phys.A:Math.Gen. 32: 8793-8802 (1999)

    [80] 99-NN-003 [Abstract] [Postscript]
    Equitable Partitions, Coherent Algebras and Random Walks: Applications to the Correlation Structure of Landscapes Peter F. Stadler and Gottfried Tinhofer
    MATCH 40: 215-261 (1999)

    [79] 99-NN-12 [Postscript]
    An Efficient Potential for Protein Sequence Design
    Günter Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
    Computer Science in Biology. Univ. Bielefeld, D. GCB'99 Proceedings, Hannover, 1999. Pages 107-112.

    [78] 99-NN-13 [Postscript]
    Conserved Secondary Structures in Hepatitis B Virus RNA
    Roman Stocsits, Ivo L. Hofacker, Peter F. Stadler
    Computer Science in Biology. Univ. Bielefeld, D. GCB'99 Proceedings, Hannover, 1999. Pages 73-79.

    [77] 99-NN-11 [Postscript]
    Topology in Phenotype Space
    Jan Cupal, Peter Schuster, Peter F. Stadler
    In: Computer Science in Biology. Univ. Bielefeld, D. GCB'99 Proceedings, Hannover, 1999. Pages 9-15.

    [76] 97-03-08 [Abstract] [Postscript]
    Complex Adaptations and the Structure of Recombination Spaces
    G.P. Wagner, P.F. Stadler
    In: C.L. Nehaniv, M. Ito (eds.) "Algebraic Engineering"
    World Scientific 1999, pp.96-115
    (Proceedings of the Conference on Semi-Groups and Algebraic Engineering, University of Aizu, Japan)

    [75] 99-02-010 [Abstract] [Postscript]
    Viral RNA and Evolved Mutational Robustness
    A.Wagner, P.F.Stadler
    J.Exper.Zool. (Molec. Develop. Evol.) 285: 119-127 (1999)

    [74] 98-11-098 [Abstract] [Postscript]
    Nature and Evolution of Early Replicons
    P. Schuster, P.F. Stadler
    In: Origin and Evolution of Viruses, E. Domingo, R.G. Webster, J. Holland (Eds.), Academic Press, 1999, pp.1-24.
    [73] 97-03-030 [Abstract] [Postscript]
    RNA Structures with Pseudo-Knots
    C.Haslinger, P.F. Stadler
    Bull.Math.Biol. 61: 437-467 (1999)

    [72] 95-07-09 [Abstract] [Postscript]
    Random Field Models for Fitness Landscapes
    Peter F. Stadler and Robert Happel
    J.Math.Biol. 38: 435-478 (1999)

    [71] 95-07-05 [Abstract] [Postscript]
    Autocatalytic Replication in a CSTR and Constant Organization
    Robert Happel and Peter F. Stadler
    J.Math.Biol. 38: 422-434 (1999)

    [70] 99-NN-002 [Abstract] [Postscript]
    RNA in silico: The Computational Biology of RNA Secondary Structures
    Christoph Flamm,Ivo L. Hofacker, Peter F. Stadler
    Adv. Complex Syst. 2: 65-90 (1999)

    [69] 98-06-008 [Abstract] [Postscript] (SFI 98-06-58)
    Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
    Ivo L. Hofacker and Peter F. Stadler
    Comp & Chem. 23: 401-414 (1999)

    [68] 97-09-001 [Abstract] [Postscript]
    Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers
    P.F. Stadler
    J.Mol.Struct.(THEOCHEM) 463, 7-19 (1999).

    1998


    [67] 94-04-03 [Abstract] [Postscript]
    Combinatorics of RNA Secondary Structures
    Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
    Discr.Appl.Math. 88: 207-237 (1998) {in a revised version}

    [66] 97-07-065 [Abstract] [Postscript]
    Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation
    P.R. Wills, S.A. Kauffman, B.M.R. Stadler, P.F. Stadler
    Bull.Math.Biol., 60: 1073-1098 (1998)

    [65] 97-05-031 [Abstract] [Postscript]
    The Evolution of Diversity in Replicator Networks
    R. Happel, P.F. Stadler
    J.Theor.Biol. 195: 329-338 (1998)

    [64] 94-06-05 [Abstract] [Postscript]
    The Dynamics of Adaptive Parties Under Spatial Voting
    John H. Miller, Peter F. Stadler
    J.Econ.Dyn.Control 23: 171-189 (1998)

    [63] 97-12-097 [Abstract not available] [PostScript]
    Generic Properties of the Sequence-Structure Relations of Biopolymers
    Peter F. Stadler
    In: "Exobiology: Matter, Energy, and Information in the Origin of Life in the Universe",
    J. Chela-Flores and F. Raulin (eds). Kluwer, Dordrecht 1998.
    [62] 98-03-002 [Abstract] [Postscript]
    Amplitude Spectra of Fitness Landscapes
    Wim Hordijk, Peter F. Stadler
    J.Complex Systems 1:39-66 (1998)
    [61] 98-03-003 [Abstract] [Postscript] pdf ps
    Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes
    Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, Peter F. Stadler
    Nucl.Acids Res. 26: 3825-3836

    [60] 98-01-001 [Abstract] [Postscript]
    Minimal Cycle Bases of Outerplanar Graphs
    Josef Leydold, Peter F. Stadler
    Elec.J.Comb. 5: 209-222 [R16: 14 pages] (1998).

    [59] 97-12-098 [Abstract] [Postscript not available]
    Spontaneous and Engineered Deletions in the 3'-Noncoding Region of Tick-Borne Encephalitis Virus: Construction of Highly Attenuated Mutants of Flavivirus.
    Christian W. Mandl, Heidemarie Holzmann, Tamara Meixner, Susanne Rauscher, Peter F. Stadler, Steven L. Allison, Franz X. Heinz
    J. Virology 72: 2132-2140 (1998).

    [58] 96-07-01 [Abstract] [Postscript]
    The Algebraic Theory of Recombination Spaces
    P.F. Stadler and G.P. Wagner
    Evol.Comp. 5: 241-275 (1998).

    [57] 97-07-066 [Abstract] [Postscript]
    Sequence Redundancy in Biopolymers: A Study on RNA and Protein Structures
    P. Schuster, P.F. Stadler
    In: "Viral Regulatory Structures",
    G. Myers (ed.) Addison-Wesley, Reading MA, 1998, pp. 163-186.

    1997


    [56] 96-11-099 [Abstract] [Postscript]
    Neutral Networks in Protein Space
    A Computational Study Based on Knowledge-Based Potentials of Mean Force
    A. Babajide, I.L. Hofacker, M.J. Sippl and P.F. Stadler
    Folding & Design 2:261-269 (1997)

    [55] 96-12-01 [Abstract] [Postscript]
    Secondary Structure of the 3'-Non-Coding Region of Flavivirus Genomes
    Comparative Analysis of Base Pairing Probabilities
    S. Rauscher, C. Flamm, C.W. Mandl, F.X. Heinz, P.F. Stadler
    RNA 3: 779-791 (1997)

    [54] 97-01-01 [Abstract] [Postscript]
    Correlation Length, Isotropy, and Meta-stable States
    Ricardo García-Pelayo and Peter F. Stadler
    Physica D 107:240-254 (1997)

    [53] 97-12-099 [Abstract] [Postscript not available]
    RNA structures and folding: from conventional to new issues in structure predictions
    Peter Schuster, Peter F. Stadler, Alexander Renner
    Curr Opin Struct Biol 7: 229-235 (1997).

    [52] 95-07-04 [Abstract] [Postscript]
    Generic Properties of Combinatory Maps: Neural Networks of RNA Secondary Structures
    Christian Reidys, Peter F. Stadler, and Peter Schuster
    Bull.Math.Biol. 59: 339-397 (1997)

    [51] 96-05-03 [Abstract] [postscript]
    Autocatalytic Networks with Intermediates I: Irreversible Reactions
    Robert Hecht, Robert Happel, Peter Schuster, and Peter F. Stadler
    Math.Biosc. 140: 33-74 (1997)

    [50] 97-02-07 [Abstract] [Postscript]
    Density of States, Metastable States, and Saddle Points
    Exploring the Energy Landscape of an RNA Molecule
    J. Cupal, C. Flamm, A. Renner, P.F. Stadler
    In: "Proceedings, Fifth International Conference on Intelligent Systems for Molecular Biology",
    T. Gaasterland, P. Karp, K. Karplus, Ch. Ouzounis, Ch. Sander, A. Valencia (Eds.), AAAI Press, 1997, pp. 88-91

    1996


    [49] 96-12-102 [Abstract] [Postscript]
    Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures.
    Jan Cupal, Ivo L. Hofacker, Peter F. Stadler
    In: "Computer Science and Biology 96" (Prooceedings of the German Conference on Bioinformatics),
    R. Hofstädt, T. Lengauer, M. Löffler, D. Schomburg (eds.), Univ. Leipzig 1996, pp. 184-186

    [48] 96-01-03 [Abstract] [Postscript]
    Algorithm Independent Properties of RNA Secondary Structure Predictions
    Manfred Tacker, Peter F. Stadler, Erich G. Bornberg-Bauer, Ivo L. Hofacker, Peter Schuster
    Eur.Biophy.J. 25: 115-130 (1996)

    [47] 96-01-02 [Abstract] [Postscript]
    Local Minima in the Graph Bipartitioning Problem
    Bärbel Krakhofer, Peter F. Stadler
    Europhys.Lett. 34: 85-90 (1996)

    [46] 94-05-04 [Abstract] [Postscript]
    Permanence of Sparse Autocatalytic Networks
    Peter F. Stadler, Peter Schuster
    Math.Biosc. 131: 111-134 (1996)

    [45] 95-07-03 [Abstract] [Postscript]
    Base Pairing Probabilities in a Complete HIV-1 RNA
    Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, and Peter F. Stadler
    J.Comp.Biol. 3: 253-274 (1996)

    [44] 95-01-02 [Abstract] [Postscript]
    Smoothness within ruggedness: the role of neutrality in adaptation
    Martijn Huynen, Peter Stadler, and Walter Fontana
    Proc.Natl.Acad.Sci.(USA) 93: 397-401 (1996)

    [43] 95-07-06 [Abstract] [Postscript]
    Autocatalytic Networks with Translation
    Robert Happel, Robert Hecht, and Peter F. Stadler
    Bull.Math.Biol. 58: 877-905 (1996)

    [42] 95-07-08 [Abstract] [Postscript]
    Canonical Approximation of Fitness Landscapes
    Robert Happel and Peter F. Stadler
    Complexity 2: 53-58 (1996)

    [41] 95-07-07 [Abstract] [Postscript]
    Landscapes and Their Correlation Functions
    Peter F. Stadler
    J.Math.Chem. 20: 1-45 (1996)

    [40] 96-01-01./ABSTRACTS/ [Abstract] [Postscript]
    Local Minima of p-Spin Models
    Peter F. Stadler and Bärbel Krakhofer
    Rev.Mex.Fis. 42: 355-363 (1996)

    [39] 95-10-17 [Abstract] [Postscript]
    Approximate Scaling Properties of RNA Free Energy Landscapes
    Subbiah Baskaran, Peter F. Stadler, and Peter Schuster
    J.Theor.Biol. 181: 299-310 (1996)

    [38] [PostScript]
    Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers
    Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, and Paul E. Stolorz
    In: Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining,
    edited by Evangelos Simoudis, Jiawei Han, and Usama Fayyad, pp. 20-25, AAAI Press, Menlo Park CA, 1996.
    see also [33].

    [37] 95-10-12 [Abstract] [Postscript]
    Hamming-Chromatography
    Andreas Schwienhorst, Andreas Schober, Rolf Guenther, and Peter F. Stadler
    Molecular Diversity 1: 187-192 (1996)

    [36] 95-10-15 [Abstract] [Postscript]
    Bio-Molecular Shapes and Algebraic Structures
    Christian Reidys and Peter F. Stadler
    Computers Chem. 20: 85-94 (1996)

    [35,34] 95-10-16 [Abstract]
    Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
    Part One: Neutral Networks [Postscript]
    Part Two: Structure of Neutral Networks and Shape Space Covering [Postscript]
    Walter Gruener, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, Peter F. Stadler, and Peter Schuster
    [34] Monatsh.Chem. 127: 375-389 (1996)
    [35] Monatsh.Chem. 127: 355-374 (1996)

    1995


    [33] See Technical Reports (2).
    [32] [Electronic version not available]
    RNA: Genotype and Phenotype
    Peter F. Stadler
    In: "Chemical Evolution: Self-Organization of the Macromolecules of Life" [Proceedings of the Second Trieste Conference on Chemical Evolution, 25-29 October 1993]
    J. Chela-Flores, M. Chadha, A. Negron-Mendoza, T. Oshima (eds.), Deepak 1995, pp. 159-176
    [31] 95-01-01 [No Abstract] [Postscript]
    Towards a Theory of Landscapes.
    Peter F. Stadler
    In: "Complex Systems and Binary Networks" (Proceeding of the Guanajuato Lectures 1995)
    R. Lopéz-Peña, R. Capovilla, R. García-Pelayo, H. Waelbroeck, and F. Zertuche (eds.), Springer-Verlag 1995, pp.77-163.

    [30] 93-05-04 [Abstract] [Postscript]
    Random Walks and Orthogonal Functions Associated with Highly Symmetric Graphs
    Peter F. Stadler
    Discr.Math. 145: 229-238 (1995).

    [29] 94-02-02 [Abstract] [Postscript]
    Dynamics of Small Autocatalytic Reaction Networks II: Replication, Mutation, and Catalysis
    Peter F. Stadler, Wolfgang Schnabl, Christian V. Forst, and Peter Schuster
    Bull.Math.Biol. 57: 21-61 (1995).

    [28] [Electronic version not available]
    RNA: Genotype and Phenotype
    Manfred Tacker, Peter F. Stadler
    In: SFI Studies in the Sciences of Complexity VI, L. Nadel and D. L. Stein (eds.), Addison-Wesley, Reading MA 1995, pp. 579-589

    [27] [Electronic version not available]
    Evolution on Fitness Landscapes.
    Catherine A. Macken, Peter F. Stadler
    In: SFI Studies in the Sciences of Complexity VI, L. Nadel and D. L. Stein (eds.), Addison-Wesley, Reading MA 1995, pp. 43-86

    1994


    [26] See Technical Reports (1).

    [25] 93-06-06 [Abstract] [Postscript]]
    Statistics of RNA Melting Kinetics
    Manfred Tacker, Walter Fontana, Peter F. Stadler, and Peter Schuster
    Eur.Biophys.J. 23: 29-38 (1994).

    [24] 93-11-13 [Abstract] [Postscript]]
    Landscapes: Complex Optimization Problems and Biopolymer Structures
    Peter Schuster, Peter Stadler
    Computers Chem. 18: 295-314 (1994).

    [23] 93-07-08 [Abstract] [Postscript]
    From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures
    Peter Schuster, Walter Fontana, Peter F. Stadler, and Ivo L. Hofacker
    Proc.Roy.Soc.Lond.B 255: 279-284 (1994)

    [22] 93-07-07 [Abstract] [Postscript]
    Fast Folding and Comparison of RNA Secondary Structures
    Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, and Peter Schuster
    Monatsh.Chem. 125: 167-188 (1994).

    [21] 94-12-099 [Abstract] [PostScript]
    Immune Networks Modeled by Replicator Equations
    Peter F. Stadler, Peter Schuster, and Alan S. Perelson
    J.Math.Biol. 33: 111-137 (1994).

    [20]93-12-14 [Abstract] [Postscript]
    The Influence of Mutation on Autocatalytic Reaction Networks
    Peter F. Stadler, Juan Carlos Nuño
    Math.Biosci. 122: 127-160 (1994).

    [19] 93-06-05 [Abstract] [Postscript]
    Linear Operators on Correlated Landscapes
    Peter F. Stadler
    J.Phys.I France 4: 681-696 (1994).

    1993


    [18] 93-01-01 [Abstract] [Postscript]
    Why some Fitness Landscapes are Fractal
    Weinberger, Peter F. Stadler
    J.Theor.Biol. 163: 255-275 (1993).

    [17] 92-02-01 [Abstract] [PostScript (no figures)] [Figures (TAR archive)]
    Statistics of RNA Secondary Structures
    Walter Fontana, Danielle A. M. Konings, Peter F. Stadler, and Peter Schuster
    Biopolymers 33: 1389-1404 (1993).

    [16] 92-10-03 [Abstract] [Postscript]
    RNA Folding and Combinatory Landscapes
    Walter Fontana, Peter F. Stadler, Erich G. Bornberg-Bauer, Thomas Griesmacher, Ivo L. Hofacker, Manfred Tacker, Pedro Tarazona, Edward D. Weinberger, and Peter Schuster
    Phys. Rev. E 47: 2083-2099 (1993).

    [15] 93-01-02 [Abstract] [ Postscript]
    Errorthresholds on Complex Fitness Landscapes
    Bonhoeffer, Peter F. Stadler
    J.Theor.Biol. 164: 359-372 (1993).

    [14] 92-08-02 [Abstract] [PostScript (no figures)]
    RNA Multi-Structure Landscapes
    Sebastian Bonhoeffer, John S. McCaskill, Peter F. Stadler, and Peter Schuster
    Eur.Biophys.J. 22: 13-24 (1993).

    [13] 93-01-03 [Abstract] [Postscript]
    Anisotropy in Fitness Landscapes
    Peter F. Stadler, Walter Gruener
    J.Theor.Biol.: 165: 378-388 (1993).

    [12] 93-12-15 [Abstract] [Postscript]
    Random Catalytic Reaction Networks
    Peter F Stadler, Walter Fontana, John H Miller
    Physica D 63: 378-392 (1993).

    [11] 92-01-001 [Abstract] [PostScript (no figures)]
    The Probability for Permanence.
    Peter F Stadler, Robert Happel
    Math.Biosc. 113: 25-50 (1993).

    1992


    [10] [Abstract]
    Correlation in Landscapes of Combinatorial Optimization Problems.
    Peter F Stadler
    Europhys.Lett. 20: 479-482 (1992)

    [9] 92-01-002 [Abstract] [PostScript]
    Correlation Structure of the Landscape of the Graph-Bipartitioning-Problem.
    Peter F Stadler, Robert Happel
    J.Phys.A:Math.Gen. 25: 3103-3110 (1992).

    [8] 92-01-003 [Abstract] [PostScript (no figures)]
    The Landscape of the Travelling Salesman Problem.
    Peter F Stadler, Wolfgang Schnabl
    Phys.Lett.A 161: 337-344 (1992).

    92-01-004 [Abstract] [PostScript (no figures)]
    [7] Mutation in Autocatalytic Networks - An Analysis Based on Perturbation Theory.
    Peter F Stadler and Peter Schuster
    J.Math.Biol. 30: 597-631 (1992).

    1991


    [6]
    Dynamics of Small Autocatalytic Reaction Networks III: Monotonous Growth Functions.
    Bärbel M R Stadler, Peter F Stadler
    Bull.Math.Biol. 53: 469-485 (1991).

    [5] 91-00-004 [Abstract] [PostScript (No Figures)]
    Full Characterization of a Strange Attractor. Chaotic Dynamics in Low Dimensional Replicator Systems.
    Wolfgang Schnabl, Peter F Stadler, Christian V Forst, Peter Schuster
    Physica D 48: 65-90 (1991).

    [4] 91-00-003 [Abstract] [PostScript (No Figures)]
    Statistics of Landscapes Based on Free Energies, Replication and Degradation Rate Constants of RNA Secondary Structures.
    Walter Fontana, Thomas Griesmacher, Wolfgang Schnabl, Peter F Stadler, Peter Schuster
    Monatsh.Chem. 122: 795-819 (1991).

    [3] 91-00-001 [Abstract] [PostScript (No Figures)]
    Complementary Replication.
    Peter F Stadler
    Math.Biosc. 107: 83-109 (1991).

    [2] 91-00-002 [Abstract] [PostScript (No Figures)]
    Dynamics of Small Autocatalytic Reaction Network IV: Inhomogeneous Replicator Equations.
    Peter F Stadler
    BioSystems 26: 1-19 (1991).

    1990


    [1]
    Dynamics of Small Autocatalytic Reaction Networks: Bifurcations, Permanence and Exclusion.
    Peter F Stadler, Peter Schuster
    Bull.Math.Biol. 52: 485-508 (1990)

    Last modified: 2004-04-25 18:02:20 studla