List of Publications

This list is outdated.


Please see my complete PDF List of publications and consult the group's Preprint and Publications Server for preprint versions.


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