Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
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Publications of the bioinformatics group 2005
Replicator Dynamics in Protocells
Peter F. Stadler, Bärbel M. R. Stadler
In: <em>Protocells</em>, Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard, Peter F. Stadler (eds), MIT Press, Cambridge MA, 2008.
PREPRINT 05-034: [ Abstract ] [ PDF ]
In: <em>Protocells</em>, Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard, Peter F. Stadler (eds), MIT Press, Cambridge MA, 2008.
PREPRINT 05-034: [ Abstract ] [ PDF ]
An analysis of Andes Frogs {Phrynopus: Leptodactylidae} phylogeny based on 12S and 16S mitochondrial DNA sequences
E. Lehr, G. Fritzsch, A. Müller
Zoologica Scripta 34: 593-603 (2005).
PREPRINT 05-033:
[ Publishers's page ]
Zoologica Scripta 34: 593-603 (2005).
PREPRINT 05-033:
[ Publishers's page ]
The Atlas Mountains, not the Strait of Gibraltar, as biogeographic barrier for Mauremys leprosa {Reptilia: Testudines}
U. Fritz, G. Fritzsch, E. Lehr, J.-M. Ducotterd, A Müller
Salamandra 41{3}: 97-106 (2005).
PREPRINT 05-032:
Salamandra 41{3}: 97-106 (2005).
PREPRINT 05-032:
Molecular insights into speciation in the Agrilus viridis-complex and the genus Trachys {Coleoptera: Buprestidae}
D. Bernhard, G. Fritzsch, P. Glöckner, C. Wurst
Eur. J. Entomol. 102{4}: 559-605 (2005).
PREPRINT 05-031:
[ Publishers's page ]
Eur. J. Entomol. 102{4}: 559-605 (2005).
PREPRINT 05-031:
[ Publishers's page ]
Globalization, polarization and cultural drift
Konstantin Klemm, Victor M. Eguiluz, Raul Toral, Maxi San Miguel
J. Econ. Dyn. Control 29, 321 (2005)
PREPRINT 05-030:
[ Publishers's page ]
J. Econ. Dyn. Control 29, 321 (2005)
PREPRINT 05-030:
[ Publishers's page ]
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)
PREPRINT 05-029: [ PDF ] [ PS ]
[ Publishers's page ]
Networks, 46: 119-12346: 119-12346: 119-12346: 119-123 (2005)
PREPRINT 05-029: [ PDF ] [ PS ]
[ Publishers's page ]
Binary and Multivariate Stochastic Models of Consensus Formation
Maxi San Miguel, Victor M. Eguiluz, Raul Toral, Konstantin Klemm
Computing in Science and Engineering 7, 67 (2005)
PREPRINT 05-028: [ Abstract ]
[ Publishers's page ]
Computing in Science and Engineering 7, 67 (2005)
PREPRINT 05-028: [ Abstract ]
[ Publishers's page ]
Nodal Domain Theorems and Bipartite Subgraphs
Türker Biyikoglu, Josef Leydold, Peter F. Stadler
Elec.J.Lin.Alg. 13: 344-351 (2005)
PREPRINT 05-022: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Elec.J.Lin.Alg. 13: 344-351 (2005)
PREPRINT 05-022: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Neutral Networks of Interacting RNA Secondary Structures
Camille Stephan-Otto Attolini, Peter F. Stadler
Adv. Complex Syst, 8: 275-284 (2005)
PREPRINT 05-016: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Adv. Complex Syst, 8: 275-284 (2005)
PREPRINT 05-016: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artifical Chemistry
Gil Benkö, Christoph Flamm, Peter F. Stadler
LNCS 3630: 725-733 (2005)
PREPRINT 05-015: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
LNCS 3630: 725-733 (2005)
PREPRINT 05-015: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Emergence of regulatory networks in simulated evolutionary processes
Dirk Drasdo, Matthias Kruspe
Adv. Complex Syst., 2 & 3, 285-318 (2005).
PREPRINT 05-014: [ Abstract ] [ PDF ]
Adv. Complex Syst., 2 & 3, 285-318 (2005).
PREPRINT 05-014: [ 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)
PREPRINT 05-013: [ Abstract ]
[ Publishers's page ]
RNA 11: 1181-1191 (2005)
PREPRINT 05-013: [ Abstract ]
[ Publishers's page ]
<tt>CelloS</tt>: A Multi-level Approach to Evolutionary Dynamics
Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
LNCS 3630: 500-509 (2005)
PREPRINT 05-012: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
LNCS 3630: 500-509 (2005)
PREPRINT 05-012: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Non-coding RNAs in <i>Ciona intestinalis</i>
Kristin Missal, Dominic Rose, Peter F. Stadler
Bioinformatics, 21(S2): i77-i78 (2005)
PREPRINT 05-008: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Bioinformatics, 21(S2): i77-i78 (2005)
PREPRINT 05-008: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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)
PREPRINT 05-005: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Nature Biotech. 23: 1383-1390 (2005)
PREPRINT 05-005: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
BMC Bioinformatics 6: 160 [epub] (2005)
PREPRINT 05-004: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
BMC Bioinformatics 6: 160 [epub] (2005)
PREPRINT 05-004: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Fast and reliable prediction of noncoding RNAs
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
Proc.Natl.Acad.Sci.USA (2005)
PREPRINT 05-003: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Proc.Natl.Acad.Sci.USA (2005)
PREPRINT 05-003: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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).
PREPRINT 05-001: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Th.Biosci. 123: 301-369 (2005).
PREPRINT 05-001: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Stable and unstable attractors in Boolean networks
Konstantin Klemm, Stefan Bornholdt
Phys. Rev. E 72, 055101(R) (2005).
PREPRINT 04-023: [ Abstract ]
[ Publishers's page ]
Phys. Rev. E 72, 055101(R) (2005).
PREPRINT 04-023: [ Abstract ]
[ Publishers's page ]
Topology of biological networks and reliability of information processing
Konstantin Klemm, Stefan Bornholdt
Proc. Natl. Acad. Sci. USA 102, 18414-18419 (2005).
PREPRINT 04-022: [ Abstract ]
[ Publishers's page ]
Proc. Natl. Acad. Sci. USA 102, 18414-18419 (2005).
PREPRINT 04-022: [ Abstract ]
[ Publishers's page ]
Scaling in the structure of directory trees in a computer cluster
Konstantin Klemm, Victor M. Eguiluz, Maxi San Miguel
Phys. Rev. Lett. 95, 128701 (2005).
PREPRINT 04-021: [ Abstract ]
[ Publishers's page ]
Phys. Rev. Lett. 95, 128701 (2005).
PREPRINT 04-021: [ Abstract ]
[ Publishers's page ]
Comparative promoter region analysis powered by <tt>CORG</tt>
Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Ropcke, Peter F Arndt, Peter F Stadler, Martin Vingron
BMC Genomics 6: 24 [10pages] (2005)
PREPRINT 04-017: [ Abstract ] [ PDF ]
[ Publishers's page ]
BMC Genomics 6: 24 [10pages] (2005)
PREPRINT 04-017: [ Abstract ] [ PDF ]
[ Publishers's page ]
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).
PREPRINT 04-016: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Gene 345: 3-12 (2005).
PREPRINT 04-016: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Molecular Evolution of Duplicated Ray Finned Fish 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).
PREPRINT 04-014: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
J.Mol.Evol. 60: 665-676 (2005).
PREPRINT 04-014: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
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).
PREPRINT 04-013: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
J.Exp.Zool.(Mol.Dev.Evol.) 304B: 75-85 (2005).
PREPRINT 04-013: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Multiple sequence alignment with user-defined constraints at GOBICS
Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler
Bioinformatics 21: 1271-1273 (2005).
PREPRINT 04-011: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Bioinformatics 21: 1271-1273 (2005).
PREPRINT 04-011: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
On a Notion of Linear Replicator Equations
Nihat Ay, Ionas Erb
J. Dyn. Diff. Eqns. 17:427-451 (2005)
PREPRINT 03-022: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J. Dyn. Diff. Eqns. 17:427-451 (2005)
PREPRINT 03-022: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]