Publications - Published papers

Please find below publications of our group. Currently, we list 454 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 (access) 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 ]

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 ]  paperID

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:   paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]

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 ]  paperID

<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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID