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 2006

Impact of mountain chains, sea straits and peripheral populations on genetic and taxonomic structure of a freshwater turtle, Mauremys leprosa {Reptilia, Testudines, Geoemydidae}

U. Fritz, M. Barata, St. Busack, G. Fritzsch, R. Castilho
Zoologica Scripta 35: 97-108 (2006)
PREPRINT 06-028:
[ Publishers's page ]  paperID

Geoemyda silvatica, an enigmatic turtle of the Geoemydidae {Reptilia: Testudines}, represents a distinct genus

P. Praschag, Ch. Schmidt, G. Fritzsch, A. Müller, R. Gemel, U. Fritz
ODE 6: 151-162 (2006)
PREPRINT 06-027:
[ Publishers's page ]  paperID

From terrestrial to aquatic habitats and back again - molecular insights into the evolution and phylogeny of Hydrophiloidea {Coleoptera} using multigene analyses

Detlef Bernhard, Claudia Schmidt, Anja Korte, Guido Fritzsch, Rolf G. Beutel
ODE 6: 151-162 (2006)
PREPRINT 06-026:
[ Publishers's page ]  paperID

Multiple sequence alignment with user-defined anchor points

Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pohler, Peter F. Stadler
Alg.Mol.Biol. 1:6 (2006).
PREPRINT 06-025: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

Evolution of MicroRNAs

Andrea Tanzer, Peter F. Stadler
MicroRNA Protocols, Humana Press, Totowa, NJ, Methods in Molecular Biology 342: 335-350 (2006).
PREPRINT 06-024: [ Abstract ]
[ Publishers's page ]  paperID

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)
PREPRINT 06-023: [ Abstract ]
[ Publishers's page ]  paperID

Genotype Phenotype Maps

Peter F. Stadler, Bärbel M. R. Stadler
Biological Theory 3: 268-279 (2006)
PREPRINT 06-022: [ Abstract ]
[ Publishers's page ]  paperID

Local versus global interactions in nonequilibrium transitions: A model of social dynamics

J. C. Gonzalez-Avella, V. M. Eguiluz, M. G. Cosenza, K. Klemm, J. L. Herrera, M. San Miguel
Phys. Rev. E 73, 046119 (2006)
PREPRINT 06-021: [ Abstract ]
[ Publishers's page ]  paperID

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.***-***.
PREPRINT 06-019:   paperID

Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs

Axel Mosig, Ivo L. Hofacker, Peter F. Stadler
Proceedings GCB 2006, Lecture Notes in Informatics P-83: 93-102 (2006)
PREPRINT 06-008: [ Abstract ]  [ PDF ]  [ Software ]

Visualization of Lattice-Based Protein Folding Simulations

Sebastian Pötzsch, Gerik Scheuermann, Michael T. Wolfinger, Christoph Flamm, Peter F. Stadler
IEEE Information Visualization 2006, 89-94. (2006). doi: 10.1109/IV.2006.127.
PREPRINT 06-004: [ Abstract ]
[ Publishers's page ]  paperID

Hairpins in a Haystack: Recognizing microRNA Precursors in Comparative Genomics Data

Jana Hertel, Peter F. Stadler
Bioinformatics 22: e197-e202 (2006)
PREPRINT 06-002: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

<tt>miRNAMap</tt>: 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).
PREPRINT 05-027: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

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).
PREPRINT 05-026: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

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)
PREPRINT 05-025: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

Local RNA Base Pairing Probabilities in Large Sequences

Stephan Bernhart, Ivo L. Hofacker, Peter F. Stadler
Bioinformatics 22: 614-615 (2006).
PREPRINT 05-024: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

Prediction of Structured Non-Coding RNAs in the Genomes of the Nematodes <i>Caenorhabditis elegans</i> and <i>Caenorhabditis briggsae</i>

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).
PREPRINT 05-023: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

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: <small>Sten Heinze, Alexander ''muppet'' Donath, Sven Findeiß, Stephanie Keller, Kevin Peter, Julian Jöris, Jakob Mühmel, Marco Dienelt, Lisa aus Jena, Maiko Lohet, Holger Schmidtchen, Nick Jagiella, Andrej Aderhold, Paul-Robert Kästerer, Thomas Skodawessely (in Leipzig), Martina Hödl, Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits, Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor Neumayr, Reinhard Wohlfart (in Vienna).</small>
BMC Genomics, 7: 15 (2006).
PREPRINT 05-021: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

Statistics of cycles in large networks

Konstantin Klemm, Peter F. Stadler
Phy.Rev.E, 73: 025101 (2006)
PREPRINT 05-020: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

Thermodynamics of RNA-RNA Binding

Ulrike M&uuml;ckstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler, Ivo L. Hofacker
Bioinformatics 22: 1177-1182 (2006)
PREPRINT 05-019: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

Memory Efficient Folding Algorithms for Circular RNA Secondary Structures

Ivo L. Hofacker, Peter F. Stadler
Bioinformatics 22: 1172-1176 (2006)
PREPRINT 05-018: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

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).
PREPRINT 05-017: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

A Prime Factor Theorem for a Generalized Direct Product

Wilfried Imrich, Peter F. Stadler
Discussiones Math. Graph Th. 26: 135-140 (2006)
PREPRINT 05-010: [ Abstract ]  [ PDF ]  [ PS ]

Evolution of the Vertebrate Parahox Clusters

Sonja J. Prohaska, Peter F. Stadler
J. Exp. Zool.: Mol. Dev. Evol. 306B: 481-487 (2006).
PREPRINT 05-007: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

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)
PREPRINT 05-006: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

<tt>fragrep</tt>: Efficient Search for Fragmented Patterns in Genomic Sequences

Axel Mosig, Katrin Sameith, Peter F. Stadler
Geno. Prot. Bioinfo. 4: 56-60 (2006).
PREPRINT 04-019: [ Abstract ]  [ PDF ]  [ PS ]  [ Software ]   paperID

Alignments of Mitochondrial Genome Arrangements: Applications to Metazoan Phylogeny

Guido Fritzsch, Martin Schlegel, Peter F. Stadler
J.Theor.Biol., 240: 511-520 (2006)
PREPRINT 04-015: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution

Camille Stephan-Otto Attolini, Peter F. Stadler
Physica D 217: 143-141 (2006).
PREPRINT 04-012: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

Modeling RNA Folding

Ivo L. Hofacker, Peter F. Stadler
Thomas S. Deisboeck and J. Yasha Kresh, editors, Complex Systems Science in BioMedicine, pages 227245. Springer, New York, 2006
PREPRINT 03-013: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID