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.
|
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 ]
Zoologica Scripta 35: 97-108 (2006)
PREPRINT 06-028:
[ Publishers's page ]
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 ]
ODE 6: 151-162 (2006)
PREPRINT 06-027:
[ Publishers's page ]
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 ]
ODE 6: 151-162 (2006)
PREPRINT 06-026:
[ Publishers's page ]
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 ]
Alg.Mol.Biol. 1:6 (2006).
PREPRINT 06-025: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
MicroRNA Protocols, Humana Press, Totowa, NJ, Methods in Molecular Biology 342: 335-350 (2006).
PREPRINT 06-024: [ Abstract ]
[ Publishers's page ]
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 ]
IEEE Trans. Vis. Comp. Graphics 12: 781-788 (2006)
PREPRINT 06-023: [ Abstract ]
[ Publishers's page ]
Genotype Phenotype Maps
Peter F. Stadler, Bärbel M. R. Stadler
Biological Theory 3: 268-279 (2006)
PREPRINT 06-022: [ Abstract ]
[ Publishers's page ]
Biological Theory 3: 268-279 (2006)
PREPRINT 06-022: [ Abstract ]
[ Publishers's page ]
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 ]
Phys. Rev. E 73, 046119 (2006)
PREPRINT 06-021: [ Abstract ]
[ Publishers's page ]
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:
In: HOX Gene Expression, S. Papageorgiou (ed), Landes Bioscience & Springer, 2006, pp.***-***.
PREPRINT 06-019:
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 ]
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 ]
IEEE Information Visualization 2006, 89-94. (2006). doi: 10.1109/IV.2006.127.
PREPRINT 06-004: [ Abstract ]
[ Publishers's page ]
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 ]
Bioinformatics 22: e197-e202 (2006)
PREPRINT 06-002: [ Abstract ] [ PDF ]
[ Publishers's page ]
<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 ]
Nucleic Acids Res. 34: D135-D139 (2006).
PREPRINT 05-027: [ Abstract ] [ PDF ]
[ Publishers's page ]
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 ]
Europhys. Lett. 74: 726-732 (2006).
PREPRINT 05-026: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
Alg.Mol.Biol. 1:3 (2006)
PREPRINT 05-025: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
Bioinformatics 22: 614-615 (2006).
PREPRINT 05-024: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
J.Exp.Zool.(Mol.Dev.Evol.) 306B: 379-392 (2006).
PREPRINT 05-023: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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 ]
BMC Genomics, 7: 15 (2006).
PREPRINT 05-021: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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 ]
Phy.Rev.E, 73: 025101 (2006)
PREPRINT 05-020: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Thermodynamics of RNA-RNA Binding
Ulrike Mückstein, 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 ]
Bioinformatics 22: 1177-1182 (2006)
PREPRINT 05-019: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
Bioinformatics 22: 1172-1176 (2006)
PREPRINT 05-018: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
BMC Bioinformatics, 7: 67 (2006).
PREPRINT 05-017: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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 ]
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 ]
J. Exp. Zool.: Mol. Dev. Evol. 306B: 481-487 (2006).
PREPRINT 05-007: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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 ]
Mol.Biol.Evol. 23: 121-136 (2006)
PREPRINT 05-006: [ Abstract ] [ PDF ]
[ Publishers's page ]
<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 ]
Geno. Prot. Bioinfo. 4: 56-60 (2006).
PREPRINT 04-019: [ Abstract ] [ PDF ] [ PS ] [ Software ]
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 ]
J.Theor.Biol., 240: 511-520 (2006)
PREPRINT 04-015: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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 ]
Physica D 217: 143-141 (2006).
PREPRINT 04-012: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Modeling RNA Folding
Ivo L. Hofacker, Peter F. Stadler
Thomas S. Deisboeck and J. Yasha Kresh, editors, Complex Systems Science in BioMedicine, pages 227–245. Springer, New York, 2006
PREPRINT 03-013: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Thomas S. Deisboeck and J. Yasha Kresh, editors, Complex Systems Science in BioMedicine, pages 227–245. Springer, New York, 2006
PREPRINT 03-013: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]