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 2004
The freshwater turtle genus Mauremys {Testudines, Geoemydidae} - a textbook example of an east-west disjunction or a taxonomic misconcept
D. Barth, D. Bernhard, G. Fritzsch, U. Fritz
Zoologica Scripta 33: 213-221 (2004).
PREPRINT 04-028:
Zoologica Scripta 33: 213-221 (2004).
PREPRINT 04-028:
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).
PREPRINT 04-027:
In: Handbook of Computational Chemistry and Biology; J. Crabbe, A. Konopka, and M. Drew, eds. Marcel Dekker, Inc., pp 187-221 (2004).
PREPRINT 04-027:
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.
PREPRINT 04-026:
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.
PREPRINT 04-026:
RNA Folding <i>in silico</i>
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.
PREPRINT 04-025:
In: Evolutionary Methods in Biotechnology, Susanne Brakmann, Andreas Schwienhost (eds.), Wiley-VCH, Weinheim, Germany, 2004; pp. 177-190.
PREPRINT 04-025:
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)
PREPRINT 04-024:
[ Publishers's page ]
Science 303: 963-965 (2004)
PREPRINT 04-024:
[ Publishers's page ]
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].
PREPRINT 04-010: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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].
PREPRINT 04-010: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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).
PREPRINT 04-009: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J.Theor.Biol 231: 197-202 (2004).
PREPRINT 04-009: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Simon Ando Decomposability and Fitness Landscapes
Max Shpak, Peter F. Stadler, Günter P. Wagner, Lee Altenberg
Th. Biosci., 123: 139-180 (2004).
PREPRINT 04-008: [ Abstract ] [ PDF ]
[ Publishers's page ]
Th. Biosci., 123: 139-180 (2004).
PREPRINT 04-008: [ Abstract ] [ PDF ]
[ Publishers's page ]
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)
PREPRINT 04-007: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Mol.Biol.Evol. 21: 2116-2121 (2004)
PREPRINT 04-007: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
The Duplication of the Hox Gene Clusters in Teleost Fishes
Sonja J. Prohaska, Peter F. Stadler
Th. Biosci., 123: 89-110 (2004)
PREPRINT 04-006: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Th. Biosci., 123: 89-110 (2004)
PREPRINT 04-006: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Graph Grammars as Models for the Evolution of Developmental Pathways
Martin Beck, Gil Benkö, Gunther J. Eble, Christoph Flamm Stefan Müller, Peter F. Stadler
The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, H Schaub, F. Detje, U. Brüggemann (eds.), IOS Press, Akademische Verlagsgesellschaft, Berlin, pp. 8-15 (2004)
PREPRINT 04-005: [ Abstract ] [ PDF ] [ PS ]
The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, H Schaub, F. Detje, U. Brüggemann (eds.), IOS Press, Akademische Verlagsgesellschaft, Berlin, pp. 8-15 (2004)
PREPRINT 04-005: [ Abstract ] [ PDF ] [ PS ]
Interactions in oligonucleotide hybrid duplexes on microarrays
Hans Binder, Toralf Kirsten, Ivo L. Hofacker, Markus Loeffler, Peter F. Stadler
J.Phys.Chem.B 108: 18015-18025 (2004)
PREPRINT 04-004: [ Abstract ]
[ Publishers's page ]
J.Phys.Chem.B 108: 18015-18025 (2004)
PREPRINT 04-004: [ Abstract ]
[ Publishers's page ]
The sensitivity of microarray oligonucleotide probes: variability and the effect of base composition
Hans Binder, Toralf Kirsten, Markus Loeffler, Peter F. Stadler
J.Phys.Chem.B 108: 18003-18014 (2004)
PREPRINT 04-003: [ Abstract ]
[ Publishers's page ]
J.Phys.Chem.B 108: 18003-18014 (2004)
PREPRINT 04-003: [ Abstract ]
[ Publishers's page ]
Molecular Evolution of a MicroRNA Cluster
Andrea Tanzer, Peter F. Stadler
J.Mol.Biol. 339: 327-335 (2004)
PREPRINT 04-002: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
J.Mol.Biol. 339: 327-335 (2004)
PREPRINT 04-002: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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).
PREPRINT 04-001: [ Abstract ] [ PDF ] [ PS ] [ Software ]
[ Publishers's page ]
IEEE/ACM Trans.Comp.Biol.Bioinf. 1: 66-77 (2004).
PREPRINT 04-001: [ Abstract ] [ PDF ] [ PS ] [ Software ]
[ Publishers's page ]
Assessing the robustness of disparity estimates: the impact of morphometric scheme, temporal scale, and taxonomic level in spatangoid echinoids
Loïc Villier and Gunther J. Eble
Paleobiology, 30, 652–665. (2004)
PREPRINT 03-031: [ Abstract ] [ PDF ]
[ Publishers's page ]
Paleobiology, 30, 652–665. (2004)
PREPRINT 03-031: [ Abstract ] [ PDF ]
[ Publishers's page ]
The Partition Function Variant of Sankoff's Algorithm
Ivo L. Hofacker, Peter F. Stadler
Marian Bubak, Geert Dick van Albada, Peter M. A. Sloot, and Jack J. Dongarra (Eds.): <i>Computational Science - ICCS 2004, Part IV</i>, Lecture Notes in Computer Science LNCS 3039, Springer Verlag, Heidelberg, 2004, pp 728-735.
PREPRINT 03-030: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Marian Bubak, Geert Dick van Albada, Peter M. A. Sloot, and Jack J. Dongarra (Eds.): <i>Computational Science - ICCS 2004, Part IV</i>, Lecture Notes in Computer Science LNCS 3039, Springer Verlag, Heidelberg, 2004, pp 728-735.
PREPRINT 03-030: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Multi-Phase Artificial Chemistry
Gil Benkö, Christoph Flamm, Peter F. Stadler
The Logic of Artificial Life - Proceedings of the 6th German Workshop on Artificial Life (GWAL 2004),<br/>H. Schaub, F. Detje, U. Brüggemann (Eds.) Akademische Verlagsgesellschaft Aka GmbH, Berlin, 2004, pp. 16-22.
PREPRINT 03-029: [ Abstract ] [ PDF ] [ PS ]
The Logic of Artificial Life - Proceedings of the 6th German Workshop on Artificial Life (GWAL 2004),<br/>H. Schaub, F. Detje, U. Brüggemann (Eds.) Akademische Verlagsgesellschaft Aka GmbH, Berlin, 2004, pp. 16-22.
PREPRINT 03-029: [ Abstract ] [ PDF ] [ PS ]
Computational Chemistry with RNA Secondary Structures
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Kemija u indistriji 53: 315-322 (2004), Proceedings of CEC-2 2003
PREPRINT 03-028: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Kemija u indistriji 53: 315-322 (2004), Proceedings of CEC-2 2003
PREPRINT 03-028: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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)
PREPRINT 03-027: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J.Phys.A: Math.Gen. 37: 4731-4741 (2004)
PREPRINT 03-027: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Alignment of RNA Base Pairing Probability Matrices
Ivo L. Hofacker, Stephan H.F. Bernhart, Peter F. Stadler
Bioinformatics 20 (14): 2222-2227 (2004)
PREPRINT 03-026: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Bioinformatics 20 (14): 2222-2227 (2004)
PREPRINT 03-026: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Exclusion of Repetitive DNA Elements from Gnathostome Hox Clusters
Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
J.Exp.Zool., Mol.Dev.Evol. 302B: 165-173 (2004)
PREPRINT 03-025: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J.Exp.Zool., Mol.Dev.Evol. 302B: 165-173 (2004)
PREPRINT 03-025: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Evidence for independent Hox gene 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 Phylogenet Evol. 32(3):686-94 (2004).
PREPRINT 03-024: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Mol Phylogenet Evol. 32(3):686-94 (2004).
PREPRINT 03-024: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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)
PREPRINT 03-023: [ Abstract ] [ Supplement ]
[ Publishers's page ]
Gene 329: 103-114 (2004)
PREPRINT 03-023: [ Abstract ] [ Supplement ]
[ Publishers's page ]
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)
PREPRINT 03-021: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J.Chem.Inf.Comput.Sci. 44: 332-338 (2004)
PREPRINT 03-021: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Conserved RNA Secondary Structures in Viral Genomes: A Survey
Ivo L. Hofacker, Peter F. Stadler, Roman Stocsits
Bioinformatics 20: 1495-1499 (2004).<br/>Proceedings of the German Conference on Bioinformatics. Volume I. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer (Eds.), belleville Verlag Michael Farin, München, 2003, p.57-62.
PREPRINT 03-020: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Bioinformatics 20: 1495-1499 (2004).<br/>Proceedings of the German Conference on Bioinformatics. Volume I. H.-W. Mewes, V. Heun, D. Frishman, S. Kramer (Eds.), belleville Verlag Michael Farin, München, 2003, p.57-62.
PREPRINT 03-020: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Multi-Information in the Thermodynamic Limit
Ionas Erb, Nihat Ay
Journal of Statistical Physics 115 (3-4), 949-976 (2004)
PREPRINT 03-016: [ Abstract ] [ PDF ] [ PS ]
Journal of Statistical Physics 115 (3-4), 949-976 (2004)
PREPRINT 03-016: [ Abstract ] [ PDF ] [ PS ]
Conserved RNA Secondary Structures in Flaviviridae Genomes
Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
J Gen Virol 85 (2004), 1113-1124
PREPRINT 03-015: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J Gen Virol 85 (2004), 1113-1124
PREPRINT 03-015: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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)
PREPRINT 03-012: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
J.Chem.Inf.Comput.Sci. 44: 323-331 (2004)
PREPRINT 03-012: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
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)
PREPRINT 03-010: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
J.Mol.Evol 58: 212-217 (2004)
PREPRINT 03-010: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Prediction of Locally Stable RNA Secondary Structures for Genome-Wide Surveys
Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
Bioinformatics 20: 191-198 (2003)
PREPRINT 03-009: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Bioinformatics 20: 191-198 (2003)
PREPRINT 03-009: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Aggregation of Variables and System Decomposition: Applications to Fitness Landscape Analysis
Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson
Theory in Biosciences 123: 33-68 (2004)
PREPRINT 03-008: [ Abstract ] [ PDF ]
[ Publishers's page ]
Theory in Biosciences 123: 33-68 (2004)
PREPRINT 03-008: [ Abstract ] [ PDF ]
[ Publishers's page ]
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
C-H. 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)
PREPRINT 03-007: [ Abstract ] [ Supplement ]
[ Publishers's page ]
Genome Res. 14: 11-17 (2004)
PREPRINT 03-007: [ Abstract ] [ Supplement ]
[ Publishers's page ]
The Macroevolution of Phenotypic Integration
Gunther J. Eble
Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes, Pigliucci, M. and Preston, K. (eds.), Oxford, Oxford University Press. pp. 253-273
PREPRINT 03-005: [ PDF ]
Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes, Pigliucci, M. and Preston, K. (eds.), Oxford, Oxford University Press. pp. 253-273
PREPRINT 03-005: [ PDF ]
The Topology of Evolutionary Biology
Bärbel M.R. Stadler and Peter F. Stadler
G.Ciobanu, G. Rozenberg (Eds.): Modeling in Molecular Biology,<br/>Springer Verlag, Natural Computing Series 2004; pp. 267-286
PREPRINT 03-003: [ Abstract ] [ PDF ] [ PS ]
G.Ciobanu, G. Rozenberg (Eds.): Modeling in Molecular Biology,<br/>Springer Verlag, Natural Computing Series 2004; pp. 267-286
PREPRINT 03-003: [ Abstract ] [ PDF ] [ PS ]
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)
PREPRINT 03-002: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
Mol.Evol.Phylog. 31: 581-604 (2004)
PREPRINT 03-002: [ Abstract ] [ PDF ] [ PS ] [ Supplement ]
[ Publishers's page ]
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)
PREPRINT 02-005: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Orig. Life Evol. Biosph. 34: 171-180 (2004)
PREPRINT 02-005: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements
Türker Biyikoglu, Wim Hordijk, Josef Leydold, Tomaz Pisanski, and Peter F. Stadler
Linear algebra appl. Volume 390, pp. 155-174, 2004. ISSN 0024-3795
PREPRINT 02-002: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Linear algebra appl. Volume 390, pp. 155-174, 2004. ISSN 0024-3795
PREPRINT 02-002: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]