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 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:   paperID

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:

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:   paperID

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:   paperID

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 ]  paperID

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 ]

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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, 652665. (2004)
PREPRINT 03-031: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

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 ]  paperID

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 ]

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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, M&uuml;nchen, 2003, p.57-62.
PREPRINT 03-020: [ Abstract ]  [ PDF ]  [ PS ]
[ Publishers's page ]  paperID

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 ]   paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]

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 ]

Surveying Phylogenetic Footprints in Large Gene Clusters: Applications to Hox Cluster Duplications

Sonja Prohaska, Claudia Fried, Christoph Flamm, G&uuml;nter P. Wagner, Peter F. Stadler
Mol.Evol.Phylog. 31: 581-604 (2004)
PREPRINT 03-002: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

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 ]  paperID

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 ]  paperID