TBI WORKING PAPERS 2003

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TBI Working Papers are usually works in progress or papers submitted for publication in refereed scientific journals. They contain accounts of the scientific work of the author(s) and do not necessarily represent the views of the TBI.

©NOTICE: All papers are copyrighted by the authors; revised versions that appear in print are copyrighted by the publication in which each appears. If you would like to use all or a portion of any paper, please contact the author.

BIOINF 03-030 [Abstract] [PostScript] [PDF]
The Partition Function Variant of Sankoff's Algorithm
Ivo L. Hofacker, Peter F. Stadler
Appeared in Lecture Notes in Computer Science, 3039, ICCS 2004

BIOINF 03-028 [Abstract] [PostScript] [PDF]
Computational Chemistry with RNA Secondary Structures
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Appeared in Kemija u industriji; Proceedings of CECM-2 2003

BIOINF 03-027 [Abstract] [PostScript] [PDF]
Exact Folding Dynamics of RNA Secondary Structures
Michael T. Wolfinger, W. Andreas Svrcek-Seiler Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Appeared in J.Phys.A: Math.Gen. 37: 4731-4741 (2004)

BIOINF 03-023 [Abstract] [Full Text Not Yet Available] [Supplemental Material]
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
appeared in Gene 329: 102-114 (2004).

BIOINF 03-026 [Abstract] [PostScript] [PDF]
Alignment of RNA Base Pairing Probability Matrices
Ivo L. Hofacker, Stephan H.F. Bernhart, Peter F. Stadler
Appeared in Bioinformatics, 20, 2222-2227, (2004).

BIOINF 03-020 [Abstract] [PostScript] [PDF]
Conserved RNA Secondary Structures in Viral Genomes: A Survey
Ivo L. Hofacker, Peter F. Stadler, Roman Stocsits
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.

BIOINF 03-015 [Abstract] [PostScript] [PDF]
Conserved RNA Secondary Structures in Flaviviridae Genomes
Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
appeared in J. Gen. Virol, 85: 1113-1124 (2004)

BIOINF 03-013 [Abstract] [PostScript] [PDF]
Modeling RNA Folding
Ivo L. Hofacker, Peter F. Stadler
to appear in Complex Systems in Biomedicine
edited by Thomas S Deisboeck, J. Yasha Kresh, and Thomas B Kepler.

BIOINF 03-009 [Abstract] [PostScript] [PDF]
Prediction of Locally Stable RNA Secondary Structures for Genome-Wide Surveys
Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
appeared in Bioinformatics 20: 191-198 (2004).

BIOINF 03-006 [ Abstract] [Postscript] [PDF]
Generic Properties of Chemical Networks:
Artificial Chemistry Based on Graph Rewriting
Gil Benkö, Christoph Flamm, Peter F. Stadler
submitted (2003) to ECAL 2003

TBI 03-nagel [Abstract]
The Refolding Mechanism of the Metastable Structure at the 5′-end of the hok mRNA of Plasmid R1
J.H.A. Nagel, J. Møller-Jensen, C. Flamm, K.J. Öistämö, J. Besnard, I.L. Hofacker,
A.P. Gultyaev, M.H. de Smit, P.K. Schuster, K. Gerdes, C.W.A. Pleij
submitted (2003) to Proc. Natl. Acad. Sci. USA

TBI 03-02-001 [Abstract] [Postscript] [PDF]
The Vienna RNA Secondary Structure Server
Ivo L. Hofacker
appeared in Nucl. Acids Res. 31: 3429-3431 (2003)

BIOINF 03-002 [ Abstract] [Postscript] [PDF] [ PDF with pixelgraphics]
[Supplemental Material]
Surveying Phylogenetic Footprints in Large Gene Clusters:
Applications to Hox Cluster Duplications
Sonja Prohaska, Claudia Fried, Christoph Flamm, Günter P. Wagner, Peter F. Stadler
submitted (2003) to J.Mol.Biol.

BIOINF 03-001 [ Abstract] [Postscript] [PDF]
Phase transition and landscape statistics of the number partitioning problem
Peter F. Stadler, Wim Hordijk, José F. Fontanari
submitted (2003) to Phys.Rev.E

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Ivo Hofacker, <ivo@tbi.univie.ac.at>
Institut für theoretische Chemie, Währingerstr. 17, A-1090 Wien, Austria

Last modified: 2007-08-22 12:35:21 xtof