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TBI WORKING PAPERS 2005

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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.


TBI 05-10-001 [Abstract] [Postscript] [PDF]
Local Base Pairing Probabilities in Large RNAs
Stephan Bernhart, Ivo L. Hofacker, Peter F. Stadler
submitted to Bioinformatics
TBI 05-10-002 [Abstract] [Postscript] [PDF]
miRNAMap: 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. in press (2005)
TBI 05-08-001 [Abstract] [Postscript] [PDF] [Supplementary Material]
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: Sten Heinze, Alexander "muppet" Donath, Sven Findeß, Stephanie Keller, Kevin Peter, Julian Jöris, Jokab Mühmel, Marco Dienelt (in Leipzig), Martina Hödl, Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits, Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor Neumayr, Reinhard Wohlfart (in Vienna).
submitted to BMC Genomics
TBI 05-07-002 [Abstract] [Postscript] [PDF]
Thermodynamics of RNA-RNA Binding
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler, Ivo L. Hofacker
appeared in: Proceedings of the GCB 2005
TBI 05-07-001 [Abstract] [Postscript] [PDF]
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures
Ivo L. Hofacker, Peter F. Stadler
appeared in: Proceedings of the GCB 2005
TBI 05-04-003 [Abstract] [Postscript] [PDF] [Software]
Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation
Christian Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
submitted to BMC Biofinformarics
TBI 05-04-002 [Abstract] [PDF] [Supplement] [Additional supplementary data]
A benchmark of multiple sequence alignment programs upon structural RNAs
Paul P. Gardner, Andreas Wilm, Stefan Washietl
appeared in: Nucleic Acids Res. 33(8):2433-2439

Full text available free of charge: http://nar.oupjournals.org/cgi/content/full/33/8/2433
TBI 05-04-001 [Abstract] [Postscript] [PDF]
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry
Gil Benkö, Christoph Flamm, Peter F. Stadler
appeared in: Proc. 8th ECAL, LNAI 3630, pp. 725-733, 2005
BIOINF 05-03-003
[Abstract] [Postscript] [PDF]
Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
published in BMC Bioinformatics 6:160 (2005)
TBI 05-03-002 [Abstract] [Postscript] [PDF] [Software]
SBML ODE Solver Library: a command-line tool and library for numerical analysis of reaction networks
Rainer Machne, Andrew Finney, Stefanie Widder, Stefan Müller, Christoph Flamm
submitted to Bioinformatics 2005
TBI 05-03-001 [Abstract] [Postscript] [PDF] [Supplements]
CelloS: a Multi-level Approach to Evolutionary Dynamics
Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
appeared in: Proc. 8th ECAL, LNAI 3630, pp. 500-509, 2005
TBI 05-02-001 [Abstract] [Postscript] [PDF]
Fast and reliable prediction of noncoding RNAs
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
appeared in: Proc. Natl. Acad. Sci. USA 102: 2454-2459 (2005).
TBI 05-01-002 [Abstract] [Postscript] [PDF] [Supplements]
Evolutionary patterns of non-coding RNAs
Athanasius F. Bompfünewerera, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M.R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl and Christina Witwer
appeared in: Theor. Biosci. 123: 301-369 (2005).
TBI 05-01-001 [Abstract] [Postscript] [PDF]
The ToyChem Package: A Computational Toolkit Implementing a Realistic Artificial Chemistry Model
Gil Benkö, Christoph Flamm, Peter F. Stadler
submitted to Math/Chem/Comp 2005
For comments on this page
Ivo Hofacker, <ivo@tbi.univie.ac.at>
Institut für theoretische Chemie, Währingerstr. 17, A-1090 Wien, AUSTRIA

Last modified: 2007-08-22 12:32:54 xtof