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TBI WORKING PAPERS 2008

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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.
Dinucleotide Controlled Null Models for Comparative RNA Gene Prediction.

Author: Tanja Gesell & Stefan Washietl
ID: TBI-p-2008-1
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [BMC Bioinformatics. 9:248 [2008]]

Beyond Energy Minimization: Approaches to the kinetic Folding of RNA.

Author: Christoph Flamm, Ivo L. Hofacker
ID: TBI-p-2008-2
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Arthropod 7SK RNA

Author: Gruber AR, Kilgus C, Mosig A, Hofacker IL, Hennig W, Stadler PF
ID: TBI-p-2008-3
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]
Link to publication: [Mol. Biol. Evol. 25(9):1923-30 (2008)]

Invertebrate 7SK snRNAs

Author: Gruber AR, Koper-Emde D, Marz M, Tafer H, Bernhart S, Obernosterer G, Mosig A, Hofacker IL, Stadler PF, Benecke BJ
ID: TBI-p-2008-4
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]
Link to publication: [J. Mol. Evol. 66(2):107-15 (2008)]

The Vienna RNA websuite

Author: Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL
ID: TBI-p-2008-5
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [Nucleic Acids Res. 36(Web Server issue):W70-4 (2008)]

Strategies for measuring evolutionary conservation of RNA secondary structures

Author: Gruber AR, Bernhart SH, Hofacker IL, Washietl S
ID: TBI-p-2008-6
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [BMC Bioinformatics 9:122 (2008)]

RNAalifold: improved consensus structure prediction for RNA alignments

Author: Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF
ID: TBI-p-2008-7
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [BMC Bioinformatics 9:474 (2008)]

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

Author: Gruber AR, Neuböck R, Hofacker IL, Washietl S
ID: TBI-p-2008-8
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Nucleic Acids Res. 35(Web Server issue):W335-8 (2007)]

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

Author: Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, and Ivo L. Hofacker o
ID: TBI-p-2008-9
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [Bioinformatics Research and Development, vol 13 of Communications in Computer and Information Science, pages 114–127. Springer.]