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TBI WORKING PAPERS 2013

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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.
Computational Design of RNAs with Complex Energy Landscapes

Author: Christian Höner zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L Hofacker, Christoph Flamm, and Peter F Stadler
ID: TBI-p-2013-1
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics

Author: Stephan A. Müller, Sven Findeiß, Sandy R. Pernitzsch, Dirk K. Wissenbach, Peter F. Stadler, Ivo L. Hofacker, Martin von Bergen, Stefan Kalkhof
ID: TBI-p-2013-2
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]
Link to publication: [Journal of Proteomics]

Barrier trees for metabolic adjustment landscapes

Author: {Flamm, Christoph and Hemmingsen, Chris and Merkle, Daniel
ID: TBI-p-2013-3
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

TSSAR: TSS Annotation Regime for dRNA-seq data

Author: Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Peter F. Stadler, Ivo L. Hofacker and Sven Findeiß
ID: TBI-p-2013-4
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]

De novo design of a synthetic riboswitch that regulates transcription termination

Author: Manja Wachsmuth, Sven Findeiß, Nadine Weissheimer, Peter F. Stadler and Mario Mörl
ID: TBI-p-2013-5
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [Nucleic Acids Research]

Generic Strategies for Chemical Space Exploration

Author: Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
ID: TBI-p-2013-6
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Mapping the RNA-Seq Trash Bin: Unusual Transcripts in Prokaryotic Transcriptome Sequencing Data

Author: Doose, Gero and Alexis, Maria and Kirsch, Rebecca and Findeiß, Sven and Langenberger, David and Machne, Rainer and Moerl, Mario and Hoffmann, Steve and Stadler, Peter F.
ID: TBI-p-2013-7
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]
Link to publication: [RNA biology]

How to Multiply Dynamic Programming Algorithms

Author: Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
ID: TBI-p-2013-8
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted

Automated identification of 3D modules with discriminative power in RNA structural alignments

Author: Corinna Theis, Christian Höner zu Siederdissen, Ivo L. Hofacker, and Jan Gorodkin
ID: TBI-p-2013-9
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Nucleic Acids Research. 41, no. 22. 41. : 9999–10009]

CMCompare webserver: comparing RNA families via covariance models

Author: Florian Eggenhofer, Ivo L. Hofacker, and Christian Höner zu Siederdissen
ID: TBI-p-2013-10
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Nucleic Acids Research. 41, no. W1. 41. : W499–W503]

2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction

Author: Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, and Peter F. Stadler
ID: TBI-p-2013-11
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [IEEE/ACM Transactions on Computation Biology and Bioinformatics]

Systematic analysis and evolution of 5S ribosomal DNA in metazoans

Author: Joaquin Vierna, Stefanie Wehner, Christian Höner zu Siederdissen, Andrés Martínez-Lage, and Manja Marz
ID: TBI-p-2013-12
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Heredity. 111, no. 5. 111. : 410–21]