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TBI WORKING PAPERS 2014

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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.
Bioinformatics of Prokaryotic RNAs

Author: Rolf Backofen, Fabian Amman, Fabrizio Costa, Sven Findeiß , Andreas S. Richter and Peter F. Stadler
ID: TBI-p-2014-1
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]

Computational design of a circular RNA with prion-like behavior

Author: Stefan Badelt, Christoph Flamm and Ivo L. Hofacker
ID: TBI-p-2014-2
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Towards an Optimal DNA-Templated Molecular Assembler

Author: Jakob L Andersen, Christoph Flamm, Martin M Hanczyc, Daniel Merkle
ID: TBI-p-2014-3
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Adaptable probabilistic mapping of short reads using position specific scoring matrices

Author: Peter Kerpedjiev, Jes Frellsen, Stinus Lindgreen and Anders Krogh
ID: TBI-p-2014-4
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Supplements: [Link to Supplements]
Link to publication: [BMC Bioinformatics]

Anomalous scaling in an age-dependent branching model

Author: Stephanie Keller-Schmidt, Murat Tugrul, Victor M. Eguiluz, Emilio Hernandez-Garcia, Konstantin Klemm
ID: TBI-p-2014-14
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Basin Hopping Graph: A computational framework to characterize RNA folding landscapes

Author: Kucharík, Marcel and Hofacker, Ivo L. and Stadler, Peter F. and Qin, Jing
ID: TBI-p-2014-6
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]

Memory efficient RNA energy landscape exploration

Author: Martin Mann, Marcel Kucharík, Christoph Flamm and Michael T. Wolfinger
ID: TBI-p-2014-7
Status: submitted
Abstract:         [Abstract]
PDF: No pdf submitted

50 Shades of Rule Composition: From Chemical Reactions to Higher Levels of Abstraction

Author: Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
ID: TBI-p-2014-8
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Predicting 3D RNA structure using a coarse-grain helix-centered model

Author: Peter Kerpedjiev, Christian Höner zu Siederdissen, and Ivo L. Hofacker
ID: TBI-p-2014-9
Status: submitted
Abstract:         [Abstract]
PDF: No pdf submitted

Comparative Detection of Processed Small RNAs in Archaea

Author: Christian Höner zu Siederdissen, Sarah Berkemer, Fabian Amman, Axel Wintsche, Sebastian Will, Sonja J. Prohaska, and Peter F. Stadler
ID: TBI-p-2014-10
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Supplements: [Link to Supplements]

Product Grammars for Alignment and Folding

Author: Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
ID: TBI-p-2014-11
Status: submitted
Abstract:         [Abstract]
PDF: No pdf submitted

The HERMIT in the stream: fusing stream fusion’s concatMap

Author: Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill
ID: TBI-p-2014-12
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.]

Boolean networks with veto functions

Author: Haleh Ebadi, Konstantin Klemm
ID: TBI-p-2014-13
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Anomalous scaling in an age-dependent branching model

Author: Stephanie Keller-Schmidt, Murat Tugrul, Victor M. Eguiluz, Emilio Hernandez-Garcia, Konstantin Klemm
ID: TBI-p-2014-14
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Thermodynamic and kinetic folding of Riboswitches.

Author: Stefan Badelt, Stefan Hammer, Christoph Flamm, Ivo L Hofacker
ID: TBI-p-2014-15
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [Methods in Enzymology]

Engineering synthetic riboswitches acting on transcription

Author: Wachsmuth M, Lorenz R, Serfling R, Findeiß S, Stadler PF and Mörl M
ID: TBI-p-2014-16
Status: submitted
Abstract:         [Abstract]
PDF: No pdf submitted

Design of Transcription Regulating Riboswitches

Author: Findeiß S, Wachsmuth M, Mörl M and Stadler PF
ID: TBI-p-2014-17
Status: submitted
Abstract:         [Abstract]
PDF: No pdf submitted