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TBI WORKING PAPERS 2012

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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.
Microstructure Alignment of Wood Density Profiles – An Approach to Equalize Radial Differences in Growth Rate

Author: Bela J. Bender, Martin Mann, Rolf Backofen, and Heinrich Spiecker
ID: TBI-p-2012-1
Status: in press
Abstract:         [Abstract]
PDF: [Link to PDF]

Sneaking Around concatMap: Efficient Combinators for Dynamic Programming

Author: Christian Hoener zu Siederdissen
ID: TBI-p-2012-2
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Link to publication: [Proceedings of the 17th ACM SIGPLAN international conference on Functional programming]

CARNA - Alignment of RNA Structure Ensembles

Author: Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, and Sebastian Will
ID: TBI-p-2012-3
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]
Link to publication: [NAR, Webserver Issue (2012)]

Producing high-accuracy lattice models from protein atomic co-ordinates including side chains

Author: Martin Mann and Rhodri Saunders and Cameron Smith and Rolf Backofen and Charlotte M. Deane
ID: TBI-p-2012-4
Status: published
Abstract:         [Abstract]
PDF: [Link to PDF]
Supplements: [Link to Supplements]
Link to publication: [Advances in Bioinformatics 2012]

Atom Mapping with Constraint Programming

Author: Martin Mann, Heinz Ekker, Peter F. Stadler, and Christoph Flamm
ID: TBI-p-2012-5
Status: in press
Abstract:         [Abstract]
PDF: [Link to PDF]

Folding RNA/DNA hybrid duplexes

Author: Ronny Lorenz, Ivo L Hofacker and Stephan H Bernhart
ID: TBI-p-2012-6
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Inferring chemical reaction patterns using rule composition in graph grammars.

Author: Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
ID: TBI-p-2012-7
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Exploring Chemistry using SMT

Author: Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters
ID: TBI-p-2012-8
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

Generalized topologies: Hypergraphs, chemical reactions and biological evolution.

Author: Christoph Flamm, Bärbel MR Stadler, Peter F Stadler
ID: TBI-p-2012-9
Status: submitted
Abstract:         [Abstract]
PDF: [Link to PDF]

RNA Folding Algorithms with G-Quadruplexes

Author: Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, and Peter F. Stadler
ID: TBI-p-2012-10
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Brazilian Symposium on Bioinformatics (BSB 2012). Lecture Notes in Bioinformatics 7409]

Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida

Author: Conrad Helm, Stephan H. Bernhart, Christian Höner zu Siederdissen, Birgit Nickel, and Christoph Bleidorn
ID: TBI-p-2012-11
Status: published
Abstract:         [Abstract]
PDF: No pdf submitted
Link to publication: [Molecular Phylogenetics and Evolution]