Publications - Published papers

Please find below publications of our group. Currently, we list 54 papers. Some of the publications are in collaboration with the group of Peter Stadler and are also listed in the publication list for his group. Access to published papers (access) is restricted to our local network and chosen collaborators.
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©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

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Publications of the Computational EvoDevo group 2014

CEM-Designer: Design of custom expression microarrays in the post-ENCODE Era.

Arnold C, Externbrink F, Hackermüller J, Reiche K
J Biotechnol. 2014 Nov 10;189:154-6
PREPRINT 15-002: [ Abstract ]
[ Publishers's page ]

Dynamic Programming for Set Data Types

Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler
In Conference Proceedings of Brasilian Symposium on Bioinformatics BSB ’14, Belo Horizonte, MG, Brazil. Lect. Notes Comp Sci. 2014
PREPRINT 14-015: [ Abstract ]  [ Software ]

A priori assessment of data quality in molecular phylogenetics

Bernhard Misof, Karen Meusemann, Björn M von Reumont, Patrick Kück, Sonja J Prohaska and Peter F Stadler
Algorithms for Molecular Biology 9.1 (2014): 22.
PREPRINT 14-014: [ Abstract ]
[ Publishers's page ]  paperID

Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin

Thimo Rohlf, Lydia Steiner, Jens Przybilla, Sonja Prohaska, Hans Binder, Joerg Galle
Vol. 4, No. 2, Pages 205-219 , DOI 10.2217/epi.11.117
PREPRINT 14-013: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Analyzing Chromatin Using Tiled Binned Scatterplot Matrices

Dirk Zeckzer, Daniel Gerighausen, Lydia Steiner, Sonja J Prohaska
BioVis 2014 conference proceedings
PREPRINT 14-011: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The transcription factor p53: Not a repressor, solely an activator

Martin Fischer, Lydia Steiner, Kurt Engeland
Cell Cycle 13:19, 3037--3058
PREPRINT 14-010: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Orthology detection combining clustering and synteny for very large datasets

Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thévenin, Jens Stoye, Roland K. Hartmann, Sonja J. Prohaska, Peter F. Stadler
PLoS ONE 9(8): e105015
PREPRINT 14-009: [ Abstract ]
[ Publishers's page ]  paperID

The CHR site: definition and genome-wide identification of a cell cycle transcriptional element

Gerd A. Müller, Axel Wintsche, Konstanze Stangner, Sonja J. Prohaska, Peter F. Stadler, and Kurt Engeland
Nucl. Acids Res. (2014)
PREPRINT 14-003: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya

Arli Aditya Parikesit, Lydia Steiner, Peter F Stadler, Sonja J Prohaska
Malaysian Journal of Fundamental and Applied Sciences, Vol 10, No 2 (2014)
PREPRINT 13-033: [ Abstract ]  [ PDF ]   paperID