Publications - Published papers

Please find below publications of our group. Currently, we list 363 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©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 bioinformatics group 2014

The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies

Martin Machyna, Stephanie Kehr, Korinna Straube, Dennis Kappei, Frank Buchholz, Falk Butter, Jernej Ule, Jana Hertel, Peter F. Stadler, Karla M. Neugebauer
Molecular Cell,Volume 56, Issue 3, 6 November 2014, Pages 389–399
PREPRINT 14-016: [ Abstract ]
[ Publishers's page ]  paperID

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

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. doi:10.1371/journal.pone.0105015
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) doi: 10.1093/nar/gku696
PREPRINT 14-003: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The HERMIT in the Stream

Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill
Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation: 97--108
PREPRINT 14-002: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Convex Cycle Bases

Hellmuth, Marc and Leydold, Josef and Stadler, Peter F
Acta Math. Con- temp. 7:123–140 (2014)
PREPRINT 13-044: [ Abstract ]  [ PDF ]   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

Computational prediction of microRNA genes

Jana Hertel, David Langenberger, and Peter F. Stadler
In Jan Gorodkin and Larry Ruzzo, editors, An introduction to RNA Bioinformatics , volume 1097 of Meth. Mol. Biol. Humana Press, New York, 2014. in press.
PREPRINT 13-029:

Class-specific prediction of ncRNAs

Peter F. Stadler
In Jan Gorodkin and Larry Ruzzo, editors, An introduction to RNA Bioinformatics , volume 1097 of Meth. Mol. Biol. Humana Press, New York, 2014. in press.
PREPRINT 13-028:

Geometry and Coarse-Grained Representations of Landscapes

Konstantin Klemm, Jing Qin, Peter F. Stadler
Recent Advances in the Theory and Application of Fitness Landscapes Emergence, Complexity and Computation Volume 6: 153-176 (2014)
PREPRINT 13-024: [ Abstract ]

The genome of the recently domesticated crop plant sugar beet Beta vulgaris

Juliane C. Dohm, Andre E. Minoche, Daniela Holtgrawe, Salvador Capella Gutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Thomas Rosleff S ̈oren sen, Ralf Stracke, Richard Reinhardt, Alexander Goesmann, Britta Schulz, Peter F. Stadler, Thomas Schmidt, Toni Gabaldon, Hans Lehrach, Bernd Weisshaar, and Heinz Himmelbauer
Nature 505: 546-549 (2014)
PREPRINT 13-023:
[ Publishers's page ]  paperID

A First Glimpse at the Genome of the Baikalian Amphipod Eulimnogammarus verrucosus

Lorena Rivarola-Duarte*, Christian Otto*, Frank Jühling, Stephan Schreiber, Daria Bedulina, Lena Jakob, Anton Gurkov, Denis Axenov-Gribanov, Abdullah H. Sahyoun, Magnus Lucassen, Jörg Hackermüller, Steve Hoffmann, Franz Sartoris, Hans-Otto Pörtner, Maxim Timofeyev, Till Luckenbach, Peter F. Stadler
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume 322, Issue 3, pages 177–189, May 2014,DOI: 10.1002/jez.b.22560
PREPRINT 13-003: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Simulation of Gene Family Histories

BMC Bioinformatics 15(Suppl 3):A8 (2014)
PREPRINT 12-017: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID