Publications - Published papers

Please find below publications of our group. Currently, we list 565 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 2010

Detection of Protein Domains in Eukaryotic Genome Sequences. In: Advances in Bioinformatics and Computational Biology, Carlos E. Ferreira, Satoru Miyano, Peter F. Stadler (eds.), Springer, Heidelberg, Lect. Note.

Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010
PREPRINT 10-045:   [ PDF ]   paperID

In Silico Analysis of Hemagglutinin, Neuraminidase, and Matrix2 of H5N1 Virus Indonesian Strain Related to Its High Pathgenicity

Usman Sumo Friend Tambunan, Agus Limanto and Arli Aditya Parikesit
IIOABJ, 2010; Vol.1 (3): 17-24
PREPRINT 10-042:
[ Publishers's page ]

Cracking The Genetic Code of Human Virus by using Open Source Bioinformatics tools

Usman Sumo Friend Tambunan, and Arli Aditya Parikesit
Journal of Fundamental Sciences Vol 6, No 1 (2010). 42-50
PREPRINT 10-041:
[ Publishers's page ]

Quantitative Comparison of Genomic-Wide Protein Domain Distributions

Arli A. Parikesit , Peter F. Stadler & Sonja J. Prohaska
GCB2010 conference proceeding. Vol P-173: pp 93-102
PREPRINT 10-034: [ Abstract ]  [ PDF ]   paperID

Optimization of Parameters for Coverage of Low Molecular Weight Proteins

Stephan A. Müller, Tibor Kohajda, Sven Findeiß, Peter F. Stadler, Stefan Washietl, Manolis Kellis, Martin von Bergen and Stefan Kalkhof
Analytical and Bioanalytical Chemistry
PREPRINT 10-031: [ Abstract ]
[ Publishers's page ]  paperID

Robustness of Boolean dynamics under knockouts

Gunnar Boldhaus, Nils Bertschinger, Johannes Rauh, Eckehard Olbrich, Konstantin Klemm
Phys. Rev E 82:021916 (2010)
PREPRINT 10-030: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism.

Dominik Schilling, Sven Findeiß, Andreas S Richter, Jenny A Taylor, Ulrike Gerischer
Archives of Microbiology, 2010 Jun 18.
PREPRINT 10-028: [ Abstract ]   paperID

bcheck: a wrapper tool for detecting RNase P RNA genes

YDilmurat Yusuf, Manja Marz, Peter F. Stadler, and Ivo L. Hofacker
BMC Bioinformatics 11: 432 (2010).
PREPRINT 10-024: [ Abstract ]  [ Software ]
[ Publishers's page ]  paperID

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

Christian Arnold, and Peter F. Stadler
Alg. Mol. Biol. 5: 25 (2010)
PREPRINT 10-022: [ Abstract ]  [ PDF ]  [ Software ]   paperID

Visual Network Analysis of Dynamic Metabolic Pathways

Markus Rohrschneider, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, and Gerik Scheuermann
Lect.\ Notes Comp.\ Sci. 6453: 316-327 (2010) [Advances in Visual Computing (ISVC 2010)]
PREPRINT 10-020:
[ Publishers's page ]  paperID

Visualization of Graph Products

Stefan Jänicke, Christian Heine, Marc Hellmuth, Peter F. Stadler, and Gerik Scheuermann
IEEE Trans Vis Comput Graph. 16: 1082-1089 (2010)
PREPRINT 10-019: [ Abstract ]
[ Publishers's page ]  paperID

Evolution of Metabolic Networks: A Computational Framework

Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider,Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker, Peter F. Stadler
J.Syst.Chem 1: 4 (2010)
PREPRINT 10-015: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Reconstruction of pedigrees in clonal plant populations

Markus Riester, Peter F. Stadler, Konstantin Klemm
Theor. Popul. Biol. 78:109-117 (2010)
PREPRINT 10-014: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε

Peter F. Stadler
In: <em>Advances in Bioinformatics and Computational Biology</em>,<br> Carlos E. Ferreira, Satoru Miyano, Peter F. Stadler (eds.), <br>Springer, Heidelberg, Lect. Notes Comp. Sci. 6268 (2010), pp.1-12<br>
PREPRINT 10-011: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

A Differentiation-Based Phylogeny of Cancer Subtypes

Markus Riester, Camille Stephan-Otto Attolini, Robert J. Downey, Samuel Singer, Franziska Michor
PLoS Comput Biol 6(5): e1000777. doi:10.1371/journal.pcbi.1000777
PREPRINT 10-009: [ Abstract ]
[ Publishers's page ]  paperID

Simple models for scaling in phylogenetic trees

Emilio Hernandez-Garcia, Murat Tugrul, E. Alejandro Herrada, Victor M. Eguiluz, Konstantin Klemm
International Journal of Bifurcation and Chaos 20:805-811 (2010)
PREPRINT 10-008: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.

Mario Fasold, Peter F. Stadler, Hans Binder
BMC Bioinformatics 2010, 11:207
PREPRINT 10-007: [ Abstract ]
[ Publishers's page ]  paperID

The primary transcriptome of the major human pathogen Helicobacter pylori

Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jeremy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler and Jörg Vogel
Nature. 2010 Mar 11;464(7286):250-5
PREPRINT 10-006: [ Abstract ]
[ Publishers's page ]  paperID

Combinatorial Vector Fields and the Valley Structure of Fitness Landscapes

Bärbel M. R. Stadler, Peter F. Stadler
J Math Biol. 61: 877–898 (2010)
PREPRINT 10-003: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Innovation in Gene Regulation: The Case of Chromatin Computation

Sonja J. Prohaska, Peter F. Stadler, David C. Krakauer
J.Theor.Biol. 265: 27-44 (2010)
PREPRINT 10-002: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Genomic Organization of Eukaryotic tRNAs

Clara Bermudez-Santana, Camille Stephan-Otto Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J. Prohaska, Stephan Steigele, Peter F. Stadler
BMC Genomics 11: 270 (2010)
PREPRINT 09-050:   [ Supplement ]
[ Publishers's page ]  paperID

Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata

Marleen Perseke, Detlef Bernhard, Guido Fritzsch, Franz Br&uuml;mmer, Peter F Stadler, Martin Schlegel
Mol. Phylog. Evol. 56: 201-211 (2010).
PREPRINT 09-049: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

BarMap: RNA folding on dynamics energy landscapes

Ivo L. Hofacker, Christoph Flamm, Christian Heine, Michael T. Wolfinger, Gerik Scheuermann, and Peter F. Stadler.
PREPRINT 09-048: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

A novel family of plasmid-transferred anti-sense ncRNAs

Sven Findeiß, Cornelius Schmidtke, Peter F. Stadler ,and Ulla Bonas
RNA Biol. 7: 120-124 (2010)
PREPRINT 09-041: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (<em>Meleagris gallopavo</em>): Genome Assembly and Analysis

Rami A Dalloul, Julie A Long, Aleksey V Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W Burt, Oswald Crasta, Richard P M A Crooijmans, Kristal Cooper, Roger A Coulombe, Supriyo De, Mary E Delany, Jerry B Dodgson, Jennifer J Dong, Clive Evans, Karin M Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A M Groenen, Tim T Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R Paton, William S Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L Salzberg, Michael C Schatz, Chantel Scheuring, Carl J Schmidt, Steven Schroeder, Stephen M J Searle, Edward J Smith, Jacqueline Smith, Tad S Sonstegard, Peter F Stadler, Hakim Tafer, Zhijian (Jake) Tu, Curtis P Van Tassell, Albert J Vilella, Kelly P Williams, James A Yorke, Liqing Zhang, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M Reed
PLoS Biology 8: e1000475 (2010
PREPRINT 09-037: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication

Jörg Lehmann, Carina Eisenhardt, Peter F. Stadler, Veiko Krauss
BMC Evol. Biol. 10: 156 (2010)
PREPRINT 09-036: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Target prediction and a statistical sampling algorithm for RNA-RNA interaction

Fenix Huang, Jing Qin, Christian M Reidys, Peter F Stadler
Bioinformatics 26:175-181 (2010)
PREPRINT 09-032: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

RNAz 2.0: improved noncoding RNA detection

Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker and Peter F. Stadler
Pac Symp Biocomput. 2010:69-79 (2010)
PREPRINT 09-026: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]
[ Publishers's page ]  paperID

<tt>RNAsnoop</tt>: efficient target prediction for box H/ACA snoRNAs. Submitted.

Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
Bioinformatics. 26: 610-616 (2010)
PREPRINT 09-025: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Nematode sbRNAs: homologs of vertebrate Y RNAs

Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, Peter F. Stadler
J. Mol. Evol. 70: 346-358 (2010)
PREPRINT 09-020: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Regulatory networks and connected components of the neutral space - A Look At Functional Islands

Gunnar Boldhaus, Konstantin Klemm
Eur. J. Phys. B 77: 233 (2010)
PREPRINT 09-011: [ Abstract ]  [ PDF ]   paperID

Temperature-Dependent Structural Variability of RNAs: Spliced Leader RNAs and their Evolutionary History

Manja Marz, Nathalie Vanzo, Peter F. Stadler
J Bioinform Comput Biol. 8: 1-17 (2010)
PREPRINT 09-009: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

Chris T. Amemiya, Thomas P. Powers, Sonja J. Prohaska, Jane Grimwood, Jeremy Schmutz, Mark Dickson, Tsutomu Miyake, Michael A. Schoenborn, Richard M. Myers, Francis H. Ruddle, Peter F. Stadler
Proc. Natl. Acad. Sci. USA 107: 3622-3627 (2010)
PREPRINT 09-002: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Non-Coding RNAs

Alexander Donath, Sven Findeiß, Jana Hertel, Manja Marz, Wolfgang Otto, Christine Schulz, Peter F. Stadler, Stefan Wirth
In: <em>Evolutionary Genomics and Systems Biology</em>, G. Caetano Anolles, eds. Wiley-Blackwell, Hoboken NJ, 2010, pp.251-293
PREPRINT 08-018: [ Abstract ]  [ PDF ]
[ Publishers's page ]

Evolutionary Genomics of MicroRNAs and Their Relatives

Andrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler
In: <em>Evolutionary Genomics and Systems Biology</em>, G. Caetano Anolles, eds. Wiley-Blackwell, Hoboken NJ, 2010, pp.295-327
PREPRINT 08-017: [ Abstract ]  [ PDF ]
[ Publishers's page ]