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 2012

Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida.

Helm, Conrad and Bernhart, Stephan H. and Siederdissen, Christian and Nickel, Birgit and Bleidorn, Christoph
Molecular phylogenetics and evolution 64 (1): 198--203
PREPRINT 18-036: [ Abstract ]

From event-labeled gene trees to species trees

Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T Huber, Vincent Moulton, and Peter F Stadler
BMC Bioinformatics 13(Suppl 19):S6 (2012)
PREPRINT 12-036: [ Abstract ]  [ PDF ]   paperID

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D
Mol Syst Biol. 8:593 (2012)
PREPRINT 12-035: [ Abstract ]  [ PDF ]   paperID

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing

Julia Richter, Matthias Schlesner, Steve Hoffmann, Markus Kreuz, Ellen Leich, Birgit Burkhardt, Maciej Rosolowski, Ole Ammerpohl, Rabea Wagener, Stephan H Bernhart, Dido Lenze, Monika Szczepanowski, Maren Paulsen, Simone Lipinski, Robert B Russell, Sabine Adam-Klages, Gordana Apic, Alexander Claviez, Dirk Hasenclever, Volker Hovestadt, Nadine Hornig, Jan O Korbel, Dieter Kube, David Langenberger, Chris Lawerenz, et al.
Nature Genetics 44:1316–1320 (2012)
PREPRINT 12-034: [ Abstract ]

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A. M. Groenen, Alan L. Archibald, Hirohide Uenishi, Christopher K. Tuggle, Yasuhiro Takeuchi, Max F. Rothschild, Claire Rogel-Gaillard, Chankyu Park, Denis Milan, Hendrik-Jan Megens, Shengting Li, Denis M. Larkin, Heebal Kim, Laurent A. F. Frantz, Mario Caccamo, Hyeonju Ahn, Bronwen L. Aken, Anna Anselmo, Christian Anthon, Loretta Auvil, Bouabid Badaoui, Craig W. Beattie, Christian Bendixen, Daniel Berman, Frank Blecha, et al.
Nature 491:393–398 (2012)
PREPRINT 12-033: [ Abstract ]  [ PDF ]   paperID

A Visual Cross-Database Comparison of Metabolic Networks

Markus Rohrschneider, Peter F. Stadler, Gerik Scheuermann
Advances in Visual Computing Lecture Notes in Computer Science 7432:678-687 (2012)
PREPRINT 12-032: [ Abstract ]  [ PDF ]   paperID

Clustering Rfam 10.1: Clans, families, and classes

Felipe A. Lessa, Taina Raiol, Marcelo M. Brigido, Daniele S. B. Martins Neto, Maria Emilia M. T. Walter, and Peter F. Stadler
Genes 3(3), 378-390 (2012)
PREPRINT 12-031: [ Abstract ]  [ PDF ]   paperID

Minimum cycle bases of lexicographic products

Marc Hellmuth, Philipp-Jens Ostermeier, Peter F. Stadler
Ars Math. Comptemp. 5:219–230 (2012)
PREPRINT 12-029: [ Abstract ]  [ PDF ]   paperID

A Survey on Hypergraph Products

Marc Hellmuth, Lydia Ostermeier, and Peter F. Stadler
Math. Comp. Sci. 6: 1-32 (2012)
PREPRINT 12-027: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

In silico Genetic Variation Pathogenicity Analysis of Hemagglutinin, Matrix 1, and Non Structural 1 Protein of Human H5N1 Indonesian Strain

Tambunan, U.S.F., Danang Febrianto and A.A. Parikesit
IIOABJ. Vol.3 (3):5-14
PREPRINT 12-024:
[ Publishers's page ]

Boolean networks as modeling framework

Florian Greil
Frontiers in Plant Science 3:178 (2012)
PREPRINT 12-021: [ Abstract ]
[ Publishers's page ]

Folding RNA/DNA hybrid duplexes

Ronny Lorenz, Ivo L Hofacker, Stephan H Bernhart
Bioinformatics 28: 2530-2531 (2012)
PREPRINT 12-018: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]

Detection of differentially expressed segments in tiling array data

Otto C, Reiche K, Hackermüller J
Bioinformatics. (2012) Jun; 28:(11) 1471-1479
PREPRINT 12-016:   [ PDF ]  [ Supplement ]  [ Software ]

Fast and sensitive mapping of bisulfite-treated sequencing data

Otto C, Stadler PF, Hoffmann S
Bioinformatics. (2012) Jul; 28:(13) 1698-1704
PREPRINT 12-015:   [ PDF ]  [ Supplement ]  [ Software ]

Armless Mitochondrial tRNAs in Enoplea (Nematoda)

Frank Jühling, Joern Pütz, Catherine Florentz, Peter F. Stadler
RNA Biology 9:1161-1166 (2012)
PREPRINT 12-014: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Atom Mapping with Constraint Programming

Martin Mann, Heinz Ekker, Peter F. Stadler, Christoph Flamm
In: Proceedings of the Workshop on Constraint Based Methods for Bioinformatics WCB12. Rolf Backofen and Sebastian Will (eds.), Univ. Freiburg 2012, pp. 23-29
PREPRINT 12-013: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Hypothesis for the modern RNA world: a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity.

Lozada-Chavez I, Stadler PF, Prohaska SJ
Orig Life Evol Biosph. 2011 Dec;41(6):587-607
PREPRINT 12-012:   paperID

Structure of transfer RNAs: similarity and variability

Richard Giegé, Frank Jühling, Joern Pütz, Peter Stadler, Claude Sauter, Catherine Florentz
WIREs RNA 2012, 3: 37-61
PREPRINT 12-011: [ Abstract ]   paperID

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF
Nucleic Acids Res. 2012 Apr 1;40(7):2833-2845. Epub 2011 Dec 1.
PREPRINT 12-010:   [ PDF ]  [ Supplement ]   paperID

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

Washietl S, Hofacker IL, Stadler PF, Kellis M
Nucleic Acids Res. 40(10):4261-72 (2012)
PREPRINT 12-009:   [ PDF ]   paperID

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R
RNA. 2012 May;18(5):900-14. Epub 2012 Mar 26
PREPRINT 12-008:   [ PDF ]   paperID

RNA Folding Algorithms with G-Quadruplexes

Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
Advances in Bioinformatics and Computational Biology Lecture Notes in Computer Science 7409:49-60 (2012)
PREPRINT 12-006: [ Abstract ]  [ Supplement ]  [ Software ]   paperID

Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera

Oliver Niehuis*, Gerrit Hartig*, Sonja Grath*, Hans Pohl, Jörg Lehmann, Hakim Tafer, Alexander Donath, Veiko Krauss, Carina Eisenhardt, Jana Hertel, Malte Petersen, Christoph Mayer, Karen Meusemann, Ralph S. Peters, Peter F. Stadler, Rolf G. Beutel, Erich Bornberg-Bauer, Duane D. McKenna, Bernhard Misof
Current Biology 22:1309–13 (2012)
PREPRINT 12-004: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

A global genome segmentation method for exploration of epigenetic patterns

Lydia Steiner, Lydia Hopp, Henry Wirth, Jörg Galle, Hans Binder, Sonja J Prohaska, Thimo Rohlf
PLoS ONE 7(10): e46811. doi:10.1371/journal.pone.0046811
PREPRINT 12-002: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID

Impact of individual nodes in Boolean network dynamics

Fakhteh Ghanbarnejad, Konstantin Klemm
Europhysics Letters 99:58006 (2012)
PREPRINT 11-027: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

A model of macroevolution as a branching process based on innovations

Stephanie Keller-Schmidt, Konstantin Klemm
Adv. Compl. Syst. 15:1250043 (2012)
PREPRINT 11-025: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Evolution of the let-7 microRNA Family

Jana Hertel, Sebastian Bartschat, Axel Wintsche, Christian Otto, The Students of the Bioinformatics Computer Lab 2011, Peter F Stadler
RNA Biology 9: 231-241 (2012)
PREPRINT 11-022: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

Hidden treasures in unspliced EST data

Jan Engelhardt, Peter F. Stadler
Th. Biosci. 131: 49-57 (2012)
PREPRINT 11-020: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

A measure of individual role in collective dynamics

Konstantin Klemm, M. Angeles Serrano, Victor M. Eguiluz, Maxi San Miguel
Scientific Reports 2:292 (2012)
PREPRINT 11-006: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Landscape Encodings Enhance Optimization

Konstantin Klemm, Anita Mehta, Peter F. Stadler
PLoS One 7: e34780 (2012)
PREPRINT 11-005: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

Cornelius Schmidtke, Sven Findeiß, Cynthia M. Sharma, Juliane Kuhfuß, Steve Hoffmann, Jörg Vogel, Peter F. Stadler, Ulla Bonas
Nucleic Acids Res. 40(5):2020-31 (2012)
PREPRINT 10-035: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID

Symmetric Circular Matchings and RNA Folding

Ivo L. Hofacker, Christian M. Reidys, and Peter F. Stadler
Discrete Mathematics 312:100–112 (2012)
PREPRINT 10-025:   paperID

The Cartesian Product of Hypergraphs

Lydia Ostermeier, Marc Hellmuth, Peter F. Stadler
J. Graph Theory 70: 180-196 (2012)
PREPRINT 10-012: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Diagonalized Cartesian Products of S-prime graphs are S-prime

Marc Hellmuth, Lydia Gringmann, Peter F. Stadler
Discrete Mathematics 312:74–80 (2012)
PREPRINT 09-035: [ Abstract ]  [ PDF ]   paperID