Publications - Published papers

Please find below publications of our group. Currently, we list 454 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 2009

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia Sharma, Philipp Khaitovich, Peter F. Stadler, and Jörg Hackermüller.
PLoS Comp. Biol., 5:e1000502, 2009
PREPRINT 09-045:
[ Publishers's page ]  paperID

Automatic classification of embryonic fruit fly gene expression patterns

Andreas Heffel, Sonja J. Prohaska, Peter F. Stadler, Gerhard Kauer, and Jens-Peer Kuska.
In H.-P. Meinzer, Th. M. Deserno, H. Handels, and Th. Tolxdorff, editors, Bildverarbeitung für die Medizin 2009: Algorithmen Systeme Anwendungen, pages 415419, Heidelberg, 2009. Springer.
PREPRINT 09-044:
[ Publishers's page ]  paperID

Sequence assembly

Karsten Scheibye-Alsing, Steve Hoffmann, Annett M. Frankel, Peter Jensen, Peter F. Stadler, Yuan Mang, Niels Tommerup, Mike J Gilchrist, Ann-Britt N. Hillig, Susanna Cirera, Claus B Jørgensen, Merete Fredholm, and Jan Gorodkin.
Comp. Biol. Chem., 33:121136, 2009.
PREPRINT 09-043: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Extended Shapes for the Combinatorial Design of RNA Sequences

Marc Hellmuth, Daniel Merkle, Martin Middendorf
Int. J. of Computational Biology and Drug Design, 2, 4, 371 - 384, 2009
PREPRINT 09-039: [ Abstract ]
[ Publishers's page ]  paperID

Identification and Classification of Small RNAs in Transcriptome Sequence Data

D. Langenberger, C.I. Bermudez-Santana, P.F. Stadler, S. Hoffmann
Pac Symp Biocomput. 2010:80-7
PREPRINT 09-034: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

On the Design of RNA Sequences for Realizing Extended Shapes

Marc Hellmuth, Daniel Merkle, Martin Middendorf
Bioinformatics, Systems Biology and Intelligent Computing, IJCBS '09. 167-173 (2009)
PREPRINT 09-033: [ Abstract ]
[ Publishers's page ]  paperID

The Genome of the Stick Insect Medauroidea extradentata Is Strongly Methylated within Genes and Repetitive DNA

Veiko Krauss, Carina Eisenhardt und Tina Unger
PLoS ONE 4(9): e7223.
PREPRINT 09-030: [ Abstract ]
[ Publishers's page ]  paperID

Comparative Analysis of Eukaryotic U3 snoRNA

Manja Marz, Peter F. Stadler
RNA Biol., 6:503507
PREPRINT 09-021: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Local algorithms for the prime factorization of strong product graphs

Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler
Mathematics in Computer Science: DOI 10.1007/s11786-009-0073-y
PREPRINT 09-018: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Converting DNA to Music: ComposAlign

Todd Ingalls, Georg Martius, Marc Hellmuth, Manja Marz, Sonja J. Prohaska
Proceedings of the German Conference on Bioinformatics 2009, LNI. 2009; P-157:93-103.
PREPRINT 09-017: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID

Solvent exposure imparts similar selective pressures across a range of yeast proteins.

Gavin C. Conant, Peter F. Stadler
Mol. Biol. Evol. 26: 1155-1161 (2009)
PREPRINT 09-016: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data

David Langenberger, Clara Bermudez-Santana, Jana Hertel, Philipp Khaitovich, Steve Hoffmann, Peter F. Stadler
Bioinformatics. 2009 Sep 15;25(18):2298-301.
PREPRINT 09-015: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

Conservation laws for voter-like models on random directed networks

M. Angeles Serrano, Konstantin Klemm, Federico Vazquez, Victor M. Eguiluz, Maxi San Miguel
J. Stat. Mech. (2009) P10024
PREPRINT 09-014: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Customized strategies for discovering distant ncRNA homologs

Axel Mosig, Liang Zhu, Peter F. Stadler
Brief. Funct. Genom. Proteom. 8(6):451-460
PREPRINT 09-012: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Evolution of 7SK RNA and Its Protein Partners in Metazoa

Manja Marz*, Alexander Donath*, Nina Verstraete, Van Trung Nguyen, Peter F. Stadler, Olivier Bensaude
Mol Biol Evol. 2009 Dec;26(12):2821-30.
PREPRINT 09-010: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Partition Function and Base Pairing Probabilities for RNA-RNA Interaction Prediction

Fenix W. D. Huang, Jin Qin, Christian M. Reidys, Peter F. Stadler
Bioinformatics 25:2646-2654 (2009)
PREPRINT 09-008: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Measuring Transcription Factor Binding Site Turnover: A Maximum Likelihood Approach using Phylogenies

Wolfgang Otto, Peter F. Stadler, Francesc López-Gialdéz, Jeffrey Townsend, Vincent Lynch, Günter P. Wagner
Genome Biol. Evol. 1:85-98 (2009)
PREPRINT 09-007: [ Abstract ]  [ Software ]
[ Publishers's page ]  paperID

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

Roman R. Stocsits, Harald Letsch, Jana Hertel, Bernhard Misof , Peter F. Stadler
Nucleic Acids Res. 2009 Oct;37(18):6184-93.
PREPRINT 09-006: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

A Note on Quasi-Robust Cycle Bases

Philipp-Jens Ostermeier, Marc Hellmuth, Konstantin Klemm, Josef Leydold, Peter F. Stadler
Ars Math. Contemp. 2, 2, 231-240 (2009)
PREPRINT 09-005: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Largest eigenvalues of the discrete p-Laplacian of trees with degree sequences

Türker Biyikoglu, Marc Hellmuth and Josef Leydold
ELA volume 18 (2009), pages 202-210
PREPRINT 09-004: [ Abstract ]   paperID

Mutate Now, Die Later

Andreea Munteanu, Peter F. Stadler
J Theor Biol. 260:412-421 (2009)
PREPRINT 09-003: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

A survey of nematode SmY RNAs

Thomas A. Jones, Wolfgang Otto, Manja Marz, Sean R. Eddy, Peter F. Stadler
RNA Biology 6:1; 5-8
PREPRINT 09-001: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

<em>Hox</em> cluster duplications in the basal teleost <em>Hiodon alosoides</em> (Osteoglossomorpha)

Karen E. Chambers, Ryan McDaniell, Jeremy F. Raincrow, Maya Deshmukh, Peter F Stadler, Chi-hua Chiu
Th. Biosci [online first] (2009)
PREPRINT 08-029: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

The tedious task of RNA homology search

Peter Menzel, Jan Gorodkin and Peter F. Stadler
RNA 15:2075-2082 (2009)
PREPRINT 08-025: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Non-Coding RNA Annotation of the Genome of <em>Trichoplax adhaerens</em>

Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler
Nucleic Acids Res. 37: 1602-1615 (2009)
PREPRINT 08-024: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz
Nucleic. Acids Res. 37: D159-D162 (2009)
PREPRINT 08-023: [ Abstract ]
[ Publishers's page ]  paperID

Evolution of vault RNAs

Peter F. Stadler, Julian J.-L. Chen, Jörg Hackermüller, Steve Hoffmann, Friedemann Horn, Phillip Khaitovich, Antje Kretzschmar, Axel Mosig, Sonja J. Prohaska, Xiaodong Qi, Katharina Schutt, Kerstin Ullmann
Mol Biol Evol. 2009; 26(9):1975-91
PREPRINT 08-022: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Conserved Introns Reveal Novel Transcripts in Drosophila melanogaster.

Hiller M, Findeiss S, Nickel C, Lein S, Marz M, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF.
Genome Res. 2009; 19(7):1289-300
PREPRINT 08-021:   [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Approximate Graph Products

Marc Hellmuth, Wilfried Imrich, Werner Kl&ouml;ckl, Peter F. Stadler
Europ. J. of Combinatorics, 30, 5, Part Special Issue on Metric Graph Theory, 1119-1133 (2009)
PREPRINT 08-020: [ Abstract ]
[ Publishers's page ]  paperID

Homology-Based Annotation of Non-coding RNAs in the Genomes of <i>Schistosoma mansoni</i> and <i>Schistosoma japonicum</i>

Claudia S. Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J. Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan Otto-Attolini, Peter F. Stadler
BMC Genomics 2009, 10:464.
PREPRINT 08-014: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

<tt>FRANz</tt>: Fast reconstruction of wild pedigrees

Markus Riester, Peter F. Stadler, Konstantin Klemm
Bioinformatics 25:2134-2139 (2009)
PREPRINT 08-011: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

A note on fundamental, non-fundamental, and robust cycle bases

Konstantin Klemm, Peter F. Stadler
Discrete Appl. Math. 157:2432-2438 (2009)
PREPRINT 07-005: [ Abstract ]
[ Publishers's page ]  paperID

A Topological Approach to Chemical Organization

Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler
Alife 15: 71-88 (2009)
PREPRINT 06-011: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Discovering cis-regulatory modules by optimizing barbecues

Axel Mosig, Türker Biyikoglu, Sonja J. Prohaska, Peter F. Stadler
Discr. Appl. Math. 157: 2458-2468 (2009)
PREPRINT 04-020: [ Abstract ]  [ PDF ]  [ PS ]  [ Software ]
[ Publishers's page ]  paperID