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 2011

A comprehensively molecular haplotype-resolved genome of a European individual.

Suk, EK., McEwen, G.K., Duitama, J., Nowick, K., Schulz, S., Palczewski, S., Schreiber, S., Holloway, D., McLaughlin S., Peckham, H., Lee, C., Huebsch, T., and Hoehe, M.R.
Genome Research, Epub 2011/08/05
PREPRINT 11-042: [ Abstract ]
[ Publishers's page ]  paperID

Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species

Nowick K, Fields C, Gernat T, Caetano-Anolles D, Kholina N, Stubbs L
PLoS One 6: e21553
PREPRINT 11-041: [ Abstract ]   paperID

In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)

Tambunan, U.S.F., N Bramantya and A.A. Parikesit
BMC Bioinformatics.12(Suppl 13):S23
PREPRINT 11-040:
[ Publishers's page ]

RNA interactions

Marz M, Stadler PF
Advances in Experimental Medicine and Biology 2011, 1, Volume 722, RNA Infrastructure and Networks, Pages 20-38
PREPRINT 11-033:   [ PDF ]

A comprehensively molecular haplotype-resolved genome of a European individual

Eun-Kyung Suk, Gayle K. McEwen, Jorge Duitama, Katja Nowick, Sabrina Schulz, Stefanie Palczewski, Stefan Schreiber,2 Dustin T. Holloway, Stephen McLaughlin, Heather Peckham, Clarence Lee, Thomas Huebsch, and Margret R. Hoehe
Genome Res. 2011 21: 1672-1685
PREPRINT 11-032: [ Abstract ]   paperID

Gain, Loss and Divergence in Primate Zinc-Finger Genes: A Rich Resource for Evolution of Gene Regulatory Differences between Species

Katja Nowick, Christopher Fields, Tim Gernat, Derek Caetano-Anolles, Nadezda Kholina, Lisa Stubbs
PLoS ONE 6(6): e21553
PREPRINT 11-031: [ Abstract ]   paperID

Topology and prediction of RNA pseudoknots

Christian M. Reidys, Fenix W.D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, and Markus E. Nebel
Bioinformatics (2011) 27 (8): 1076-1085
PREPRINT 11-030: [ Abstract ]  [ PDF ]   paperID

ViennaRNA Package 2.0

Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler , Ivo L Hofacker
Algorithms for Molecular Biology 2011, 6:26
PREPRINT 11-029: [ Abstract ]  [ PDF ]   paperID

Animal snoRNAs and scaRNAs with exceptional structures

Manja Marz, Andreas R. Gruber, Christian Höner zu Siederdissen, Fabian Amman, Stefan Badelt, Sebastian Bartschat, Stephan H. Bernhart, Wolfgang Beyer, Stephanie Kehr, Ronny Lorenz, Andrea Tanzer, Dilmurat Yusuf, Hakim Tafer, Ivo L. Hofacker and Peter F. Stadler
RNA Biology 8:6, 938-946; November/December 2011
PREPRINT 11-028: [ Abstract ]   paperID

Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions

Arli A. Parikesit, Peter F. Stadler, Sonja Prohaska
Genes 2, no. 4: 912-924 (2011)
PREPRINT 11-024: [ Abstract ]   paperID

deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns

David Langenberger, Sachin Pundhir, Claus T. Ekstrøm, Peter F. Stadler, Steve Hoffmann, and Jan Gorodkin
Bioinformatics (2011) doi: 10.1093/bioinformatics/btr598
PREPRINT 11-023: [ Abstract ]   paperID

RNAcentral: A vision for an international database of RNA sequences

Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C
RNA. 2011 Sep 22. [Epub ahead of print]
PREPRINT 11-021: [ Abstract ]   paperID

Evolution of Domain Co-occurrences: Some Striking Results

Arli A. Parikesit, Peter F. Stadler, and Sonja J. Prohaska
GCB2011 Extended Abstract, Poster Track PT-141
PREPRINT 11-019: [ Abstract ]  [ PDF ]

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

Irma Lozada-Chávez, Peter F. Stadler, Sonja J. Prohaska
Orig Life Evol Biosph. 41: 587-607 (2011)
PREPRINT 11-014: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Protein-Coding Structured RNAs<br> A Computational Survey of Conserved RNA Secondary Structures Overlapping Coding Regions in Drosophilids

Sven Findeiß, Jan Engelhardt, Sonja J. Prohaska and Peter F. Stadler
Biochimie
PREPRINT 11-012: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID

Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis

Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F Stadler, Sonja J. Prohaska
BMC Bioinformatics 2011, 12:124
PREPRINT 11-010: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]   paperID

DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments

Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, Steve Hoffmann
Nucleic Acids Res. (Web Server Issue)
PREPRINT 11-009:   [ PDF ]
[ Publishers's page ]  paperID

MicroRNA or Not MicroRNA?

David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, and Peter F. Stadler
Lecture Notes Comp. Sci. 6832: 1-9 (2011) [Brasilian Symposium of Bioinformatics 2011]
PREPRINT 11-008:   [ PDF ]
[ Publishers's page ]  paperID

Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript

Dominic Rose, Peter F. Stadler
Frontiers in Genetics, 2:69. Epub 2011 Oct 5
PREPRINT 11-007: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Stability of Boolean and continuous dynamics

Fakhteh Ghanbarnejad, Konstantin Klemm
Phys. Rev. Lett. 107: 188701 (2011)
PREPRINT 11-004: [ Abstract ]  [ PDF ]   paperID

A Folding Algorithm for Extended RNA Secondary Structures

Christian H&ouml;ner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
Bioinformatics (2011) 27 (13): i129-i136
PREPRINT 11-002: [ Abstract ]  [ PDF ]   paperID

Fast local fragment chaining using sum-of-pair gap costs

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler
Algorithms for Molecular Biology 2011, 6:4
PREPRINT 10-039: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]   paperID

A Pipeline for Computational Historical Linguistics

Lydia Steiner, Peter F. Stadler, Michael Cysouw
Language Dynamics and Change
PREPRINT 10-038: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID

Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data

Sven Findeiß, David Langenberger, Peter F. Stadler, Steve Hoffmann
Biol. Chem., Vol. 392 (April 2011)
PREPRINT 10-036: [ Abstract ]  [ PDF ]  [ Supplement ]

PLEXY: Efficient Target Prediction for Box C/D snoRNAs

Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler and Hakim Tafer
Bioinformatics (2011) 27 (2): 279-280
PREPRINT 10-032: [ Abstract ]  [ PDF ]  [ Software ]   paperID

Finding attractors in asynchronous Boolean dynamics

Thomas Skodawessely, Konstantin Klemm
Advances in Complex Systems 14: 439-449 (2011)
PREPRINT 10-029: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Computational discovery of human coding and non-coding transcripts with conserved splice sites

Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler
Bioinformatics
PREPRINT 10-010: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

Peter Menzel, Peter F. Stadler, Jan Gorodkin
Bioinformatics (2011) 27 (3): 317-325
PREPRINT 10-005: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]   paperID

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data

Stefan Washietl, Sven Findeiß Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß, Nick Goldman
RNA 2011 Apr;17(4):578-594
PREPRINT 10-001: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny

Jeremy D. Raincrow, Ken Dewar, Li-Zhi Gao, Claudia Stocsits, Sonja J. Prohaska, Ken Dewar, Chris T. Amemiya, Peter F. Stadler, Chi-hua Chiu
J Exp Zool B Mol Dev Evol. 316: 451-64 (2011)
PREPRINT 09-040: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Efficient exploration of discrete energy landscapes

Martin Mann, Konstantin Klemm
Physical Review E 83: 011113 (2011)
PREPRINT 09-031: [ Abstract ]  [ PDF ]   paperID

Deletion analysis of the 3&#039; long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs as sufficient for first strand transfer

Andrea Tramontano, Alexander Donath, Stefan H. Bernhart, Kristin Reiche, Gudrun Böhmdorfer, Peter F. Stadler, and Andreas Bachmair
Virology (2011)
PREPRINT 09-029: [ Abstract ]
[ Publishers's page ]  paperID