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 2013

How to multiply dynamic programming algorithms

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
In Joao C. Setubal and Nalvo F. Almeida, editors, Advances in Bioinformatics and Computational Biology, 8th BSB , volume 8213 of Lect. Notes Comp. Sci. , pages 8293 (2013)
PREPRINT 13-047: [ Abstract ]  [ PDF ]   paperID

ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation

Wosley Arruda, Célia G. Ralha, Tainá Raiol, Marcelo M. Brigido, Maria Emilia M. T. Walter, Peter F. Stadler
In Joao C. Setubal and Nalvo F. Almeida, editors, Advances in Bioinformatics and Computational Biology, 8th BSB , volume 8213 of Lect. Notes Comp. Sci. , pages 136147 (2013)
PREPRINT 13-046: [ Abstract ]   paperID

Generalized topologies: hypergraphs, chemical reactions, and biological evolution

Christoph Flamm, Bärbel M. R. Stadler, and Peter F. Stadler
In Subhash C. Basak, Guillermo Restrepo, and Jose Luis Villaveces, editors, Advances in Mathematical Chemistry: With applications to chemoinformatics, bioinformatics, drug d iscovery, and Predictive toxicology. Bentham (2013)
PREPRINT 13-045: [ Abstract ]  [ PDF ]

The Trouble with Long-Range Base Pairs in RNA Folding

Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. H ofacker, Jing Qin, Peter F. Stadler, The Students of the Bioinformatics II Lab Class 201 3, and Sebastian Will
Advances in Bioinformatics and Computational Biology Lecture Notes in Computer Science Volume 8213:1-11 (2013)
PREPRINT 13-043: [ Abstract ]   paperID

Computational design of RNAs with complex energy landscapes

Höner Zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF
Biopolymers 99: 11241136 (2013)
PREPRINT 13-042: [ Abstract ]  [ PDF ]   paperID

Inferring chemical reaction patterns using rule composition in graph grammars

Jakob L Andersen, Christoph Flamm, Daniel Merkle, and Peter F Stadler
Journal of Systems Chemistry 4:4 (2013)
PREPRINT 13-041: [ Abstract ]  [ PDF ]   paperID

Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures

Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler
Algorithms in Bioinformatics Lecture Notes in Computer Science Volume 8126:112-125 (2013)
PREPRINT 13-040: [ Abstract ]  [ PDF ]   paperID

The RNAsnp web server: predicting SNP effects on local RNA secondary structure

Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J
Nucleic Acids Res. 41(Web Server issue):W475-9 (2013)
PREPRINT 13-039: [ Abstract ]  [ PDF ]   paperID

Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach

Li Y, Podlevsky JD, Marz M, Qi X, Hoffmann S, Stadler PF, Chen JJ
RNA. 19(6):852-60 (2013)
PREPRINT 13-038: [ Abstract ]   paperID

Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data

Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF
RNA Biol. 10(7):1204-10 (2013)
PREPRINT 13-037: [ Abstract ]

Efficient detection of local RNA secondary structure changes induced by SNPs

Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J
Hum. Mut. 34:546556 (2013)
PREPRINT 13-036: [ Abstract ]  [ PDF ]   paperID

Computational biology of RNA interactions

Christoph Dieterich, Peter F. Stadler
WIREs RNA, 4: 107120
PREPRINT 13-035: [ Abstract ]   paperID

Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks

Lesca M. Holdt, Steve Hoffmann, Kristina Sass, David Langenberger, Markus Scholz, Knut Krohn, Knut Finstermeier, Anika Stahringer, Wolfgang Wilfert, Frank Beutner, Stephan Gielen, Gerhard Schuler, Gabor G ̈abel, Hendrick Bergert, Ingo Bachmann, Peter F. Stadler, Joachim Thiery, and Daniel Teupser
PLoS Genet. 9:e1003588 (2013)
PREPRINT 13-032: [ Abstract ]  [ PDF ]   paperID

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Yinhua Huang, Yingrui Li, David W Burt, Hualan Chen, Yong Zhang, Wubin Qian, Heebal Kim, Shangquan Gan, Yiqiang Zhao, Jianwen Li, Kang Yi, Huapeng Feng, Pengyang Zhu, Bo Li, Qiuyue Liu, Suan Fairley, Katharine E Magor, Zhenlin Du, Xiaoxiang Hu, Laurie Goodman, Hakim Tafer, Alain Vignal, Taeheon Lee, Kyu-Won Kim, Zheya Sheng, et al.
Nature Genetics 45:776783 (2013)
PREPRINT 13-031: [ Abstract ]  [ PDF ]   paperID

Homology search for small structured ncRNAs

Manja Marz, Stefanie Wehner and Peter F Stadler
In: Homology Search for Small Structured ncRNAs A. Schoen, Eric Westhof, Albrecht Bindereif, Roland Hartmann (2013)
PREPRINT 13-027:

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

Will S, Siebauer MF, Heyne S, Engelhardt J, Stadler PF, Reiche K, Backofen R
Algorithms Mol Biol. 8(1):14 (2013)
PREPRINT 13-026: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The african coelacanth genome provides insights into tetrapod evolution

Chris T. Amemiya, Jessica Alföldi, Alison P. Lee, Shaohua Fan, Hervé Philippe, Iain MacCallum, Ingo Braasch, Tereza Manousaki, Igor Schneider, Nicolas Rohner, Chris Organ, Domitille Chalopin, Jeramiah J. Smith, Mark Robinson, Rosemary A. Dorrington, Marco Gerdol, Bronwen Aken, Maria Assunta Biscotti, Marco Barucca, Denis Baurain, Aaron M. Berlin, Gregory L. Blatch, Francesco Buonocore, Thorsten Burmester, Michael S. Campbell, et al.
Nature 496: 311-316 (2013)
PREPRINT 13-025: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Mitogenomics and metazoan evolution

Schierwater B, Stadler P, Desalle R, Podsiadlowski L.
Mol Phylogenet Evol 69(2): 311312 (2013)
PREPRINT 13-022:   paperID

On the Complexity of Reconstructing Chemical Reaction Networks

Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
Math. Comp. Sci. 7(3):275-292 (2013)
PREPRINT 13-021: [ Abstract ]

snoStrip: a snoRNA annotation pipeline

Bartschat S, Kehr S, Tafer H, Stadler PF, Hertel J
Bioinformatics , 2013. doi: 10.1093/bioinformat- ics/btt604
PREPRINT 13-020: [ Abstract ]  [ PDF ]   paperID

Atypical RNAs in the coelacanth transcriptome

Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF
J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-10 (2013)
PREPRINT 13-019: [ Abstract ]  [ PDF ]   paperID

Biological evidence for the worlds smallest tRNAs

Wende S, Platzer EG, Jühling F, Pütz J, Florentz C, Stadler PF, Mörl M
Biochimie , 2013. doi: 10.1016/j.biochi.2013.07.034
PREPRINT 13-018: [ Abstract ]
[ Publishers's page ]  paperID

Widespread purifying selection on RNA structure in mammals

Martin A. Smith, Tanja Gesell, Peter F. Stadler, and John S. Mattick
Nucleic Acids Res. 41:82208236 (2013)
PREPRINT 13-016: [ Abstract ]  [ PDF ]   paperID

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, and Peter F. Stadler
Entropy 15:40664083 (2013)
PREPRINT 13-015: [ Abstract ]  [ PDF ]   paperID

Translation in Mammalian Mitochondria: Order and Disorder Linked to tRNAs and Aminoacyl-tRNA Synthetases

Catherine Florentz, Joern Pütz, Frank Jühling, Hagen Schwenzer, Peter F. Stadler, Bernard Lorber, Claude Sauter, Marie Sissler
In: Anne-Marie Duchene, editor, Translation in Mitochondria and Other Organelles , pages 5585. Springer, Heidelberg, 2013
PREPRINT 13-014: [ Abstract ]

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny

Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, Jühling F, Meusemann K, Middendorf M, Misof B, Perseke M, Podsiadlowski L, von Reumont B, Schierwater B, Schlegel M, Schrödl M, Simon S, Stadler PF, Stöger I, Struck TH
Mol. Phylog. Evol. , 69:352364 (2013)
PREPRINT 13-013: [ Abstract ]  [ PDF ]   paperID

Genetic aspects of mitochondrial genome evolution

Bernt M, Braband A, Schierwater B, Stadler PF
Mol. Phylog. Evol. 69:328338 (2013)
PREPRINT 13-012: [ Abstract ]  [ PDF ]   paperID

Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences

Bernt M, Braband A, Middendorf M, Misof B, Rota-Stabelli O, Stadler PF
Mol. Phylog. Evol. 69:320327 (2013)
PREPRINT 13-011: [ Abstract ]  [ PDF ]   paperID

Mitochondrial Genome Evolution

Matthias Bernt, Rainer Machne, Abdullah H Sahyoun, Martin Middendorf, Peter F Stadler
eLS. doi: 10.1002/9780470015902.a0025142
PREPRINT 13-010: [ Abstract ]   paperID

The correlation of genome size and DNA methylation rate in metazoans

Marcus Lechner, Manja Marz, Christian Ihling, Andrea Sinz, Peter F. Stadler, Veiko Krauss
Th. Biosci. 132:4760 (2013)
PREPRINT 13-009: [ Abstract ]  [ PDF ]   paperID

Polo-like kinase 4 transcription is activated via CRE and NRF1 elements, repressed by DREAM through CDE/CHR sites and deregulated by HPV E7 protein

Martin Fischer, Marianne Quaas, Axel Wintsche, Gerd A. Müller and Kurt Engeland
Nucleic Acids Research, 2013, 118
PREPRINT 13-007: [ Abstract ]
[ Publishers's page ]  paperID

Chromatin Computation: Epigenetic Inheritance as a Pattern Reconstruction Problem

Christian Arnold, Peter F. Stadler, Sonja J. Prohaska
Journal of Theoretical Biology 336:6174 (2013)
PREPRINT 13-006: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

Beyond genealogies: mutual information of causal paths to analyse single cell tracking data

Nico Scherf, Thomas Zerjatke, Konstantin Klemm, Ingmar Glauche, Ingo Roeder
Proc IEEE Int Symp Biomed Imaging 2013, 440-443
PREPRINT 13-005: [ Abstract ]  [ PDF ]
[ Publishers's page ]

Temporal networks: slowing down diffusion by long lasting interactions

Naoki Masuda, Konstantin Klemm, Victor M. Eguiluz
Phys. Rev. Lett. 111: 188701 (2013)
PREPRINT 13-004: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The common ancestral core of vertebrate and fungal telomerase RNAs

Qi X, Li Y, Honda S, Hoffmann S, Marz M, Mosig A, Podlevsky JD, Stadler PF, Selker EU, Chen JJ
Nucleic Acids Res.41:450462 (2013)
PREPRINT 12-037: [ Abstract ]  [ PDF ]   paperID

Relations Between Graphs

Jan Hubička, Jürgen Jost, Yangjing Long and Peter F. Stadler
Ars Math Contemp 6: 323-350 (2013)
PREPRINT 12-028: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

De novo design of a synthetic riboswitch that regulates transcription termination

Manja Wachsmuth, Sven Findeiß, Nadine Weissheimer, Peter F. Stadler and Mario Mörl
Nucleic Acids Res. 41:25412551 (2013)
PREPRINT 12-026: [ Abstract ]  [ PDF ]   paperID

2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction

Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
IEEE/ACM Trans Comput Biol Bioinform. 10: 832-844 (2013)
PREPRINT 12-025: [ Abstract ]  [ Supplement ]  [ Software ]
[ Publishers's page ]  paperID

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics

Stephan A. Müller, Sven Findeiß, Sandy R. Pernitzsch, Dirk K. Wissenbach, Peter F. Stadler, Ivo L. Hofacker, Martin von Bergen, Stefan Kalkhof
Journal of Proteomics 86:27-42 (2013)
PREPRINT 12-023: [ Abstract ]  [ Supplement ]   paperID

Matching of Soulmates: Coevolution of SnoRNAs and Their Targets

Stephanie Kehr, Sebastian Bartschat, Hakim Tafer, Peter F. Stadler, Jana Hertel
Mol Biol Evol (2013) doi: 10.1093/molbev/mst209
PREPRINT 12-022: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

Searchability of central nodes in networks

Konstantin Klemm
J. Stat. Phys. 151:707-719 (2013)
PREPRINT 12-020: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Dicer-Processed Small RNAs: Rules and Exceptions

David Langenberger, M. Volkan C, Steve Hoffmann, Peter F. Stadler
J.Exp.Zool.B Mol.Dev.Evol. 320: 35-46 (2012)
PREPRINT 12-005: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Orthology Relations, Symbolic Ultrametrics, and Cographs

Marc Hellmuth, Maribel Hernandez-Rosales, Katharina T. Huber, Vincent Moulton, Peter F. Stadler, Nicolas Wieseke
J.Math.Biol. 66: 399-420 (2013)
PREPRINT 11-026: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Prediction of lethal and synthetically lethal knock-outs in regulatory networks

Gunnar Boldhaus, Florian Greil, Konstantin Klemm
Theory in Biosciences 132:17-25 (2013)
PREPRINT 11-018: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Near Intron Pairs and the Metazoan Tree

Jörg Lehmann, Peter F. Stadler, Veiko Krauss
Mol. Phylogenet. Evol. 66(3):811-823 (2013)
PREPRINT 11-003: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

MITOS: Improved <i>de novo</i> Metazoan Mitochondrial Genome Annotation

Matthias Bernt, Alexander Donath, Frank Jühling, Fabian Externbrink, Catherine Florentz, Guido Fritzsch, Joern Pütz, Martin Middendorf, and Peter F. Stadler
Mol. Phylog. Evol. 69:313319 (2013)
PREPRINT 09-028: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID