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 (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) 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 82–93 (2013)
PREPRINT 13-047: [ Abstract ] [ PDF ]
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 82–93 (2013)
PREPRINT 13-047: [ Abstract ] [ PDF ]
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 136–147 (2013)
PREPRINT 13-046: [ Abstract ]
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 136–147 (2013)
PREPRINT 13-046: [ Abstract ]
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 ]
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 ]
Advances in Bioinformatics and Computational Biology Lecture Notes in Computer Science Volume 8213:1-11 (2013)
PREPRINT 13-043: [ Abstract ]
Computational design of RNAs with complex energy landscapes
Höner Zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF
Biopolymers 99: 1124–1136 (2013)
PREPRINT 13-042: [ Abstract ] [ PDF ]
Biopolymers 99: 1124–1136 (2013)
PREPRINT 13-042: [ Abstract ] [ PDF ]
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 ]
Journal of Systems Chemistry 4:4 (2013)
PREPRINT 13-041: [ Abstract ] [ PDF ]
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 ]
Algorithms in Bioinformatics Lecture Notes in Computer Science Volume 8126:112-125 (2013)
PREPRINT 13-040: [ Abstract ] [ PDF ]
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 ]
Nucleic Acids Res. 41(Web Server issue):W475-9 (2013)
PREPRINT 13-039: [ Abstract ] [ PDF ]
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 ]
RNA. 19(6):852-60 (2013)
PREPRINT 13-038: [ Abstract ]
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 ]
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. 34:546–556 (2013)
PREPRINT 13-036: [ Abstract ] [ PDF ]
Hum. Mut. 34:546–556 (2013)
PREPRINT 13-036: [ Abstract ] [ PDF ]
Computational biology of RNA interactions
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 ]
PLoS Genet. 9:e1003588 (2013)
PREPRINT 13-032: [ Abstract ] [ PDF ]
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 45:776–783 (2013)
PREPRINT 13-031: [ Abstract ] [ PDF ]
Nature Genetics 45:776–783 (2013)
PREPRINT 13-031: [ Abstract ] [ PDF ]
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:
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 ]
Algorithms Mol Biol. 8(1):14 (2013)
PREPRINT 13-026: [ Abstract ] [ PDF ]
[ Publishers's page ]
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 ]
Nature 496: 311-316 (2013)
PREPRINT 13-025: [ Abstract ] [ PDF ]
[ Publishers's page ]
Mitogenomics and metazoan evolution
Schierwater B, Stadler P, Desalle R, Podsiadlowski L.
Mol Phylogenet Evol 69(2): 311–312 (2013)
PREPRINT 13-022:
Mol Phylogenet Evol 69(2): 311–312 (2013)
PREPRINT 13-022:
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 ]
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 ]
Bioinformatics , 2013. doi: 10.1093/bioinformat- ics/btt604
PREPRINT 13-020: [ Abstract ] [ PDF ]
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 ]
J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-10 (2013)
PREPRINT 13-019: [ Abstract ] [ PDF ]
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 ]
Biochimie , 2013. doi: 10.1016/j.biochi.2013.07.034
PREPRINT 13-018: [ Abstract ]
[ Publishers's page ]
Widespread purifying selection on RNA structure in mammals
Martin A. Smith, Tanja Gesell, Peter F. Stadler, and John S. Mattick
Nucleic Acids Res. 41:8220–8236 (2013)
PREPRINT 13-016: [ Abstract ] [ PDF ]
Nucleic Acids Res. 41:8220–8236 (2013)
PREPRINT 13-016: [ Abstract ] [ PDF ]
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 15:4066–4083 (2013)
PREPRINT 13-015: [ Abstract ] [ PDF ]
Entropy 15:4066–4083 (2013)
PREPRINT 13-015: [ Abstract ] [ PDF ]
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 55–85. Springer, Heidelberg, 2013
PREPRINT 13-014: [ Abstract ]
In: Anne-Marie Duchene, editor, Translation in Mitochondria and Other Organelles , pages 55–85. 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. , 69:352–364 (2013)
PREPRINT 13-013: [ Abstract ] [ PDF ]
Mol. Phylog. Evol. , 69:352–364 (2013)
PREPRINT 13-013: [ Abstract ] [ PDF ]
Genetic aspects of mitochondrial genome evolution
Bernt M, Braband A, Schierwater B, Stadler PF
Mol. Phylog. Evol. 69:328–338 (2013)
PREPRINT 13-012: [ Abstract ] [ PDF ]
Mol. Phylog. Evol. 69:328–338 (2013)
PREPRINT 13-012: [ Abstract ] [ PDF ]
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. 69:320–327 (2013)
PREPRINT 13-011: [ Abstract ] [ PDF ]
Mol. Phylog. Evol. 69:320–327 (2013)
PREPRINT 13-011: [ Abstract ] [ PDF ]
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 ]
eLS. doi: 10.1002/9780470015902.a0025142
PREPRINT 13-010: [ Abstract ]
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. 132:47–60 (2013)
PREPRINT 13-009: [ Abstract ] [ PDF ]
Th. Biosci. 132:47–60 (2013)
PREPRINT 13-009: [ Abstract ] [ PDF ]
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, 1–18
PREPRINT 13-007: [ Abstract ]
[ Publishers's page ]
Nucleic Acids Research, 2013, 1–18
PREPRINT 13-007: [ Abstract ]
[ Publishers's page ]
Chromatin Computation: Epigenetic Inheritance as a Pattern Reconstruction Problem
Christian Arnold, Peter F. Stadler, Sonja J. Prohaska
Journal of Theoretical Biology 336:61–74 (2013)
PREPRINT 13-006: [ Abstract ] [ PDF ] [ Software ]
[ Publishers's page ]
Journal of Theoretical Biology 336:61–74 (2013)
PREPRINT 13-006: [ Abstract ] [ PDF ] [ Software ]
[ Publishers's page ]
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 ]
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 ]
Phys. Rev. Lett. 111: 188701 (2013)
PREPRINT 13-004: [ Abstract ] [ PDF ]
[ Publishers's page ]
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.41:450–462 (2013)
PREPRINT 12-037: [ Abstract ] [ PDF ]
Nucleic Acids Res.41:450–462 (2013)
PREPRINT 12-037: [ Abstract ] [ PDF ]
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 ]
Ars Math Contemp 6: 323-350 (2013)
PREPRINT 12-028: [ Abstract ] [ PDF ]
[ Publishers's page ]
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. 41:2541–2551 (2013)
PREPRINT 12-026: [ Abstract ] [ PDF ]
Nucleic Acids Res. 41:2541–2551 (2013)
PREPRINT 12-026: [ Abstract ] [ PDF ]
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 ]
IEEE/ACM Trans Comput Biol Bioinform. 10: 832-844 (2013)
PREPRINT 12-025: [ Abstract ] [ Supplement ] [ Software ]
[ Publishers's page ]
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 ]
Journal of Proteomics 86:27-42 (2013)
PREPRINT 12-023: [ Abstract ] [ Supplement ]
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 ]
Mol Biol Evol (2013) doi: 10.1093/molbev/mst209
PREPRINT 12-022: [ Abstract ] [ Supplement ]
[ Publishers's page ]
Searchability of central nodes in networks
Konstantin Klemm
J. Stat. Phys. 151:707-719 (2013)
PREPRINT 12-020: [ Abstract ] [ PDF ]
[ Publishers's page ]
J. Stat. Phys. 151:707-719 (2013)
PREPRINT 12-020: [ Abstract ] [ PDF ]
[ Publishers's page ]
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 ]
J.Exp.Zool.B Mol.Dev.Evol. 320: 35-46 (2012)
PREPRINT 12-005: [ Abstract ] [ PDF ]
[ Publishers's page ]
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 ]
J.Math.Biol. 66: 399-420 (2013)
PREPRINT 11-026: [ Abstract ] [ PDF ]
[ Publishers's page ]
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 ]
Theory in Biosciences 132:17-25 (2013)
PREPRINT 11-018: [ Abstract ] [ PDF ]
[ Publishers's page ]
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 ]
Mol. Phylogenet. Evol. 66(3):811-823 (2013)
PREPRINT 11-003: [ Abstract ] [ Supplement ]
[ Publishers's page ]
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. 69:313–319 (2013)
PREPRINT 09-028: [ Abstract ] [ PDF ] [ Supplement ]
Mol. Phylog. Evol. 69:313–319 (2013)
PREPRINT 09-028: [ Abstract ] [ PDF ] [ Supplement ]