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:

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Publications of the bioinformatics group 2015

The ViennaRNA web services.

Gruber, Andreas R. and Bernhart, Stephan H. and Lorenz, Ronny
Methods in molecular biology (Clifton, N.J.) 1269: 307--326
PREPRINT 18-034: [ Abstract ]
[ Publishers's page ]

The PCBP1 gene encoding poly(rC) binding protein I is recurrently mutated in Burkitt lymphoma.

Wagener, Rabea and Aukema, Sietse M. and Schlesner, Matthias and Haake, Andrea and Burkhardt, Birgit and Claviez, Alexander and Drexler, Hans G. and Hummel, Michael and Kreuz, Markus and Loeffler, Markus and Rosolowski, Maciej and L\'opez, Cristina and Möller, Peter and Richter, Julia and Rohde, Marius and Betts, Matthew J. and Russell, Robert B. and Bernhart, Stephan H. and Hoffmann, Steve and Rosenstiel, Philip and Schilhabel, Markus and Szczepanowski, Monika and Trümper, Lorenz and Klapper, Wolfram and Siebert, Reiner and ICGC MMML-Seq-Project, and ``Molecular Mechanisms in Malignant Lymphomas'' Network Project of the Deutsche Krebshilfe,
Genes, chromosomes \& cancer 54 (9): 555--564
PREPRINT 18-033: [ Abstract ]
[ Publishers's page ]

MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells.

Doose, Gero and Haake, Andrea and Bernhart, Stephan H. and L\'opez, Cristina and Duggimpudi, Sujitha and Wojciech, Franziska and Bergmann, Anke K. and Borkhardt, Arndt and Burkhardt, Birgit and Claviez, Alexander and Dimitrova, Lora and Haas, Siegfried and Hoell, Jessica I. and Hummel, Michael and Karsch, Dennis and Klapper, Wolfram and Kleo, Karsten and Kretzmer, Helene and Kreuz, Markus and Küppers, Ralf and Lawerenz, Chris and Lenze, Dido and Loeffler, Markus and Mantovani-Löffler, Luisa and Möller, Peter and Ott, German and Richter, Julia and Rohde, Marius and Rosenstiel, Philip and Rosenwald, Andreas and Schilhabel, Markus and Schneider, Markus and Scholz, Ingrid and Stilgenbauer, Stephan and Stunnenberg, Hendrik G. and Szczepanowski, Monika and Trümper, Lorenz and Weniger, Marc A. and ICGC MMML-Seq Consortium, and Hoffmann, Steve and Siebert, Reiner and Iaccarino, Ingram
Proceedings of the National Academy of Sciences of the United States of America 112 (38): E5261--E5270
PREPRINT 18-032: [ Abstract ]
[ Publishers's page ]

The Relativity of Biological Function

Laubichler, Manfred D. and Stadler, Peter F. and Prohaska, Sonja J. and Nowick, Katja
Th. Biosci. 143: 143-147
PREPRINT 16-011:
[ Publishers's page ]

Linking differential DNA methylation in gene regions with the mutational landscape of Burkitt lymphoma

Kretzmer, Helene and Bernhart, Stephan H. and Wang, Wei and Haake, Andrea and Weniger, Marc A. and Bergmann, Anke K. and Betts, Matthew J. Betts and Carrillo-de-Santa-Pau, Enrique and Doose, Gero and Gutwein, Jana and Richter, Julia and Hovestadt, Volker and Huang, Bingding and Rico, Daniel and Jühling, Frank and Kolarova, Julia and Lu, Qianhao and Otto, Christian and Wagner, Rabea and Arnolds, Judith and Burkhardt, Birgit and Claviez, Alexander and Drexler, Hans G. and Eberth, Sonja and Eils, Roland and Flicek, Paul and Haas, Siegfried and Hummel, Michael and Karsch, Dennis and Kerstens, Hinrik H. D. and Klapper, Wolfram and Kreuz, Markus and Lawerenz, Chris and Lenze, Dido and Löffler, Markus and L\'opez, Cristina and MacLeod, Roderick A. F. and Martens, Joost H. A. Martens and Martín-Subero, José Ignacio and Möller, Peter and Nagel, Inga and Picelli, Simone and Vater, Inga and Rohde, Marius and Rosenstiel, Philip and Rosolowski, Maciej and Russell, Robert B. and Schilhabel, Markus and Schlesner, Matthias and Stadler, Peter F. and Szczepanowski, Monika and Trümper, Lorenz and Stunnenberg, Hendrik G. and Küppers, Ralf and Ammerpohl, Ole and Lichter, Peter and Siebert, Reiner and Hoffmann, Steve and Radlwimmer, Bernhard
Nature Gen. 47: 1316-1325
PREPRINT 16-010:
[ Publishers's page ]

Model guided identification and therapeutic implications of an ammonia sink mechanism

Ghallab, A and Henkel, S G and Cellière, G and Driesch, D and Hoehme, S and Hofmann, U and Zellmer, S and Godoy, P and Sachinidis, A and Blaszkewicz, M and Reif, R. and Marchan, R and Kuepfer, L. and Häussinger, D and Drasdo, D and Gebhardt, R. and Hengstler, J G
J. Hepatology
PREPRINT 16-008:
[ Publishers's page ]

The use of RNA 3D modules can enhance genome-wide predictions of RNA 2D structure

Theis, Corinna and Zirbel, Craig and Siederdissen, Christian and Anthon, Christian and Hofacker, Ivo L and Nielsen, Henrik and Gorodkin, Jan
PLOS One 10: e0139900
PREPRINT 16-007:
[ Publishers's page ]

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

Will, Sebastian and Otto, Christina and Miladi, Milad and M\
Bioinformatics 31: 2489--2496
PREPRINT 16-006:
[ Publishers's page ]

Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction

Will, Sebastian and Jabbari, Hosna
Algorithms in Bioinformatics WABI '15
PREPRINT 16-005:
[ Publishers's page ]

Mereology of quantitative structure-activity relationships models

Restrepo, Guillermo and Harr\e
HYLE Int J Phil Chem 21: 19--38
PREPRINT 16-004:
[ Publishers's page ]

Gene-pseudogene evolution: a probabilistic approach

Mahmudi, O and Sennblad, B and Arvestad, L and Nowick, K and Lagergren, J
BMC Genomics 16: S12
PREPRINT 16-003:
[ Publishers's page ]

A novel method to analyze 5-hydroxymethylcytosine in CpG sequences using maintenance DNA methyltransferase, DNMT1

Takahashi, Saori and Suetake, Isao and Engelhardt, Jan and Tajima, Shoji
FEBS Open Bio 5: 741--747
PREPRINT 15-063:
[ Publishers's page ]

Evolution of RNA-Based Networks

Stadler, Peter F.
Quasispecies: From Theory to Experimental Systems
PREPRINT 15-062:
[ Publishers's page ]

SHAPE directed RNA folding

Lorenz, Ronny and Luntzer, Dominik and Hofacker, Ivo L. and Stadler, Peter F. and Wolfinger, Michael T.
PREPRINT 15-061:
[ Publishers's page ]

Improvement of RNA structure probabilities by sequence extensions using RNAcop

Hecker, Nikolai and Christensen-Dalsgaard, Mikkel and Seemann, Stefan E. and Havgaard, Jakob Hull and Stadler, Peter F. and Hofacker, Ivo L. and Nielsen, Henrik and Gorodkin, Jan
Nucleic Acids Res.
PREPRINT 15-060:
[ Publishers's page ]

Knowledge-based reasoning to annotate noncoding RNA using multi-agent system

Arruda, Wosley C and Souza, Daniel S. and Ralha, Célia G and Walter, Maria Emila M. T. and Raiol, Tainá and Brigido, Marcelo M. and Stadler, Peter F.
J. Bioinf. Comp. Biol. :
PREPRINT 15-059:
[ Publishers's page ]

Towards a Comprehensive Picture of Alloacceptor tRNA Remolding in Metazoan Mitochondrial Genomes

Sahyoun, Abdullah H. and Hölzer, Martin and Jühling, Frank and Siederdissen, Christian and Al-Arab, Marwa and Tout, Kifah and Marz, Manja and Middendorf, Martin and Stadler, Peter F. and Bernt, Matthias
Nucleic Acids Res.
PREPRINT 15-058:
[ Publishers's page ]

Spiders can be recognized by counting their legs

Berkemer, Sarah and Chaves, Ricardo and Fritz, Adrian and Hellmuth, Marc and Hernandez-Rosales, Maribel and Stadler, Peter F.
Math. Comp. Sci.
PREPRINT 15-057:
[ Publishers's page ]

Evolution of the unspliced transcriptome

Engelhardt, Jan and Stadler, Peter F.
BMC Evol Biol 15: 166
PREPRINT 15-056:
[ Publishers's page ]

Third Report on Chicken Genes and Chromosomes 2015

Schmid, M and Smith, J and Burt, D W and Aken, B L and Antin, P B and Archibald, AL and Ashwell, C and Blackshear, P J and Boschiero, C and Brown, CT and Burgess, S C and Cheng, H H and Chow, W and Coble, D J and Cooksey, A and Crooijmans, R P and Damas, J and Davis, R V and Koning, D J and Delany, M E and Derrien, T and Desta, T T and Dunn, I C and Dunn, M and Ellegren, H and Eöry, L and Erb, I and Farré, M and Fasold, M and Fleming, D and Flicek, P and Fowler, K E and Frésard, L and Froman, D P and Garceau, V and Gardner, P P and Gheyas, A A and Griffin, D K and Groenen, M A and Haaf, T and Hanotte, O and Hart, A and Häsler, J and Hedges, S B and Hertel, J and Howe, K and Hubbard, A and Hume, D A and Kaiser, P and Kedra, D and Kemp, S J and Klopp, C and Kniel, K E and Kuo, R and Lagarrigue, S and Lamont, S J and Larkin, D M and Lawal, R A and Markland, S M and McCarthy, F and McCormack, H A and McPherson, M C and Motegi, A and Muljo, S A and Münsterberg, A and Nag, R and Nanda, I and Neuberger, M and Nitsche, A and Notredame, C and Noyes, H and O'Connor, R and O'Hare, EA and Oler, A J and Ommeh, S C and Pais, H and Persia, M and Pitel, F and Preeyanon, L and Prieto, P and Pritchett, E M and Rhoads, D D and Robinson, C M and Romanov, M N and Rothschild, M and Roux, P F and Schmidt, C J and Schneider, A S and Schwartz, M G and Searle, S M and Skinner, M A and Smith, C A and Stadler, P F and Steeves, T E and Steinlein, C and Sun, L and Takata, M and Ulitsky, I and Wang, Q and Wang, Y and Warren, W C and Wood, J M and Wragg, D and Zhou, H
Cytogenet Genome Res 145: 78-179
PREPRINT 15-055:
[ Publishers's page ]

In silico Support for Eschenmoser's Glyoxylate Scenario

Andersen, Jakob L. and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.
Israel J. Chem. 55: 919-933
PREPRINT 15-054:
[ Publishers's page ]

Unusual Novel snoRNA-like RNAs in Drosophila melanogaster

Angrisani, Alberto and Tafer, Hakim and Stadler, Peter F. and Furia, Maria
ncRNA 1: 139-150
PREPRINT 15-053:
[ Publishers's page ]

Kiwi genome provides insights into nocturnal adaptation

Le Duc, Diana and Renaud, Gabriel and Krishnan, Arunkumar and Sällman Almén, Markus and Huynen, Leon and Prohaska, Sonja J. and Ongyerth, Matthias and Bitarello, Bárbara D. and Schiöth, Helgi B. and Hofreiter, Michael and Stadler, Peter F. and Prüfer, Kay and Lambert, David and Kelso, Janet and Schöneberg, Torsten
Genome Biology 16: 147
PREPRINT 15-052:
[ Publishers's page ]

Developmentally regulated expression and expression strategies of Drosophila snoRNAs

Angrisani, Alberto and Tafer, Hakim and Stadler, Peter F and Furia, Maria
Insect Biochem Mol Biol 61: 69-78
PREPRINT 15-051:
[ Publishers's page ]

Conservation and Losses of Non-Coding RNAs in Avian Genomes

Fasold, Mario and Burge, Sarah W. and Ninova, Maria and Hertel, Jana and Kehr, Stephanie and Steeves, Tammy E. and Griffiths-Jones, Sam and Stadler, Peter F.
PLoS One 10: e0121797
PREPRINT 15-050:
[ Publishers's page ]

A Simple Data-Adaptive Probabilistic Variant Calling Model

Hoffmann, Steve and Stadler, Peter F. and Strimmer, Korbinian
Alg. Mol. Biol. 10: 10
PREPRINT 15-049:
[ Publishers's page ]

Indications for potential parent of origin effects within the FTO gene

Liu, Xuanshi and Scholz, Markus and Tönjes, Anke and Stumvoll, Michael and Stadler, Peter F. and Böttcher, Yvonne
PLoS ONE 10: e0119206
PREPRINT 15-048:
[ Publishers's page ]

Prevalent and distinct spliceosomal 3'-end processing mechanisms for fungal telomerase RNA

Qi, X and Rand, D P and Podlevsky, J D and Li, Y and Mosig, A and Stadler, P F and Chen, J J
Nat Commun. 6: 6105
PREPRINT 15-047: [ Abstract ]
[ Publishers's page ]

The relaxed square property

Hellmuth, Marc and Marc, Tilen and Ostermeier, Lydia and Stadler, Peter F.
Australasian Journal of Combinatorics Vol 62: No. 3 240-770 (2015)
PREPRINT 15-045: [ Abstract ]
[ Publishers's page ]  paperID

The Grid Property and Product-Like Hypergraphs

Ostermeier, Lydia and Stadler, Peter F.
Graphs and Combinatorics 31(3): 757-770 (2015)
PREPRINT 15-044: [ Abstract ]  [ PDF ]
[ Publishers's page ]

Algebraic dynamic programming over general data structures

Christian Höner zu Siederdissen, Sonja J. Prohaska, Peter F. Stadler
BMC Bioinformatics 16: 19:S2
PREPRINT 15-043: [ Abstract ]
[ Publishers's page ]

Predicting RNA 3D structure using a coarse-grain helix-centered model

Peter Kerpedjiev, Christian Höner zu Siederdissen, Ivo L. Hofacker
RNA 2015. 21: 1110-1121
PREPRINT 15-042: [ Abstract ]
[ Publishers's page ]

Anomalous scaling in an age-dependent branching model

Stephanie Keller-Schmidt, Murat Tuğrul, Víctor M. Eguíluz, Emilio Hernández-García, and Konstantin Klemm
Physical Review E 91.2 (2015): 022803.
PREPRINT 15-041:
[ Publishers's page ]

Design criteria for synthetic riboswitches acting on transcription

Manja Wachsmuth, Gesine Domin, Ronny Lorenz, Robert Serfling, Sven Findeiß, Peter F Stadler & Mario Mörl
RNA Biology 12: 221-231 (2015)
PREPRINT 15-040: [ Abstract ]
[ Publishers's page ]  paperID

Phylogenomics with paralogs

Hellmuth, Marc and Wieseke, Nicolas and Lechner, Marcus and Lenhof, Hans-Peter and Middendorf, Martin and Stadler, Peter F.
Proceedings of the National Academy of Sciences USA
PREPRINT 15-039: [ Abstract ]
[ Publishers's page ]  paperID

Processed Small RNAs in Archaea and BHB Elements

Sarah J. Berkemer, Christian Höner zu Siederdissen, Fabian Amman, Axel Wintsche, Sebastian Will, Ivo L. Hofacker, Sonja J. Prohaska, Peter F. Stadler
GCB, Vol. 1, No. 1 (2015): e18
PREPRINT 15-038: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]

The Expansion of Animal MicroRNA Families Revisited

Jana Hertel, Peter F. Stadler
Life (ISSN 2075-1729)
PREPRINT 15-037: [ Abstract ]  [ Supplement ]  [ Software ]
[ Publishers's page ]  paperID

The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer

Heike Betat, Tobias Mede, Sandy Tretbar, Lydia Steiner, Peter F. Stadler, Mario Mörl, and Sonja J. Prohaska
Nucleic Acids Res. 2015 Jun 27. pii: gkv631
PREPRINT 14-017: [ Abstract ]  [ Supplement ]
[ Publishers's page ]

Phylogenetics from Paralogs

Marc Hellmuth, Nicolas Wieseke, Markus Lechner, Hans-Peter Lenhof, Martin Middendorf, Peter F. Stadler
Proc. Natl. Acad. Sci. USA 112:2058-2063
PREPRINT 14-004: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]

Comparison of splice sites reveals that long non-coding RNAs are evolutionarily well conserved

Anne Nitsche, Dominic Rose, Mario Fasold, Kristin Reiche, and Peter F. Stadler
RNA May 2015 21: 801-812; Published in Advance March 23, 2015
PREPRINT 12-001: [ Abstract ]  [ Supplement ]
[ Publishers's page ]