Publications - Published papers

Please find below publications of our group. Currently, we list 560 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 2018

Identification and Characterization of Novel Conserved RNA Structures in \emphDrosophila

Kirsch, Rebecca and Seemann, Stefan Ernst and Ruzzo, Walter Larry and Cohen, Stephen Michael and Stadler, Peter F. and Gorodkin, Jan
BMC Genomics 19: 899
PREPRINT 18-090: [ Abstract ]
[ Publishers's page ]  paperID

Superbubbles revisited

Gärtner, Fabian and Müller, Lydia and Stadler, Peter F.
Alg. Mol. Biol. 13: 16
PREPRINT 18-089: [ Abstract ]
[ Publishers's page ]  paperID

Patterning the insect eye: from stochastic to deterministic mechanisms

Ebadi, Haleh and Perry, Michael and Short, Keith and Klemm, Konstantin and Desplan, Claude and Stadler, Peter F. and Mehta, Anita
PLoS Comp. Biol. 14: e1006363
PREPRINT 18-088: [ Abstract ]
[ Publishers's page ]  paperID

Phylogenetics beyond biology

Retzlaff, Nancy and Stadler, Peter F.
Th. Biosci. 137: 133-143
PREPRINT 18-087: [ Abstract ]
[ Publishers's page ]  paperID

Reconstructing Gene Trees From Fitch's Xenology Relation

Geiß, Manuela and Anders, John and Stadler, Peter F. and Wieseke, Nicolas and Hellmuth, Marc
J. Math. Biol. 77: 1459-1491
PREPRINT 18-086: [ Abstract ]
[ Publishers's page ]  paperID

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis

Kutsche, Lisa K. and Gysi, Deisy M. and Fallmann, Jörg and Lenk, Kerstin and Petri, Rebecca and Swiersy, Anka and Klapper, Simon D. and Pircs, Karolina and Stadler, Peter F. and Khattak, Shahryar and Jakobsson, Johan and Nowick, Katja and Busskamp, Volker
Cell Syst. 7: 438-452
PREPRINT 18-085: [ Abstract ]
[ Publishers's page ]  paperID

Beyond the 3' UTR binding–microRNA-induced protein truncation via DNA binding

von Brandenstein, Melanie and Bernhart, Stephan H. and Pansky, Andreas and Richter, Claudia and Kohl, Tobias and Deckert, Martina and Heidenreich, Axel and Stadler, Peter F. and Montesinos-Rongen, Manuel and Fries, Jochen W. U.
OncoTarget 9: 32855-32867
PREPRINT 18-084: [ Abstract ]
[ Publishers's page ]  paperID

Studying Language Evolution in the Age of Big Data

Bhattacharya, Tanmoy and Blasi, Damian and Croft, William and Cysouw, Michael and Hruschka, Daniel and Maddieson, Ian and Müller, Lydia and Retzlaff, Nancy and Smith, Eric and Stadler, Peter F. and Starostin, George and Youn, Hyejin
J. Language Evol. 3: 94-129
PREPRINT 18-083: [ Abstract ]
[ Publishers's page ]  paperID

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes

Waldl, Maria and Thiel, Bernhard and Ochsenreiter, Roman and Holzenleiter, Alexander and Araujo Oliveira, Joao Victor and Walter, Maria Emília M T and Wolfinger, Michael T and Stadler, Peter F
Genes 9: 372
PREPRINT 18-082: [ Abstract ]
[ Publishers's page ]  paperID

Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction

Kamm, Kai and Osigius, Hans-Jürgen and Stadler, Peter F. and DeSalle, Rob and Schierwater, Bernd
Sci. Rep. 11168: 8
PREPRINT 18-081: [ Abstract ]
[ Publishers's page ]  paperID

Split-Inducing Indels in Phylogenomic Analysis

Donath, Alexander and Stadler, Peter F.
Alg. Mol. Biol. 13: 12
PREPRINT 18-079: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]
[ Publishers's page ]  paperID

Cover-Encodings of Fitness Landscapes

Klemm, Konstantin and Mehta, Anita and Stadler, Peter F.
Bull. Math. Biol. 80: 2154-2176
PREPRINT 18-078: [ Abstract ]
[ Publishers's page ]  paperID

Towards Mechanistic Prediction of Mass Spectra Using Graph Transformation

Andersen, Jakob Lykke and Fagerberg, Rolf and Flamm, Christoph and Kianian, Rojin and Merkle, Daniel and Stadler, Peter F.
MATCH Commun. Math. Comput. Chem. 80: 705-731
PREPRINT 18-077: [ Abstract ]
[ Publishers's page ]  paperID

Rule Composition in Graph Transformation Models of Chemical Reactions

Andersen, Jakob Lykke and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.
MATCH Commun. Math. Comput. Chem. 80: 661-704
PREPRINT 18-076: [ Abstract ]
[ Publishers's page ]  paperID

Reachability, Connectivity, and Proximity in Chemical Spaces

Stadler, Bärbel M. R. and Stadler, Peter F.
MATCH Commun. Math. Comput. Chem. 80: 639-659
PREPRINT 18-075: [ Abstract ]
[ Publishers's page ]  paperID

Accurate Mapping of tRNA Reads

Hoffmann, Anne and Fallmann, Jörg and Vilardo, Elisa and Mörl, Mario and Stadler, Peter F. and Amman, Fabian
Bioinformatics 34: 1116-1124
PREPRINT 18-074: [ Abstract ]
[ Publishers's page ]  paperID

Inferring Phylogenetic Trees from the Knowledge of Rare Evolutionary Events

Hellmuth, Marc and Hernandez-Rosales, Maribel and Long, Yangjing and Stadler, Peter F.
J. Math. Biol. 76: 1623-1653
PREPRINT 18-073: [ Abstract ]
[ Publishers's page ]  paperID

Partially Local Multi-Way Alignments

Retzlaff, Nancy and Stadler, Peter F.
Math. Comp. Sci. 12: 207-234
PREPRINT 18-072: [ Abstract ]
[ Publishers's page ]  paperID

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors

Sutandy, F X Reymond and Ebersberger, Stefanie and Huang, Lu and Busch, Anke and Bach, Maximilian and Kang, Hyun Seo and Fallmann, Jörg and Maticzka, Daniel and Backofen, Rolf and Stadler, Peter F. and Zarnack, Kathi and Sattler, Michael and Legewie, Stefan and König, Julian
Genome Res. 28: 699-713
PREPRINT 18-071: [ Abstract ]
[ Publishers's page ]  paperID

Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa

Lokits, Alyssa D. and Indrischek, Henrike and Meiler, Jens and Hamm, Heidi E. and Stadler, Peter F.
BMC Evolutionary Biology 18: 51
PREPRINT 18-070: [ Abstract ]
[ Publishers's page ]  paperID

Finding the K Best Synthesis Plans

Fagerberg, Rolf and Flamm, Christoph and Kianian, Rojin and Merkle, Daniel and Stadler, Peter F.
J. Cheminformatics 10: 19
PREPRINT 18-069: [ Abstract ]
[ Publishers's page ]  paperID

Towards a Mechanistic Explanation of Phenotypic Evolution: The Need for a Theory of Theory Integration

Laubichler, Manfred and Prohaska, Sonja J. and Stadler, Peter F.
J. Exp. Zool.: Mol. Dev. Evol. 330: 5-14
PREPRINT 18-068: [ Abstract ]
[ Publishers's page ]  paperID

A Short Note on Undirected Fitch Graphs

Hellmuth, Marc and Long, Yangjing and Geiß, Manuela and Stadler, Peter F.
Art Discr. Appl. Math. 1: P1.08
PREPRINT 18-067: [ Abstract ]
[ Publishers's page ]  paperID

The Fungal snoRNAome

Canzler, Sebastian and Stadler, Peter F. and Schoor, Jana
RNA 24: 342-360
PREPRINT 18-066: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

Time-Consistent Reconciliation Maps and Forbidden Time Travel

Nojgaard, Nikolai and Geiß, Manuela and Merkle, Daniel and Stadler, Peter F. and Wieseke, Nicolas and Hellmuth, Marc
Alg. Mol. Biol. 13: 2
PREPRINT 18-065: [ Abstract ]
[ Publishers's page ]  paperID

Detailed Secondary Structure Models of Invertebrate 7SK RNAs

Yazbeck, Ali and Tout, Kifah R. and Stadler, Peter F.
RNA Biology 15: 158-164
PREPRINT 18-064: [ Abstract ]
[ Publishers's page ]  paperID

Temporal Ordering of Substitutions in RNA Evolution: Uncovering the Structural Evolution of the Human Accelerated Region 1

Walter Costa, Maria Beatriz and Siederdissen, Christian and Tulpan, Dan and Stadler, Peter F. and Nowick, Katja
J. Theor. Biol. 438: 143-150
PREPRINT 18-063: [ Abstract ]
[ Publishers's page ]  paperID

Comparative RNA Genomics

Backofen, Rolf and Gorodkin, Jan and Hofacker, Ivo L. and Stadler, Peter F.
Comparative Genomics (Methods in Molecular Biology)
PREPRINT 18-062: [ Abstract ]
[ Publishers's page ]  paperID

Gene Phyologenies and Orthologous Groups

Setubal, Joao C. and Stadler, Peter F.
Comparative Genomics (Methods in Molecular Biology)
PREPRINT 18-061: [ Abstract ]
[ Publishers's page ]  paperID

Axiomatic Characterization of Transit Functions of Hierarchies

Changat, Manoj and Nezhad, Ferdoos Hossein and Stadler, Peter F.
Ars Math. Contemp. 14: 117-128
PREPRINT 18-060: [ Abstract ]
[ Publishers's page ]  paperID

Coordinate systems for supergenomes

Gärtner, Fabian and Siederdissen, Christian and Müller, Lydia and Stadler, Peter F.
Algorithms for Molecular Biology 13 (1): 15
PREPRINT 18-057: [ Abstract ]
[ Publishers's page ]  paperID

RNApuzzler: Efficient Outerplanar Drawing of RNA-Secondary Structures

Wiegreffe, Daniel and Alexander, Daniel and Stadler, Peter F. and Zeckzer, Dirk
Bioinformatics (2018): bty817
PREPRINT 18-056: [ Abstract ]
[ Publishers's page ]  paperID

Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes

Skrzypczyk, Aniela and Kehr, Stephanie and Krystel, Ilona and Bernhart, Stephan H and Giri, Shibashish and Bader, Augustinus and Stadler, Peter F
Stem Cells International, vol. 2018, Article ID 5692840, 15 pages
PREPRINT 18-055: [ Abstract ]
[ Publishers's page ]  paperID

Nonprotein-Coding RNAs as Regulators of Development in Tunicates

Velandia-Huerto, Cristian A and Brown, Federico D and Gittenberger, Adriaan and Stadler, Peter F and Bermúdez-Santana, Clara I
Marine Organisms as Model Systems in Biology and Medicine(2018)
PREPRINT 18-053: [ Abstract ]
[ Publishers's page ]  paperID

The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments

Daniel Wiegreffe, and Lydia Müller, and Jens Steuck, and Dirk Zeckzer, and Peter F. Stadler,
BMC Research Notes
PREPRINT 18-052: [ Abstract ]
[ Publishers's page ]  paperID

Analyzing Histone Modifications Using Tiled Binned Clustering and 3D Scatter Plots

Dirk Zeckzer, and Daniel Wiegreffe, and Lydia Müller,
Journal of WSCG 26
PREPRINT 18-051: [ Abstract ]
[ Publishers's page ]  paperID

Customized biomedical informatics

Singh, Abhishek Narain
Big Data Analytics 3 (1): 6
PREPRINT 18-049: [ Abstract ]
[ Publishers's page ]  paperID

A translational silencing function of MCPIP1/Regnase-1 specified by the target site context

Behrens, Gesine and Winzen, Reinhard and Rehage, Nina and Dörrie, Anneke and Barsch, Monika and Hoffmann, Anne and Hackermüller, Jörg and Tiedje, Christopher and Heissmeyer, Vigo and Holtmann, Helmut
Nucleic Acids Research: gky106
PREPRINT 18-046: [ Abstract ]
[ Publishers's page ]  paperID

Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA

Rehage, Nina and Davydova, Elena and Conrad, Christine and Behrens, Gesine and Maiser, Andreas and Stehklein, Jenny E. and Brenner, Sven and Klein, Juliane and Jeridi, Aicha and Hoffmann, Anne and Lee, Eunhae and Dianzani, Umberto and Willemsen, Rob and Feederle, Regina and Reiche, Kristin and Hackermüller, Jörg and Leonhardt, Heinrich and Sharma, Sonia and Niessing, Dierk and Heissmeyer, Vigo
Nature Communications 9: 299
PREPRINT 18-045: [ Abstract ]
[ Publishers's page ]  paperID