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 2019

Improved Annotation of Protein-Coding Genes Boundaries in Metazoan Mitochondrial Genomes

Donath, Alexander and Jühling, Frank and Al-Arab, Marwa and Berhart, Stephan H. and Reihardt, Franziska and Stadler, Peter F and Middendorf, Martin and Bernt, Matthias
Nucleic Acids Res. 47: 10543-10552
PREPRINT 19-028: [ Abstract ]
[ Publishers's page ]  paperID

Automatic Curation of Large Comparative Animal MicroRNA Data Sets

Yazbeck, Ali M. and Stadler, Peter F. and Tout, Kifah and Fallmann, Jörg
Bioinformatics 35: 4553-4559
PREPRINT 19-027: [ Abstract ]  [ Supplement ]
[ Publishers's page ]  paperID

DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation

Uxa, Sigrid and Bernhart, Stephan H and Mages, Christina and Fischer, Martin and Kohler, Robin and Hoffmann, Steve and Stadler, Peter F. and Engeland, Kurt and Müller, Gerd A.
Nucleic Acids Res. 47: 9087-9103
PREPRINT 19-026: [ Abstract ]
[ Publishers's page ]  paperID

A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro

Kirsch, Rebecca and Olzog, Vanessa Janett and Bonin, Sonja and Weinberg, Christina E and Betat, Heike and Stadler, Peter F and Mörl, Mario
BioTechniques 67: 178-183
PREPRINT 19-025: [ Abstract ]
[ Publishers's page ]  paperID

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods

Drozdova, Polina and Rivarola-Duarte, Lorena and Bedulina, Daria and Schreiber, Stephan and Axenov-Gribanov, Denis and Gurkov, Anton and Shatilina, Zhanna and Vereshchagina, Kseniya and Lubyaga, Yulia and Madyarova, Ekaterina and Otto, Christian and Jühling, Frank and Busch, Wibke and Jakob, Lena and Lucassen, Magnus and Sartoris, Franz Josef and Hackermüller, Jörg and Hoffmann, Steve and Pörtner, Hans-Otto and Luckenbach, Till and Timofeyev, Maxim and Stadler, Peter F.
BMC Genomics 20: 712
PREPRINT 19-024: [ Abstract ]
[ Publishers's page ]  paperID

Selection Pressures on RNA Sequences and Structures

Nowick, Katja and Walter Costa, Maria Beatriz and Siederdissen, Christian and Stadler, Peter F.
Evol. Bioinf. 15: 1-4
PREPRINT 19-023: [ Abstract ]
[ Publishers's page ]  paperID

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies

Garcia Sousa, Isabel and Rodrigues Simi, Kelly Cristina and Almo, Manuela and Gomes Bezerra, Maryani Andressa and Doose, Gero and Raiol, Tainá a and Stadler, Peter F. and Hoffmann, Steve and Queiroz Maranhao, Andréa and Macedo Brigido, Marcelo
BMC Genomics 20: 593
PREPRINT 19-022: [ Abstract ]
[ Publishers's page ]  paperID

The exploration of the chemical space and its three historical regimes

Llanos, Eugenio J. and Leal, Wilmer and Luu, Duc H. and Jost, Jürgen and Stadler, Peter F. and Restrepo, Guillermo
Proc. Natl. Acad. Sci. USA 116: 12660-12665
PREPRINT 19-021: [ Abstract ]
[ Publishers's page ]  paperID

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species

Gurkov, Anton and Rivarola-Duarte, Lorena and Bedulina, Daria and Fernández Casas, Irene and Michael, Hendrik and Drozdova, Polina and Nazarova, Anna and Govorukhina, Ekaterina and Timofeyev, Maxim and Stadler, Peter F and Luckenbach, Till
BMC Evol. Biol. 19: 138
PREPRINT 19-020: [ Abstract ]
[ Publishers's page ]  paperID

The RNA workbench 2.0: next generation RNA data analysis

Fallmann, Jörg and Videm, Pavankumar and Bagnacani, Andrea and Batut, Bérénice and Doyle, Maria and Klingström, Tomas and Eggenhofer, Florian and Stadler, Peter F. and Backofen, Rolf and Grüning, Björn
Nucleic Acids Res. 47: W511-W515
PREPRINT 19-019: [ Abstract ]
[ Publishers's page ]  paperID

Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods

Drozdova, Polina and Bedulina, Daria and Madyarova, Ekaterina and Rivarola-Duarte, Lorena and Schreiber, Stephan and Stadler, Peter F. and Luckenbach, Till and Timofeyev, Maxim
Sci. Rep. 9: 8907
PREPRINT 19-017: [ Abstract ]
[ Publishers's page ]  paperID

Best Match Graphs

Geiß, Manuela and Chávez, Edgar and González Laffitte, Marcos and Lopez Sánchez, Alitzel and Stadler, Bärbel M R and Valdivia, Dulce I. and Hellmuth, Marc and Hernández Rosales, Maribel and Stadler, Peter F
J. Math. Biol. 78: 2015-2057
PREPRINT 19-016: [ Abstract ]
[ Publishers's page ]  paperID

Exploring plant sesquiterpene diversity by generating chemical networks

da Silva, Waldeyr M. C. and Andersen, Jakob Lykke and Holanda, Maristela and Walter, Maria Emília M. T. and Brigido, Marcel M. and Stadler, Peter F. and Flamm, Christoph
Processes 7: 240
PREPRINT 19-015: [ Abstract ]
[ Publishers's page ]  paperID

Direct Superbubble Detection

Gärtner, Fabian and Stadler, Peter F.
Algorithms 12: 81
PREPRINT 19-014: [ Abstract ]
[ Publishers's page ]  paperID

Ryuto: network-flow based transcriptome reconstruction

Gatter, Thomas and Stadler, Peter F.
BMC Bioinformatics 20: 190
PREPRINT 19-013: [ Abstract ]
[ Publishers's page ]  paperID

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

Lopez, Cristina and Kleinheinz, Kortine and Aukema, Sietse and Rohde, Marius and Bernhart, Stephan H. and Wagener, Rabea and Hübschmann, Daniel and Toprak, Umut and Raimondi, Francesco and Kreuz, Markus and Waszak, Sebastian and Huang, Zhiqin and Sieverling, Lina and Paramasivam, Nagarajan and Seufert, Julian and Sungalee, Stephanie and Russell, Robert and Bausinger, Julia and Kretzmer, Helene and Ammerpohl, Ole and Bergman, Anke and Binder, Hans and Borkhardt, Arndt and Brors, Benedikt and Claviez, Alexander and Doose, Gero and Feuerbach, Lars and Haake, Andrea and Hansmann, Martin-Leo and Höll, Jessica and Hummel, Michael and Korbel, Jan and Lawerenz, Christian and Lenze, Dido and Radlwimmer, Bernhard and Richter, Julia and Rosenstiel, Philip and Rosenwald, Andreas and Schilhabel, Markus and Stein, Harald and Stilgenbauer, Stephan and Stadler, Peter F. and Szczepanowski, Monika and Weniger, Marc and Zapatka, Marc and Eils, Roland and Lichter, Peter and Loeffler, Markus and Moeller, Peter and Trümper Lorenz, and Klapper, Wolfram and Hoffmann, Steve and Kuppers, Ralf and Burkhardt, Birgit and Schlesner, Matthias and Siebert, Reiner
Nature Comm. 10: 1459
PREPRINT 19-012: [ Abstract ]
[ Publishers's page ]  paperID

Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows

Andersen, Jakob Lykke and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.
IEEE/ACM Trans. Comp. Biol. 16: 510-523
PREPRINT 19-011: [ Abstract ]
[ Publishers's page ]  paperID

A General Framework for Exact Partially Local Alignments

Kirchner, Falco and Retzlaff, Nancy and Stadler, Peter F.
PREPRINT 19-010: [ Abstract ]
[ Publishers's page ]  paperID

SSS-test: A Novel Test for Detecting Positive Selection on RNA Secondary Structure

Walter Costa, Maria Beatriz and Siederdissen, Christian and Dunjic, Marko and Stadler, Peter F. and Nowick, Katja
BMC Bioinformatics 20: 151
PREPRINT 19-009: [ Abstract ]
[ Publishers's page ]  paperID

Divergent evolution in the genomes of closely-related lacertids, Lacerta viridis and L. bilineata and implications for speciation

Kolora, Sree Rohit Raj and Weigert, Anne and Saffari, Amin and Kehr, Stephanie and Walter Costa, Maria and Spröer, Cathrin and Indrischek, Henrike and Chintalapati, Manjusha and Lohse, Konrad and Doose, Gero and Overmann, Jörg and Bunk, Boyke and Bleidorn, Christoph and Grimm-Seyfarth, Annegret and Henle, Klaus and Nowick, Katja and Faria, Rui and Stadler, Peter F and Schlegel, Martin
GigaScience 8: giy160
PREPRINT 19-008: [ Abstract ]
[ Publishers's page ]  paperID

RNAcentral: a hub of information for non-coding RNA sequences

The RNA Central Consortium,
Nucleic Acids Res. 47: D221-D229
PREPRINT 19-007: [ Abstract ]
[ Publishers's page ]  paperID

Axiomatic Characterization of Transit Functions of Weak Hierarchies

Changat, Manoj and Narasimha-Shenoi, Prasanth G. and Stadler, Peter F.
Art Discr. Appl. Math. 2: P1.01
PREPRINT 19-006: [ Abstract ]
[ Publishers's page ]  paperID

Evolving methods for rational de novo design of functional RNA molecules

Stefan Hammer, and Christian Günzel, and Mario Mörl, and Sven Findeiß,
Methods 161: 54 - 63
PREPRINT 19-003: [ Abstract ]
[ Publishers's page ]  paperID