Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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Recent Publications

All our recent publications (from this year) are on display right here on this page. For older publications choose a period from the menu.

Preliminary versions of most of our work can be found on our pre-print server.

2020

20-001
Doo Nam Kim, Bernhard C. Thiel, Tyler Mrozowich, Scott P. Hennelly, Ivo L. Hofacker, Trushar R. Patel, Karissa Y. Sanbonmatsu
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution
Nature Communications volume 11, Article number: 148 (2020), doi:10.1038/s41467-019-13942-4
20-002
Kamonpan Sanachai, Panupong Mahalapbutr, Kiattawee Choowongkomon, Rungtiva P. Poo-arporn, Peter Wolschann, Thanyada Rungrotmongko
Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases
ACS Omega 2020, 5, 1, 369-377, 2020, doi:10.1021/acsomega.9b0280076
20-003
Helmut Viernstein, Peter Wolschann
Cyclodextrin inclusion complexation and pharmaceutical applications
ScienceAsia 46 (2020): 254–262, doi:10.2306/scienceasia1513-1874.2020.048
20-004
Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, and Rolf Backofen
The locality dilemma of Sankoff-like RNA alignments
Bioinformatics, 36:i242–i250, 2020, doi:10.1093/bioinformatics/btaa431
20-005
Denisa Petrácková, Mariam R Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Dilip Kumar, Jakub Drzmísek, Ivo L. Hofacker, Maria Eugenia Rodriguez, and Branislav Vecerek
Transcriptional profiling of human macrophages during infection with bordetella pertussis
RNA biology, 17:731–742, 2020, doi:10.1080/15476286.2020.1727694
20-006
Keating, Sarah M et al (+140 Coauthors)
SBML Level 3: an extensible format for the exchange and reuse of biological models
Mol Sys Biol 16(8):e9110 (2020), doi:10.15252/msb.20199110
20-007
Ronny Lorenz Christoph Flamm, Ivo L Hofacker Peter F Stadler
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) Vol 3, pp 23-31, 2020, ISBN: 978-989-758-398-8, doi:10.5220/0008916600230031
20-008
Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F Stadler
Generic Context-Aware Group Contributions
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020, doi:10.1109/TCBB.2020.2998948
20-009
Christida E. Wastika, Hayato Harima, Michihito Sasaki, Bernard M. Hang'ombe, Yuki Eshita, Yongjin Qiu, William W. Hall, Michael T. Wolfinger, Hirofumi Sawa, Yasuko Orba
Discoveries of exoribonuclease-resistant structures of insect-specific flaviviruses isolated in Zambia
Viruses 12(9):1017 (2020), doi:10.3390/v12091017
20-010
Elisabeth Sonnleitner, Petra Pusic, Michael T. Wolfinger, Udo Bläsi
Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq
Front. Microbiol. 11:1001 (2020), doi:10.3389/fmicb.2020.01001
20-011
Balogh, G., Bernhart, S. H., Stadler, P. F. & Schor, J.
A probabilistic version of Sankoff's maximum parsimony algorithm
Journal of Bioinformatics and Computational Biology (JBCB). 18, 1, 19 S., 2050004, doi:10.1142/S0219720020500043
20-012
Nitsche, A., Arnold, C., Ueberham, U., Reiche, K., Fallmann, J., Hackermueller, J., Horn, F., Stadler, P. F. & Arendt, T.
Alzheimer-related genes show accelerated evolution
Molecular Psychiatry. 7 S., doi:10.1038/s41380-020-0680-1
20-013
Hordijk, W., Kauffman, S. A. & Stadler, P. F.
Average Fitness Differences on NK Landscapes
Theory in Biosciences. 139, 1, S. 1-7 7 S., doi:10.1007/s12064-019-00296-0
20-014
Geiss, M., Gonzalez Laffitte, M. E., Lopez Sanchez, A., Valdivia, D. I., Hellmuth, M., Hernandez Rosales, M. & Stadler, P. F.
Best match graphs and reconciliation of gene trees with species trees
Journal of Mathematical Biology. 37 S., doi:10.1007/s00285-020-01469-y
20-015
Hellmuth, M., Geiss, M. & Stadler, P. F.
Complexity of modification problems for reciprocal best match graphs
Theoretical Computer Science. 809, S. 384-393 10 S., doi:10.1016/j.tcs.2019.12.033
20-016
Hotarat, W., Nutho, B., Wolschann, P., Rungrotmongkol, T. & Hannongbua, S.
Delivery of Alpha-Mangostin Using Cyclodextrins through a Biological Membrane: Molecular Dynamics Simulation
Molecules. 25, 11, 17 S., 2532, doi:10.3390/molecules25112532
20-017
Breitfeld, J., Kehr, S., Mueller, L., Stadler, P. F., Boettcher, Y., Blueher, M., Stumvoll, M. & Kovacs, P.
Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity
Frontiers in Endocrinology. 11, 18 S., 138, doi:10.3389/fendo.2020.00138
20-018
Long, Y. & Stadler, P.
Exact-2-relation graphs
Discrete Applied Mathematics. 285, S. 212-226 15 S., doi:10.1016/j.dam.2020.05.015
20-019
Stadler, P. F., Geiss, M., Schaller, D., Sanchez, A. L., Laffitte, M. G., Valdivia, D. I., Hellmuth, M. & Rosales, M. H.
From pairs of most similar sequences to phylogenetic best matches
Algorithms for Molecular Biology. 15, 1, 20 S., 5., doi:10.1186/s13015-020-00165-2
20-020
Vilardo, E., Amman, F., Toth, U., Kotter, A., Helm, M. & Rossmanith, W.
Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B
Nucleic Acids Research. 48, 11, S. 6157-6169 13 S., doi:10.1093/nar/gkaa353
20-021
Hellmuth, M., Seemann, C. R. & Stadler, P. F.
Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees
Discrete Applied Mathematics. 283, S. 495-511 17 S, doi:10.1016/j.dam.2020.01.036
20-022
Berkemer, S. J., Maier, L-K., Amman, F., Bernhart, S. H., Woertz, J., Maerkle, P., Pfeiffer, F., Stadler, P. F. & Marchfelder, A.
Identification of RNA 3 ' ends and termination sites in Haloferax volcanii
RNA Biology. 14 S., doi:10.1080/15476286.2020.1723328
20-023
Binder, S., Zipfel, I., Friedrich, M., Riedel, D., Ende, S., Kaempf, C., Wiedemann, K., Buschmann, T., Puppel, S-H., Reiche, K., Stadler, P. F. & Horn, F.
Master and servant: LINC00152-a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma
Bmc medical genomics. 13, 1, 13 S., doi:10.1186/s12920-020-0692-3
20-024
Entzian, G. & Raden, M.
pourRNA-a time- and memory-efficient approach for the guided exploration of RNA energy landscapes
Bioinformatics. 36, 2, S. 462-469 8 S., doi:10.1093/bioinformatics/btz583
20-025
Antonio Corona-Gomez, J., Jair Garcia-Lopez, I., Stadler, P. F. & Fernandez-Valverde, S. L.
Splicing conservation signals in plant long noncoding RNAs
RNA. 26, 7, S. 784-793 10 S., doi:10.1261/rna.074393.119
20-026
Kammarabutr, J., Mahalapbutr, P., Okumura, H., Wolschann, P. & Rungrotmongkol, T.
Structural dynamics and susceptibility of anti-HIV drugs against HBV reverse transcriptase
Journal of biomolecular structure & dynamics. 10 S., doi:10.1080/07391102.2020.1751715
20-027
Shatilina, Z., Drozdova, P., Bedulina, D., Rivarola-Duarte, L., Schreiber, S., Otto, C., Juehling, F., Aulhorn, S., Busch, W., Lubyaga, Y., Kondrateva, E., Pobezhimova, T., Jakob, L., Lucassen, M., Sartoris, F. J., Hackermueller, J., Poertner, H-O., Stadler, P. F., Luckenbach, T. & Timofeyev, M.
Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species
Comparative biochemistry and physiology d-Genomics & proteomics. 33, 7 S., 100630., doi:10.1016/j.cbd.2019.100630
20-028
Erber, L., Hoffmann, A., Fallmann, J., Hagedorn, M., Hammann, C., Stadler, P. F., Betat, H., Prohaska, S. & Moerl, M.
Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes inDictyostelium discoideum
International Journal of Molecular Sciences. 21, 15, 16 S., 5210, doi:10.3390/ijms21155210
20-029
Seal, R. L., Chen, L-L., Griffiths-Jones, S., Lowe, T. M., Mathews, M. B., O'Reilly, D., Pierce, A. J., Stadler, P. F., Ulitsky, I., Wolin, S. L. & Bruford, E. A.
A guide to naming human non-coding RNA genes
MBO Journal. 39, 6, 18 S., 103777, doi:10.15252/embj.2019103777
20-030
Alexandra Popa, Jakob-Wendelin Genger, Michael Nicholson, Thomas Penz, Daniela Schmid, Stephan W Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique Colaco, Mark Smyth, Michael Schuster, Miguel L. Grau, Francisco Martinez-Jimenez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Martin Senekowitsch, Jan Laine, Judith H Aberle, Monika Redlberger-Fritz, Mario Karolyi, Alexander Zoufaly, Sabine Maritschnik, Martin Borkovec, Peter Hufnagl, Manfred Nairz, Günter Weiss, Michael T. Wolfinger, Dorothee von Laer, Giulio Superti-Furga, Nuria Lopez-Bigas, Elisabeth Puchhammer-Stöckl, Franz Allerberger, Franziska Michor, Christoph Bock, Andreas Bergthaler
Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
Sci. Transl. Med. eabe2555 (2020), doi:10.1126/scitranslmed.abe2555
20-031
Waldl M., Will S., Wolfinger M.T., Hofacker I.L., Stadler P.F.
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2019. Lecture Notes in Computer Science, vol 12313. Springer, Cham., doi:10.1007/978-3-030-63061-4_15
20-032
Sen, R., Fallmann, J., Walter, M. E. M. T. & Stadler, P. F.
Are spliced ncRNA host genes distinct classes of lncRNAs?
Theory in Biosciences. 11 S., doi:10.1007/s12064-020-00330-6
20-033
Guenzel, C., Kuehnl, F., Arnold, K., Findeiss, S., Weinberg, C. E., Stadler, P. F. & Moerl, M.
Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches
RNA Biology. 11 S., doi:10.1080/15476286.2020.1816336
20-034
Keller, M., Yaskolka Meir, A., Bernhart, S. H., Gepner, Y., Shelef, I., Schwarzfuchs, D., Tsaban, G., Zelicha, H., Hopp, L., Mueller, L., Rohde, K., Boettcher, Y., Stadler, P. F., Stumvoll, M., Blueher, M., Kovacs, P. & Shai, I.
DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial
Genome Medicine. 12, 1, 18 S., 97., doi:10.1186/s13073-020-00794-7
20-035
Miladi, M., Raden, M., Will, S. & Backofen, R.
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains
Algorithms for Molecular Biology. 15, 1, 11 S., 19., doi:10.1186/s13015-020-00179-w
20-036
Schwarz, T. S., Berkemer, S. J., Bernhart, S. H., Weiss, M., Ferreira-Cerca, S., Stadler, P. F. & Marchfelder, A.
Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea
Frontiers in Microbiology. 11, 15 S., 594838., doi:10.3389/fmicb.2020.594838