Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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Quickly jump to the following years directly: 2020, 2021


S Zayni, S Damiati, S Moreno-Flores, F Amman, I Hofacker, D Jin, ...
Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence—An Experimental Study of the Human Voltage-Dependent Anion Channel
Membranes 11 (10), 741, doi:10.3390/membranes11100741
MT Wolfinger, R Ochsenreiter, IL Hofacker
Functional RNA Structures in the 3′ UTR of Mosquito-Borne Flaviviruses
Virus Bioinformatics, 65-100, doi:10.1201/9781003097679-5
G Entzian, IL Hofacker, Y Ponty, R Lorenz, A Tanzer
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes
Bioinformatics 37 (15), 2126-2133, doi:10.1093/bioinformatics/btab066
Devadatta Gosavi, Iwona Wower, Irene K Beckmann, Ivo L Hofacker, Jacek Wower, Michael T Wolfinger, Joanna Sztuba-Solinska
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
bioRxiv 2021.05.13.444024, doi:10.1101/2021.05.13.444024
Anastasia Cianciulli Sesso, Branislav Lilić, Fabian Amman, Michael T. Wolfinger, Elisabeth Sonnleitner, Udo Bläsi
Gene Expression Profiling of Pseudomonas Aeruginosa Upon Exposure to Colistin and Tobramycin
Front. Microbiol. 12:937 (2021), doi:10.3389/fmicb.2021.626715
Hayato Harima, Yasuko Orba, Shiho Torii, Yongjin Qiu, Masahiro Kajihara, Yoshiki Eto, Naoya Matsuta, Bernard M. Hang’ombe, Yuki Eshita, Kentaro Uemura, Keita Matsuno, Michihito Sasaki, Kentaro Yoshii, Ryo Nakao, William W. Hall, Ayato Takada, Takashi Abe, Michael T. Wolfinger, Martin Simuunza, Hirofumi Sawa
An African Tick Flavivirus Forming an Independent Clade Exhibits Unique Exoribonuclease-Resistant RNA Structures in the Genomic 3’-Untranslated Region
Sci. Rep. 11:4883 (2021), doi: 10.1038/s41598-021-84365-9
Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
Genes 12 (2):239 (2021), doi:10.3390/genes12020239
Esther Heid, Samuel Goldman, Karthik Sankaranarayanan, Connor W Coley, Christoph Flamm, William H Green
EHreact: Extended Hasse diagrams for the extraction and scoring of enzymatic reaction templates
J Chem Inf Model Publication Date:September 29, 2021 Online ahead of print, doi:10.1021/acs.jcim.1c00921
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe VFP Laurent, Daniel Merkle and Nikolai Nøjgaard
Graph Transformation for Enzymatic Mechanisms
Bioinformatics 37(1):i392-i400 2021, doi:10.1093/bioinformatics/btab296
Nino Lauber, Christoph Flamm, Kepa Ruiz-Mirazo
Minimal metabolism: a key concept to investigate the origins and nature of biological systems
BioEssays, 2021:2100201, doi:10.1002/bies.202100103
Ronny Lorenz, Christoph Flamm, Ivo L Hofacker Peter F Stadler
Efficient Algorithms for Co-folding of Multiple RNAs.
In: Ye X. et al. (eds) Biomedical Engeneering Systems and Technologies. BIOSTEC 2020. Communications in Computer and Information Science, vol 1400, pp 193-214, 2021 ISBN: 978-3-030-72378-1, doi:10.1007/978-3-030-72379-8_10
Kerdpol, K., Daengngern, R., Sattayanon, C., Namuangruk, S., Rungrotmongkol, T., Wolschann, P., Kungwan, N., Hannongbua, S.
Effect of Water Microsolvation on the Excited-State Proton Transfer of 3-Hydroxyflavone Enclosed in gamma-Cyclodextrin
Molecules, 26(4), [843], doi:10.3390/molecules26040843
Dienstbier, A., Amman, F., Petrackova, D., Stipl, D., Capek, J., Zavadilova, J., Fabianova, K., Drzmisek, J., Kumar, D., Wildung, M., Pouchnik, D., Vecerek, B.
Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution
Emerging infectious diseases, 27(1), 57-68, doi:10.3201/eid2701.191541
Lorenz, R., Stadler, P. F.
Rna secondary structures with limited base pair span: Exact backtracking and an application
Genes, 12(1), 1-9. [14], doi:10.3390/genes12010014
Ponty, Y., Hammer, S., Yao, H. T., Will, S.
Advanced Design of Structural RNAs Using RNARedPrint
in Methods in Molecular Biology (Band 2284, S. 1-15). Springer-Nature. Methods in Molecular Biology Band 2284, doi:10.1007/978-1-0716-1307-8_1
Anders, J., Petruschke, H., Jehmlich, N., Haange, S-B., von Bergen, M., Stadler, P. F.
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations
BMC Bioinformatics, 22 (1), [277], doi:10.1186/s12859-021-04159-8
Kolora, S. R. R., Gysi, D. M., Schaffer, S., Grimm-Seyfarth, A., Szabolcs, M., Faria, R., Henle, K., Stadler, P. F., Schlegel, M., Nowick, K.
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards
Genome Biology and Evolution, 13(8), [109], doi:10.1093/gbe/evab109
Stadler, P. F.
Alignments of biomolecular contact maps
Interface Focus, 11(4), [20200066], doi:10.1098/rsfs.2020.0066
Vieira, L. M., Jorge, N. A. N., de Sousa, J. B., Setubal, J. C., Stadler, P. F., Walter, M. E. M. T.
Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction
Frontiers in Oncology , 11, [681579], doi:10.3389/fonc.2021.681579
Schaller, D., Geiss, M., Stadler, P. F., Hellmuth, M.
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs
Journal of Mathematical Biology, 82(3), [20], doi:10.1007/s00285-021-01564-8
Schaller, D., Stadler, P. F., Hellmuth, M.
Complexity of modification problems for best match graphs
Theoretical Computer Science, 865, 63-84, doi:10.1016/j.tcs.2021.02.037
Lipaeva, P., Vereshchagina, K., Drozdova, P., Jakob, L., Kondrateva, E., Lucassen, M., Bedulina, D., Timofeyev, M., Stadler, P., Luckenbach, T.
Different ways to play it cool: Transcriptomic analysis sheds light on different activity patterns of three amphipod species under long-term cold exposure
Molecular Ecology, doi:10.1111/mec.16164
Yaskolka Meir, A., Keller, M., Mueller, L., Bernhart, S. H., Tsaban, G., Zelicha, H., Rinott, E., Kaplan, A., Gepner, Y., Shelef, I., Schwarzfuchs, D., Ceglarek, U., Stadler, P., Blueher, M., Stumvoll, M., Kovacs, P., Shai, I.
Effects of lifestyle interventions on epigenetic signatures of liver fat: Central randomized controlled trial
Liver international, doi:10.1111/liv.14916
Leal, W., Restrepo, G., Stadler, P. F., Jost, J.
Advances in Complex Systems, 24(01), [2150003], doi:10.1142/S021952592150003X
Hellmuth, M., Seemann, C. R., Stadler, P. F.
Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees
Discrete mathematics and theoretical computer science, 23(1), [13], doi:10.46298/dmtcs.6040
Schaller, D., Geiss, M., Hellmuth, M., & Stadler, P. F.
Heuristic algorithms for best match graph editing
Algorithms for Molecular Biology, 16(1), [19], doi:10.1186/s13015-021-00196-3
Doncheva, N. T., Palasca, O., Yarani, R., Litman, T., Anthon, C., Groenen, M. A. M., Stadler, P. F., Pociot, F., Jensen, L. J.,Gorodkin, J.
Human pathways in animal models: possibilities and limitations
Nucleic Acids Research, 49(4), 1859-1871, doi:10.1093/nar/gkab012
Schaller, D., Lafond, M., Stadler, P. F., Wieseke, N., Hellmuth, M
Indirect identification of horizontal gene transfer
Journal of Mathematical Biology, 83(1), [10], doi:10.1007/s00285-021-01631-0
Gatter, T., von Loehneysen, S., Fallmann, J., Drozdova, P., Hartmann, T., Stadler, P. F
LazyB: fast and cheap genome assembly
Algorithms for Molecular Biology, 16(1), [8], doi:10.1186/s13015-021-00186-5
Yaskolka Meir, A., Keller, M., Bernhart, S. H., Rinott, E., Tsaban, G., Zelicha, H., Kaplan, A., Schwarzfuchs, D., Shelef, I., Gepner, Y., Li, J., Lin, Y., Blueher, M., Ceglarek, U., Stumvoll, M., Stadler, P. F., Stampfer, M. J., Kovacs, P., Liang, L., Shai, I.
Lifestyle weight-loss intervention may attenuate methylation aging: the CENTRAL MRI randomized controlled trial
Clinical epigenetics, 13(1), [48], doi:10.1186/s13148-021-01038-0
Ender, A., Etzel, M., Hammer, S., Findeiss, S., Stadler, P., Moerl, M.
Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch
Nucleic Acids Research, 49(3), 1784-1800, doi:10.1093/nar/gkaa1282
Velandia-Huerto, C. A., Fallmann, J., Stadler, P. F.
miRNAture-Computational Detection of microRNA Candidates
Genes, 12(3), [348], doi:10.3390/genes12030348
Bedulina, D., Drozdova, P., Gurkov, A., von Bergen, M., Stadler, P. F., Luckenbach, T., Timofeyev, M., Kalkhof, S.
Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus
Science of the Total Environment, 763, [143008], doi:10.1016/j.scitotenv.2020.143008
Jakob, L., Vereshchagina, K. P., Tillmann, A., Rivarola-Duarte, L., Axenov-Gribanov, D., Bedulina, D. S., Gurkov, A. N., Drozdova, P., Timofeyev, M. A., Stadler, P. F., Luckenbach, T., Poertner, H-O., Sartoris, F. J., Lucassen, M.
Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species
Scientific Reports, 11(1), [4562], doi:10.1038/s41598-021-83748-2
Schaller, D., Geiss, M., Chavez, E., Gonzalez Laffitte, M., Lopez Sanchez, A., Stadler, B. M. R., Valdivia, D. I., Hellmuth, M., Hernandez Rosales, M., Stadler, P. F.
Best match graphs (vol 78, 2015, 2019)
Journal of Mathematical Biology, 82(6), [47], doi:10.1007/s00285-021-01601-6


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
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
Helmut Viernstein, Peter Wolschann
Cyclodextrin inclusion complexation and pharmaceutical applications
ScienceAsia 46 (2020): 254–262, doi:10.2306/scienceasia1513-1874.2020.048
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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