Publications
Quickly jump to the following years directly: 2020, 2021, 2022
Quickly jump to the following years directly: 2020, 2021, 2022
22-001 Suriyan Thengyai, Yuewei Guo, Khanit Suwanborirux, Heinz Berner, Helmut Spreitzer, Peter Wolschann, Supa Hannongbua and Anuchit Plubrukarn 2D‐QSAR and CoMFA Models for Antitubercular Activity of Scalarane‐Type Sesterterpenes Sci. Pharm. 2022, 90, 47, doi:10.3390/scipharm90030047 |
22-002 Amy Oo, Panupong Mahalapbutr, Kuakarun Krusong, Ponsiri Liangsakul, Sariyarach Thanasansurapong, Vichai Reutrakul, Chutima Kuhakarn, Phornphimon Maitarad, Atit Silsirivanit, Peter Wolschann, Siyaporn Putthisen, Khanittha Kerdpol, Thanyada Rungrotmongkol Inclusion complexation of emodin with various b-cyclodextrin derivatives: Preparation, characterization, molecular docking, and anticancer activity Journal of Molecular Liquids Volume 367, Part A, 1 December 2022, 120314, doi:10.1016/j.molliq.2022.120314 |
22-003 Stadler, P. F., & Will, S. Bi-alignments with affine gaps costs. Algorithms for Molecular Biology, 17(1), [10], doi:10.1186/s13015-022-00219-7 |
22-004 D'Souza, M. H., Mrozowich, T., Badmalia, M. D., Geeraert, M., Frederickson, A., Henrickson, A., Demeler, B., Wolfinger,M. T., & Patel, T. R. Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Research, 50(10), 5881-5898, doi:10.1093/nar/gkac414 |
22-005 Wortz, J., Smith, V., Fallmann, J., Koenig, S., Thuraisingam, T., Walther, P., Urlaub, H., Stadler, P. F., Allers, T., Hille, F., & Marchfelder, A. Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair. Frontiers in Microbiology, 13, [822304], doi:10.3389/fmicb.2022.822304 |
22-006 Engelhardt, J., Scheer, O., Stadler, P. F., & Prohaska, S. J. Evolution of DNA Methylation Across Ecdysozoa. Journal of Molecular Evolution, 90(1), 56-72, doi:10.1007/s00239-021-10042-0 |
22-007 Reinhardt, F., & Stadler, P. F. ExceS-A: an exon-centric split aligner. Journal of Integrative Bioinformatics, 19(1), doi:10.1515/jib-2021-0040 |
22-008 Flamm, C., Hellmuth, M., Merkle, D., Nojgaard, N., & Stadler, P. F. Generic Context-Aware Group Contributions. I E E E - A C M Transactions on Computational Biology and Bioinformatics, 19(1), 429-442, doi:10.1109/TCBB.2020.2998948 |
22-009 Gosavi, D., Wower, I., Beckmann, I. K., Hofacker, I. L., Wower, J., Wolfinger, M. T., & Sztuba-Solinska, J. Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus internal Ribosome Entry Site. RNA Biology, 19 (1), 496-506, doi:10.1080/15476286.2022.2058818 |
22-010 Ender, A., Grafl, N., Kolberg, T., Findeiss, S., Stadler, P. F., & Moerl, M. Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes. RNA, 28(4), 551-567, doi:10.1261/rna.078814.121 |
22-011 Mrozowich, T., Park, S. M., Wolfinger, M. T., & Patel, T. R. Investigating flaviviral genomic cyclization. Biophysical Journal, 121(3), 311A-311A, doi:10.1016/j.bpj.2021.11.1203 |
22-012 Park, S. M., Mrozowich, T., Wolfinger, M. T., & Patel, T. R. Investigating Japanese encephalitis virus long-range terminal region interactions. Biophysical Journal, 121(3), 206A-206A, doi:10.1016/j.bpj.2021.11.1703 |
22-013 Kamonpan Sanachai, Tuanjai Somboon, Patcharin Wilasluck, Peerapon Deetanya, Peter Wolschann, Thierry Langer, Vannajan Sanghiran Lee, Kittikhun Wangkanont, Thanyada Rungrotmongkol, Supot Hannongbua Identification of repurposing therapeutics toward SARS-CoV-2 main protease by virtual screening PLoS ONE 17(6): e0269563, doi:10.1371/journal.pone.0269563 |
22-014 Anderson, J. L., Fagerberg, R., Flamm, C., Fontana, W., Kolcak, J., Laurent, C. V. F. P., Merkle, D. & Nojgaard, N. Representing Catalytic Mechanisms with Rule Composition Journal of Chemical Information and Modeling. 62, 22, S. 5513-5524 12 S., doi:10.1021/acs.jcim.2c00426 |
22-015 Müller, S., Flamm, C. & Stadler, P. F. What makes a reaction network "chemical"? Journal of Cheminformatics. 14, 1, 24 S., 63, doi:10.1186/s13321-022-00621-8 |
22-016 Hartman, T., Bannach, M., Middendorf, M., Stadler, P., Wieseke, N. & Hellmuth, M. Complete edge-colored permutation graphs Advances in Applied Mathematics. 139, 34 S., 102377., doi:10.1016/j.aam.2022.102377 |
22-017 Hellmuth, M., Schaller, D. & Stadler, P. F. Compatibility of partitions with trees, hierarchies, and split systems Discrete Applied Mathematics. 314, S. 265-283 19 S., doi:10.1016/j.dam.2022.03.014 |
22-018 Bruckmann, C., Stadler, P. F. & Hellmuth, M. From modular decomposition trees to rooted median graphs Discrete Applied Mathematics. 310, S. 1-9 9 S., doi:10.1016/j.dam.2021.12.017 |
22-019 Christoph Flamm, Julia Wielach, Michael T Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L Hofacker Caveats to deep learning approaches to RNA secondary structure prediction. Front Bioinf 2:835422, 2022 , doi:10.3389/fbinf.2022.835422 |
22-020 Nitchakan Darai, Panupong Mahalapbutr, Peter Wolschann, Vannajan Sanghiran Lee, Michael T. Wolfinger, Thanyada Rungrotmongkol Theoretical studies on RNA recognition by Musashi 1 RNA–binding protein Sci. Rep. 12:12137 (2022), doi:10.1038/s41598-022-16252-w |
22-021 Marlena Rozner, Ella Nukarinen, Michael T. Wolfinger, Fabian Amman, Wolfram Weckwerth, Udo Blaesi, Elisabeth Sonnleitner Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq Front. Microbiol. 13:919539 (2022), doi:10.3389/fmicb.2022.919539 |
22-022 Lena S. Kutschera, Michael T. Wolfinger Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology Virus Evol. (8):1 veac051 (2022), doi:10.1093/ve/veac051 |
22-023 Guzman, G. E. C., Stadler, P. F. & Fujita, A. Efficient eigenvalue counts for tree-like networks Journal of complex networks. 10, 5, 15 S., 040., doi:10.1093/comnet/cnac040 |
22-024 Santiago Arguello, A., Montellano-Ballesteros, J. J. & Stadler, P. F. Hamiltonicity in power graphs of a class of abelian groups Journal of Algebraic Combinatorics, doi:10.1007/s10801-022-01172-9 |
22-025 Nunn, A., Otto, C., Fasold, M., Stadler, P. F. & Langenberger, D. Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches BMC Genomics. 23, 1, 10 S., 477, doi:10.1186/s12864-022-08691-6 |
22-026 Gornik, S. G., Flores, V., Reinhardt, F., Erber, L., Salas-Leiva, D. E., Douvropoulou, O., Lassadi, I., Einarsson, E., Mörl, M., Git, A., Stadler, P. F., Pain, A. & Waller, R. F. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes Molecular Biology and Evolution. 39, 10, msac191, doi:10.1093/molbev/msac191 |
22-027 Sanachai, K., Mahalapbutr, P., Hengphasatporn, K., Shigeta, Y., Seetaha, S., Tabtimmai, L., Langer, T., Wolschann, P., Kittikool, T., Yotphan, S., Choowongkomon, K. & Rungrotmongkol, T. Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases ACS Omega. 7, 37, S. 33548-33559 12 S, doi:10.1021/acsomega.2c0453533548ACS |
21-001 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 |
21-002 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 |
21-003 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 |
21-004 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 |
21-005 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 |
21-006 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 |
21-007 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 |
21-008 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 |
21-009 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 |
21-010 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 |
21-011 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 |
21-012 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 |
21-013 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 |
21-014 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 |
21-015 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 |
21-016 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 |
21-017 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 |
21-018 Stadler, P. F. Alignments of biomolecular contact maps Interface Focus, 11(4), [20200066], doi:10.1098/rsfs.2020.0066 |
21-019 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 |
21-020 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 |
21-021 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 |
21-022 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 |
21-023 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 |
21-024 Leal, W., Restrepo, G., Stadler, P. F., Jost, J. FORMAN-RICCI CURVATURE FOR HYPERGRAPHS Advances in Complex Systems, 24(01), [2150003], doi:10.1142/S021952592150003X |
21-025 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 |
21-026 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 |
21-027 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 |
21-028 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 |
21-029 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 |
21-030 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 |
21-031 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 |
21-032 Velandia-Huerto, C. A., Fallmann, J., Stadler, P. F. miRNAture-Computational Detection of microRNA Candidates Genes, 12(3), [348], doi:10.3390/genes12030348 |
21-033 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 |
21-034 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 |
21-035 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 |
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 |