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.
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.
23-001 Farman, M. R., Petrackova, D., Kumar, D., Drzmisek, J., Saha, A., Curnova, I., Capek, J., Hejnarova, V., Amman, F., Hofacker, I. & Vecerek, B. Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment Emerging microbes & infections. 12, 1, 16 p., 2146536, doi:10.1080/22221751.2022.2146536 |
23-002 Chonnikan Hanpaibool, Natharin Ngamwongsatit, Puey Ounjai, Sirilata Yotphan, Peter Wolschann, Adrian J. Mulholland, James Spencer, and Thanyada Rungrotmongkol Pyrazolones Potentiate Colistin Activity against MCR-1-Producing Resistant Bacteria: Computational and Microbiological Study ACS Omega 2023, 8, 9, 8366-8376 (Article), doi:10.1021/acsomega.2c07165 |
23-003 Stefan Badelt, Ronny Lorenz, Ivo L Hofacker DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model Bioinformatics, Volume 39, Issue 1, January 2023, btad034, doi:10.1093/bioinformatics/btad034 |
23-004 Roman Ochsenreiter and Michael T. Wolfinger Strukturierte RNAs in Viren (in German) BIOspektrum 02.23:156 (2023), doi:10.1007/s12268-023-1907-x |
23-005 Tyler Mrozowich, Sean Park, Maria Waldl, Amy Henrickson, Scott Tersteeg, Corey R. Nelson, Anneke Deklerk, Borries Demeler, Ivo L. Hofacker, Michael T. Wolfinger, Trushar R. Patel Investigating RMA-RNA interactiona through computational and biophysical analysis Nucleic Acids Res. (2023), doi:10.1093/nar/gkad223 |
23-006 Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol and Ryuhei Harada A Structural Refinement Technique for Protein-RNA Complexes Using Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein Bulletin of the Chemical Society of Japan, doi:10.1246/bcsj.20230092 |
23-007 Phoomintara Longsompurana, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 PLoS ONE 18(10): e0293263., doi:10.1371/journal.pone.0293263 |
23-008 Malinee Promkatkaew, Pornthip Boonsri, Songwut Suramitr, Thitinun Karpkird, Peter Wolschann, Supa Hannongbua Stability improvement of UV-filter between methoxy cinnamic acid derivatives and cyclodextrins inclusion complexes based on DFT and TD-DFT investigations Journal of Molecular Graphics and Modelling 125 (2023) 108619, doi:10.1016/j.jmgm.2023.108619 |
23-009 P. Pojtanadithee, K. Hengphasatporn, A. Suroengrit, S. Boonyasuppayakorn, P. Wilasluck, P. Deetanya, K. Wangkanont, I.P. Sukanadi, W. Chavasiri, P. Wolschann, Th. Langer, Y. Shigeta, Ph. Maitarad, K. Sanachai, Th. Rungrotmongkol Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 ECLpro through Structure-Based Virtual Screning and Experimental Approaches J Chem Inf Model 63, 5244-5258 (2023), doi:10.1021/acs.jcim.3c00663 |
23-010 Siriluk Rattanabunyong, Khuanjarat Choengpanya, Chonticha Suwattanasophon, Duangnapa Kiriwan, Peter Wolschann, Thomanai Lamtha, Abdul Rajjak Shaikh, Jatuporn Rattanasrisomporn, and Kiattawee Choowongkomon Biochemical and structural comparisons of non-nucleoside reverse transcriptase inhibitors against feline immunodeficiency virus and human immunodeficiency virus J Vet Sci. 2023;24:e67, doi:10.4142/jvs.22326 |
23-011 Aamir Aman, Saba Ali, Panupong Mahalapbutr, Kuakarun Krusong, Peter Wolschann and Thanyada Rungrotmongkol Enhancing solubility and stability of sorafenib through cyclodextrin-based inclusion complexation: in silico and in vitro studies RSC Adv., 2023, 13, 27244, doi:10.1039/d3ra03867j |
23-012 Piyatida Pojtanadithee, Kulpornsorn Isswanich, Koonchira Buaban, Supakarn Chamni, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Thierry Langer, Peter Wolschann, Kamonpan Sanachai, Thanyada Rungrotmongkol A combination of structure-based virtual screening and experimentali strategies to identify the potency of caffeic acid ester derivatives as SARS-CoV-2 3CLpro inhibitor from an in-house database Biophysical Chemistry 304 (2024) 107125, doi:10.1016/j.bpc.2023.107125 |
23-013 Mariam R Farman, Denisa Petráčková, Dilip Kumar, Jakub Držmıšek, Argha Saha, Ivana Čurnová, Jan Čapek, Václava Hejnarová, Fabian Amman, Ivo L. Hofacker, and Branislav Vevcerek Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment Emerging Microbes & Infections, 12:e2146536, 2023, doi:10.1080/22221751.2022.2146536 |
23-014 Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K Beckmann, Ivo L Hofacker, Sarah Von Lohneysen, and Peter F Stadler Local RNA folding revisisted Journal of Bioinformatics and Computational Biology, 2023, doi:10.1142/S0219720023500166 |
23-015 Anda Ramona Tanasie, Peter Kerpedjiev, Stefan Hammer, Stefan Badelt DrForna: visualization of cotranscriptional folding Bioinformatics, 2023, 39(9), doi:10.1093/bioinformatics/btad555 |
23-016 Jakob L Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F Stadler On the Realisability of Chemical Pathways LNBI 14348, pp 409-419, 2023, doi:10.1007/978-981-99-7074-2_32 |
23-017 Sven Findeiß, Christoph Flamm, Yann Ponty Rational Design of RiboNucleic Acids Dagstuhl Reports, 12(9):121–149, 2023, doi:10.4230/DagRep.12.9.121 |
23-018 Nino Lauber, Ondřej Ticháček, Rudra Bose, Christoph Flamm, Luca Leuzzi, T-Y Dora Tang, Kepa Ruiz-Mirazo, Daniele De Martino Statistical mechanics of biomolecular condensates via cavity methods iScience 26:106300, 2023, doi:10.1016/j.isci.2023.106300 |
23-019 Badelt S, Lorenz R A guide to computational cotranscriptional folding featuring the SRP RNA bioRxiv (2023) page(s): 2023--06 |
23-020 Yao, H. T., Lorenz, R., Hofacker, I. L. & Stadler, P. F. Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package Biology. 18, 1, 8, doi:10.1186/s13015-023-00236-0 |
23-021 Darren Gemmill, Corey Nelson, Maulik Badmalia, Higor Pereira, Michael T. Wolfinger, and Trushar Patel The 3’ terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17 Biochem. Cell Biol (2023), doi:10.1139/bcb-2023-0036 |
23-022 Nitchakan Darai, Kowit Hengphasatporn, Peter Wolschann, Michael T. Wolfinger, Yasuteru Shigeta, Thanyada Rungrotmongkol, Ryuhei Harada A Structural Refinement Technique for Protein-RNA Complexes Using a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein B. Chem. Soc. Jpn. 96(7):677–685 (2023), doi:10.1246/bcsj.20230092 |
23-023 Gemmill, D. L., Pereira, H. S., Badmalia, M. D., Nelson, C. R., Wolfinger, M. T. & Patel, T. R. Identification and characterisation of G-quadruplexes from viral genomes Biophysical Journal. 122, 3, S. 444A-444A Meeting Abstract: 2159-Plat |
23-024 Fiedler, L., Bernt, M., Middendorf, M. & Stadler, P. F. Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs BMC Bioinformatics. 24, 1, 235, doi:10.1186/s12859-023-05371-4 |
23-025 Avila Santos, A. P., Kabiru Nata’ala, M., Kasmanas, J. C., Bartholomäus, A., Keller-Costa, T., Jurburg, S. D., Tal, T., Camarinha-Silva, A., Saraiva, J. P., Ponce de Leon Ferreira de Carvalho, A. C., Stadler, P. F., Sipoli Sanches, D. & Rocha, U. The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes Animal Microbiome. 5, 1, 48, doi:10.1186/s42523-023-00267-3 |
23-026 Hellmuth, M., Schaller, D. & Stadler, P. F Clustering systems of phylogenetic networks Theory in Biosciences. 142, 4, S. 301-358 58 S, doi:10.1007/s12064-023-00398-w |
23-027 Klapproth, C., Zötzsche, S., Kühnl, F., Fallmann, J., Stadler, P. F. & Findeiß, S., Sep. 2023 Tailored machine learning models for functional RNA detection in genome-wide screens NAR: Genomics and Bioinformatics. 5, 3, S. lqad072 lqad072, doi:10.1093/nargab/lqad072 |
23-028 Hellmuth, M., Huber, K. T., Moulton, V., Scholz, G. E. & Stadler, P. F. Injective Split Systems Graphs and Combinatorics. 39, 4, 65, doi:10.1007/s00373-023-02660-w |
23-029 Schaller, D., Geiss, M., Hellmuth, M. & Stadler, P. F. Best Match Graphs with Binary Trees IEEE/ACM Transactions on Computational Biology and Bioinformatics. 20, 3, S. 1679-1690, doi:10.1109/TCBB.2022.3143870 |
23-030 Kolberg, T., von Löhneysen, S., Ozerova, I., Wellner, K., Hartmann, R. K., Stadler, P. F. & Mörl, M. Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA Nucleic Acids Research. 51, 11, S. e63-e63, doi:10.1093/nar/gkad312 |
23-031 Seemann, C. R., Moulton, V., Stadler, P. F. & Hellmuth, M. Planar median graphs and cubesquare-graphs Discrete Applied Mathematics. 331, S. 38-58 21 S, doi:10.1016/j.dam.2023.01.022 |
23-032 Korchmaros, A., Schaller, D., Hellmuth, M. & Stadler, P. F. Quasi-best match graphs Discrete Applied Mathematics. 331, S. 104-125 22 S, doi:10.1016/j.dam.2023.01.015 |
23-033 Bran, A. M., Stadler, P. F., Jost, J. & Restrepo, G. The six stages of the convergence of the periodic system to its final structure Communications Chemistry. 6, 1, 87, doi:10.1038/s42004-023-00883-9 |
23-034 Santiago Arguello, A., Montellano-Ballesteros, J. J. & Stadler, P. F. Hamiltonicity in power graphs of a class of abelian groups Journal of Algebraic Combinatorics. 57, 1, S. 313-328 16 S, doi:10.1007/s10801-022-01172-9 |
23-035 González Laffitte, M. E., Beier, N., Domschke, N. & Stadler, P. F. Comparison of Atom Maps Match. 90, 1, S. 75-102 28 S, doi:10.46793/match.90-1.075G |
23-036 Schaller, D., Hellmuth, M. & Stadler, P. ORIENTATION OF FITCH GRAPHS AND RECONCILIATION-FREE INFERENCE OF HORIZONTAL GENE TRANSFER IN GENE TREES SIAM Journal on Discrete Mathematics. 37, 3, S. 2172-2207 |
23-037 Domingo, E., Schuster, P., Elena, S. F. & Perales, C. Viral Fitness and Evolution Band 439. S. 341-344 (Current Topics in Microbiology and Immunology) |
23-038 Schuster, P. & Stadler, P. Virus Evolution on Fitness Landscapes Band 439. S. 1-94 (Current Topics in Microbiology and Immunology) |
23-039 Sangkhawasi, M., Kerdpol, K., Ismail, A., Nutho, B., Hanpiboon, C., Wolschann, P., Krusong, K., Rungrotmongkol, T. & Hannongbua, S. In Vitro and In Silico Study on the Molecular Encapsulation of α-Tocopherol in a Large-Ring Cyclodextrin International Journal of Molecular Sciences. 24, 5, 4425, doi:10.3390/ijms24054425 |
23-040 Avila Santos, A. P., Kabiru Nata’ala, M., Kasmanas, J. C., Bartholomäus, A., Keller-Costa, T., Jurburg, S. D., Tal, T., Camarinha-Silva, A., Saraiva, J. P., Ponce de Leon Ferreira de Carvalho, A. C., Stadler, P. F., Sipoli Sanches, D., Rocha, U. The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes Animal Microbiome. 5, 1, 48., doi:10.1186/s42523-023-00267-3 |
23-041 Klapproth, C., Zötzsche, S., Kühnl, F., Fallmann, J., Stadler, P. F. & Findeiß, S. Tailored machine learning models for functional RNA detection in genome-wide screens NAR: Genomics and Bioinformatics. 5, 3, S. lqad072 lqad072, doi:10.1093/nargab/lqad072 |
23-042 Anders, J. & Stadler, P. F. RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions Journal of Integrative Bioinformatics. 20, 3, 20220046, doi:10.1515/jib-2022-0046 |
23-043 Rocha, U., Coelho Kasmanas, J., Kallies, R., Saraiva, J. P., Toscan, R. B., Štefanič, P., Bicalho, M. F., Borim Correa, F., Baştürk, M. N., Fousekis, E., Viana Barbosa, L. M., Plewka, J., Probst, A. J., Baldrian, P. & Stadler, P. F. MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy Molecular Ecology Resources, doi:10.1111/1755-0998.13904 |