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SnakeLines: integrated set of computational pipelines for sequencing reads.
Budiš J, Krampl W, Kucharík M, Hekel R, Goga A, Sitarčík J, Lichvár M, Smol'ak D, Böhmer M, Baláž A, Ďuriš F, Gazdarica J, Šoltys K, Turňa J, Radvánszky J, Szemes T. Budiš J, et al. Among authors: krampl w. J Integr Bioinform. 2023 Aug 21;20(3):20220059. doi: 10.1515/jib-2022-0059. eCollection 2023 Sep 1. J Integr Bioinform. 2023. PMID: 37602733 Free PMC article.
Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations.
Sládeček T, Gažiová M, Kucharík M, Zaťková A, Pös Z, Pös O, Krampl W, Tomková E, Hýblová M, Minárik G, Radvánszky J, Budiš J, Szemes T. Sládeček T, et al. Among authors: krampl w. Sci Rep. 2023 Jun 29;13(1):10531. doi: 10.1038/s41598-023-37352-1. Sci Rep. 2023. PMID: 37386017 Free PMC article.
WarpSTR: determining tandem repeat lengths using raw nanopore signals.
Sitarčík J, Vinař T, Brejová B, Krampl W, Budiš J, Radvánszky J, Lucká M. Sitarčík J, et al. Among authors: krampl w. Bioinformatics. 2023 Jun 1;39(6):btad388. doi: 10.1093/bioinformatics/btad388. Bioinformatics. 2023. PMID: 37326967 Free PMC article.
Mitochondrial DNA copy number changes, heteroplasmy, and mutations in plasma-derived exosomes and brain tissue of glioblastoma patients.
Soltész B, Pös O, Wlachovska Z, Budis J, Hekel R, Strieskova L, Liptak JB, Krampl W, Styk J, Németh N, Keserű JS, Jenei A, Buglyó G, Klekner Á, Nagy B, Szemes T. Soltész B, et al. Among authors: krampl w. Mol Cell Probes. 2022 Dec;66:101875. doi: 10.1016/j.mcp.2022.101875. Epub 2022 Nov 12. Mol Cell Probes. 2022. PMID: 36379303
Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic-One Year Experience.
Rusňáková D, Sedláčková T, Radvák P, Böhmer M, Mišenko P, Budiš J, Bokorová S, Lipková N, Forgáčová-Jakúbková M, Sládeček T, Sitarčík J, Krampl W, Gažiová M, Kaliňáková A, Staroňová E, Tichá E, Vrábľová T, Ševčíková L, Kotvasová B, Maďarová L, Feiková S, Beňová K, Reizigová L, Onderková Z, Ondrušková D, Loderer D, Škereňová M, Danková Z, Janíková K, Halašová E, Nováková E, Turňa J, Szemes T. Rusňáková D, et al. Among authors: krampl w. Viruses. 2022 Nov 2;14(11):2432. doi: 10.3390/v14112432. Viruses. 2022. PMID: 36366530 Free PMC article.
Automated prediction of the clinical impact of structural copy number variations.
Gažiová M, Sládeček T, Pös O, Števko M, Krampl W, Pös Z, Hekel R, Hlavačka M, Kucharík M, Radvánszky J, Budiš J, Szemes T. Gažiová M, et al. Among authors: krampl w. Sci Rep. 2022 Jan 11;12(1):555. doi: 10.1038/s41598-021-04505-z. Sci Rep. 2022. PMID: 35017614 Free PMC article.