Publications

• 2024

  GIUSEPPE, S.; TRAJKOVSKI, M.; CANTARA, A.; MURA, M.; MELONI, C.; GIULIA, O.; DOBROVOLNÁ, M.; PISANO, L.; GASPA, S.; SALIS, A.; DE LUCA, L.; MOCCI, F.; BRAZDA, V.; PLAVEC, J.; CARRARO, M. Complex Biophysical and Computational Analyses of G‐Quadruplex Ligands: The Porphyrin Stacks Back. CHEMISTRY-A EUROPEAN JOURNAL, 2024, vol. 30, no. 62, ISSN: 0947-6539.
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  KRATOCHVILOVÁ, L.; VOJSOVIČ, M.; VALKOVÁ, N.; BRÁZDA, V. Effect of the Presence of G-quadruplex Prone DNA Sequences on Transcription Induced by Cancer-relevant P53 Tumor Suppressor Mutants. Czech Chemical Society Symposium Series. Czech Chemical Society, 2024. p. 23-24. ISSN: 2336-7210.
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  BRÁZDA, V.; ŠISLEROVÁ, L.; MERGNY, J.; CUCCHIARINI, A. G-quadruplex propensity in H. neanderthalensis, H. sapiens and Denisovans mitochondrial genomes. NAR Genomics and Bioinformatics, 2024, vol. 6, no. 2, p. 1-10. ISSN: 2631-9268.
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  KRATOCHVILOVÁ, L.; VOJSOVIČ, M.; VALKOVÁ, N.; ŠISLEROVÁ, L.; EL RASHED, Z.; INGA, A.; MONTI, P.; BRÁZDA, V. G-quadruplex forming sequences modulate the P53 family proteins transactivation. Terst, Itálie: 2024. p. 67-67.
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  DOBROVOLNÁ, M.; ŠISLEROVÁ, L.; BRÁZDA, V.; BARTAS, M.; ČERVEŇ, J.; VALKOVÁ, N.; VOLNÁ, A.; BALDVINSSON, H.; PEČINKA, P.;. RNA analysis of the longest living vertebrate Greenland shark revealed an abundance of LINE-like elements in its transcriptome. Czech Polar Reports, 2024, vol. 13, no. 2, p. 210-227. ISSN: 1805-0689.
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  VOJSOVIČ, M.; KRATOCHVILOVÁ, L.; VALKOVÁ, N.; ŠISLEROVÁ, L.; EL RASHED, Z.; MENICHINI, P.; INGA, A.; MONTI, P.; BRÁZDA, V. Transactivation by partial function P53 family mutants is increased by the presence of G-quadruplexes at a promoter site. BIOCHIMIE, 2024, vol. 216, no. January 2024, p. 14-23. ISSN: 0300-9084.
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  BRÁZDA, V.; VÁLKOVÁ, N.; DOBROVOLNÁ, M.; MERGNY, J. Abundance of G-Quadruplex Forming Sequences in the Hepatitis Delta Virus Genomes. ACS OMEGA, 2024, vol. 9, no. 3, p. 4096-4101. ISSN: 2470-1343.
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• 2023

  KRATOCHVILOVÁ, L.; VOJSOVIČ, M.; VALKOVÁ, N.; ŠISLEROVÁ, L.; EL RASHED, Z.; INGA, A.; MONTI, P.; BRÁZDA, V. The presence of a G-quadruplex prone sequence upstream of a minimal promoter increases transcriptional activity in the yeast Saccharomyces cerevisiae. BIOSCIENCE REPORTS, 2023, vol. 43, no. 12, ISSN: 0144-8463.
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  BRÁZDA, V.; KRATOCHVILOVÁ, L.; VOJSOVIČ, M.; VALKOVÁ, N.; ŠISLEROVÁ, L.; EL RASHED, Z.; MONTI, P.; INGA, A. G-quadruplex forming sequences modulate basal transcription of a yeast reporter and impact the transactivation by P53 family proteins. The EuroBiotech Journal. 2023. p. 15-15. ISSN: 2564-615X.
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  KRATOCHVILOVÁ, L.; VALKOVÁ, N.; BRÁZDA, V. Study of IFI16 Protein Binding to DNA G-quadruplex Secondary Structure. Studentská odborná konference Chemie je život 2023 Sborník abstraktů. Purkyňova 464/118, 612 00 Brno: Vysoké učení technické v Brně, Fakulta chemická, 2023. p. 55-56. ISBN: 978-80-214-6204-5.
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  KRATOCHVILOVÁ, L.; VALKOVÁ, N.; BRÁZDA, V. Study of IFI16 protein interaction with G4 prone DNA sequences and its influence on p53 transcription activity. The EuroBiotech Journal. 2023. p. 38-39. ISSN: 2564-615X.
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  PORUBIAKOVÁ, O.; HAVLÍK, J.; INDU, M.; ŠEDŸ, M.; PŘEPECHALOVÁ, V.; BARTAS, M.; BIDULA, S.; ŠŤASTNÝ, J.; FOJTA, M.; BRÁZDA, V. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiology spectrum, 2023, vol. 11, no. 4, p. 1-11. ISSN: 2165-0497.
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  HAVLÍK, J.; BRÁZDA, V.; STANĚK, K.; JEŽEK, M.; ŠŤASTNÝ, J. Feature-overlapper: The tool for DNA analysis overlap. Software Impacts, 2023, vol. 16, no. 5, p. 1-4. ISSN: 2665-9638.
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  BOHÁLOVÁ, N.; CANTARA, A.; BARTAS, M.; KAURA, P.; ŠŤASTNÝ, J.; PEČINKA, P.; FOJTA, M.; BRÁZDA, V. Tracing dsDNA Virus-Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences. In Impacts of Molecular Structure on Nucleic Acid-Protein Interactions. 2023. p. 39-50. ISBN: 978-3-0365-7444-8.
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  GAJARSKÝ, M.; STADLBAUER, P.; CUCCHIARINI, A.; ŠPONER, J.; DOBROVOLNÁ, M.; BRÁZDA, V.; MERGNY, J.; TRANTÍREK, L. LENARCIC ZIVKOVIC, M. DNA Quadruplex Structure with a Unique Cation Dependency. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2023, vol. 63, no. 7, ISSN: 1433-7851.
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  BRÁZDA, V.; DOBROVOLNÁ, M.; BOHÁLOVÁ, N.; MERGNY, J. G-quadruplexes in the evolution of hepatitis B virus. Nucleic Acids Research, 2023, vol. 51, no. 14, p. 7198-7204. ISSN: 1362-4962.
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  VALKOVÁ, N.; KRATOCHVILOVÁ, L.; MARTINKOVÁ, L.; BRÁZDA, V. Dual mode of IFI16 binding to supercoiled and linear DNA: A closer insight. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2023, vol. 667, no. 30.07.2023, p. 89-94. ISSN: 0006-291X.
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  Natália Bohálová, Michaela Dobrovolná, Václav Brázda, Stefan Bidula. Conservation and over-representation of G-quadruplex sequences in regulatory regions of mitochondrial DNA across distinct taxonomic sub-groups. BIOCHIMIE, 2023, vol. 194, no. 194, p. 28-34. ISSN: 1638-6183.
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• 2022

  DOBROVOLNÁ, M.; WARNER E. F.; BIDULA S.; BRÁZDA, V. Inverted repeats in the monkeypox virus genome are hot spots for mutation. JOURNAL OF MEDICAL VIROLOGY, 2022, vol. 95, no. 1, ISSN: 0146-6615.
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  DOBROVOLNÁ, M.; BRÁZDA, V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. International Journal of Molecular Sciences, 2022, vol. 23, no. 15, ISSN: 1661-6596.
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  CANTARA, A.; LUO, Y.; DOBROVOLNÁ, M.; BOHALOVA, N.; FOJTA, M.; VERGA, D.; GUITTAT, L.; CUCCHIARINI, A.; SAVRIMOUTOU, S.; HÄBERLI, C.; GUILLON, J.; KEISER, J.; MERGNY, J-L.; BRÁZDA, V. G-quadruplexes in helminth parasites. Nucleic Acids Research, 2022, vol. 50, no. 5, p. 2719-2735. ISSN: 1362-4962.
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• 2021

  BOHÁLOVÁ, N.; CANTARA, A.; BARTAS, M.; KAURA, P.; ŠŤASTNÝ, J.; PEČINKA, P.; FOJTA, M.; MERGNY, J.; BRÁZDA, V. Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection. BIOCHIMIE, 2021, vol. 186, no. 1, p. 13-27. ISSN: 0300-9084.
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  BRÁZDA, V.; HAVLÍK, J.; KOLOMAZNÍK, J.; TRENZ, O.; ŠŤASTNÝ, J. R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences. International Journal of Molecular Sciences, 2021, vol. 22, no. 23, p. 1-8. ISSN: 1422-0067.
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  PORUBIAKOVÁ, O.; CANTARA, A.; PŘEPECHALOVÁ, V.; BRÁZDA, V. Comparison between synthetic and natural G4-ligands and the effects of their binding to DNA. 2021. p. 1 (1 s.).
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  BRÁZDA, V.; BARTAS, M.; ČERVEŇ, J.; PEČINKA, P. Ancient brothers of the human p53 tumour suppressor. FEBS Open Bio. 2021. p. 91-91. ISSN: 2211-5463.
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  BOHÁLOVÁ, N.; CANTARA, A.; BARTAS, M.; KAURA, P.; ŠŤASTNÝ, J.; PEČINKA, P.; FOJTA, M.; BRÁZDA, V. Tracing dsDNA Virus–Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences. International Journal of Molecular Sciences, 2021, vol. 22, no. 7, p. 1-12. ISSN: 1422-0067.
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  MONTI, P.; BRÁZDA, V.; BOHÁLOVÁ, N.; PORUBIAKOVÁ, O.; MENICHINI, P.; SPECIALE, A.; BOCCIARDI, R.; INGA, A.; FRONZA, G. Evaluating the Influence of a G-Quadruplex Prone Sequence on the Transactivation Potential by Wild-Type and/or Mutant P53 Family Proteins through a Yeast-Based Functional Assay. Genes, 2021, vol. 12, no. 2, p. 1-13. ISSN: 2073-4425.
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  BRÁZDA, V.; PORUBIAKOVÁ, O.; CANTARA, A.; BOHÁLOVÁ, N.; COUFAL, J.; BARTAS, M.; FOJTA, M.; MERGNY, J. G-quadruplexes in H1N1 influenza genomes. BMC GENOMICS, 2021, vol. 22, no. 1, p. 1-11. ISSN: 1471-2164.
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• 2020

  PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; BRÁZDA, V. The influence of non-canonical structures on the p53 isoforms binding to DNA. 2020.
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  PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; BRÁZDA, V. The influence of non-canonical structures on the p53 isoform binding to DNA. Sborník príspevků. 2020. p. 185-192. ISBN: 978-80-214-5921-2.
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  BRÁZDA, V.; KOLOMAZNÍK, J.; MERGNY, J.; ŠŤASTNÝ, J. G4Killer web application: a tool to design G-quadruplex mutations. BIOINFORMATICS, 2020, vol. 36, no. 10, p. 3246-3247. ISSN: 1367-4803.
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  ČUTOVÁ, M.; MANTA, J.; PORUBIAKOVÁ, O.; KAURA, P.; ŠŤASTNÝ, J.; BRÁZDOVÁ JÁGELSKÁ, E.; GOSWAMI, P.; BARTAS, M.; BRÁZDA, V. Divergent distributions of inverted repeats and G-quadruplex forming sequences in Saccharomyces cerevisiae. GENOMICS, 2020, vol. 112, no. 2, p. 1897-1901. ISSN: 0888-7543.
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  PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; INGA, A.; VADOVIČOVÁ, N.; COUFAL, J.; FOJTA, M.; BRÁZDA, V. The influence of quadruplex structure in proximity to p53 target sequences on the transactivation potential of p53alpha isoforms. International Journal of Molecular Sciences, 2020, vol. 21, no. 1, p. 1-15. ISSN: 1422-0067.
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  BARTAS, M.; BRÁZDA, V.; BOHÁLOVÁ, N.; CANTARA, A.; VOLNÁ, A.; STACHUROVÁ, T.; MALACHOVÁ, K.; BRÁZDOVÁ JAGELSKÁ, E.; PORUBIAKOVÁ, O.; CERVEN, J.; PEČINKA, P. In-depth Bioiformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles. Frontiers in Microbiology, 2020, vol. 11, no. 1, p. 1-29. ISSN: 1664-302X.
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  PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; BRÁZDA, V. G-quasruplex structure in proximity of p53 target sequence causes significant inhibition on transactivation potential of p53 isoforms. Sborník abstraktů. 2020. ISBN: 978-80-214-5920-0.
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  BRÁZDA, V.; LUO, Y.; BARTAS, M.; KAURA, P.; PORUBIAKOVÁ, O.; ŠŤASTNÝ, J.; PEČINKA, P.; VERGA, D.; DA CUNHA, V.; S. TAKAHASHI, T.; FORTERRE, P.; MYLLYKALLIO, H.; FOJTA, M.; MERGNY, J. G-quadruplexes in the Archaea Domain. Biomolecules, 2020, vol. 10, no. 9, p. 1-23. ISSN: 2218-273X.
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• 2019

  PORUBIAKOVÁ, O.; BRÁZDA, V.; BOHÁLOVÁ, N. p53alpha protein isoforms binds preferentially to cruciform in transactivation yeast isogenic system. 2019.
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  BRÁZDA, V.; PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; INGA, A.; FOJTA, M. Attenuation of p53-alpha isoform transactivation by inverted repeat sequernces in p53 target sites. 2019. p. 1 (1 s.).
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  PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; INGA, A.; BRÁZDA, V. Attenuation of p53-alpha isoform transactivation by inverted repeat sequences in p53 target sites. FEBS Open Bio. 2019. p. 1 (1 s.). ISSN: 2211-5463.
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  BRÁZDA, V.; JAGELSKÁ, E. B.; KOLOMAZNÍK, J.; LÝSEK, J.; KAURA, P.; BARTAS, M.; COUFAL, J.; ŠŤASTNÝ, J. DNA analyser, a new powerful tool to identify and analyse local DNA structures in genomes. FEBS Open Bio. 2019. p. 149-149. ISSN: 2211-5463.
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  BARTAS, M.; ČUTOVÁ, M.; BRÁZDA, V.; KAURA, P.; ŠŤASTNÝ, J.; KOLOMAZNÍK, J.; COUFAL, J.; GOSWAMI, P.; ČERVEŇ, J.; PEČINKA, P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. MOLECULES, 2019, vol. 24, no. 9, p. 1-13. ISSN: 1420-3049.
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  BRÁZDA, V.; KOLOMAZNÍK, J.; LÝSEK, J.; BARTAS, M.; FOJTA, M.; ŠŤASTNÝ, J.; MERGNY, J.-L. G4Hunter web application: a web server for G-quadruplex prediction. BIOINFORMATICS, 2019, vol. 35, no. 18, p. 3493-3495. ISSN: 1367-4803.
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  PORUBIAKOVÁ, O.; BOHÁLOVÁ, N.; BRÁZDA, V.; INGA, A. Attenuation of p53-alpha isoform binding to DNA by inverted repeat abolishment in p53 target. 2019.
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• 2018

  BRÁZDA, V.; TOMANOVÁ, B.; COUFAL, J., Něměček M. YEAST ISOGENIC SYSTEM AS A TOOL FOR STUDY P53 PROTEIN INTERACTION WITH DNA. 34th Annual Conference on Yeasts, Book of abstracts. Bratislava: SAV, 2018. p. 27-27. ISSN: 1336-4839.
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  KONEČNÁ, J.; CHVALKOVSKÁ, E.; KNÁPKOVÁ, M.; ŠPANOVÁ, A.; RITTICH, B.; BRÁZDA, V. High resolution melting analysis for identification of strains beloging to the Lactobacillus casei group. In Študentská vedecká konferencia PriF UK 2018 Zborník recenzovaných príspevkov. 2018. p. 302-307. ISBN: 978-80-223-4517-0.
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  BRÁZDA, V.; TOMANOVÁ, B.; COUFAL, J. Yeast isogenic system as a tool for study protein interaction with DNA structures. FEBS Open Bio. FEBS, 2018. p. 191-191. ISSN: 2211-5463.
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