Výpis publikací

ŠÁMALOVÁ, Markéta, Alesia MELNIKAVA, Kareem ELSAYAD, Alexis PEAUCELLE, Evelína GAHUROVÁ, Jaromír GUMULEC, Ioannis SPYROGLOU, Elena V ZEMLYANSKAYA, Elena V UBOGOEVA, Darina BALKOVÁ, Martin DEMKO, Nicolas BLAVET, Panagiotis ALEXIOU, Vladimir BENES, Gregory MOUILLE a Jan HEJÁTKO. Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth. Online. Plant Physiology. CARY: OXFORD UNIV PRESS INC, roč. 194, č. 1, s. 209-228. ISSN 0032-0889. Dostupné z: https://dx.doi.org/10.1093/plphys/kiad228

HEJRET, Václav, Nandan Mysore VARADARAJAN, Eva KLIMENTOVÁ, Katarína GREŠOVÁ, Ilektra-Chara GIASSA, Štěpánka VAŇÁČOVÁ a Panagiotis ALEXIOU. Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation. Online. Scientific Reports. Nature Research, roč. 13, č. 1, s. 1-9. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-023-49757-z

TIMOFEYENKO, Kseniya, Dzmitry KANAVALAU, Panagiotis ALEXIOU, Maria KALYNA a Kamil RŮŽIČKA. CATSNAP: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. Online. New Phytologist. Wiley, roč. 238, č. 4, s. 1722-1732. ISSN 0028-646X. Dostupné z: https://dx.doi.org/10.1111/nph.18799

GREŠOVÁ, Katarína, Vlastimil MARTINEK, David ČECHÁK, Petr ŠIMEČEK a Panagiotis ALEXIOU. Genomic benchmarks: a collection of datasets for genomic sequence classification. Online. BMC Genomic Data. 2730-6844: BMC, roč. 24, č. 1, s. 1-9. ISSN 2730-6844. Dostupné z: https://dx.doi.org/10.1186/s12863-023-01123-8

FULNEČEK, Jaroslav, Eva KLIMENTOVÁ, Albert CAIRO CALZADA, Soňa BUKOVČÁKOVÁ, Panagiotis ALEXIOU, Zbyněk PROKOP a Karel ŘÍHA. The SAP domain of Ku facilitates its efficient loading onto DNA ends. Online. Nucleic Acids Research. Oxford: Oxford University Press, roč. 51, č. 21, s. 11706-11716. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad850

VACULÍK, Ondřej, Eliška CHALUPOVÁ, Katarína GREŠOVÁ, Tomáš MAJTNER a Panagiotis ALEXIOU. Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes. Online. Biology. MDPI, roč. 12, č. 10, s. 1-19. ISSN 2079-7737. Dostupné z: https://dx.doi.org/10.3390/biology12101276

GREŠOVÁ, Katarína, Ondřej VACULÍK a Panagiotis ALEXIOU. Using Attribution Sequence Alignment to Interpret Deep Learning Models for miRNA Binding Site Prediction. Online. Biology. Basel: MDPI, roč. 12, č. 3, s. 1-16. ISSN 2079-7737. Dostupné z: https://dx.doi.org/10.3390/biology12030369

CHALUPOVÁ, Eliška, Ondřej VACULÍK, Jakub POLÁČEK, Filip JOZEFOV, Tomáš MAJTNER a Panagiotis ALEXIOU. ENNGene: an Easy Neural Network model building tool for Genomics. Online. BMC Genomics. BioMed Central, roč. 23, č. 1, s. 248-258. ISSN 1471-2164. Dostupné z: https://dx.doi.org/10.1186/s12864-022-08414-x

GREŠOVÁ, Katarína, Petr ŠIMEČEK, Vlastimil MARTINEK, David ČECHÁK a Panagiotis ALEXIOU. Genomic Benchmarks: A Collection of Datasets for Genomic Sequence Classification. Online. ISBN 978-80-7592-127-7

KLIMENTOVÁ, Eva, Václav HEJRET, Katarína GREŠOVÁ, Ilektra-Chara GIASSA a Panagiotis ALEXIOU. miRBind: a Deep Learning method for miRNA binding classification. Online. ISBN 978-80-7592-127-7

KLIMENTOVÁ, Eva, Václav HEJRET, Ján KRČMÁŘ, Katarína GREŠOVÁ, Ilektra-Chara GIASSA a Panagiotis ALEXIOU. miRBind: A Deep Learning Method for miRNA Binding Classification. Online. GENES. MDPI, roč. 13, č. 12, s. 2323-2335. ISSN 2073-4425. Dostupné z: https://dx.doi.org/10.3390/genes13122323

HEJRET, Václav, Nandan Mysore VARADARAJAN, Eva KLIMENTOVÁ, Ilektra-Chara GIASSA, Štěpánka VAŇÁČOVÁ a Panagiotis ALEXIOU. Noncanonical small RNA chimeras identified by AGO2-CLASH. Online. In 16th Microsymposium on RNA Biology

BHAGAT, Kriti, Ilektra-Chara GIASSA a Panagiotis ALEXIOU. PENGUINN-RNA: prediction of RNA G-quadruplexes using interpretable Neural Networks. Online. ISBN 978-80-7592-127-7

GREŠOVÁ, Katarína, Panagiotis ALEXIOU a Ilektra-Chara GIASSA. Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. Online. BIOLOGY-BASEL. BASEL: MDPI, roč. 11, č. 12, s. 1798-1821. ISSN 2079-7737. Dostupné z: https://dx.doi.org/10.3390/biology11121798

GIASSA, Ilektra-Chara a Panagiotis ALEXIOU. Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements. Online. BIOLOGY-BASEL. BASEL: MDPI, roč. 10, č. 9, s. 896-917. ISSN 2079-7737. Dostupné z: https://dx.doi.org/10.3390/biology10090896

PERDIKOPANIS, N., Georgios GEORGAKILAS, D. GRIGORIADIS, V. PIERROS, I. KAVAKIOTIS, Panagiotis ALEXIOU a A. HATZIGEORGIOU. DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. Online. Nucleic acids research. Oxford: Oxford University Press, roč. 49, D1, s. "D151"-"D159", 9 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa1060

ŠTĚTKOVÁ, Monika, Kateřina GROWKOVÁ, Petr FOJTÍK, Barbora VALČÍKOVÁ, Veronika PALUŠOVÁ, Amandine VERLANDE, Radek JORDA, Vladimír KRYŠTOF, Václav HEJRET, Panagiotis ALEXIOU, Vladimír ROTREKL a Stjepan ULDRIJAN. CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells. Online. CELL DEATH & DISEASE. LONDON: NATURE PUBLISHING GROUP, roč. 11, č. 9, s. 1-14. ISSN 2041-4889. Dostupné z: https://dx.doi.org/10.1038/s41419-020-02971-3

GEORGAKILAS, Georgios, Andrea GRIONI, Konstantinos G. LIAKOS, Eliška CHALUPOVÁ, Fotis C. PLESSAS a Panagiotis ALEXIOU. Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci. Online. Scientific reports. London: Nature Research, roč. 10, č. 1, s. 1-10. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-020-66454-3

KLIMENTOVÁ, Eva, Jakub POLÁČEK, Petr ŠIMEČEK a Panagiotis ALEXIOU. PENGUINN: Precise Exploration of Nuclear G-Quadruplexes Using Interpretable Neural Networks. Online. Frontiers in Genetics. Lausanne: Frontiers, roč. 11, OCT, s. 568546-568552. ISSN 1664-8021. Dostupné z: https://dx.doi.org/10.3389/fgene.2020.568546

GRIONI, Andrea, Georgios GEORGAKILAS a Panagiotis ALEXIOU. Dicier: a Fine-tuned Bioinformatics Pipeline to Detect Micro-RNA Chimeric Reads. Online. In ASCB / EMBO 2019 meeting