Publication Records

YAMOUNE, Amel, Markéta ŽĎÁRSKÁ, Thomas DEPAEPE, Anna RUDOLFOVÁ, Jan SKALÁK, Kenneth Wayne BERENDZEN, Virtudes MIRA-RODADO, Michael FITZ, Blanka PEKÁROVÁ, Katrina Leslie MALÁ, Paul TARR, Eliška ŠPAČKOVÁ, Lucia TOMOVIČOVÁ, Barbora PARIZKOVA, Abigail FRANCZYK, Ingrid KOVÁČOVÁ, Vladislav DOLGIKH, Elena ZEMLYANSKAYA, Markéta PERNISOVÁ, Ondrej NOVAK, Elliot MEYEROWITZ, Klaus HARTER, Dominique VAN DER STRAETEN and Jan HEJÁTKO. Cytokinins regulate spatially specific ethylene production to control root growth in Arabidopsis. 2024. Available from: https://dx.doi.org/10.1016/j.xplc.2024.101013.

MARTINEK, Vlastimil, Jessica MARTIN, Cedric BELAIR, Matthew J PAYEA, Sulochan MALLA, Panagiotis ALEXIOU and Manolis MARAGKAKIS. Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics. NAR Genomics and Bioinformatics. Oxford University Press (OUP), 2024, Vol. 6, Issue 3. Available from: https://dx.doi.org/10.1093/nargab/lqae116.

VETEŠNÍKOVÁ ŠIMKOVÁ, Andrea, Kristína KŘÍŽOVÁ, Kristýna VOŘÍŠKOVÁ, Lukáš VETEŠNÍK, Václav HEJRET, Lenka GETTOVÁ, Jiří VOREL, Nikol RESLOVÁ and Vojtěch BYSTRÝ. Heterosis versus breakdown in cyprinid hybrids associated with SVCV infection revealed by transcriptome profile analysis of head kidney. Aquaculture. AMSTERDAM: ELSEVIER, 2024, vol. 578, January, p. "740083", 14 pp. ISSN 0044-8486. Available from: https://dx.doi.org/10.1016/j.aquaculture.2023.740083.

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 and Jan HEJÁTKO. Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth. Plant Physiology. CARY: OXFORD UNIV PRESS INC, 2024, vol. 194, No 1, p. 209-228. ISSN 0032-0889. Available from: https://dx.doi.org/10.1093/plphys/kiad228.

REDMER, Torben, Martin RAIGEL, Christina STERNBERG, Roman ZIEGLER, Clara PROBST, Desiree LINDNER, Astrid AUFINGER, Tanja LIMBERGER, Karolína TRACHTOVÁ, Petra KODAJOVA, Sandra HOEGLER, Michaela SCHLEDERER, Stefan STOIBER, Monika OBERHUBER, Marco BOLIS, Heidi A NEUBAUER, Sara MIRANDA, Martina TOMBERGER, Nora S HARBUSCH, Garces de los Fayos Alonso INES, Felix STERNBERG, Richard MORIGGL, Jean-Philippe THEURILLAT, Boris TICHÝ, Vojtěch BYSTRÝ, Jenny L PERSSON, Stephan MATHAS, Fritz ABERGER, Birgit STROBL, Šárka POSPÍŠILOVÁ, Olaf MERKEL, Gerda EGGER, Sabine LAGGER and Lukas KENNER. JUN mediates the senescence associated secretory phenotype and immune cell recruitment to prevent prostate cancer progression. Molecular Cancer. LONDON: BioMed Central Ltd, 2024, vol. 23, No 1, p. 1-21. ISSN 1476-4598. Available from: https://dx.doi.org/10.1186/s12943-024-02022-x.

SIKORA, Maciej, Eva KLIMENTOVÁ, Dawid UCHAL, Denisa ŠRÁMKOVÁ, Agata P PERLINSKA, Mai Lan NGUYEN, Marta KORPACZ, Roksana MALINOWSKA, Szymon NOWAKOWSKI, Pawel RUBACH, Petr ŠIMEČEK and Joanna I SULKOWSKA. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model. Protein Science. HOBOKEN: WILEY, 2024, vol. 33, No 7, p. 1-21. ISSN 0961-8368. Available from: https://dx.doi.org/10.1002/pro.4998.

JACQUES, Florian, Tomas TICHOPAD, Martin DEMKO, Vojtech BYSTRY, Kristína KŘÍŽOVÁ, Mária SEIFERTOVÁ, Kristýna VOŘÍŠKOVÁ, Md Mehedi Hasan FUAD, Lukáš VETEŠNÍK and Andrea VETEŠNÍKOVÁ ŠIMKOVÁ. Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction. BMC Genomics. London: BioMed Central Ltd, 2024, vol. 25, No 1, p. 1-22. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-024-10462-4.

KADLČÍK, Marek, Michal ŠTEFÁNIK, Ondřej SOTOLÁŘ and Vlastimil MARTINEK. Self-Training Language Models in Arithmetic Reasoning. In ICLR 2024 Workshop on Large Language Model (LLM) Agents. 2024.

HOFERKOVÁ, Eva, Václav ŠEDA, Soňa CESNÁRIKOVÁ, Jan VERNER, Tomáš LOJA, Květoslava MATULOVÁ, Hana SKUHROVÁ FRANCOVÁ, Eva ONDROUŠKOVÁ, Daniel FILIP, Nicolas BLAVET, Miroslav BOUDNÝ, Gabriela MLADONICKÁ PAVLASOVÁ, Josef VEČEŘA, Laura ONDRIŠOVÁ, Petra PAVELKOVÁ, Kryštof HLAVÁČ, Lenka KOŠŤÁLOVÁ, Androniki MICHAELOU, Šárka POSPÍŠILOVÁ, Jana DORAZILOVÁ, Václav CHOCHOLA, Josef JAROŠ, Michael DOUBEK, Marie JAROŠOVÁ, Aleš HAMPL, Lucy VOJTOVÁ, Leoš KŘEN, Jiří MAYER and Marek MRÁZ. Stromal cells engineered to express T cell factors induce robust CLL cell proliferation in vitro and in PDX co-transplantations allowing the identification of RAF inhibitors as anti-proliferative drug. Leukemia. LONDON: SPRINGERNATURE, 2024, vol. 38, No 8, p. 1-13. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-024-02284-w.

LYČKA, Martin, Michal BUBENÍK, Michal ZÁVODNÍK, Vratislav PESKA, Petr FAJKUS, Martin DEMKO, Jiří FAJKUS and Miloslava FOJTOVÁ. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Research. Oxford: Oxford University Press, 2024, vol. 52, D1, p. "D311"-"D321", 11 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad672.

ŠIMONÍK, Jan, Pavla BOUCHALOVÁ, Petr LAPČÍK, David POTĚŠIL, Ján PODHOREC, Lucia JANÁČOVÁ, Hlobilková ALICE, Kateřina JURÁSKOVÁ, Alexandr POPRACH, Hora MILAN, Fiala ONDŘEJ and Pavel BOUCHAL. Transmembrane glycoprotein GPNMB is a candidate predictive biomarker and potentially a therapeutic target in metastatic renal cell carcinoma. In Human Proteome Organization 2024. 2024.

FUAD, Md Mehedi Hasan, Tomas TICHOPAD, Marketa ONDRACKOVA, Kristína KŘÍŽOVÁ, Mária SEIFERTOVÁ, Kristýna VOŘÍŠKOVÁ, Martin DEMKO, Lukáš VETEŠNÍK and Andrea VETEŠNÍKOVÁ ŠIMKOVÁ. Trematode Diplostomum pseudospathaceum inducing differential immune gene expression in sexual and gynogenetic gibel carp (Carassius gibelio): parasites facilitating the coexistence of two reproductive forms of the invasive species. Frontiers in immunology. LAUSANNE: Frontiers Media S.A., 2024, vol. 15, June, p. "1392569", 16 pp. ISSN 1664-3224. Available from: https://dx.doi.org/10.3389/fimmu.2024.1392569.

HEJRET, Václav, Nandan Mysore VARADARAJAN, Eva KLIMENTOVÁ, Katarína GREŠOVÁ, Ilektra-Chara GIASSA, Štěpánka VAŇÁČOVÁ and Panagiotis ALEXIOU. Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation. Scientific Reports. Nature Research, 2023, vol. 13, No 1, p. 1-9. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-023-49757-z.

KADLČÍK, Marek, Michal ŠTEFÁNIK, Ondřej SOTOLÁŘ and Vlastimil MARTINEK. Calc-X and Calcformers: Empowering Arithmetical Chain-of-Thought through Interaction with Symbolic Systems. Online. In Houda Bouamor, Juan Pino, Kalika Bali. Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing: Main track. Singapore: Association for Computational Linguistics, 2023, p. 12101-12108. ISBN 979-8-89176-060-8. Available from: https://dx.doi.org/10.18653/v1/2023.emnlp-main.742.

ZÁVACKÁ, Kristýna, Petr TAUŠ, Karol PÁL, Jakub Paweł PORC, Šárka PAVLOVÁ, Jitka MALČÍKOVÁ, Kamila STRÁNSKÁ, Marcela ŽENATOVÁ, Boris TICHÝ, Nicolas BLAVET, Anna PANOVSKÁ, Michael DOUBEK, Šárka POSPÍŠILOVÁ and Karla PLEVOVÁ. Clonal competition and disrupted molecular processes in chronic lymphocytic leukemia. In XXVIIth Biochemistry congress. 2023. ISBN 978-80-8240-048-2.

PESCHELOVÁ, Helena, Veronika MANČÍKOVÁ, Lenka DOSTÁLOVÁ, Adriana LADUNGOVÁ, Dominika ŠKRNOVÁ, Václav HEJRET and Michal ŠMÍDA. CRISPR/Cas9 technology as a useful tool in the study of chornic lymphocytic leukemia. In CRISPR as a research tool in cancer and regenerative medicine, Stockholm, Švédsko. 2023.

PESCHELOVÁ, Helena, Veronika KOZLOVÁ, Veronika MANČÍKOVÁ, Lenka DOSTÁLOVÁ, Adriana LADUNGOVÁ, Dominika ŠKRNOVÁ, Václav HEJRET and Michal ŠMÍDA. CRISPR/Cas9 technology as a useful tool in the study of chronic lymphocytic leukemia. In PhD and PostDoc RETREAT, Sněžné, Milovy. 2023.

MANČÍKOVÁ, Veronika, Michaela PEŠOVÁ, Šárka PAVLOVÁ, Robert HELMA, Kristýna ZÁVACKÁ, Václav HEJRET, Petr TAUŠ, Jakub HYNŠT, Karla PLEVOVÁ, Jitka MALČÍKOVÁ and Šárka POSPÍŠILOVÁ. Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in the activation of circumjacent pathways upon DNA damage. MOLECULAR ONCOLOGY. ENGLAND: WILEY, 2023, vol. 17, No 1, p. 82-97. ISSN 1574-7891. Available from: https://dx.doi.org/10.1002/1878-0261.13337.

PEŠOVÁ, Michaela, Veronika MANČÍKOVÁ, Robert HELMA, Šárka PAVLOVÁ, Václav HEJRET, Petr TAUŠ, Jakub HYNŠT, Karla PLEVOVÁ, Jana KOTAŠKOVÁ, Jitka MALČÍKOVÁ and Šárka POSPÍŠILOVÁ. Distinct p53 Phosphorylation Patterns in Chronic Lymphocytic Leukemia: Where They Come from and How They Affect p53 Function. In PhD and PostDoc RETREAT, Sněžné, Milovy. 2023.

SOUČKOVÁ, Kamila, Matej JASÍK, Iva SOVADINOVÁ, Alexandr SEMBER, Eliška SYCHROVÁ, Anna KONIECZNA, Vojtěch BYSTRÝ, Iva DYKOVÁ, Radim BLAŽEK, Karolína LUKŠÍKOVÁ, Tomáš PAVLICA, Marek JANKÁSEK, Marie ALTMANOVÁ, Jakub ŽÁK, Adriána ZBONČÁKOVÁ, Martin REICHARD and Ondřej SLABÝ. From fish to cells: Establishment of continuous cell lines from embryos of annual killifish Nothobranchius furzeri and N. kadleci. Aquatic Toxicology. Elsevier, 2023, vol. 259, June, p. 1-16. ISSN 0166-445X. Available from: https://dx.doi.org/10.1016/j.aquatox.2023.106517.

GREŠOVÁ, Katarína, Vlastimil MARTINEK, David ČECHÁK, Petr ŠIMEČEK and Panagiotis ALEXIOU. Genomic benchmarks: a collection of datasets for genomic sequence classification. BMC Genomic Data. 2730-6844: BMC, 2023, vol. 24, No 1, p. 1-9. ISSN 2730-6844. Available from: https://dx.doi.org/10.1186/s12863-023-01123-8.

BALAKHONOVA, Veronika, Tereza DOBISOVÁ, Zuzana BENEDIKTY, Klara PANZAROVA, Jaromir PYTELA, Radka KOCI, Ioannis SPYROGLOU, Ingrid KOVÁČOVÁ, Dominique ARNAUD, Jan SKALÁK, Martin TRTILEK and Jan HEJÁTKO. iReenCAM: automated imaging system for kinetic analysis of photosynthetic pigment biosynthesis at high spatiotemporal resolution during early deetiolation. Frontiers in Plant Science. Frontiers Media SA, 2023, vol. 14, April, p. 1-15. ISSN 1664-462X. Available from: https://dx.doi.org/10.3389/fpls.2023.1093292.

ATANASOVA, Velina S, Crhistian de Jesus CARDONA, Václav HEJRET, Andreas TIEFENBACHER, Theresia MAIR, Loan TRAN, Janette PFNEISSL, Kristina DRAGANIC, Carina BINDER, Julijan KABILJO, Janik CLEMENT, Katharina WOERAN, Barbara NEUDERT, Sabrina WOHLHAUPTER, Astrid HAASE, Sandra DOMAZET, Markus HENGSTSCHLAEGER, Markus MITTERHAUSER, Leonhard MUELLAUER, Boris TICHÝ, Michael BERGMANN, Gabriele SCHWEIKERT, Markus HARTL, Helmut DOLZNIG and Gerda EGGER. Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model. CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY. UNITED STATES: ELSEVIER INC, 2023, vol. 15, No 6, p. 1391-1419. ISSN 2352-345X. Available from: https://dx.doi.org/10.1016/j.jcmgh.2023.02.014.

HRACHOVINOVÁ, Šárka, Pavla BOUCHALOVÁ, Petr LAPČÍK, David POTĚŠIL, Kateřina JURÁSKOVÁ, Vojtěch BYSTRÝ, Boris TICHÝ, Rudolf NENUTIL, Roman HRSTKA and Pavel BOUCHAL. Proteogenomic Classification of Triple-Negative Breast Cancer for Prognosis and Targeted Therapy. In Abstract Book of Doctoral conference 2023, Brno, CZ, 1.6.2023. 2023.

SPIELVOGEL, Clemens P, Stefan STOIBER, Laszlo PAPP, Denis KRAJNC, Marko GRAHOVAC, Elisabeth GURNHOFER, Karolína TRACHTOVÁ, Vojtěch BYSTRÝ, Asha LEISSER, Bernhard JANK, Julia SCHNOELL, Lorenz KADLETZ, Gregor HEIDUSCHKA, Thomas BEYER, Marcus HACKER, Lukas KENNER and Alexander R HAUG. Radiogenomic markers enable risk stratification and inference of mutational pathway states in head and neck cancer. European Journal of Nuclear Medicine and Molecular Imaging. NEW YORK: SPRINGER, 2023, vol. 50, No 2, p. 546-558. ISSN 1619-7070. Available from: https://dx.doi.org/10.1007/s00259-022-05973-9.

LUKAVSKY, Peter, Dalibor BLAŽEK, Vojtěch BYSTRÝ, Anna HELÁNOVÁ and Barbora TRUKSOVÁ. RNA Summer School 2023. 2023.

FULNEČEK, Jaroslav, Eva KLIMENTOVÁ, Albert CAIRO CALZADA, Soňa BUKOVČÁKOVÁ, Panagiotis ALEXIOU, Zbyněk PROKOP and Karel ŘÍHA. The SAP domain of Ku facilitates its efficient loading onto DNA ends. Nucleic Acids Research. Oxford: Oxford University Press, 2023, vol. 51, No 21, p. 11706-11716. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad850.

JEDLIČKOVÁ, Veronika, Václav HEJRET, Martin DEMKO, Pavel JEDLIČKA, Marie ŠTEFKOVÁ and Helene ROBERT BOISIVON. Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus. BMC Genomics. London: BioMed Central Ltd, 2023, vol. 24, No 1, p. 1-15. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-023-09316-2.

VETEŠNÍKOVÁ ŠIMKOVÁ, Andrea, Kristína KŘÍŽOVÁ, Kristýna VOŘÍŠKOVÁ, Lukáš VETEŠNÍK, Vojtěch BYSTRÝ and Martin DEMKO. Transcriptome Profile Analyses of Head Kidney in Roach (Rutilus rutilus), Common Bream (Abramis brama) and Their Hybrids: Does Infection by Monogenean Parasites in Freshwater Fish Reveal Differences in Fish Vigour among Parental Species and Their Hybrids? Biology. Basel: MDPI, 2023, vol. 12, No 9, p. 1-29. ISSN 2079-7737. Available from: https://dx.doi.org/10.3390/biology12091199.

PÍREK, Pavlína, Karolína KRYŠTOFOVÁ, Ingrid KOVÁČOVÁ, Anna KROMEROVÁ, Dagmar ZACHOVÁ, Ondřej HELIA, Klara PANZAROVA, Jiří FAJKUS, Zbyněk ZDRÁHAL, Gabriela LOCHMANOVÁ and Miloslava FOJTOVÁ. Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors. PLANTS-BASEL. BASEL: MDPI, 2023, vol. 12, No 24, p. 1-16. ISSN 2223-7747. Available from: https://dx.doi.org/10.3390/plants12244177.

ČERMÁK, Milan, Tatiana FRITZOVÁ, Vít RUSŇÁK and Denisa ŠRÁMKOVÁ. Using relational graphs for exploratory analysis of network traffic data. Forensic Science International: Digital Investigation. 2023, vol. 45, S, p. 1-10. ISSN 2666-2825. Available from: https://dx.doi.org/10.1016/j.fsidi.2023.301563.

DRÁBOVÁ, Klára, Petra POKORNÁ, Hana PÁLOVÁ, Sabina ADAMCOVÁ, Vojtěch BYSTRÝ, Robin JUGAS, Ondřej SLABÝ and Jaroslav ŠTĚRBA. Výsledky celoexomového sekvenování germinální DNA u dětských pacientů se solidními tumory (Results of whole-exome sequencing of germline DNA in pediatric patients with solid tumors). In Kaprasův den 2023, Praha. 2023.

SKLENÁŘ, Vladimír, Radovan FIALA, Jiří NOVÁČEK, Josef HOUSER, Jan PŘIBYL, Zbyněk ZDRÁHAL, Milan EŠNER, Michal MIKL, Boris TICHÝ, Vojtěch BYSTRÝ and Radka SVOBODOVÁ. CF Day Meeting. 2022.

DOSTÁLOVÁ, Lenka, Aneta LEDEREROVÁ, Helena PESCHELOVÁ, Václav HEJRET and Michal ŠMÍDA. CRISPR/Cas9 knockout screening revealed genes involved in CD20 regulation. In Annual PhD conference Biomedical sciences, Brno. 2022.

PEŠOVÁ, Michaela, Veronika MANČÍKOVÁ, Robert HELMA, Šárka PAVLOVÁ, Václav HEJRET, Petr TAUŠ, Jakub HYNŠT, Karla PLEVOVÁ, Jana KOTAŠKOVÁ, Jitka MALČÍKOVÁ and Šárka POSPÍŠILOVÁ. Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in circumjacent pathways activation upon DNA damage. In Mendel genetics Conference 2022. 2022.

PEŠOVÁ, Michaela, Veronika MANČÍKOVÁ, Robert HELMA, Šárka PAVLOVÁ, Václav HEJRET, Petr TAUŠ, Jakub HYNŠT, Karla PLEVOVÁ, Jana KOTAŠKOVÁ, Jitka MALČÍKOVÁ and Šárka POSPÍŠILOVÁ. Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in circumjacent pathways activation upon DNA damage. In EHA 2022 in HemaSphere 2022; 6(S3): 976. 2022.

PEŠOVÁ, Michaela, Veronika MANČÍKOVÁ, Robert HELMA, Šárka PAVLOVÁ, Václav HEJRET, Petr TAUŠ, Jakub HYNŠT, Karla PLEVOVÁ, Jana KOTAŠKOVÁ, Jitka MALČÍKOVÁ and Šárka POSPÍŠILOVÁ. Distinct p53 phospohrylation patterns in chronic lymphocytic leukemia patients are reflected in circumjacent pathways activation upon DNA damage. In PhD retreat 2022, Telč. 2022.

CHALUPOVÁ, Eliška, Ondřej VACULÍK, Jakub POLÁČEK, Filip JOZEFOV, Tomáš MAJTNER and Panagiotis ALEXIOU. ENNGene: an Easy Neural Network model building tool for Genomics. BMC Genomics. BioMed Central, 2022, vol. 23, No 1, p. 248-258. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-022-08414-x.

FROHLICH, Jan, Kristina KOVACOVICOVA, Marco RAFFAELE, Tereza VIRGLOVA, Eliska CIZKOVA, Jan KUČERA, Julie DOBROVOLNÁ, Martin WABITSCH, Marion PEYROU, Francesca BONOMINI, Rita REZZANI, George N. CHALDAKOV, Anton B. TONCHEV, Michelino DI ROSA, Nicolas BLAVET, Václav HEJRET and Manlio VINCIGUERRA. GDF11 inhibits adipogenesis and improves mature adipocytes metabolic function via WNT/beta-catenin and ALK5/SMAD2/3 pathways. Cell Proliferation. 2022, vol. 55, No 10, p. 1-15. ISSN 0960-7722. Available from: https://dx.doi.org/10.1111/cpr.13310.

VALISKOVA, Barbora, Sona GREGOROVA, Diana LUSTYK, Petr ŠIMEČEK, Petr JANSA and Jiri FOREJT. Genic and chromosomal components of Prdm9-driven hybrid male sterility in mice (Mus musculus). Genetics. BETHESDA (USA): GENETICS SOCIETY AMERICA, 2022, vol. 222, No 1, p. 1-14. ISSN 0016-6731. Available from: https://dx.doi.org/10.1093/genetics/iyac116.

GREŠOVÁ, Katarína, Petr ŠIMEČEK, Vlastimil MARTINEK, David ČECHÁK and Panagiotis ALEXIOU. Genomic Benchmarks: A Collection of Datasets for Genomic Sequence Classification. 2022. ISBN 978-80-7592-127-7.

NEMERGUT, Michal, Tereza BÁŤKOVÁ, Dana VIGAŠOVÁ, Milan BARTOŠ, Martina HLOZANKOVA, Andrea SMITH, Barbora LIŠKOVÁ, Kateřina SHEARDOVÁ, Martin VYHNALEK, Jakub HORT, Jan LACZO, Ingrid KOVÁČOVÁ, Michal ŠITINA, Radoslav MATEJ, Radim JANČÁLEK, Martin MAREK and Jiří DAMBORSKÝ. Increased occurrence of Treponema spp. and double-species infections in patients with Alzheimer's disease. Science of the Total Environment. Amsterdam: Elsevier Science, 2022, vol. 844, October 2022, p. 1-7. ISSN 0048-9697. Available from: https://dx.doi.org/10.1016/j.scitotenv.2022.157114.

LIMBERGER, Tanja, Michaela SCHLEDERER, Karolína TRACHTOVÁ, Ines Garces de los Fayos ALONSO, Jiaye YANG, Sandra HOEGLER, Christina STERNBERG, Vojtěch BYSTRÝ, Jan OPPELT, Boris TICHÝ, Margit SCHMEIDL, Petra KODAJOVA, Anton JAEGER, Heidi A NEUBAUER, Monika OBERHUBER, Belinda S SCHMALZBAUER, Šárka POSPÍŠILOVÁ, Helmut DOLZNIG, Wolfgang WADSAK, Zoran CULIG, Suzanne Dawn TURNER, Gerda EGGER, Sabine LAGGER and Lukas KENNER. KMT2C methyltransferase domain regulated INK4A expression suppresses prostate cancer metastasis. Molecular Cancer. LONDON: BioMed Central, 2022, vol. 21, No 1, p. 89-107. ISSN 1476-4598. Available from: https://dx.doi.org/10.1186/s12943-022-01542-8.

POPPOVÁ, Lucie, Šárka PAVLOVÁ, Beatriz GONZALEZ, Jana KOTAŠKOVÁ, Karla PLEVOVÁ, Gabrijela DUMBOVIC, Pavlína JANOVSKÁ, Vojtěch BYSTRÝ, Anna PANOVSKÁ, Lucie BEZDĚKOVÁ, Stanislava MAŠLEJOVÁ, Yvona BRYCHTOVÁ, Michael DOUBEK, Marcela KRZYŽÁNKOVÁ, Marek BORSKÝ, Jiří MAYER, Vítězslav BRYJA, Sergio ALONSO and Šárka POSPÍŠILOVÁ. Memory B-cell like chronic lymphocytic leukaemia is associated with specific methylation profile of WNT5A promoter and undetectable expression of WNT5A gene. Epigenetics. Philadelphia: TAYLOR & FRANCIS INC, 2022, vol. 17, No 12, p. 1628-1635. ISSN 1559-2294. Available from: https://dx.doi.org/10.1080/15592294.2022.2050004.

KLIMENTOVÁ, Eva, Václav HEJRET, Katarína GREŠOVÁ, Ilektra-Chara GIASSA and Panagiotis ALEXIOU. miRBind: a Deep Learning method for miRNA binding classification. 2022. ISBN 978-80-7592-127-7.

KLIMENTOVÁ, Eva, Václav HEJRET, Ján KRČMÁŘ, Katarína GREŠOVÁ, Ilektra-Chara GIASSA and Panagiotis ALEXIOU. miRBind: A Deep Learning Method for miRNA Binding Classification. GENES. MDPI, 2022, vol. 13, No 12, p. 2323-2335. ISSN 2073-4425. Available from: https://dx.doi.org/10.3390/genes13122323.

HEJRET, Václav, Nandan Mysore VARADARAJAN, Eva KLIMENTOVÁ, Ilektra-Chara GIASSA, Štěpánka VAŇÁČOVÁ and Panagiotis ALEXIOU. Noncanonical small RNA chimeras identified by AGO2-CLASH. In 16th Microsymposium on RNA Biology. 2022.

BHAGAT, Kriti, Ilektra-Chara GIASSA and Panagiotis ALEXIOU. PENGUINN-RNA: prediction of RNA G-quadruplexes using interpretable Neural Networks. 2022. ISBN 978-80-7592-127-7.

HAKL, Roman, Pavel KUKLÍNEK, Marta SOBOTKOVA, Irena KRCMOVA, Pavlina KRALICKOVA, Martina VACHOVA, Jana HANZLIKOVA, Martina NOVACKOVA, Michal SVOBODA, Ingrid KOVÁČOVÁ and Jiří LITZMAN. Registry-based analysis of Icatibant and C1-inhibitor use in treatment of laryngeal attacks of hereditary angioedema. CLINICAL AND EXPERIMENTAL ALLERGY. HOBOKEN: WILEY, 2022, vol. 52, No 8, p. 994-997. ISSN 0954-7894. Available from: https://dx.doi.org/10.1111/cea.14182.

BYSTRÝ, Vojtěch, Viktor MAŠÍČEK, Nicolas MOKRIŠ and Martin DEMKO. SeqUIa: Softwarová platforma pro zpracování sekvenování nové generace skrze grafické rozhraní (SeqUIa: Software platform for GUI based next generation sequencing data analysis). 2022.

GREŠOVÁ, Katarína, Panagiotis ALEXIOU and Ilektra-Chara GIASSA. Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. BIOLOGY-BASEL. BASEL: MDPI, 2022, vol. 11, No 12, p. 1798-1821. ISSN 2079-7737. Available from: https://dx.doi.org/10.3390/biology11121798.

MARTINO, Fabiana, Nandan Mysore VARADARAJAN, Ana Rubina PERESTRELO, Václav HEJRET, Helena DURIKOVA, Dragana VUKIĆ, Vladimir HORVATH, Francesca CAVALIERI, Frank CARUSO, Waleed S ALBIHLAL, Andre P GERBER, Mary Anne O'CONNELL, Štěpánka VAŇÁČOVÁ, Stefania PAGLIARI and Giancarlo FORTE. The mechanical regulation of RNA binding protein hnRNPC in the failing heart. Science Translational Medicine. Washington: American Association for the Advancement of Science, 2022, vol. 14, No 672, p. 1-17. ISSN 1946-6234. Available from: https://dx.doi.org/10.1126/scitranslmed.abo5715.

MURESAN, Ximena M., Eva SLABÁKOVÁ, Jiřina PROCHÁZKOVÁ, Stanislav DRÁPELA, Radek FEDR, Markéta PÍCKOVÁ, Ondřej VACEK, Ráchel VÍCHOVÁ, Tereza SUCHÁNKOVÁ, Jan BOUCHAL, Daniela KÜRFÜRSTOVÁ, Milan KRÁL, Tereza HULÍNOVÁ, Radek P. SÝKORA, Vladimír ŠTUDENT, Václav HEJRET, Wytske M. VAN WEERDEN, Martin PUHR, Václav PUSTKA, David POTĚŠIL, Zbyněk ZDRÁHAL, Zoran CULIG and Karel SOUČEK. Toll-Like Receptor 3 Overexpression Induces Invasion of Prostate Cancer Cells, whereas Its Activation Triggers Apoptosis. American Journal of Pathology. Elsevier, 2022, vol. 192, No 9, p. 1321-1335. ISSN 0002-9440. Available from: https://dx.doi.org/10.1016/j.ajpath.2022.05.009.

MURESAN, Ximena M., Eva SLABÁKOVÁ, Jiřina PROCHÁZKOVÁ, Stanislav DRÁPELA, Radek FEDR, Markéta PÍCKOVÁ, Ondřej VACEK, Ráchel VÍCHOVÁ, Tereza SUCHÁNKOVÁ, Jan BOUCHAL, Daniela KÜRFÜRSTOVÁ, Milan KRÁL, Tereza HULÍNOVÁ, Radek P. SÝKORA, Vladimír ŠTUDENT, Václav HEJRET, Wytske M. VAN WEERDEN, Martin PUHR, Václav PUSTKA, David POTĚŠIL, Zbyněk ZDRÁHAL, Zoran CULIG and Karel SOUČEK. Toll-Like Receptor 3 Overexpression Induces Invasion of Prostate Cancer Cells, whereas Its Activation Triggers Apoptosis. American Journal of Pathology. Elsevier, 2022, vol. 192, No 9, p. 1321-1335. ISSN 0002-9440. Available from: https://dx.doi.org/10.1016/j.ajpath.2022.05.009.

DRÁBOVÁ, Klára, Petra POKORNÁ, Hana PÁLOVÁ, Soňa ADAMCOVÁ, Vojtěch BYSTRÝ, Robin JUGAS, Ondřej SLABÝ and Jaroslav ŠTĚRBA. Výsledky celoexomového sekvenování germinální DNA u dětských pacientů se solidními tumory. In XXV. Biologické dny. 2022.

GIASSA, Ilektra-Chara and Panagiotis ALEXIOU. Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements. BIOLOGY-BASEL. BASEL: MDPI, 2021, vol. 10, No 9, p. 896-917. ISSN 2079-7737. Available from: https://dx.doi.org/10.3390/biology10090896.

PEŠOVÁ, Michaela, Veronika MANČÍKOVÁ, Šárka PAVLOVÁ, Robert HELMA, Jitka MALČÍKOVÁ, Marcela ŽENATOVÁ, Václav HEJRET, Petr TAUŠ, Jana KOTAŠKOVÁ, Karla PLEVOVÁ, Michael DOUBEK, Jiří MAYER and Šárka POSPÍŠILOVÁ. Fosforylace proteinu p53: vliv na aktivitu dráhy p53 po poškození DNA u chronické lymfocytární leukémie. In II. Český hematologický a transfuziologický sjezd v Transfuze a Hematologie Dnes (2021). 2021.

DYKOVÁ, Iva, Jakub ŽÁK, Martin REICHARD, Kamila SOUČKOVÁ, Ondřej SLABÝ, Vojtěch BYSTRÝ and Radim BLAŽEK. Histopathology of laboratory-reared Nothobranchius fishes: Mycobacterial infections versus neoplastic lesions. Journal of Fish Diseases. Hoboken: Wiley, 2021, vol. 44, No 8, p. 1179-1190. ISSN 0140-7775. Available from: https://dx.doi.org/10.1111/jfd.13378.

PEŠOVÁ, Michaela, Veronika MANČÍKOVÁ, Šárka PAVLOVÁ, Robert HELMA, Jitka MALČÍKOVÁ, Marcela ŽENATOVÁ, Václav HEJRET, Petr TAUŠ, Jana KOTAŠKOVÁ, Karla PLEVOVÁ, Michael DOUBEK, Jiří MAYER and Šárka POSPÍŠILOVÁ. Phosphorylation patterns of tumor suppressor P53 and their impact on the P53 pathway activity in chronic lymphocytic leukemia. In XIX International Workshop on Chronic Lymphocytic Leukemia (iwCLL). 2021.

LOBELLO, Cosimo, Boris TICHÝ, Vojtěch BYSTRÝ, Lenka RADOVÁ, Daniel FILIP, Marek MRÁZ, I.A. MONTES-MOJARRO, N. PROKOPH, H. LAROSE, H.C. LIANG, G.G. SHARMA, L. MOLOGNI, D. BELADA, K. KAMARADOVA, F. FEND, C. GAMBACORTI-PASSERINI, O. MERKEL, Suzanne Dawn TURNER, Andrea JANÍKOVÁ and Šárka POSPÍŠILOVÁ. STAT3 and TP53 mutations associate with poor prognosis in anaplastic large cell lymphoma. Leukemia. London: Nature Publishing Group, 2021, vol. 35, No 5, p. 1500-1505. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-020-01093-1.

LYČKA, Martin, Vratislav PEŠKA, Martin DEMKO, Ioannis SPYROGLOU, Agata Magdalena KILAR, Jiří FAJKUS and Miloslava FOJTOVÁ. WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. BMC Bioinformatics. London: BioMed Central, 2021, vol. 22, No 1, p. "145", 14 pp. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-021-04064-0.

LOBELLO, Cosimo, Boris TICHÝ, Vojtěch BYSTRÝ, Lenka RADOVÁ, Daniel FILIP, Marek MRÁZ, IA. MONTES-MOJARO, Andrea JANÍKOVÁ and Šárka POSPÍŠILOVÁ. Analysis mutational landscape in systemic anaplastic large cell lymphoma identifies novel prognostic markers. In 20. Pražské hematologické dny (Hematologie 2020), Praha. 2020.

ŠTĚTKOVÁ, Monika, Kateřina GROWKOVÁ, Petr FOJTÍK, Barbora VALČÍKOVÁ, Veronika PALUŠOVÁ, Amandine VERLANDE, Radek JORDA, Vladimír KRYŠTOF, Václav HEJRET, Panagiotis ALEXIOU, Vladimír ROTREKL and Stjepan ULDRIJAN. CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells. CELL DEATH & DISEASE. LONDON: NATURE PUBLISHING GROUP, 2020, vol. 11, No 9, p. 1-14. ISSN 2041-4889. Available from: https://dx.doi.org/10.1038/s41419-020-02971-3.

ŠKOLÁKOVÁ, Petra, Zahra BADRI, Silvie TRANTÍRKOVÁ, Jan RYNEŠ, Jiří ŠPONER, Miloslava FOJTOVÁ, Jiří FAJKUS, Radek MAREK, Michaela VORLÍČKOVÁ, Jean-Louis MERGNY and Lukáš TRANTÍREK. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. BBA - General Subjects. Elsevier B.V., 2020, vol. 1864, No 9, p. 129651-129659. ISSN 0304-4165. Available from: https://dx.doi.org/10.1016/j.bbagen.2020.129651.

PESCHELOVÁ, Helena, Veronika KOZLOVÁ, Veronika MANČÍKOVÁ, Adriana LADUNGOVÁ, Václav HEJRET and Michal ŠMÍDA. CRISPR/CAS9 technology: a useful tool in the study of chronic lymphocytic leukemia. In XXth Interdisciplinary meeting of young researchs and students in the field of chemistry, biochemistry, molecular biology and biomaterials in Chemické listy. 2020. ISSN 2336-7202.

PESCHELOVÁ, Helena, Lenka DOSTÁLOVÁ, Veronika KOZLOVÁ, Aneta LEDEREROVÁ, Václav HEJRET and Michal ŠMÍDA. Genome-wide CRISPR/Cas9 screening reveals novel target genes, whose inactivation is able to upregulate surface expression of immunotherapy target CD20. In 25th Congress of European Hematology Association, Amsterdam, Nizozemsko, in HemaSphere. 2020.

GIASSA, Ilektra-Chara, Andrea VAVRINSKÁ, Jiří ZELINKA, Jakub ŠEBERA, Vladimír SYCHROVSKÝ, Rolf BOELENS, Radovan FIALA and Lukáš TRANTÍREK. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. ChemPlusChem. Weinheim: Wiley - Verlag Chemie, 2020, vol. 85, No 9, p. 2177-2185. ISSN 2192-6506. Available from: https://dx.doi.org/10.1002/cplu.202000505.

REIGL, Tomáš, Jakub Paweł PORC, Kamila STRÁNSKÁ, Karol PÁL, Veronika NAVRKALOVÁ, Jakub HYNŠT, Vojtěch BYSTRÝ, Šárka POSPÍŠILOVÁ, Nikos DARZENTAS and Karla PLEVOVÁ. High throughput sequencing data analysis of IG/TR rearranged genes in leukemie clinical research. In CEITEC PhD Conference, Brno, únor 2020. 2020.

KEENAN, B.T., R.J. GALANTE, J. LIAN, Petr ŠIMEČEK, D.M. GATTI, L. ZHANG, D.C. LIM, K.L. SVENSON, G.A. CHURCHILL and A.I. PACK. High-throughput sleep phenotyping produces robust and heritable traits in Diversity Outbred mice and their founder strains. SLEEP. CARY: OXFORD UNIV PRESS INC, 2020, vol. 43, No 5, p. nestrankovano, 17 pp. ISSN 0161-8105. Available from: https://dx.doi.org/10.1093/sleep/zsz278.

LOBELLO, Cosimo, Vojtěch BYSTRÝ, Lenka RADOVÁ, Daniel FILIP, Marek MRÁZ, IA. MONTES-MOJARRO, N. PROKOPH, H. LAROSE, HCh. LIANG, G. SHARMA, L. MOLOGNI, D. BELADA, K. KAMARÁDOVÁ, F. FEND, C. GAMBACORTI-PASSERINI, O. MERKEL, S. TURNER, Andrea JANÍKOVÁ and Šárka POSPÍŠILOVÁ. Mutational landscape analysis in systematic anaplastic large cell lymphoma identifies novel prognostic markers. In CEITEC PhD Conference, Brno, 2020. 2020.

KLIMENTOVÁ, Eva, Jakub POLÁČEK, Petr ŠIMEČEK and Panagiotis ALEXIOU. PENGUINN: Precise Exploration of Nuclear G-Quadruplexes Using Interpretable Neural Networks. Frontiers in Genetics. Lausanne: Frontiers, 2020, vol. 11, OCT, p. 568546-568552. ISSN 1664-8021. Available from: https://dx.doi.org/10.3389/fgene.2020.568546.

PESCHELOVÁ, Helena, Veronika KOZLOVÁ, Veronika MANČÍKOVÁ, Adriana LADUNGOVÁ, Václav HEJRET and Michal ŠMÍDA. The use of CRISPR/Cas9 technology in the study of chronic lymphocytic leukemia. In CEITEC PhD Conference. 2020.

GRIONI, Andrea, G. FAZIO, S. RIGAMONTI, Vojtěch BYSTRÝ, G. DANIELE, Zuzana DOSTÁLOVÁ, M. QUADRI, C. SAITTA, D. SILVESTRI, S. SONGIA, C.T. STORLAZZI, A. BIONDI, Nikos DARZENTAS and G. CAZZANIGA. A Simple RNA Target Capture NGS Strategy for Fusion Genes Assessment in the Diagnostics of Pediatric B-cell Acute Lymphoblastic Leukemia. HEMASPHERE. PHILADELPHIA: LIPPINCOTT WILLIAMS & WILKINS, 2019, vol. 3, No 3, p. 1-9. ISSN 2572-9241. Available from: https://dx.doi.org/10.1097/HS9.0000000000000250.

ZÁPRAŽNÁ, Kristína, Kamila RÉBLOVÁ, V. SVOBODOVA, Lenka RADOVÁ, Vojtěch BYSTRÝ, Jiří BALOUN, Kristina ĎURECHOVÁ, Nikola TOM, Tomáš LOJA, Martina BUREŠOVÁ, Kamila STRÁNSKÁ, Alexandra OLTOVÁ, Michael DOUBEK, M.L. ATCHISON, Martin TRBUŠEK, Jitka MALČÍKOVÁ and Šárka POSPÍŠILOVÁ. Activation-induced deaminase and its splice variants associate with trisomy 12 in chronic lymphocytic leukemia. Annals of hematology. New York: Springer Verlag, 2019, vol. 98, No 2, p. 423-435. ISSN 0939-5555. Available from: https://dx.doi.org/10.1007/s00277-018-3520-5.

VEČEŘA, Marek, Jan OPPELT, Radim LIPINA, Martin SMRČKA, Radim JANČÁLEK, Michal FILIP, Markéta HERMANOVÁ, Leoš KŘEN, Jiří ŠÁNA and Ondřej SLABÝ. Analýza dlouhých nekódujících RNA v tkáni multiformního glioblastomu a jejich asociace s celkovým přežíváním. In Klinická onkologie. 2019. ISSN 0862-495X.

RAČEK, Tomáš, Ondřej SCHINDLER, Vladimír HORSKÝ, Jaroslav KOČA, Dominik TOUŠEK and Radka SVOBODOVÁ VAŘEKOVÁ. AtomicChargeCalculator II. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Tarakaramji MOTURU, Veronika NAVRÁTILOVÁ, Jaroslav KOČA, Karel BERKA and Radka SVOBODOVÁ VAŘEKOVÁ. Automated family-wide annotation of secondary structure elements. In Alexander E. Kister. Protein supersecondary structures: Methods and protocols. Second Edition. New York: Humana Press, 2019, p. 47-71. Methods in Molecular Biology. ISBN 978-1-4939-9160-0. Available from: https://dx.doi.org/10.1007/978-1-4939-9161-7_3.

MUSILOVÁ, Kateřina, Kateřina AMRUZ ČERNÁ, Sonali SHARMA, Václav ŠEDA, Gabriela MLADONICKÁ PAVLASOVÁ, Jan OPPELT, Daniel FILIP, Veronika ŠANDOVÁ, Laura ONDRIŠOVÁ, Šárka POSPÍŠILOVÁ, Eva VOJÁČKOVÁ, Pedro FARIA ZENI, Jiří MAYER and Marek MRÁZ. B Cell Receptor Signalling Regulation by Non-coding RNAs. In EU-LIFE Scientific Meeting 2019, Cambridge, UK. 2019.

ŠAFRÁNEK, David, Matej TROJÁK, Vojtěch BRŮŽA, Tomáš VEJPUSTEK, Jan PAPOUŠEK, Martin DEMKO, Samuel PASTVA, Aleš PEJZNOCH and Luboš BRIM. Barbaric Robustness Monitoring Revisited for STL* in Parasim. In Bortolussi L., Sanguinetti G. Computational Methods in Systems Biology (CMSB 2019). LNBI 11773. Neuveden: Springer, 2019, p. 356-359. ISBN 978-3-030-31303-6. Available from: https://dx.doi.org/10.1007/978-3-030-31304-3_26.

HYNŠT, Jakub, Karla PLEVOVÁ, Lenka RADOVÁ, Vojtěch BYSTRÝ, Karol PÁL and Šárka POSPÍŠILOVÁ. Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants. PeerJ. London: PEERJ INC, 2019, vol. 7, JUN, p. 7071-7086. ISSN 2167-8359. Available from: https://dx.doi.org/10.7717/peerj.7071.

MLADONICKÁ PAVLASOVÁ, Gabriela, Veronika ŠANDOVÁ, Marek BORSKÝ, Jan OPPELT, Václav ŠEDA, Yvona BRYCHTOVÁ, Šárka POSPÍŠILOVÁ, Michael DOUBEK, Jiří MAYER and Marek MRÁZ. CD20 in the context of microenvironmental interactions of malignant B cells: Implications for targeted therapy. In XXV. Pařízkovy dny, Ostrava. 2019.

DEMKO, Martin, Lukáš CHRÁST, Pavel DVOŘÁK, Jiří DAMBORSKÝ and David ŠAFRÁNEK. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms. Basel: MDPI, 2019, vol. 7, No 11, p. 553-581. ISSN 2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms7110553.

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA, Karel BERKA and Radka SVOBODOVÁ VAŘEKOVÁ. Creation and visualization of secondary structure consensus for protein families. In XX. setkání biochemiků a molekulárních biologů. 2019.

PESCHELOVÁ, Helena, Veronika KOZLOVÁ, Václav HEJRET and Michal ŠMÍDA. CRISPR/Cas9 gene editing and functional screening in chronic lymphocytic leukemia. In Joint retreat 2019, Kouty u Ledče nad Sázavou. 2019. ISBN 978-80-210-9300-3.

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

REIGL, Tomáš, Kamila STRÁNSKÁ, Vojtěch BYSTRÝ, Adam KREJČÍ, Andrea GRIONI, Šárka POSPÍŠILOVÁ, Nikos DARZENTAS and Karla PLEVOVÁ. Encyklopedie subsetů CLL – Unikátní bio informatický nástroj a databáze pro analýzu subsetů stereotypních B buněčných receptorů u CLL (Encyclopedia of CLL subsets - a unique bioinformatics tool and database for analysis of subsets of stereotypical B-Cell receptors in CLL). In Klinická Onkologie. ČR: ČLS JEP, 2019, p. 167-170. ISSN 0862-495X.

REIGL, Tomáš, Kamila STRÁNSKÁ, Vojtěch BYSTRÝ, Adam KREJČÍ, Andrea GRIONI, Šárka POSPÍŠILOVÁ, Nikos DARZENTAS and Karla PLEVOVÁ. Encyklopedie subsetů CLL – unikátní bioinformatický nástroj a databáze pro analýzu subsetů stereotypních B buněčných receptorů u CLL. In XLIII. Brněnské onkologické dny v Klinická Onkologie, Brno. 2019.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB. In XX. setkání biochemiků a molekulárních biologů. 2019. ISBN 978-80-210-9420-8.

FAZIO, G., V. MASSA, Andrea GRIONI, Vojtěch BYSTRÝ, S. RIGAMONTI, C. SAITTA, M. GALBIATI, C. RIZZARI, C. CONSARINO, A. BIONDI, A. SELICORNI and G. CAZZANIGA. First evidence of a paediatric patient with Cornelia de Lange syndrome with acute lymphoblastic leukaemia. Journal of clinical pathology. London: BMJ Publishing Group, 2019, vol. 72, No 8, p. 558-561. ISSN 0021-9746. Available from: https://dx.doi.org/10.1136/jclinpath-2019-205707.

SOUČKOVÁ, Kamila, Radim BLAŽEK, Vojtěch BYSTRÝ, Iva DYKOVÁ, J. ŽÁK, Markéta HERMANOVÁ, Matej JASÍK, Matej POLAČIK, Martin REICHARD and Ondřej SLABÝ. Halančíci jako nový model pro studium věkem podmíněné spontánní karcinogeneze. In XLIII. Brněnské onkologické dny v Klinická Onkologie, Brno. 2019.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB. In CEITEC Joint Retreat 2019. 2019. ISBN 978-80-210-9300-3.

ONDRIŠOVÁ, Laura, Václav ŠEDA, Kateřina AMRUZ ČERNÁ, Gabriela MLADONICKÁ PAVLASOVÁ, Eva VOJÁČKOVÁ, Jan OPPELT, Daniel FILIP, Veronika ŠANDOVÁ, Jiří MAYER and Marek MRÁZ. Mechanism of leukemia cell adaptation to targeted therapy in chronic lymphocytic leukemia. In XIX. Interdisciplinary meeting of young life scientists in Czech Chemical Society Symposium Series. 2019.

AMRUZ ČERNÁ, Kateřina, Jan OPPELT, Václav CHOCHOLA, Kateřina MUSILOVÁ, Václav ŠEDA, Gabriela PAVLASOVÁ, Lenka RADOVÁ, M. ARIGONI, R.A. CALOGERO, V. BENES, Martin TRBUŠEK, Yvona BRYCHTOVÁ, Michael DOUBEK, Jiří MAYER, Šárka POSPÍŠILOVÁ and Marek MRÁZ. MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells (MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells.). Leukemia. London: Nature Publishing Group, 2019, vol. 33, No 2, p. 403-414. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-018-0230-x.

WAYHELOVÁ, Markéta, Jan OPPELT, Jan SMETANA, Eva HLADÍLKOVÁ, Hana FILKOVÁ, Eva MAKATUROVÁ, Petra NIKOLOVÁ, Rastislav BEHARKA, Renata GAILLYOVÁ and Petr KUGLÍK. Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay. Molecular Medicine Reports. Athens: SPANDIDOS PUBL LTD, 2019, vol. 20, No 1, p. 505-512. ISSN 1791-2997. Available from: https://dx.doi.org/10.3892/mmr.2019.10303.

SCHINDLER, Ondřej, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. Partial atomic charges for proteins. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

POPPOVÁ, Lucie, Pavlína JANOVSKÁ, B. GONZALEZ, Karla PLEVOVÁ, Vojtěch BYSTRÝ, Karol PÁL, Hana PLEŠINGEROVÁ, Marek BORSKÝ, Helena OLBERTOVÁ, Jana KOTAŠKOVÁ, BRYCHTOVÁ, Michael DOUBEK, PAVLOVÁ, S ALONSO, Vítězslav BRYJA and Šárka POSPÍŠILOVÁ. Promoter Methylation of ROR1 Ligand WNT5A associates with Its Expression in Chronic Lymphocytic Leukemia. In XIX. Interdisciplinary meeting of young life scientists in Czech Chemical Society Symposium Series. 2019.

BURLEY, S.K., H.M. BERMAN, C. BHIKADIYA, C.X. BI, L. CHEN, L. DI COSTANZO, C. CHRISTIE, J.M. DUARTE, S. DUTTA, Z.K. FENG, S. GHOSH, D.S. GOODSELL, R.K. GREEN, V. GURANOVIC, D. GUZENKO, B.P. HUDSON, Y.H. LIANG, R. LOWE, E. PEISACH, I. PERISKOVA, C. RANDLE, A. ROSE, M. SEKHARAN, CH. SHAO, Y.P. TAO, Y. VALASATAVA, M. VOIGT, J. WESTBROOK, J. YOUNG, C. ZARDECKI, M. ZHURAVLEVA, G. KURISU, H. NAKAMURA, Y. KENGAKU, H. CHO, J. SATO, J.Y. KIM, Y. IKEGAWA, A. NAKAGAWA, R. YAMASHITA, T. KUDOU, G.J. BEKKER, H. SUZUKI, T. IWATA, M. YOKOCHI, N. KOBAYASHI, T. FUJIWARA, S. VELANKAR, G.J. KLEYWEGT, S. ANYANGO, D.R. ARMSTRONG, J.M. BERRISFORD, M.J. CONROY, J.M. DANA, M. DESHPANDE, P. GANE, Romana GÁBOROVÁ, D. GUPTA, A. GUTMANAS, Jaroslav KOČA, L. MAK, S. MIR, A. MUKHOPADHYAY, N. NADZIRIN, S. NAIR, A. PATWARDHAN, T. PAYSAN-LAFOSSE, Lukáš PRAVDA, O. SALIH, David SEHNAL, M. VARADI, Radka SVOBODOVÁ VAŘEKOVÁ, J.L. MARKLEY, J.C. HOCH, P.R. ROMERO, K. BASKARAN, D. MAZIUK, E.L. ULRICH, J.R. WEDELL, H.Y. YAO, M. LIVNY and Y.E. IOANNIDIS. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Research. Oxford: Oxford University Press, 2019, vol. 47, D1, p. "D520"-"D528", 9 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky949.

KNECHT, H., Tomáš REIGL, M. KOTROVA, F. APPELT, P. STEWART, Vojtěch BYSTRÝ, Adam KREJČÍ, A. GRIONI, Karol PÁL, Kamila STRÁNSKÁ, Karla PLEVOVÁ, J. RIJNTJES, S. SONGIA, M. SVATON, E. FRONKOVA, J. BARTRAM, B. SCHEIJEN, D. HERRMANN, R. GARCIA-SANZ, J. HANCOCK, J. MOPPETT, J.J.M. VAN DONGEN, G. CAZZANIGA, F. DAVI, P.J.T.A. GROENEN, M. HUMMEL, E.A. MACINTYRE, K. STAMATOPOULOS, J. TRKA, A.W. LANGERAK, D. GONZALEZ, C. POTT, M. BRUGGEMANN and Nikos DARZENTAS. Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS. Leukemia. London: Nature Publishing Group, 2019, vol. 33, No 9, p. 2254-2265. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-019-0499-4.

BRUGGEMANN, M., M. KOTROVA, H. KNECHT, J. BARTRAM, M. BOUDJOGRHA, Vojtěch BYSTRÝ, G. FAZIO, E. FRONKOVA, M. GIRAUD, A. GRIONI, J. HANCOCK, D. HERRMANN, C. JIMENEZ, Adam KREJČÍ, J. MOPPETT, Tomáš REIGL, M. SALSON, B. SCHEIJEN, M. SCHWARZ, S. SONGIA, M. SVATON, J.J.M. VAN DONGEN, P. VILLARESE, S. WAKEMAN, G. WRIGHT, G. CAZZANIGA, F. DAVI, R. GARCIA-SANZ, D. GONZALEZ, P.J.T.A. GROENEN, M. HUMMEL, E.A. MACINTYRE, K. STAMATOPOULOS, C. POTT, J. TRKA, Nikos DARZENTAS and A.W. LANGERAK. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. Leukemia. London: Nature Publishing Group, 2019, vol. 33, No 9, p. 2241-2253. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-019-0496-7.

VEČEŘA, Marek, Jiří ŠÁNA, Jan OPPELT, Boris TICHÝ, Alena KOPKOVÁ, R. LIPINA, Martin SMRČKA, Radim JANČÁLEK, Markéta HERMANOVÁ, Leoš KŘEN and Ondřej SLABÝ. Testing of library preparation methods for transcriptome sequencing of real life glioblastoma and brain tissue specimens: A comparative study with special focus on long non-coding RNAs. Plos one. San Francisco: Public Library of Science, 2019, vol. 14, No 2, p. 1-18. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0211978.

ISON, Jon, Hans IENASESCU, Piotr CHMURA, Emil RYDZA, Hervé MÉNAGER, Matúš KALAŠ, Veit SCHWÄMMLE, Björn GRÜNING, Niall BEARD, Rodrigo LOPEZ, Severine DUVAUD, Heinz STOCKINGER, Bengt PERSSON, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RAČEK, Jiří VONDRÁŠEK, Hedi PETERSON, Ahto SALUMETS, Inge JONASSEN, Rob HOOFT, Tommi NYRÖNEN, Alfonso VALENCIA, Salvador CAPELLA, Josep GELPÍ, Federico ZAMBELLI, Babis SAVAKIS, Brane LESKOŠEK, Kristoffer RAPACKI, Christophe BLANCHET, Rafael JIMENEZ, Arlindo OLIVEIRA, Gert VRIEND, Olivier COLLIN, Jacques van HELDEN, Peter LØNGREEN and Søren BRUNAK. The bio.tools registry of software tools and data resources for the life sciences. GENOME BIOLOGY. LONDON: BIOMED CENTRAL LTD, 2019, vol. 20, No 164, p. 1-4. ISSN 1474-760X. Available from: https://dx.doi.org/10.1186/s13059-019-1772-6.

PLASIL, M., S. WIJKMARK, J.P. ELBERS, Jan OPPELT, P.A. BURGER and P. HORIN. The major histocompatibility complex of Old World camelids: Class I and class I-related genes. HLA. HOBOKEN: WILEY, 2019, vol. 93, No 4, p. 203-215. ISSN 2059-2302. Available from: https://dx.doi.org/10.1111/tan.13510.

AMRUZ ČERNÁ, Kateřina, Kateřina MUSILOVÁ, Gabriela MLADONICKÁ PAVLASOVÁ, Václav ŠEDA, Jan OPPELT, Daniel FILIP, Veronika ŠANDOVÁ, Eva VOJÁČKOVÁ, Sonali SHARMA, Pedro FARIA ZENI, Jiří MAYER and Marek MRÁZ. The surprising role of microRNAs in the DNA damage and B cell receptor signalling in malignant B cells. In XXXIII. Olomoucké hematologické dny, Olomouc. 2019.

PESCHELOVÁ, Helena, Veronika KOZLOVÁ, Václav HEJRET and Michal ŠMÍDA. The use of CRISPR/Cas9 technology in the study of chronic lymphocytic leukemia. In Biomania, Brno. 2019.

HORSKÝ, Vladimír, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Dominik TOUŠEK and Jaroslav KOČA. ValTrendsDB: bringing Protein Data Bank validation information closer to the user. In ELIXIR - EXCELERATE All Hands meeting 2019. 2019.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. ValTrendsDB: bringing Protein Data Bank validation information closer to the user. Bioinformatics. Oxford (UK): Oxford University Press, 2019, vol. 35, No 24, p. 5389-5390. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz532.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. ValTrendsDB: Database of biomacromolecular structure validation trends. 2019.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

GIASSA, Ilektra-Chara, Jan RYNEŠ, T. FESSL, Silvie TRANTÍRKOVÁ and Lukáš TRANTÍREK. Advances in the cellular structural biology of nucleic acids. FEBS LETTERS. HOBOKEN: WILEY, 2018, vol. 592, No 12, p. 1997-2011. ISSN 1873-3468. Available from: https://dx.doi.org/10.1002/1873-3468.13054.

PLEVOVÁ, Karla, Tobias RAUSCH, Marie JAROŠOVÁ, Jakub HYNŠT, Kristýna ZÁVACKÁ, Šárka PAVLOVÁ, Vojtěch BYSTRÝ, Eva ONDROUŠKOVÁ, Kamila STRÁNSKÁ, Jana KOTAŠKOVÁ, Lenka RADOVÁ, Jitka MALČÍKOVÁ, Yvona BRYCHTOVÁ, Richard ROSENQUIST, Michael DOUBEK, Vladimír BENEŠ and Šárka POSPÍŠILOVÁ. Analýza rozsáhlých přestaveb genomu u chronické lymfocytární leukémie (Analysis of extensive reconstruction of the genome in chronic lymphocytic leukemia). In 22. celostátní konference DNA diagnostiky, České Budějovice. 2018.

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Karel BERKA. Annotation of protein secondary structure elements for whole protein families. In ECCB 2018, Athens, Greece. 2018.

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Tarakaramji MOTURU, Veronika NAVRÁTILOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Karel BERKA. Automated Annotation of Secondary Structure Elements for Entire Protein Families. In National Bioinformatic Conference ENBIK. 2018.

TRACHTOVÁ, Karolína, Jan OPPELT, Kateřina AMRUZ ČERNÁ and Marek MRÁZ. Bioinformatic analysis of microRNAs and long non-coding RNAs in malignant B cells. In RNA and Disease, Uppsala, Sweden. 2018.

REIGL, Tomáš, Kamila STRÁNSKÁ, Karol PÁL, Vojtěch BYSTRÝ, Adam KREJČÍ, Šárka POSPÍŠILOVÁ, Nikos DARZENTAS and Karla PLEVOVÁ. Bioinformatická platforma pro rutinní využití v diagnostice pacientů s chronickou lymfocytární leukémií (Bioinformatic Platform for Routine Use in Diagnostics of Patients with Chronic Lymphocytic Leukemia). In XLII. Brněnské onkologické dny, Brno in Klinická Onkologie. 2018.

REIGL, Tomáš, Kamila STRÁNSKÁ, Karol PÁL, Vojtěch BYSTRÝ, Adam KREJČÍ, Šárka POSPÍŠILOVÁ, Nikos DARZENTAS and Karla PLEVOVÁ. Bioinformatics platform for routine diagnostics of chronic lymphocytic leukemia patients. In CEITEC PHD and POSTDOC RETREAT 2018, Telč. 2018.

REIGL, Tomáš, Kamila STRÁNSKÁ, Karol PÁL, Vojtěch BYSTRÝ, Adam KREJČÍ, Šárka POSPÍŠILOVÁ, Nikos DARZENTAS and Karla PLEVOVÁ. Bioinformatics platform for routine diagnsotics of chronic lymphocytic leukemia patients. In ENBIK2018 conference proceedings, Skalský dvůr. 2018.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Dan POLANSKÝ, Karel BERKA and Jaroslav KOČA. bio.tools Sum – tool for exploration of summary information about bioinformatics services in bio.tools. In F1000Research. 2018. Available from: https://dx.doi.org/10.7490/f1000research.1115564.1.

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Bringing validation information closer to the user. In CEITEC PhD and Postdoc Retreat 2018. 2018. ISBN 978-80-210-8941-9.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. CCL - Charge Calculation Language. In ELIXIR CZ Annual Conference 2018. 2018. ISBN 978-80-86241-60-9.

CHIRACKAL MANAVALAN, Anil Paul, Květa PILAŘOVÁ, M. KLUGE, Koen BARTHOLOMEEUSEN, Jan OPPELT, PrashantKumar KHIRSARIYA, Kamil PARUCH, Lumír KREJČÍ, C. FRIEDEL and Dalibor BLAŽEK. CDK12 kinase activity controls G1/S progression by regulating optimal transcription of core DNA replication genes. In 2018 ASCB | EMBO Annual Meeting. 2018.

PAVLASOVÁ, Gabriela, Veronika SVOBODOVÁ, Marek BORSKÝ, Jan OPPELT, J. NOVOTNÁ, Kateřina AMRUZ ČERNÁ, Kateřina MUSILOVÁ, Václav ŠEDA, Yvona BRYCHTOVÁ, Michael DOUBEK, Šárka POSPÍŠILOVÁ, Jiří MAYER and Marek MRÁZ. CD20 is a direct regulator of B-cell receptor signaling in the microenvironment of chronic lymphocytic leukemia. 2018.

MRÁZ, Marek, Gabriela PAVLASOVÁ, Veronika SVOBODOVÁ, Marek BORSKÝ, Jan OPPELT, Kateřina AMRUZ ČERNÁ, Kateřina MUSILOVÁ, Václav ŠEDA, Yvona BRYCHTOVÁ, Michael DOUBEK, Šárka POSPÍŠILOVÁ and Jiří MAYER. CD20 reguluje signalizaci přes B-buněčný receptor v mikroprostředí chronické lymfocytární leukémie (CD20 regulates signaling via the B-cell receptor in the microenvironment of chronic lymphocytic leukemia). In I. Český hematologický a transfuziologický sjezd, Praha. 2018.

PAVLASOVÁ, Gabriela, Marek BORSKÝ, Veronika SVOBODOVÁ, Jan OPPELT, Kateřina AMRUZ ČERNÁ, Jitka NOVOTNÁ, Kateřina MUSILOVÁ, Václav ŠEDA, Eva VOJÁČKOVÁ, Yvona BRYCHTOVÁ, Michael DOUBEK, Šárka POSPÍŠILOVÁ, Jiří MAYER and Marek MRÁZ. CD20 supports BCR signaling in an intra clonal aggressive chronic lymphocytic leukemia subpopulation of cells and rituximab primarily targets these BCR proficient B cells in vivo. In AACR Annual Meeting Chicago Illinois USA. 2018.

STROUHAL, Michal, Lenka PAŠTĚKOVÁ, Jan HAVIERNIK, Sascha KNAUF, Sylvia BRUISTEN, Gerda T. NOORDHOEK, Jan OPPELT, Darina ČEJKOVÁ and David ŠMAJS. Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes. PLoS neglected tropical diseases. San Francisco: Public Library of Science, 2018, vol. 12, No 10, p. 0006867-6886. ISSN 1935-2735. Available from: https://dx.doi.org/10.1371/journal.pntd.0006867.

SUCHÁNKOVÁ, Pavla and Radka SVOBODOVÁ VAŘEKOVÁ. Connection of glycoinformatics databases with Pubchem. In ENBIK. 2018. ISBN 978-80-7592-017-1.

RAČEK, Tomáš, Ondřej SCHINDLER, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. Empirical methods for calculation of partial atomic charges – applicability for proteins? In ENBIK2018. 2018. ISBN 978-80-7592-017-1.

REIGL, Tomáš, Kamila STRÁNSKÁ, Vojtěch BYSTRÝ, Adam KREJČÍ, Andrea GRIONI, Šárka POSPÍŠILOVÁ, Karla PLEVOVÁ and Nikos DARZENTAS. Encyclopedia of CLL Subsets: An Online Knowledgebase forSubsets of CLL Cases with Stereotyped B Cell Receptors. In 23rd Congress of the European Hematology Association, Stockholm, Sweden in HemaSphere. 2018.

SVOBODOVÁ VAŘEKOVÁ, Radka, Ivana HUTAŘOVÁ VAŘEKOVÁ, Adam MIDLIK, Jan HUTAŘ, Tarakaramji MOTURU, Veronika NAVRÁTILOVÁ, Jaroslav KOČA and Karel BERKA. Family-wide annotation and schematic 2D visualization of secondary structure elements. In National Bioinformatic Conference ENBIK. 2018.

FADRUS, Pavel, Alena KOPKOVÁ, Marek VEČEŘA, Jiří ŠÁNA, Jan OPPELT, Táňa MACHÁČKOVÁ, Václav VYBÍHAL, Martin SMRČKA and Ondřej SLABÝ. Global microRNA analysis in cerebrospinal fluid in glioblastoma patients. In The 15th Meeting of the Asian Society for Neuro-Oncology (ASNO 2018), Bejing, China,. 2018.

NOVÁK, Jan, Táňa MACHÁČKOVÁ, Tereza NOVÁKOVÁ, Dalibor MLEJNEK, Július GODAVA, Petr HUDE, Víta ŽAMPACHOVÁ, Jan OPPELT, Petr NĚMEC, Helena BEDÁŇOVÁ, Ondřej SLABÝ, Julie DOBROVOLNÁ, Jan KREJČÍ and Lenka ŠPINAROVÁ. Hladiny vybraných plazmatických mikroRNA u pacientů po srdeční transplantaci odrážejí probíhající celulární rejekci štěpu - primární výsledky sekvenací (Levels of selected plasmatic microRNAs in patients after heart transplantation reflect acute cellular rejection - primary results of NGS). In 46. pracovní konference Komise experimentální kardiologie. 2018. ISSN 1801-6103.

SMETANA, Jan, Jan OPPELT, Martin ŠTORK, Luděk POUR and Petr KUGLÍK. Chromothripsis 18 in multiple myeloma patient with rapid extramedullary relapse. MOLECULAR CYTOGENETICS. BioMed Central, 2018, vol. 11, JAN, p. nestrankovano, 6 pp. ISSN 1755-8166. Available from: https://dx.doi.org/10.1186/s13039-018-0357-5.

ZWINSOVÁ, Barbora, Jan OPPELT, Petra VÍDEŇSKÁ and Eva BUDINSKÁ. Identifikace mikrobiomu kolorektálního karcinomu z RNAseq dat nádorové tkáně a jeho korelace s klinickými proměnnými a molekulárními podtypy. In Brněnské onkologické dny. 2018. ISSN 0862-495X.

SEHNAL, David, M DESHPANDE, A ROSE, Lukáš PRAVDA, Adam MIDLIK, Radka SVOBODOVÁ VAŘEKOVÁ, S MIR, K BERKA, S VELANKAR and Jaroslav KOČA. Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite. In 62nd Annual Meeting of the Biophysical-Society. 2018. Available from: https://dx.doi.org/10.1016/j.bpj.2017.11.308.

KUZAK, M., J. HARROW, R.C. JIMENEZ, P.A. MARTINEZ, F.E. PSOMOPOULOS, Radka SVOBODOVÁ VAŘEKOVÁ and A. VIA. Lesson development for Open Source Software best practices adoption. Online. In 2018 IEEE 14TH INTERNATIONAL CONFERENCE ON E-SCIENCE (E-SCIENCE 2018). NEW YORK: IEEE, 2018, p. 19-20. ISBN 978-1-5386-9156-4. Available from: https://dx.doi.org/10.1109/eScience.2018.00011.

BARTAS, Martin, Jiri ČERVEŇ, Jan OPPELT, Matus PETEJA, Petr VÁVRA, Pavel ZONČA, Vaclav PROCHÁZKA, Václav BRÁZDA and Petr PEČINKA. Liver regeneration during the associating liver partition and portal vein ligation for staged hepatectomy procedure in Sus scrofa is positively modulated by stem cells. Oncology Letters. Spandidos Publ., 2018, vol. 15, No 5, p. 6309-6321. ISSN 1792-1074. Available from: https://dx.doi.org/10.3892/ol.2018.8108.

KUBEŠOVÁ, Blanka, Šárka PAVLOVÁ, Jitka MALČÍKOVÁ, Jitka KABÁTHOVÁ, Lenka RADOVÁ, Nikola TOM, Boris TICHÝ, Karla PLEVOVÁ, Barbara KANTOROVÁ, Kristýna FIEDOROVÁ, M. SLAVIKOVA, Vojtěch BYSTRÝ, Jarmila KISSOVÁ, B. GISSLINGER, H. GISSLINGER, Miroslav PENKA, Jiří MAYER, R. KRALOVICS, Šárka POSPÍŠILOVÁ and Michael DOUBEK. Low-burden TP53 mutations in chronic phase of myeloproliferative neoplasms: association with age, hydroxyurea administration, disease type and JAK2 mutational status (Low- burden TP53 mutations in chronic phase of myeloproliferative neoplasms: association with age, hydroxyurea administration, disease type and JAK2 mutational status.). Leukemia. London: Nature Publishing Group, 2018, vol. 32, No 2, p. 450-461. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/leu.2017.230.

OPPELT, Jan, Karolína TRACHTOVÁ and Marek MRÁZ. microRNA – are you real? In ENBIK2018 conference proceedings, Skalský dvůr. 2018.

OPPELT, Jan and Marek MRÁZ. microRNA – are you real? In RNA and Disease, Uppsala, Sweden. 2018.

OPPELT, Jan, Karolína TRACHTOVÁ and Marek MRÁZ. microRNA – are you real?! In ENBIK2018 - National Bioinformatics Conference. 2018. ISBN 978-80-7592-017-1.

MUSILOVÁ, Kateřina, Ján DEVÁN, Kateřina AMRUZ ČERNÁ, Václav ŠEDA, Gabriela PAVLASOVÁ, Sonali SHARMA, Jan OPPELT, R. PYTLIK, V. PROCHAZKA, Z. PROUZOVA, Martin TRBUŠEK, L. ZLAMALIKOVA, K. LISKOVA, L. KRUZOVA, M. JAROSOVA, Andrea MAREČKOVÁ, C. KORNAUTH, I. SIMONITSCH-KLUPP, A.I. SCHIEFER, O. MERKEL, H. MOCIKOVA, P. BURDA, K.M. POLAKOVA, L. KREN, Jiří MAYER, C.S. ZENT, M. TRNENY, A.G. EVANS, Andrea JANÍKOVÁ and Marek MRÁZ. miR-150 downregulation contributes to the high-grade transformation of follicular lymphoma by upregulating FOXP1 levels. Blood. Washington DC, USA: American Society of Hematology, 2018, vol. 132, No 22, p. 2389-2400. ISSN 0006-4971. Available from: https://dx.doi.org/10.1182/blood-2018-06-855502.

MOTURU, Tarakaramji, Sravankumar THULA, R.K. SINGH, Tomasz NODZYNSKI, Radka SVOBODOVÁ VAŘEKOVÁ, J. FRIML and Sibu SIMON. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. Oxford: OXFORD UNIV PRESS, 2018, vol. 69, No 9, p. 2367-2378. ISSN 0022-0957. Available from: https://dx.doi.org/10.1093/jxb/ery097.

PRAVDA, Lukáš, David SEHNAL, Dominik TOUŠEK, Veronika NAVRÁTILOVÁ, Václav BAZGIER, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Michal OTYEPKA. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Research. Oxford: Oxford University Press, 2018, vol. 46, W1, p. "W368"-"W373", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky309.

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, David POTĚŠIL, Pavel ROUDNICKÝ, Jana ILGOVÁ, Lucie JEDLIČKOVÁ, Hana DVOŘÁKOVÁ, Libor MIKEŠ, Milan GELNAR and Martin KAŠNÝ. Monogenea, fish parasites and their unknown molecules. In International Symposium on Flatworm Biology. 2018.

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, Pavel ROUDNICKÝ, Jana ILGOVÁ, Libor MIKEŠ, Milan GELNAR and Martin KAŠNÝ. Monogeneans in the pores. In 24th Helminthological Days. 2018. ISBN 978-80-7444-057-1.

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, David POTĚŠIL, Lucie JEDLIČKOVÁ, Pavel ROUDNICKÝ, Jana ILGOVÁ, Libor MIKEŠ, Zbyněk ZDRÁHAL, Milan GELNAR and Martin KAŠNÝ. Parazitičtí jednorodí (Monogenea) - stále neznámé organismy (Parasitic monogeneans - still unknown organisms). In Zoologické dny 2018. 2018. ISBN 978-80-87189-24-5.

DEMKO, Martin, Samuel PASTVA, David ŠAFRÁNEK, Nikola BENEŠ and Luboš BRIM. PITHYA. 2018.

ŠUSTR, Filip, Táňa MACHÁČKOVÁ, Jan OPPELT, Ondřej SLABÝ, Zdeněk STÁREK and Jan NOVÁK. Použití sekvenování nové generace při hledání kandidátních mikroRNA jako biomarkerů rekurence fibrilace síní po katetrové ablaci - pilotní data (Using next generation sequencing in search of candidate microRNAs as markers of reccurence of atrial fibrilation after catheter ablation - pilot results). In 46. pracovní konference Komise experimentální kardiologie. 2018. ISSN 1801-6103.

POPPOVÁ, Lucie, Pavlína JANOVSKÁ, B. GONZALEZ, Karla PLEVOVÁ, Vojtěch BYSTRÝ, Karol PÁL, Hana PLEŠINGEROVÁ, Marek BORSKÝ, Jana KOTAŠKOVÁ, G. DUMBOVIC, J. BIAYNA, JM. MORENO, CM MORALEDA, S. JANSEN, Yvona BRYCHTOVÁ, Michael DOUBEK, Šárka PAVLOVÁ, S. ALONSO, Vítězslav BRYJA and Šárka POSPÍŠILOVÁ. Promoter methylation of ROR1 ligand WNT5A associates with its expression in CLL. In CEITEC PHD and POSTDOC RETREAT 2018, Telč. 2018.

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Adam MIDLIK, Veronika NAVRÁTILOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ and Karel BERKA. Protein family based 2D Diagrams of Secondary Structure Elements. In National Bioinformatic Conference ENBIK. 2018.

STROUHAL, Michal, Jan OPPELT, Lenka MIKALOVÁ, Natasha ARORA, Kay NIESELT, Fernando GONZÁLEZ-CANDELAS and David ŠMAJS. Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes. BMC Research Notes. London: BioMed Central Ltd., 2018, vol. 11, No 1, p. 1-5. ISSN 1756-0500. Available from: https://dx.doi.org/10.1186/s13104-017-3106-7.

PAVLASOVÁ, Gabriela, Marek BORSKÝ, Veronika ŠANDOVÁ, Jan OPPELT, Kateřina AMRUZ ČERNÁ, Jitka NOVOTNÁ, Václav ŠEDA, Miloslava FOJTOVÁ, Jiří FAJKUS, Yvona BRYCHTOVÁ, Michael DOUBEK, Šárka POSPÍŠILOVÁ, Jiří MAYER and Marek MRÁZ. Rituximab primarily targets an intra-clonal BCR signaling proficient CLL subpopulation characterized by high CD20 levels. Leukemia. London: Nature Publishing Group, 2018, vol. 32, No 9, p. 2028-2031. ISSN 0887-6924. Available from: https://dx.doi.org/10.1038/s41375-018-0211-0.

SVOBODOVÁ VAŘEKOVÁ, Radka, Adam MIDLIK, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Veronika NAVRÁTILOVÁ, Jaroslav KOČA and Karel BERKA. Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. In Biophysical Society 62nd Annual Meeting, San Francisco, California. 2018. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2017.11.307.

GRILLOVÁ, Linda, Lorenzo GIACANI, Lenka PAŠTĚKOVÁ, Michal STROUHAL, Radim STRNADEL, Christina MARRA, Arturo CENTURION-LARA, Lucy POVEDA, Giancarlo RUSSO, Darina ČEJKOVÁ, Vladimír VAŠKŮ, Jan OPPELT and David ŠMAJS. Sequencing of Treponema pallidum subsp pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material. Plos one. San Francisco: Public Library Science, 2018, vol. 13, No 8, p. 1-14. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0202619.

ALOCCI, Davide, Pavla SUCHÁNKOVÁ, Renaud COSTA, Nicolas HORY, Julien MARIETHOZ, Radka SVOBODOVÁ VAŘEKOVÁ, Philip TOUKACH and Frederique LISACEK. SugarSketcher: Quick and Intuitive Online Glycan Drawing. Molecules. Mayer und Muller, 2018, vol. 23, No 12, p. 3206-3216. ISSN 1420-3049. Available from: https://dx.doi.org/10.3390/molecules23123206.

ČULEN, Martin, Zdeňka KOSAŘOVÁ, Ivana JEŽÍŠKOVÁ, A. FOLTA, Jana CHOVANCOVÁ, Tomáš LOJA, Nikola TOM, Vojtěch BYSTRÝ, V. JANECKOVA, Dana DVOŘÁKOVÁ, Jiří MAYER and Zdeněk RÁČIL. The influence of mutational status and biological characteristics of acute myeloid leukemia on xenotransplantation outcomes in NOD SCID gamma mice. Journal of cancer research and clinical oncology. New York: Springer-Verlag, 2018, vol. 144, No 7, p. 1239-1251. ISSN 0171-5216. Available from: https://dx.doi.org/10.1007/s00432-018-2652-2.

TOM, Nikola, O. TOM, Jitka MALČÍKOVÁ, Šárka PAVLOVÁ, Blanka KUBEŠOVÁ, T. RAUSCH, M. KOLARIK, V. BENES, Vojtěch BYSTRÝ and Šárka POSPÍŠILOVÁ. ToTem: a tool for variant calling pipeline optimization. BMC Bioinformatics. London: BioMed Central, 2018, vol. 19, JUN, p. 243-251. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-018-2227-x.

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Validation information in the Protein Data Bank: What is it and why should you care? In ENBIK 2018. 2018. ISBN 978-80-7592-017-1.

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Validation of ligands in macromolecular structures determined by X-ray crystallography. Acta Crystallographica Section D. 2018, vol. 74, No 3, p. 228-236. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798318002541.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. ValTrendsDB: Viewing structure quality from macro and micro perspective. In ELIXIR CZ Annual Conference 2018. 2018.

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Worldwide Protein Data Bank validation information: usage and trends. Acta Crystallographica Section D. 2018, vol. 74, MAR, p. 237-244. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798318003303.

JANKŮJOVÁ, Marie, David POTĚŠIL, Zbyněk ZDRÁHAL, Martin DEMKO, Jan OPPELT, Martin KAŠNÝ and Jaroslav VADLEJCH. Analysis of gene expression and protein synthesis related to hypobiosis of Teladorsagia circumcincta. In The 26th International Conference of the World Association for the Advancement of Veterinary Parasitology. 2017.

STEJSKALOVA, Karla, Zuzana BAYEROVÁ, Ján FUTAS, Kristýna HRAZDILOVÁ, Marie KLUMPLEROVÁ, Jan OPPELT, Petra SPLICHALOVA, Giovanni Di GUARDO, Sandro MAZZARIOL, Cristina Esmeralda Di FRANCESCO, Gabriella Di FRANCESCO, Giuliana TERRACCIANO, Romulus-Marian PAIU, Teodor Dan URSACHE, David MODRY and Petr HOŘÍN. Candidate gene molecular markers as tools for analyzing genetic susceptibility to Morbillivirus infection in stranded Cetaceans. HLA. 2017, vol. 90, No 6, p. 343-353. ISSN 2059-2302. Available from: https://dx.doi.org/10.1111/tan.13146.

VOREL, Jiří, Marie JANKŮJOVÁ, Jan OPPELT, Filip PARDY, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Dagmar JIRSOVÁ, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)? In 6th ECIP meeting - European Centre of Ichtyoparasitology. 2017. ISBN 978-80-210-8799-6.

KIRMZIS, Antonis, Diego MOLINA-SERRANO, Vassia SCHIZA, Christis DEMOSTHENOUS, Jan OPPELT, Wei LIU, Gertrude ZISSE, Helmut BERGLER and Weiwei DANG. Epigenetic Control Of Aging In Response To Caloric Restriction. In 28th International Conference on Yeast Genetics and Molecular Biology (ICYGMB). 2017.

VOREL, Jiří, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Petr BROŽ, Dagmar JIRSOVÁ, Roman LEONTOVYČ, Lukáš VETEŠNÍK, Pavel JURAJDA, Marie JANKŮJOVÁ, Jan OPPELT, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Eudiplozoon nipponicum (Monogenea: Diplozoidae): Comparative study of transcriptome and secretome of fish parasite. In 23rd Helminthological Days. 2017. ISBN 978-80-968473-8-9.

VOREL, Jiří, Pavel ROUDNICKÝ, Jana ILGOVÁ, Hana DVOŘÁKOVÁ, Lucie JEDLIČKOVÁ, Libor MIKEŠ, Petr BROŽ, Dagmar JIRSOVÁ, Roman LEONTOVYČ, Lukáš VETEŠNÍK, Pavel JURAJDA, Marie JANKŮJOVÁ, Jan OPPELT, Božena KOUBKOVÁ, Milan GELNAR and Martin KAŠNÝ. Eudiplozoon nipponicum (Polyopisthocotylea: Diplozoidae): transcriptome and secretome analyses of hematophagous fish parasite. In 8th International Symposium on Monogenea. 2017. ISBN 978-80-210-8666-1.

SLANÝ, Michal, Jan OPPELT and Lenka ČINČÁROVÁ. Formation of Staphylococcus aureus biofilm in the presence of sub-lethal concentrations of disinfectants: a transcriptomic analysis using RNA-seq. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, 2017, vol. 83, No 24, p. nestránkováno, 13 pp. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.01643-17.

MIKALOVÁ, Lenka, Michal STROUHAL, Jan OPPELT, Philippe Alain GRANGE, Michel JANIER, Nadjet BENHADDOU, Nicolas DUPIN and David ŠMAJS. Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively. PLoS neglected tropical diseases. San Francisco: Public Library of Science, 2017, vol. 11, No 3, p. 1-14. ISSN 1935-2735. Available from: https://dx.doi.org/10.1371/journal.pntd.0005434.

ČERNÁ, Kateřina, Jan OPPELT, Václav ŠEDA, Kateřina MUSILOVÁ, Gabriela PAVLASOVÁ, Veronika SVOBODOVÁ, Jiří MAYER, Šárka POSPÍŠILOVÁ and Marek MRÁZ. MicroRNA induced by DNA damage response regulate the expression of FOXP1 and therapy response in CLL. In 2nd International Conference on the Long and the Short of Non-Coding RNAs, Heraklion, Greece. 2017.

ČERNÁ, Kateřina, Jan OPPELT, Václav ŠEDA, Kateřina MUSILOVÁ, Gabriela PAVLASOVÁ, Jiří MAYER, Šárka POSPÍŠILOVÁ and Marek MRÁZ. MicroRNA induced by DNA damage response regulates the expression of FOXP1 and therapy response in CLL. In XVII International Workshop on Chronic Lymphocytic Leukemia, USA, New York. 2017.

WAYHELOVÁ, Markéta, Jan OPPELT, Jan SMETANA, Filip PARDY, Hana FILKOVÁ, Renata GAILLYOVÁ and Petr KUGLÍK. The clinical impact of targeted „next-generation“ sequencing in molecular diagnostics of intellectual disabilities and multiple congenital abnormalities. In The Biomania Student Scientific Meeting 2017. 2017. ISBN 978-80-210-8737-8.

WAYHELOVÁ, Markéta, Jan OPPELT, Denisa VESELÁ, Jan SMETANA, Filip PARDY, Hana FILKOVÁ, Dita MATUCHOVÁ, Jana ŠOUKALOVÁ, Renata GAILLYOVÁ and Petr KUGLÍK. The clinical utility of array-CGH and targeted NGS in idiopathic intellectual disabilities and developmental delays: a case report of SCN2A p.Ala263Val variant. In The European Human Genetics Conference ESHG 2017. 2017. ISSN 1018-4813.

OPPELT, Jan and Marek MRÁZ. The impact of choice of reference gene annotation. In CEITEC PhD Retreat II. 2017. ISBN 978-80-210-8550-3.