Research Output

RP 2 – Biochemical and biophysical methods of living systems analysis

RP 2 – Biochemical methods

Method for the Synthesis of 1,3-dioxolane Derivatives Using Surface-modified Carbon Materials
Type of Protection: Patent
Number: 310226
Responsible Person (Lerco): Slovák, V.

RP 7 – Applied Research in Oncolog

Electrosurgical Biopsy Radiofrequency Ablation Needle and Instrument Set for Liver Biopsy Sampling
Type of Protection: National Patent Application
Number: D25075716
Application File Reference: PV 2025-326
Responsible Person (Lerco): Hlaváčková, M.
Implemented in cooperation with RP9

Electrosurgical Biopsy Radiofrequency Combined Sampling and Ablation Needle and Instrument Set for Liver Biopsy
Type of Protection: National Patent Application
Number: D25075721
Application File Reference: PV 2025-327
Responsible Person (Lerco): Hlaváčková, M.
Implemented in cooperation with RPVP9

Radiofrequency Ablation and Surgical Instruments
Type of Protection: International Patent Application (PCT)
Number: PCT/CZ2025/050074
Responsible Person (Lerco): Hlaváčková, M.
Implemented in cooperation with RP9

RP 1 – Molecular biology and genomics

1. Macedo, D. H., Grybchuk, D., Režnarová, J., Votýpka, J., Klocek, D., Yurchenko, T., Ševčík, J., Magri, A., Urda Dolinská, M., Záhonová, K., Lukeš, J., Servienė, E., Jászayová, A., Serva, S., Malysheva, M. N., Frolov, A. O., Yurchenko, V., Kostygov, A. Y. (2023). Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biology, 21(1), 191. https://doi.org/10.1186/s12915-023-01687-y
   
   
2. Albanaz, A. T. S., Carrington, M., Frolov, A. O., Ganyukova, A. I., Gerasimov, E. S., Kostygov, A. Y., Lukeš, J., Malysheva, M. N., Votýpka, J., Zakharova, A., Záhonová, K., Zimmer, S. L., Yurchenko, V., Butenko, A. (2023). Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of trypanosomatidae. BMC Genomics, 24(1), 471. https://doi.org/10.1186/s12864-023-09591-z
   
   
3. Kostygov, A.Y., Albanaz, A. T. S., Butenko, A., Gerasimov, E. S., Lukeš, J., Yurchenko, V. (2024). Phylogenetic framework to explore trait evolution in Trypanosomatidae. Trends in Parasitology, 40(2), 96-99. https://doi.org/10.1016/j.pt.2023.11.009
   
   
4. Opperdoes, F. R., Záhonová, K., Škodová-Sveráková, I., Bučková, B., Chmelová, L′., Lukeš, J., Yurchenko, V. (2024). In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics, 25(1), 184. https://doi.org/10.1186/s12864-024-10094-8
   
   
5. Chmelová, L., Záhonová, K., Albanaz, A.T.S., Hrebenyk, L., Horváth, A., Yurchenko, V., Škodová-Sveráková, I. (2024). Distribution and functional analysis of isocitrate dehydrogenases across kinetoplastids. Genome Biology and Evolution, 16(3), evae042. https://doi.org/10.1093/gbe/evae042
   
   
6. Usarov, G.X., Turitsin, V.S., Sattarova, X.G., Sádlová, J., Mustanov, J.A., Saura, A., Yurchenko, V. (2024). Phlebotomine sand fly (Diptera: Phlebotominae) diversity in the foci of cutaneous leishmaniasis in the Surxondaryo Region of Uzbekistan: 50 years on. Parasitology Research, 123, 179. https://doi.org/10.1007/s00436-024-08191-4
   
   
7. Rogozin, I.B., Saura, A., Poliakov, E., Bykova, A., Roche-Lima, A., Pavlov, Y.I., Yurchenko, V. (2024). Properties and mechanisms of deletions, insertions, and substitutions in the evolutionary history of SARS-CoV-2. International Journal of Molecular Sciences, 25(7), 3696. https://doi.org/10.3390/ijms25073696
   
   
8. Bartas, M., Červeň, J., Valková, N., Volná, A., Dobrovolná, M., Šislerová, L., Baldvinsson, H., Pečinka, P., Brázda, V. (2023). RNA analysis of the longest living vertebrate Greenland shark revealed an abundance of LINE-like elements in its transcriptome. Czech Polar Reports, 13(2), 210-227. https://doi.org/10.5817/CPR2023-2-17
   
   
9. Afonin, D.A., Gerasimov, E.S., Škodová-Sveráková, I., Záhonová, K., Gahura, O., Albanaz, A.T.S., Myšková, E., Bykova, A., Paris, Z., Lukeš, J., Opperdoes, F.R., Horváth, A., Zimmer, S.L., Yurchenko, V. (2024). Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucleic Acids Research, 52(7), 3870-3885. https://doi.org/10.1093/nar/gkae168
   
   
10.  Makki, A., Kereïche, S., Le, T., Kučerová, J., Rada, P., Žárský, V., Hrdý, I., Tachezy, J. (2024). A hybrid TIM complex mediates protein import into hydrogenosomes of Trichomonas vaginalis. BMC Biology, 22(1), 130. https://doi.org/10.1186/s12915-024-01928-8
    
    
11.  Grybchuk, D., Galan, A., Klocek, D., Macedo, D.H., Wolf, Y.I., Votýpka, J., Butenko, A., Lukeš, J., Neri, U., Záhonová, K., Kostygov, A.Y., Koonin, E.V., Yurchenko, V. (2024). Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evolution, 10(1), veae037. https://doi.org/10.1093/ve/veae037
    
    
12.  Chmelová, Ľ., Kraeva, N., Saura, A., Krayzel, A., Vieira, C.S., Ferreira, T.N., Soares, R.P., Bučková, B., Galan, A., Horáková, E., Vojtková, B., Sádlová, J., Malysheva, M.N., Butenko, A., Prokopchuk, G., Frolov, A.O., Lukeš, J., Horváth, A., Škodová-Sveráková, I., Feder, D., Kostygov, A.Y., Yurchenko, V. (2024). Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae). International Journal for Parasitology, 54(6), 391-400. https://doi.org/10.1016/j.ijpara.2024.04.007
    
    
13.  Williams, M. P., Flegontov, P., Maier, R., & Huber, C. D. (2024). Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA. Genetics, 228(2), iyae110. https://doi.org/10.1093/genetics/iyae110
    
    
14.  Bartas, M., Brázda, V., & Pečinka, P. (2024). Special Issue "Bioinformatics of Unusual DNA and RNA Structures". International Journal of Molecular Sciences, 25(10), 5226. https://doi.org/10.3390/ijms25105226
    
    
15.  Barcytė, D., Hodač, L., Eliáš, M. (2024). Freshwater 'microcroissants' shed light on a novel higher-level clade within Trebouxiophyceae and reveal the genus Chlorolobion as a trebouxiophyte. European Journal of Phycology, 59(4), 405-422. https://doi.org/10.1080/09670262.2024.2383626
    
    
16.  Cadena, L. R., Hammond, M., Tesařová, M., Chmelová, Ľ., Svobodová, M., Durante, I. M., Yurchenko, V., Lukeš, J. (2024). A novel nabelschnur protein regulates segregation of the kinetoplast DNA in Trypanosoma brucei. Current Biology, 34, 4803–4812.e3. https://doi.org/10.1016/j.cub.2024.08.044
    
    
17.  Kostygov, A. Y., Skýpalová, K., Kraeva, N., Kalita, E., McLeod, C., Yurchenko, V., Field, M. C., Lukeš, J., Butenko, A. (2024). Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biology, 22(1), 281. https://doi.org/10.1186/s12915-024-02080-z
    
    
18.  Kostygov, A. Y., Grybchuk, D., Heeren, S., Gerasimov, E. S., Klocek, D., Reddy, A., Sádlová, J., Pacáková, L., Kohl, A., Stejskal, F., Volf, P., Dujardin, J. C., Yurchenko, V. (2024). A novel strain of Leishmania braziliensis harbors not a toti- but a bunyavirus. PLoS Neglected Tropical Diseases, 18(4), e0012767. https://doi.org/10.1371/journal.pntd.0012767
    
    
19.  Pánek, T., Tice, A. K., Corre, P., Hrubá, P., Žihala, D., Kamikawa, R., Yazaki, E., Shiratori, T., Kume, K., Hashimoto, T., Ishida, K. I., Hradilová, M., Silberman, J. D., Roger, A., Inagaki, Y., Eliáš, M., Brown, M. W., Čepička, I. (2025). An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group. Molecular Phylogenetics and Evolution, 204, 108289. https://doi.org/10.1016/j.ympev.2025.108289
    
    
20. Terpis, K. X., Salomaki, E. D., Barcytė, D., Pánek, T., Verbruggen, H., Kolisko, M., Bailey, J. C., Eliáš, M., Lane, C. E. (2025). Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics. Current Biology, 35(3), 483–499.e8. https://doi.org/10.1016/j.cub.2024.11.065
    
    
21. Vargová, R., Chevreau, R., Alves, M., Courbin, C., Terry, K., Legrand, P., Eliáš, M., Ménétrey, J., Dacks, J. B., Jackson, C. L. (2025). The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics. Nature Microbiology, 10(4), 495–508. https://doi.org/10.1038/s41564-024-01904-6
    
    
22. Asad, M. A. U., Guan, X., Zhang, Y., Zhou, L., Bartas, M., Ullah, N., Zhou, W., Cheng, F. (2025). Nitrogen Deficiency Accelerates Rice Leaf Senescence Through ABA Signaling and Sugar Metabolic Shifts. Physiologia Plantarum, 177, e70124. https://doi.org/10.1111/ppl.70124
    
    
23. Lazaridis, I., Patterson, N., Anthony, D., Vyazov, L., Fournier, R., Ringbauer, H., Olalde, I., Khokhlov, A. A., Kitov, E. P., Shishlina, N. I., Ailincăi, S. C., Agapov, D. S., Agapov, S. A., Batieva, E., Bauyrzhan, B., Bereczki, Z., Buzhilova, A., Changmai, P., Chizhevsky, A. A., Ciobanu, I., Constantinescu, M., Csányi, M., Dani, J., Dashkovskiy, P. K., Évinger, S., Faifert, A., Flegontov, P., Reich, D. (2025). The genetic origin of the Indo-Europeans. Nature, 639(8054), 132–142. https://doi.org/10.1038/s41586-024-08531-5
    
    
24. Žárský, V., & Eliáš, M. (2025). Phylogenomics defines Streptofilum as a novel deep branch of streptophyte algae. Current Biology, 35(2), R171–R172. https://doi.org/10.1016/j.cub.2024.12.013
    
    
25. Barcytė, D. & Eliáš, M. (2025). Characterization of Lercomonas mokradensis gen. et sp. nov. enriches the phylogenetic and taxonomic diversity of Chloromonadinia (Chlorophyceae). Phycologia, 64(1), 71-83. https://doi.org/10.1080/00318884.2025.2471620
    
    
26. Gerasimov, E. S., Afonin, D. A., Škodová-Sveráková, I., Saura, A., Trusina, N., Gahura, O., Zakharova, A., Butenko, A., Baráth, P., Horváth, A., Opperdoes, F. R., Pérez-Morga, D., Zimmer, S. L., Lukeš, J., Yurchenko, V. (2025). Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatid Vickermania. Proceedings of the National Academy of Sciences of the United States of America, 122(12), e2426887122. https://doi.org/10.1073/pnas.2426887122
    
    
27. Bartas, M., Petrovič, M., Brázda, V., Trenz, O., Ďurčanský, A., Šťastný, J. (2025). CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome. Journal of Biological Chemistry, 301, 108537. https://doi.org/10.1016/j.jbc.2025.108537
    
    
28. Wiredu-Boakye, D., Higgins, L., Gahura, O., Butenko, A., Leonard, G., Freeman, M.A., Kristmundsson, Á., Moore, K., Harrison, J.W., Mac Donald, S., Yurchenko, V., Williams, B.A.P., Chahwan, R. (2025). Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes. Genome Biology and Evolution, 17(2), evaf089. https://doi.org/10.1093/gbe/evaf089
    
    
29. Bartas, M. (2024). Abiotic Stresses in Plants: From Molecules to Environment. International Journal of Molecular Sciences, 25(15), 8072. https://doi.org/10.3390/ijms25158072
    
    
30. Grybchuk, D., Kostygov, A. Y., Yurchenko, V. (2025). Analysis of Leishbuviridae from trypanosomatids. In Boshra H. (Ed.), Bunyaviruses: Methods and Protocols (pp. 151–167.) Humana, https://link.springer.com/protocol/10.1007/978-1-0716-4338-9_12
    
    
31. Tullume-Vergara, P. O., Ludwig, A., Yurchenko, V., Coelho, A. C., Coser, E. M., Krieger, M. A., Teixeira, M. M. G., Shaw, J. J., Alves, J. M. P. (2025). Comparative analysis of the mobilome yields new insights into its diversity, dynamics and evolution in parasites of the Trypanosomatidae family. Parasitology, 152(6), 602–617. https://doi.org/10.1017/S0031182025100231
    
    
32. Hughes, H. R., Ballinger, M. J., Bao, Y., Bejerman, N., Blasdell, K. R., Briese, T., Brignone, J., Carrera, J. P., De Coninck, L., de Souza, W. M., Debat, H., Dietzgen, R. G., Dürrwald, R., Erdin, M., Fooks, A. R., Forbes, K. M., Freitas-Astúa, J., Garcia, J. B.,..Kostygov, A.Y., Yurchenko, V.,.. (2025). Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal dsRNA and ssRNA(–) Viruses Subcommittee, 2025. Journal of General Virology, 106(7), 002112. https://doi.org/10.1099/jgv.0.002112
    
    
33. Zeng, T. C., Vyazov, L. A., Kim, A., Flegontov, P., Sirak, K., Maier, R., Lazaridis, I., Akbari, A., Frachetti, M., Tishkin, A. A., Ryabogina, N. E., Agapov, S. A., Agapov, D. S., Alekseev, A. N., Boeskorov, G. G., Derevianko, A. P., Dyakonov, V. M., Enshin, D. N., Fribus,A.,... Reich, D. (2025). Ancient DNA reveals the prehistory of the Uralic and Yeniseian peoples. Nature, 644(8075), 122–132. https://doi.org/10.1038/s41586-025-09189-3
    
    
34. Janowicz, N., Dohnálek, V., Zítek, J., Peña-Diaz, P., Pyrihová, E., King, M. S., Husová, M., Žárský, V., Kunji, E., Zikova, A., Hampl, V., Dolezal, P. (2025). Selective loss of ATP carriers in favour of SLC25A43 orthologues in metamonad mitochondria adapted to anaerobiosis. Open Biology, 15(8), 240202. https://doi.org/10.1098/rsob.240202
    
    
35. Záhonová, K., Füssy, Z., Albanaz, A. T. S., Butenko, A., Kachale, A., Kraeva, N., Galan, A., Zakharova, A., Stojanova, B., Votýpka, J., Kostygov, A. Y., Spodareva, V. V., Malysheva, M. N., Frolov, A. O., Rogozin, I. B., Paris, Z., Valášek, L. S., Yurchenko, V., Lukeš, J. (2025). Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio, 16(6), e0088525. https://doi.org/10.1128/mbio.00885-25
    
    
36. Galan, A., Kraeva, N., Záhonová, K., Butenko, A., Kostygov, A. Y., Paris, Z., Pergner, J., Bianchi, C., Fakih, F., Saura, A., Lukeš, J., Yurchenko, V. (2025). Converting Blastocrithidia Nonstop, a Trypanosomatid With Non-Canonical Genetic Code, Into a Genetically-Tractable Model. Molecular Microbiology, 123(6), 586–592. https://doi.org/10.1111/mmi.15365
    
    
37. Gyuris, B., Vyazov, L., Türk, A., Flegontov, P., Szeifert, B., Langó, P., Mende, B. G., Csáky, V., Chizhevskiy, A. A., Gazimzyanov, I. R., Khokhlov, A. A., Kolonskikh, A. G., Matveeva, N. P., Ruslanova, R. R., Rykun, M. P., Sitdikov, A., Volkova, E. V., Botalov, S. G., Bugrov, D. G., … Szécsényi-Nagy, A. (2025). Long shared haplotypes identify the southern Urals as a primary source for the 10th-century Hungarians. Cell, 188(21), 6064–6078.e11. https://doi.org/10.1016/j.cell.2025.09.002
    
    
38. Dobrovolná, M., Bowater, R. P., Pečinka, P., Brázda, V., Bartas, M. (2025). High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features. International Journal of Molecular Sciences, 26(20), 10180. https://doi.org/10.3390/ijms262010180
    
    
39. Barcytė, D., Žihala, D., Eliáš, M. (2025). Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles. PLoS Genetics, 21(10), e1011901. https://doi.org/10.1371/journal.pgen.1011901
    
    
40. Brázda, V., Bowater, R. P., Pečinka, P., Bartas, M. (2025). mGem: Noncanonical nucleic acid structures-powerful but neglected antiviral targets. mBio, 16(11), e0273025. https://doi.org/10.1128/mbio.02730-25
    
    
41. Votýpka, J., Jirků, M., Spodareva, V., Režnarová, J., Poloprutská, K., Pajer, P., Milner, D., Richards, T., Yurchenko, V., Ibáñez, R., Lukeš, J., Kostygov, A. Y. (2025). Trypanosomes in Neotropical frogs: unveiling hidden megadiversity and complex host-parasite patterns. Open Biology, 15(11), 250190. https://doi.org/10.1098/rsob.250190
    
    
42. Sheikh, S., Turpin Knotková, B., Benz, C., Eliáš, M., Bílý, T., Bondar, A., Tesařová, M., Stříbrná, E., Heller, J., Meinecke, M., Hashimi, H. (2025). The Core MICOS Complex Subunit mic60 has Been Substituted by Two Cryptic Mitofilin-containing Proteins in Euglenozoa. Molecular Biology and Evolution, 42(11), msaf289. https://doi.org/10.1093/molbev/msaf289
    
    
43. Petrovič, M., Bartas, M., Garratt, A. N., Pečinka, P., Dobrovolná, M., Koňaříková, K., Trenz, O., Brázda, V., Šťastný, J. (2025). Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study in Drosophila. NAR Genomics and Bioinformatics, 7(4), lqaf166. https://doi.org/10.1093/nargab/lqaf166
44. Lukeš, J., Čapková Pavlíková, Z., Yurchenko, V., Paris, Z., & Valášek, L. S. (2025). Blastocrithidia—A genetic alien from the planet Earth. Cold Spring Harbor Perspectives in Biology, 17(12), a041868. https://doi.org/10.1101/cshperspect.a041868
45. Alpizar-Sosa, E. A., Saura, A., Fajkus, P., Poláková, E., Havlová, K., Albanaz, A. T. S., Fajkus, J., & Yurchenko, V. (2025). Leishmania mexicana telomeres at high resolution: Ku80, TERT, and alternative lengthening mechanisms. BMC Genomics, 26(1), 955. https://doi.org/10.1186/s12864-025-12154-z
46. Kostygov, A. Y., Grybchuk, D., Klocek, D., Votýpka, J., Mendoza-Roldan, J. A., Lukeš, J., & Yurchenko, V. (2026). The first RNA viruses detected in a trypanosome. BMC Biology, 24(1), 27. https://doi.org/10.1186/s12915-025-02497-0
47. Kostygov, A. Y., Grybchuk, D., & Yurchenko, V. (2026). Hidden passengers: Expanding the RNA virosphere of trypanosomatids. Trends in Parasitology, 42(2), 97–101. https://doi.org/10.1016/j.pt.2025.12.004
48. Corre, P., Pilátová, J., Bílý, T., Zadrobílková, E., Čepička, I., Vancová, M., Lohr, M., Caspari, O. D., Eliáš, M., & Pánek, T. (2026). Energy metabolism and adaptation to hypoxia in the non-photosynthetic green alga Leontynka. BMC Biology, 24(1), 50. https://doi.org/10.1186/s12915-026-02529-3

RP 2 – Biochemical methods

1. Böde, K., Javornik, U., Dlouhý, O., Zsíros, O., Biswas, A., Domonkos, I., Šket, P., Karlický, V., Plavec, J., Ughy, B., Lambrev, P.H., Špunda, V., & Garab, G. (2024). Role of isotropic lipid phase in the fusion of photosystem II membranes. Photosynthesis Research, 159(1), 1-14. https://doi.org/10.1007/s11120-024-01097-3
2. Garab, G. (2024). Revisiting the nonregulatory, constitutive nonphotochemical quenching of the absorbed light energy in oxygenic photosynthetic organisms. Photosynthetica, 62(2), 204-208. https://doi.org/10.32615/ps.2024.022
3. Bartas, M., Červeň, J., Valková, N., Volná, A., Dobrovolná, M., Šislerová, L., Baldvinsson, H., Pečinka, P., Brázda, V. (2023). RNA analysis of the longest living vertebrate Greenland shark revealed an abundance of LINE-like elements in its transcriptome. Czech Polar Reports, 13(2), 210-227. https://doi.org/10.5817/CPR2023-2-17
4. Volná, A., Červeň, J., Nezval, J., Pech, R., & Špunda, V. (2024). Bridging the Gap: From Photoperception to the Transcription Control of Genes Related to the Production of Phenolic Compounds. International Journal of Molecular Sciences, 25(13), 7066. https://doi.org/10.3390/ijms25137066
5. Pech, R., Nezval, J., Volná, A., & Špunda, V. (2024). Blue Light as an Important Factor Increasing Plant Tolerance to Acute Photooxidative, Stress. Environmental and Experimental Botany, 226, 105923. https://doi.org/10.1016/j.envexpbot.2024.105923
6. Findurová, H., Urban, O., Veselá, B., Nezval, J., Pech, R., Špunda, V., & Klem, K. (2024). Acclimation of barley plants to elevated CO2 concentration and high light intensity does not increase their protection against drought, heat, and their combination. Plant Stress, 13, 100687. https://doi.org/10.1016/j.stress.2024.100687
7. Garab, G., Böde, K., Dlouhý, O., Násztor, Z., Karlický, V., Dér, A., & Špunda, V. (2025). Lipid polymorphism of plant thylakoid membranes. The dynamic exchange model – facts and hypotheses. Physiologia Plantarum, 177(2), e70230. https://doi.org/10.1111/ppl.70230
8. Böde, K., Trotta, A., Dlouhý, O., Javornik, U., Paakkarinen, V., Fujii, H., Domonkos, I., Zsíros, O., Plavec, J., Špunda, V., Aro, E.-M., & Garab, G. (2025). Lipid phase behaviour of the curvature region of thylakoid membranes of Spinacia oleracea. Physiologia Plantarum, 177(3), e70289. https://doi.org/10.1111/ppl.70289
9. Fehér, B., Nagy, G., & Garab, G. (2025). Molecular level insight into non-bilayer structure formation in thylakoid membranes: A molecular dynamics study. Photosynthesis Research, 163(3), 36. https://doi.org/10.1007/s11120-025-01156-3
10. Hällfors, M. H., Robson, T. M., Burg, S., Pentikäinen, S., Koivusaari, S. H. M., Luoto, M., Nezval, J., Pech, R., Saastamoinen, M., Schulman, L. E., Sirén, J., & Susi, H. (2025). Thermal Plasticity of Multiple Traits Varies More Within Than Between Populations of Plantago lanceolata at Its Northern Range Edge. Ecology and Evolution, 15(10), e72201https://doi.org/10.1002/ece3.72201
11. Garab, G. (2025). Revisiting the QA model of chlorophyll-a fluorescence induction: new perspectives to monitor the photochemical activity and structural dynamics of photosystem II. Photosynthesis Research, 163(6), 54. https://doi.org/10.1007/s11120-025-01178-x
12. Böde, K., Sebők-Nagy, K., Dlouhý, O., Steinbach, G., Benda, A., Garab, G., & Páli, T. (2026). Lipid assemblies mediating the fusion of photosystem-II enriched membranes characterized by DPH (1,6-diphenyl-1,3,5-hexatriene) fluorescence and fluorescence anisotropy lifetimes. Journal of Photochemistry and Photobiology B: Biology, 275, 113361. https://doi.org/10.1016/j.jphotobiol.2026.113361

RP 2 – Biophysical methods

1. Dukić, M., Sredojević, D., Férová, M., Slovak, V., Lončarević, D., Dostanić, J.,  & Nedeljković, J. M. (2024). Interfacial charge transfer complexes between ZnO and benzene derivatives: Characterization and photocatalytic hydrogen production. International Journal of Hydrogen Energy, 62, 628-636. https://doi.org/10.1016/j.ijhydene.2024.03.075
2. Férová, M. & Kalina, J. (2024). Biosynthesis of silver nanoparticles from reynoutria bohemica by hot and cold route. waste and biomass valorization, 15, 2661-2672. https://doi.org/10.1007/s12649-024-02656-4
3. Zelenka, T., Zelená, L., Abreu-Jaureguí, C., Silvestre-Albero, J., Zelenková, G., & Slovák, V. (2024). On the low-pressure hysteresis (LPH) in gas sorption isotherms of porous carbons. Small, 20, 2311990. https://doi.org/10.1002/smll.202311990
4. Lazić, V., Sredojević, D., Ćirić, A., Nedeljković, J. M., Zelenková, G., Férová, M., Zelenka, T., Chavhan, M. P., & Slovák, V. (2024). The photocatalytic ability of visible-light-responsive interfacial charge transfer complex between TiO₂ and Tiron. Journal of Photochemistry and Photobiology A: Chemistry, 449, 115394. https://doi.org/10.1016/j.jphotochem.2023.115394
5. Férová, M., Slovák, V., Nikšić, V., Lazić, V., Zeković, I., Sredojević, D., & Nedeljković, J. M. (2025). Comparative experimental and DFT study of ZnO particles prepared using Reynoutria bohemica extract. Optical Materials, 167, 117375. https://doi.org/10.1016/j.optmat.2025.117375
6. Kořená, L., Slovák, V., Flores-López, S. L., & Arenillas, A. (2025). Systematic DSC analysis of the melting point depression and the non-freezable layer width in different mesopore sizes in carbon xerogels. Thermochimica Acta, 741, 180128. https://doi.org/10.1016/j.tca.2025.180128

RP 3 – Modeling and simulation

1. Šulka, M., Šulková, K., Jurečka, P., & Dubecký, M. (2023). Dynamic and nondynamic electron correlation energy decomposition based on the node of the hartree–fock slater determinant. Journal of Chemical Theory and Computation, 19(22), 8147-8155. https://doi.org/10.1021/acs.jctc.3c00828
2. Vénosová, B., & Karlický, F. (2023). Modeling size and edge functionalization of MXene-based quantum dots and their effect on electronic and magnetic properties. Nanoscale Advances, 5(24), 7067-7076. https://doi.org/10.1039/d3na00474k
3. Novotný, M., Dubecký, M., & Karlický, F. (2024). Toward accurate modeling of structure and energetics of bulk hexagonal boron nitride. Journal of Computational Chemistry, 45(2), 115-121. https://doi.org/10.1002/jcc.27222
4. Sakhraoui, T., & Karlický, F . (2024). Prediction of induced magnetism in 2D Ti2C based MXenes by manipulating the mixed surface functionalization and metal substitution computed by xTB model Hamiltonian of the DFTB method. Physical Chemistry Chemical Physics, 26, 12862-12868. https://doi.org/10.1039/d3cp05665a
5. Saraswat, R., Kolos, M., Verma, R., Karlický, F., & Bhattacharya, S. (2024). Phonon assisted exciton processes in two-dimensional tungsten monocarbide. The Journal of Physical Chemistry C, 128(20), 8341-8350. https://doi.org/10.1021/acs.jpcc.4c02062
6. Kalmár, J., & Karlický, F. (2024). Strain-induced changes of electronic and optical properties of Zr-based MXenes. Journal of Applied Physics, 135, 244302. https://doi.org/10.1063/5.0205991
7. Vénosová, B., & Karlický, F. (2024). MXene’s surface functionalization patterns and their impacts on magnetism. Physical Chemistry Chemical Physics, 26, 18500-18509. https://doi.org/10.1039/D4CP01319K
8. Šulka, M., Šulková, K., & Dubecký, M. (2024). Unveiling hidden dynamic correlations in CASSCF correlation energies by hartree-fock nodes. The Journal of Chemical Physics, 161(11), 114112. https://doi.org/10.1063/5.0223733
9.  Kolos, M., & Karlický, F. (2025). Predicting fundamental gaps of chromium-based 2D materials using GW methods. The Journal of Physical Chemistry C, 129(5), 2782−2787. https://doi.org/10.1021/acs.jpcc.4c07981
10.  Kolos M., & Karlický, F. (2025). Computational screening of MXene-based catalysts for chlorinated hydrocarbons removal. Journal of Physics-Materials, 8(3), 035001. https://doi.org/10.1088/2515-7639/add37d
11.  Vieira de Castro, T., Richard, F., Bennett, S. H., Lamborelle, C. S., Nichol, G. S., Szabla, R., & Lawrence, A. L. (2025). Quinol−enedione rearrangement. Organic Letters, 27, 4782-4787. https://doi.org/10.1021/acs.orglett.5c01266
12.  Rossetto, D., Nader, S., Kufner, C. L., Lozano, G. G., Cerofolini, L., Fragai, M., Martin-Diaconescu, V., Zambelli, B., Ciurli, S., Guella, G., Szabla, R., Sasselov, D. D., Mansy, S. S. (2025). Preferential survival of prebiotic metallopeptides in the presence of ultraviolet light. Chemical Science, Advance online publication. https://doi.org/10.1039/d5sc02170g
13.  Suchanek, R., Błauciak, M., Spyszkiewicz, A., Dziuk, B., Boratyński, P. J., Szabla, R., & Kowalczyk, R. (2025). Tunable thiofumarate stereoselective cycloadditions via aminomefloquine catalysis. Organic Chemistry Frontiers. Advance online publication. https://doi.org/10.1039/D5QO01014D
14.  Pia, F. D., Shi, B. X., Al-Hamdani, Y. S., Alfé, D., Anderson, T. A., Barborini, M., Benali A., Casula M., Drummond N. D., Dubecký M., Filippi C., Kent P. R. C., Krogel, J. T., Ríos, P. L., Lüchow, A., Luo Y., Michaelides, A., Mitas, L., Nakano, K., … Zen, A. (2025). Reproducibility of fixed-node diffusion Monte Carlo across diverse community codes: The case of water–methane dimer. Journal of Chemical Physics, 163(10), 104110. https://doi.org/10.1063/5.0272974
15.  Sakhraoui, T., & Karlický, F. (2025). Unveiling the magnetic behavior of C3N4 2D material by defect creation, defect passivation, and transition metal adsorption. Journal of Materials Science, 60, 16984-17000. https://doi.org/10.1007/s10853-025-11399-z
16.  Fanta, R., Jurečka, P., & Dubecký, M. (2025). Why nondynamic correlation matters for ππ stacking? Lessons from the Benzene Dimer. The Journal of Physical Chemistry Letters, 16, 10982-10988. https://doi.org/10.1021/acs.jpclett.5c02576
17.  Vénosová, B., & Karlický, F. (2025). Effects of surface functionalization and size of MXene-based quantum dots on their optical properties: the exciton confinement matters. Nanoscale, 17, 24529-24540. https://doi.org/10.1039/D5NR03127C
18.  Shahrokhi, M. (2026). Stability of single-atom Pt-alloyed Cu clusters supported on γ-Al2O3: A DFT study of size and oxidizing environment effects. Computational Materials Science, 262, 114346. https://doi.org/10.1016/j.commatsci.2025.114346
19.  Sakhraoui T., & Karlický, F. (2025). Electronic and magnetic properties of ordered double transition metal MXenes: Ti2MC2T2 (M = Cr, Mo, and W; T = F, O, OH, and Cl). ACS Omega, 10, 54061. https://doi.org/10.1021/acsomega.5c05596
20.  Kumar, N., Kolos, M., & Karlický, F. (2025). Stacking-dependent interlayer excitons in BP/CrSe2 van der Waals heterostructure. Nano Letters, 25, 16608−16613. https://doi.org/10.1021/acs.nanolett.5c03389
21.  Mortazavi, B., Shojaei, F., Shahrokhi, M., & Zhuang X. (2026). Machine learning-assisted first-principles study of structural, electronic, optical, thermal, and mechanical properties of novel s-triazine-based organic framework monolayers. Carbon, 248, 121092. https://doi.org/10.1016/j.carbon.2025.121092
22.  Lech, B. K., Jurečka, P., Zgarbová, M., & Szabla, R. (2026). A-type helicity controls efficient nonenzymatic template copying of nucleic acids. Chemical Communications, 62, 897-900. https://doi.org/10.1039/D5CC05343A
23.  Shahrokhi, M., & Mortazavi, B. (2026). First-principles discovery of stable, anisotropic, semiconducting Sb2X2O (X = S, Se) and Janus Sb2SSeO nanosheets for optoelectronics and photocatalysis. Materials Today Energy, 55, 102172. https://doi.org/10.1016/j.mtener.2025.102172
24.  Mortazavi, B., Karlický, F., Zhuang, X., & Shahrokhi, M. (2026). First-principles investigation of novel stable, strong, and highly attractive semiconducting nanoporous C3N and CN monolayers. Results in Chemistry, 21, 103088. https://doi.org/10.1016/j.rechem.2026.103088
25. Rastipour, Z., Shahrokhi, M., Shojaei, F., Zhuang, X., & Martazavi, B. (2026): Hetero[8]circulene-Based 2D Materials: A DFT Study of Electronic, Mechanical, and Transport Properties. ACS Applied Energy Materials, 9, 4, 2089-2100. https://doi.org/10.1021/acsaem.5c03121

RP 4 – 4HAIE – PA and Health

1. Jandacka, D., Casula, V., Hamill, J., Vilímek, D., Jandackova, V. K., Elavsky, S., … Nieminen, M. T. (2024). Regular running is related to the knee joint cartilage structure in healthy adults. Medicine & Science in Sports & Exercise, 56(6), 1026-1035. https://doi.org/10.1249/MSS.0000000000003386
2. Cipryan, L., Litschmannova, M., Barot, T., Dostal, T., Sindler, D., Kutac, P., Jandacka, D., & Hofmann, P. (2024). Air pollution, cardiorespiratory fitness and biomarkers of oxidative status and inflammation in the 4HAIE study. Scientific Reports, 14(1), 9620. https://doi.org/10.1038/s41598-024-60388-w
3. Krajcigr, M., Kutáč, P., Elavsky, S., Jandačka, D., & Zimmermann, M. (2024). Comparison of bone mineral density of runners with inactive males: A cross-sectional 4HAIE study. PLoS ONE, 19(8), e0306715. https://doi.org/10.1371/journal.pone.0306715
4. Slovák, L., Panfilov, E., Zahradník, D., Casula, V., Nieminen, M. T., Land, W. M., ... & Abdollahipour, R. (2024). External Focus of Attention Reduces Cartilage Load During Drop Landings. Scandinavian Journal of Medicine & Science in Sports, 34(9), e14718. https://doi.org/10.1111/sms.14718
5. Cibulcova, V ., Koenig, J., Jackowska, M., & Jandackova, V. K. (2024). Influence of a 2-week transcutaneous auricular vagus nerve stimulation on memory: findings from a randomized placebo controlled trial in non-clinical adults. Clinical Autonomic Research, Advance online publication. https://doi.org/10.1007/s10286-024-01053-0
6. Jandackova, V. K., Scholes, S., Britton, A., & Steptoe, A. (2024). Midlife heart rate variability and cognitive decline: A large longitudinal cohort study. International Journal of Clinical and Health Psychology, 24(4), 100518. https://doi.org/10.1016/j.ijchp.2024.100518
7. Monte, A., Vilimek, D., Uchytil, J., Skypala, J., Cipryan, L., Casula, V., ... & Nieminen, M. T. (2024). High levels of glycated haemoglobin (HbA1c) are associated with lower knee joint cartilage quality and higher knee joint symptoms in healthy individuals. European Journal of Applied Physiology, Advance online publication. https://doi.org/10.1007/s00421-024-05646-5
8. Plesek, J., Hamill, J., Burda, M., Elavsky, S., Skypala, J., Urbaczka, J., ... & Daniel, J. (2024). Running distance and biomechanical risk factors for plantar fasciitis: A one-year prospective 4HAIE cohort study. Medicine and Science in Sports and Exercise. Advance online publication. https://doi.org/10.1249/MSS.0000000000003617
9. Dostal, T., Dankova, M., Barot, T., Sindler, D., Kutac, P., Jandackova, V., ... & Cipryan, L. (2024). Association between cardiac autonomic regulation, visceral adipose tissue, cardiorespiratory fitness and ambient air pollution: 4HAIE study (Program–4). PLoS ONE, 19(12), e0315767. https://doi.org/10.1371/journal.pone.0315767
10.  Zahradnik, D., Hamill, J., Plesek, J., Blaschova, D., Burda, M., Nieminen, M., ... & Jandačka, D. (2025). Association between T2 relaxation time and biomechanical loading of the anterior cruciate ligament in healthy individuals. Sports Biomechanics, Advance online publication. https://doi.org/10.1080/14763141.2025.2458475
11.  Farana, R., Brtva, P., Irwin, G., & Hamill, J. (2025). Head-trunk coordination during shooting skills in young floorball players. Research Quarterly for exercise and Sport. Advance online publication. https://doi.org/10.1080/02701367.2025.2461321
12.  Magris, R., Uchytil, J., Cipryan, L., Skýpala, J., Jandacka, D., & Monte, A. (2025). Elevated glycated haemoglobin affects Achilles tendon properties and walking capacity in healthy people without a diagnosis of diabetes. Scientific Reports, 15(1), Article 1219. https://doi.org/10.1038/s41598-025-01219-4
13.  Sebera, M., Skypala, J., & Elavsky, S. (2025). Psychosocial factors and running-related injuries: unraveling the connection, based on a one-year prospective study. The Journal of Sports Medicine and Physical Fitness. Advance online publication. https://doi.org/10.23736/S0022-4707.24.16398-0
14.  Elavsky, S., Brabec, M., Malý, M., Knapová, L., Kaštovská, B., Sebera, M., Ely, M., Jandačková, V.K., Keller, J., & Pavel, M. (2025). The Temporal Dynamics of the Association between Daily Physical Activity and Life Satisfaction. Annals of Behavioral Medicine. 59(1), kaaf079. https://doi.org/10.1093/abm/kaaf079
15.  Baretta, D., Koch, S., Buekers, J., Aymerich, J., Knapova, L., Elavsky, S., ... & Chevance, G. (2025). Predicting recovery after stressors using step count data derived from activity monitors. NPJ Digital Medicine. Advance online publication. https://doi.org/10.1038/s41746-025-01998-0
16.  Kutac, P., Dankova, M., Cipryan, L., Buzga, M., Jirik, V., Bunc, V., … Jandacka, D. (2025). Association of air pollution with adiposity rates in active runners and inactive people. American Journal of Human Biology, 37(10), e70159. https://doi.org/10.1002/ajhb.70159
17.  Farana, R., Brtva, P., Irwin, G., & Newell, K. M. (2025). Neck angle in the handstand changes the pattern of multi-joint variability. Journal of Motor Behavior, 57(6), 768-776. https://doi.org/10.1080/00222895.2025.2558711
18.  Slovák, L., Zahradník, D., Land, W. M., ... & Abdollahipour, R. (2026). Knee joint biomechanics under external focus instructions promoting a quiet, safe and soft landing, The Knee. 58. https://doi.org/10.1016/j.knee.2025.10.013
19.  Rygelova, M., Uchytil, J., Hamill, J., Malus, J., Torres, I. E., & Janura, M. (2025). Changes in time-continuous joint kinematics in preschool children over the stance phase of gait. Gait & Posture, 119, 203-207. https://doi.org/10.1016/j.gaitpost.2025.03.013
20.  Jandacka, D., Skypala, J., Plesek, J., Urbaczka, J., Golian, M., Burda, M., ... & Hamill, J. (2025). Biomechanical insights into Achilles tendinopathy risk and protection in runners: a large prospective study 4HAIE. British Journal of Sports Medicine. Advance online publication. https://doi.org/10.1136/bjsports-2025-110260
21.  Jackowska, M., Koenig, J., Cibulcova, V., & Jandackova, V. K. (2025). Effects of transcutaneous vagus nerve stimulation on subthreshold affective symptoms and perceived stress: Findings from a single-blinded randomized trial in community-dwelling adults. Biological Psychology, 202, 109169. https://doi.org/10.1016/j.biopsycho.2025.109169
22. Slovák, L., Singh, H., & Zahradník, D. (2026). Gender differences in technical performance of the volleyball spike jump among Czech top national league players. German Journal of Exercise and Sport Research. Advance online publication. https://doi.org/10.1007/s12662-025-01088-z
23. Cipryan, L., Skýpala, J., Litschmannová, M., Jandačka, D., Dostál, T., Šindler, D., Zahradník, D., & Hofmann, P. (2026). Baseline inflammatory markers as predictors of running-related injuries: A one-year prospective 4HAIE cohort study. Scandinavian Journal of Medicine & Science in Sports. Advance online publication. https://doi.org/10.1111/sms.70225
24. Lashinsky, A., Knapová, L., Burda, M., Kaštovská, B., Sebera, M., Blaschová, D., Filo, R., Uhrová, V., Revilla, M., & Elavsky, S. (2026). Analysis of participant-level characteristics predicting adherence to long-term EMA and Fitbit monitoring in the 4HAIE prospective cohort study. International Journal of Behavioral Medicine. Advance online publication. https://doi.org/10.1007/s12529-025-10433-3

RP 5 – Neurorehabilitation with the use of artificial intelligence

1. Filip, M., Doležel, J., Kozlovskaya, A., Kender, M., Novák, P. S., & Filipová, J. (2024). Virtuální realita v neurochirurgii: vývoj vzdělávacího modulu zaměřeného na zavádění intrakraniálního tlaku. Česká a Slovenská Neurologie a Neurochirurgie, 87(6). https://doi.org/10.48095/cccsnn2024423
2. Hečko, J., Přeček, D., Januska, J., Hudec, M., Barnova, K., Palickova Mikolaskova, M., & Jiravsky, O. (2025). Design and validation of a mixed reality workflow for structural cardiac procedures in interventional cardiology. Frontiers in Virtual Reality, 6, 1690439. https://doi.org/10.3389/frvir.2025.1690439

RP 6 – Research and development of new therapeutic methods in blood tumors

1. Venglar, O., Kapustova, V., Anilkumar Sithara, A., Zihala, D., Muronova, L., Sevcikova, T., Simicek, M., & Jelinek, T. (2023). Insight into the mechanism of CD34+ cell mobilisation impairment in multiple myeloma patients treated with anti ‐CD38 therapy. British Journal of Haematology, Advance online publication. https://doi.org/10.1111/bjh.19141 
2. Jelinek, T., Zihala, D., Sevcikova, T., Anilkumar Sithara, A., Kapustova, V., Sahinbegovic, H., Venglar, O., Muronova, L., Broskevicova, L., Nenarokov, S., Bilek, D., Popkova, T., Plonkova, H., Vrana, J., Zidlik, V., Hurnik, P., Havel, M., Hrdinka, M., Chyra, Z., Stracquadanio, G., Simicek, M., Hajek, R. (2024). Beyond the marrow: insights from comprehensive next-generation sequencing of extramedullary multiple myeloma tumors. Leukemia, 38, 1-11. https://doi.org/10.1038/s41375-024-02206-w
3. Radhakrishnan, D., Kotulová, J., Hofmanová, L., Anilkumar Sithara, A., Turi, M., Žihala, D., Ďurech, M., Vrána, J., Uleri, V., Niederlova, V., Stepanek, O., Chyra, Z., Jelínek, T., Hájek, R., & Hrdinka, M. (2025). Deubiquitinase BAP1 is crucial for surface expression of T cell receptor (TCR) complex, T cell–B cell conjugate formation, and T cell activation. Journal of Leukocyte Biology, 117(1), qiae184. https://doi.org/10.1093/jleuko/qiae184
4. Tao, Z., Chyra, Z., Kotulová, J., Celichowski, P., Mihályová, J., Charvátová, S., & Hájek, R. (2024). Impact of T cell characteristics on CAR-T cell therapy in hematological malignancies. Blood Cancer Journal, 14(1), 1-10. https://doi.org/10.1038/s41408-024-01193-6
5. Venglar, O., Radova, E., Zihala, D., Tvrda, I., Kubala, V., Kutejova, K., & Jelinek, T. (2025). Level of clonal plasma cells in hematopoietic cell autografts reflects the pre ‐transplant bone marrow minimal residual disease in multiple myeloma patients. American Journal of Hematology, Advance online publication. https://doi.org/10.1002/ajh.27590
6. Muronova, L., Soucek, O., Zihala, D., Sevcikova, T., Popkova, T., Plonkova, H., ... & Jelinek, T. (2025). Real ‐World Evidence on Prognostic Value of MRD in Multiple Myeloma Using Flow Cytometry. European Journal of Haematology, 114(1), 155-163. https://doi.org/10.1111/ejh.14316
7. Garces, J. J., Diamond, B., Sevcikova, T., Nenarokov, S., Bilek, D., Radova, E., & Jelinek, T. (2025). Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma. HemaSphere, 9(9), e70218. https://doi.org/10.1002/hem3.70218
8. Venglar, O., Radova, E., Broskevicova, L., Hajek, R., & Jelinek, T. (2025). OMIP ‐117: 40 ‐Parameter/37 ‐Color spectral cytometry panel for robust immunoprofiling of human lymphoid subsets in cancer patients. Cytometry Part A, 107(10), 641-648. https://doi.org/10.1002/cyto.a.24962
9. Fantová, T., Warmuzová, M., Charvátová, S., Stošková, K., Jelínek, T., Šimíček, M., & Bagó, J. R. (2026). Winners take it all: turning cell competition into a therapeutic ally. Cell Communication and Signaling. Advance in publication. https://doi.org/10.1186/s12964-025-02611-3
10.  Jelinek, T., Žihala, D., Zabaleta, A., Kostopoulos, I. V., Soucek, O., Venglar, O., ... & Hajek, R. (2025). Selective depletion of B-cell subsets underlies increased risk of infection in MM patients treated with anti-BCMA vs-GPRC5D bsAbs. Blood Journal, Advance in publication. https://doi.org/10.1182/blood.2025029572
11.  Anilkumar Sithara, A., Kapustova, V., Zihala, D., Venglar, O., Bilek, D., Helal, M., & Jelinek, T. (2025). Composition and functional state of T and NK cells in the extramedullary myeloma tumor microenvironment. Blood Cancer Discovery, Advance online publication. https://doi.org/10.1158/2643-3230.BCD-25-0170

RP 7 – Applied Research in Oncolog

1. Hurník, P., Režnarová, J., Chyra, Z., Motyka, O., Putnová, B. M., Čermáková, Z., & Štembírek, J. (2023). Enhancing oral squamous cell carcinoma prediction: the prognostic power of the worst pattern of invasion and the limited impact of molecular resection margins. Frontiers in Oncology, 13, Article 1287650. https://doi.org/10.3389/fonc.2023.1287650
2. Put, A., Smesny Trtkova, K., & Skarda, J. (2024). Methylation status of selected genes in non-small cell lung carcinoma: Current knowledge and future perspectives. Neoplasma. 71(6), 511-532. https://doi.org/10.4149/neo_2024_240925N403
3. Belobradová, J., Onderka, A., Timkovic, J., Hranková, V., Reguli, S., Kondé, A., Karas, R., Stránsky, J., Štembírek, J., & Bianchi, C. (2025). Possible complications of frontal sinus fractures after conservative or surgical treatment: Retrospective study. Acta Oto-Laryngologica. 145(3),  https://doi.org/10.1080/00016489.2025.2454481
4. Kratka, K., Sistik, P., Olivkova, I., Kusnierova, P., Svagera, Z., & Stejskal, D. (2024). Mass spectrometry-based proteomics in clinical diagnosis of amyloidosis and multiple myeloma: A review (2012–2024). Journal of Mass Spectrometry. 60(3), https://doi.org/10.1002/jms.5116
5. Schwarzerova, J., Mate, E. G., Idkowiak, J., Olesova, D., Kvasnicka, A., Dobesova, D., Friedecky, D., Provaznik, V., Skarda, J., Weckwerth, W., & Nägele, T. (2025). MInfer: Bridging MetaboAnalyst and Jacobian analysis for metabolomic networks. Computer Methods and Programs in Biomedicine, 263, https://doi.org/10.1016/j.cmpb.2025.108672
6. Gedeonová, D., Bianchi, C., Štembírek, J., Hrdinka, M., Chyra, Z., Buchtová, M., Hurník, P., Blažek, T., & Režnarová, J. (2025). BRCA1 and BRCA2 as prognostic markers in oral squamous cell carcinoma: A minireview. Frontiers in Oncology. 15, https://doi.org/10.3389/fonc.2025.1528822
7. Schwarzerova, J., Olesova, D., Jureckova, K., Kvasnicka, A., Kostoval, A., Friedecký, D., Sekora, J., Poměnková, J., Provaznik, V., Popelinsky, L., & Weckwerth, W. (2025). Enhanced metabolomic predictions using concept drift analysis: Identification and correction of confounding factors. Bioinformatics Advances. 5(1), https://doi.org/10.1093/bioadv/vbaf073
8. Duricová, J., Brozmanová, H., Jurica, J., Kacírová, I., Sistík, P., Kanková, K., Tomásková, H., & Kolek, M. (2025). Clindamycin, ciprofloxacin, and co-trimoxazole wound penetration in open-heart surgery patients receiving negative pressure wound therapy for deep sternal wound infection: A single-center prospective observational study. Bratislava Medical Journal. https://doi.org/10.1007/s44411-025-00194-6
9. Petroková, H., Mierzwicka, J. M., Chakraborty, P., Rašková Kafková, L., Vaculová, J., Škarda, J., Fischer, O., Kosztyu, P., Kuchař, M., Raška, M., & Malý, P. (2025). Myomedin variants developed for in vitro PD-L1 diagnostics in tissue samples of non-small cell lung carcinoma patients. Journal of Translational Medicine, 23(1). https://doi.org/10.1186/s12967-025-06699-6
10. Tichý, D., Zeleník, K., Purnell, P. R., Vaculová, J., Hurník, P., Fedorová, K., & Komínek, P. (2025). Laryngeal schwannoma in a 14-year-old girl. Otolaryngology Case Reports, 36, 100671. https://doi.org/10.1016/j.xocr.2025.100671

RP 8 – Environmental epidemiology as a tool for improving the quality of life in the industrial environment

1. Gottfriedová, N., Kovalová, M., Škerková, M., & Mrázková, E. (2024). Extended high-frequency audiometry in the elderly: A narrative review. Journal of International Advanced Otology, 20(4), 358-364. https://doi.org/10.5152/iao.2024.231217
2. Macounová, P., Bobčíková, K., Tomášková, H., Mitták, M., & Argalášová, Ľ. (2024). Functional status in patients undergoing lung resection. Archives of Medical Science, 20(4), 1339–1344. https://doi.org/10.5114/aoms/190516
3. Cibulcova, V., Koenig, J., Jackowska, M., & Jandackova, V. K. (2024). Influence of a 2-week transcutaneous auricular vagus nerve stimulation on memory: Findings from a randomized placebo-controlled trial in non-clinical adults. Clinical Autonomic Research, 34(4), 447–462. https://doi.org/10.1007/s10286-024-01053-0
4. Jandackova, V. K., Scholes, S., Britton, A., & Steptoe, A. (2024). Midlife heart rate variability and cognitive decline: A large longitudinal cohort study. International Journal of Clinical and Health Psychology, 24(4), 100518. https://doi.org/10.1016/j.ijchp.2024.100518
5. Gottfriedová, N., Škerková, M., Zbořilová, M., Kovalová, M., Tomášková, H., & Mrázková, E. (2025). Hearing thresholds at conventional and extended high frequencies in young personal listening devices’ users: A pilot study. Otolaryngologia Polska, 79(1), 1–9. https://doi.org/10.5604/01.3001.0054.8776
6. Riedlova, P., Tavandzis, S., Kana, J., & Roubec, J. (2024). Conditions and factors affecting the accuracy of olfactometric detection. Heliyon, 11(1), e41604. https://doi.org/10.1016/j.heliyon.2024.e41604
7. Riedlová, P., Tomášková, H., Slachtová, H., Babjaková, J., & Jirik, V. (2025). The impact of environmental conditions on lifestyle quality in industrial and non-industrial region in the Czech Republic. Frontiers in Public Health, 13, 1505170. https://doi.org/10.3389/fpubh.2025.1505170
8. Kramna, D., Machaczka, O., Riedlova, P., Janulkova, T., Ostrizkova, S., Siemiatkowski, G., Osrodka, L., Krajny, E., & Jirik, V. (2025). Exploring the relationship between air pollution and telomere length: Baseline findings from a comprehensive ambispective cohort study. International Journal of Hygiene and Environmental Health, 267, 114577. https://doi.org/10.1016/j.ijheh.2025.114577
9. Solecka, S., Tomášková, H., Chudy, M., Kostlivý, T., & Slonková, J. (2025). Design and validation of sleep apnea risk assessment (SARA): A screening tool for moderate-to-severe obstructive sleep apnea. Nature and Science of Sleep, 17, 1163–1174. https://doi.org/10.2147/NSS.S518391
10. Skybova, D., Slachtova, H., Tomaskova, H., Kimakova, T., Rimárová, K., Kukla, L., & Klanova, J. (2025). Self-rated health of the middle-aged population and its determinants. Bratislava Medical Journal, 126(8), 1930–1938. https://doi.org/10.1007/s44411-025-00193-7
11. Jackowska, M., Koenig, J., Cibulcová, V., & Jandackova, V. K. (2025). Effects of transcutaneous vagus nerve stimulation on subthreshold affective symptoms and perceived stress: Findings from a single-blinded randomized trial in community-dwelling adults. Biological Psychology, 204, 109169. https://doi.org/10.1016/j.biopsycho.2025.109169

RP 4 – 4HAIE – PA and Health

Silesian University of Technology
Memorandum of Understanding

Projekt MASE – The Motor Activity – Subjective Energy Project: Neurobiological and Digital Phenotyping Towards Digital Mental Health Interventions in Depression
Cooperation Agreement

RP 5 – Neurorehabilitation with the use of artificial intelligence

VR MEDIX s.r.o.

RP 1 – Molecular biology and genomics

1. Analysis of Leishbuviridae from Trypanosomatids
   Responsible Persons (Lerco): Yurchenko, V.; Kostygov, A.
2. Assembly and Annotation of Kinetoplastid and Diplonemid Mitochondrial Genomes
   Responsible Person (Lerco): Yurchenko, V.

RP 3 – Modeling and simulation

1. Decomposition of Electron Correlation Energy into Dynamic and Non-dynamic Components by Nodes of Hartree–Fock Slater Determinant and Fixed-node Diffusion Monte Carlo Method
   Responsible Person (Lerco): Dubecký, M.
2. Density functional tight-binding methods for surface modifications of 2D materials
   Responsible Person (Lerco): Sakhraoui,T.

RP 4 – 4HAIE – PA and Health

1. Automatic Segmentation of Knee Cartilage from qMRI T2 Images
   Responsible Person (Lerco): Jandačka, D., Uchytil, J.
2. Detection of Spatiotemporal Parameters from Biomechanical and Fitbit Data
   Responsible Person (Lerco): Urbaczka, J., Jandačka, D., Elavsky, S.

RP 8 – Environmental epidemiology as a tool for improving the quality of life in the industrial environment

1. Methodological Procedure for Longitudinal Monitoring of Determinants of Health Status
   Responsible Person (Lerco): Tomášková, H.

RP 2 – Biochemical and biophysical methods of living systems analysis

RP 2 – Biochemical methods

Resorbent s.r.o.
Framework Agreement on the Provision of Research, Development, and Consulting Services

RP 4 – 4HAIE – PA and Health

HAS-MOTION INC.
Memorandum of Understanding

MiracIIS, SE
Collaboration Agreement
VP4 in collaboration with VP9

RP 5 – Neurorehabilitation with the use of artificial intelligence

Medical Monitor s. r. o.
Memorandum of Understanding

Vexim s. r. o.
Collaboration Agreement
VP4 in collaboration with VP9

Krajská nemocnice T. Bati, a. s.
Collaborative Research Agreement

RP 2 – Biochemical and biophysical methods of living systems analysis

RP 2 – Biochemical methods

Doktorský studijní program Biophysics and Physics Nanostructures
Responsible Person (Lerco): Špunda, V.
Implemented in cooperation with VP3

RP 2 – Biophysical methods

Master’s Study Programme: Analytical Chemistry – New Specialisation in Bioanalytical Chemistry
Responsible Person (Lerco): Slovák, V.

RP 3 – Modeling and simulation

Doctoral Study Programme: Biophysics and Physics of Nanostructures
Responsible Person (Lerco): Karlický, F.
Implemented in cooperation with VP2 FY

RP 4 – 4HAIE – PA and Health

Habilitační řízení v oboru Human Movement Sciences
Responsible Person (Lerco): Jandačka, D.

RP 8 – Environmental epidemiology as a tool for improving the quality of life in the industrial environment

Habilitation Procedure in Hygiene, Preventive Medicine and Epidemiology
Responsible Person (Lerco): Tomášková, H.

RP 2 – Biochemical and biophysical methods of living systems analysis

RP 2 – Biophysical methods

Thermotolerance of Photosynthesis
Call: HORIZON-MSCA-2025-DN-01
Status: Under evaluation
Responsible person (LERCO): Václav Karlický

RP 3 – Modeling and simulation

Spin Symmetry Breaking in Two-Dimensional Ferromagnets and Antiferromagnets at Finite Temperature
Call: HORIZON-TMA-MSCA-PF-EF (HORIZON TMA MSCA) – Postdoctoral Fellowships (European)
Status: Not funded; resubmitted at national level
Responsible person (LERCO): F. Karlický

Erasmus+ KA2: Enhancing the Quality of Health-Related Physical Activity through Educational Feedback in Older Adults
Call: KA210-ADU-E1CC5C06
Status: Funded
Responsible person (LERCO): D. Jandačka

Brain Response to Pollution: Novel Insights from Genetic, Environmental and Lifestyle Pathways (BRIDGE)
Call: HORIZON-HLTH-2025-03-two-stage
Status: Under evaluation
Responsible persons (LERCO): V. K. Jandačková, D. Jandačka, S. Elavsky

Tumor microenvironment and clonal evolution in myeloma extramedullary disease
Call: EHA Research Grants
Status: Funded
Responsible person (LERCO): D. Žihala

Pan-European Partnership for the Prevention of Multiple Myeloma
Call: SEP-210927931, HORIZON-RIA, HORIZON-MISS-2023-CANCER-01
Status: Not funded
Responsible person (LERCO): D. Žihala

Plotting radiotherapy options to refine the individual treatment journey
Status: Under evaluation
Responsible persons (LERCO): L. Knybel, Š. Reguli

Next generation breathing management during radiotherapy, using non-invasive mechanical ventilation (NextBreathRT)
Call: COST Action
Status: Open Call Collection OC-2025-1-28575
Responsible person (LERCO): L. Knybel