Publications

22. Tretyachenko, V., Leiman, T., Morgenstern, D., Levin, Y., Asraf, O., Dahan, O., Dahary, D. & Pilpel, Y. (2026). Encoded and non-genetic protein variants expand human functional proteome. Nature. https://doi.org/10.1038/s41586-026-11124-z

21. Lobinska, G., Tretyachenko, V., Dahan, O., Nowak, M. A. & Pilpel, Y. (2024). The evolutionary safety of mutagenic drugs should be assessed before drug approval. PLOS Biology, 22(3), e3002570. https://doi.org/10.1371/journal.pbio.3002570

20. Heames, B., Buchel, F., Aubel, M., Tretyachenko, V., Loginov, D., Novák, P., Lange, A., Bornberg-Bauer, E. & Hlouchová, K. (2023). Experimental characterization of de novo proteins and their unevolved random-sequence counterparts. Nature Ecology & Evolution, 7(4), 570–580. https://doi.org/10.1038/s41559-023-02010-2

19. Tretyachenko, V., Vymětal, J., Neuwirthová, T., Vondrášek, J., Fujishima, K. & Hlouchová, K. (2022). Modern and prebiotic amino acids support distinct structural profiles in proteins. Open Biology, 12(6), 220040. https://doi.org/10.1098/rsob.220040

18. Giacobelli, V. G., Fujishima, K., Lepšík, M., Tretyachenko, V., Kadavá, T., Makarov, M., Bednárová, L., Novák, P. & Hlouchová, K. (2022). In vitro evolution reveals noncationic protein–RNA interaction mediated by metal ions. Molecular Biology and Evolution, 39(3), msac032. https://doi.org/10.1093/molbev/msac03

17. Tretyachenko, V., Leiman, T., Morgenstern, D., Levin, Y., Asraf, O., Dahan, O., Dahary, D. & Pilpel, Y. (2026). Encoded and non-genetic protein variants expand human functional proteome. Nature. https://doi.org/10.1038/s41586-026-11124-z

16. Lobinska, G., Tretyachenko, V., Dahan, O., Nowak, M. A. & Pilpel, Y. (2024). The evolutionary safety of mutagenic drugs should be assessed before drug approval. PLOS Biology, 22(3), e3002570. https://doi.org/10.1371/journal.pbio.3002570

15. Heames, B., Buchel, F., Aubel, M., Tretyachenko, V., Loginov, D., Novák, P., Lange, A., Bornberg-Bauer, E. & Hlouchová, K. (2023). Experimental characterization of de novo proteins and their unevolved random-sequence counterparts. Nature Ecology & Evolution, 7(4), 570–580. https://doi.org/10.1038/s41559-023-02010-2

14. Tretyachenko, V., Vymětal, J., Neuwirthová, T., Vondrášek, J., Fujishima, K. & Hlouchová, K. (2022). Modern and prebiotic amino acids support distinct structural profiles in proteins. Open Biology, 12(6), 220040. https://doi.org/10.1098/rsob.220040

13. Giacobelli, V. G., Fujishima, K., Lepšík, M., Tretyachenko, V., Kadavá, T., Makarov, M., Bednárová, L., Novák, P. & Hlouchová, K. (2022). In vitro evolution reveals noncationic protein–RNA interaction mediated by metal ions. Molecular Biology and Evolution, 39(3), msac032. https://doi.org/10.1093/molbev/msac032

12. Makarov, M., Meng, J., Tretyachenko, V., Srb, P., Březinová, A., Giacobelli, V. G., Bednárová, L., Vondrášek, J., Dunker, A. K. & Hlouchová, K. (2021). Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. Protein Science, 30(5), 1022–1034. https://doi.org/10.1002/pro.4068

11. Tretyachenko, V., Voráček, V., Souček, R., Fujishima, K. & Hlouchová, K. (2021). CoLiDe: Combinatorial Library Design tool for probing protein sequence space. Bioinformatics, 37(4), 482–489. https://doi.org/10.1093/bioinformatics/btaa804

10. Tretyachenko, V., Vymětal, J., Bednárová, L., Kopecký, V., Jr., Hofbauerová, K., Jindrová, H., Hubálek, M., Souček, R., Konvalinka, J., Vondrášek, J. & Hlouchová, K. (2017). Random protein sequences can form defined secondary structures and are well-tolerated in vivo. Scientific Reports, 7, 15449. https://doi.org/10.1038/s41598-017-15635-8

9. Makukhin, N., Tretyachenko, V., Moskovitz, J. & Míšek, J. (2016). A ratiometric fluorescent probe for imaging of the activity of methionine sulfoxide reductase A in cells. Angewandte Chemie International Edition, 55(41), 12727–12730. https://doi.org/10.1002/anie.201605833

8. Fejfarová, K., Kádek, A., Mrázek, H., Hausner, J., Tretyachenko, V., Koval’, T., Man, P., Hašek, J. & Dohnálek, J. (2016). Crystallization of nepenthesin I using a low-pH crystallization screen. Acta Crystallographica Section F, 72(1), 24–28. https://doi.org/10.1107/S2053230X15022323

7. Kadek, A., Tretyachenko, V., Mrazek, H., Ivanova, L., Halada, P., Rey, M., Schriemer, D. C. & Man, P. (2014). Expression and characterization of plant aspartic protease nepenthesin-1 from Nepenthes gracilis. Protein Expression and Purification, 95, 121–128. https://doi.org/10.1016/j.pep.2013.12.005

6. Makarov, M., Meng, J., Tretyachenko, V., Srb, P., Březinová, A., Giacobelli, V. G., Bednárová, L., Vondrášek, J., Dunker, A. K. & Hlouchová, K. (2021). Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. Protein Science, 30(5), 1022–1034. https://doi.org/10.1002/pro.4068

5. Tretyachenko, V., Voráček, V., Souček, R., Fujishima, K. & Hlouchová, K. (2021). CoLiDe: Combinatorial Library Design tool for probing protein sequence space. Bioinformatics, 37(4), 482–489. https://doi.org/10.1093/bioinformatics/btaa804

4. Tretyachenko, V., Vymětal, J., Bednárová, L., Kopecký, V., Jr., Hofbauerová, K., Jindrová, H., Hubálek, M., Souček, R., Konvalinka, J., Vondrášek, J. & Hlouchová, K. (2017). Random protein sequences can form defined secondary structures and are well-tolerated in vivo. Scientific Reports, 7, 15449. https://doi.org/10.1038/s41598-017-15635-8

3. Makukhin, N., Tretyachenko, V., Moskovitz, J. & Míšek, J. (2016). A ratiometric fluorescent probe for imaging of the activity of methionine sulfoxide reductase A in cells. Angewandte Chemie International Edition, 55(41), 12727–12730. https://doi.org/10.1002/anie.201605833

2. Fejfarová, K., Kádek, A., Mrázek, H., Hausner, J., Tretyachenko, V., Koval’, T., Man, P., Hašek, J. & Dohnálek, J. (2016). Crystallization of nepenthesin I using a low-pH crystallization screen. Acta Crystallographica Section F, 72(1), 24–28. https://doi.org/10.1107/S2053230X15022323

1. Kadek, A., Tretyachenko, V., Mrazek, H., Ivanova, L., Halada, P., Rey, M., Schriemer, D. C. & Man, P. (2014). Expression and characterization of plant aspartic protease nepenthesin-1 from Nepenthes gracilis. Protein Expression and Purification, 95, 121–128. https://doi.org/10.1016/j.pep.2013.12.005