Софийски университет "Св. Климент Охридски"

В лабораторията по Синтетична биология и Биоинформатика се извършват експерименти – биоинформатични и лабораторни, които водят до постигане на високи резултати с обществено значение. Те са високооценени от реферирани, индексирани и високоимпактирани списания като: Nature Biotechnology, Nature Methods, ACS Synthetic Biology, Antibiotics, RSC Chemistry World и др. Тук са показани статиите от последните 5 години:

1. Dimitrios Kaloudas, Martina Traykovska, Nikolet Pavlova, Robert Penchovsky, Design and Applications of riboregulators, ISBN:978-981-95395-6-7, Springer, Ref, Рецензирано издание, глава от книга, 2026 https://books.google.bg/books/about/Handbook_of_Synthetic_Biology.html?id=KJma0QEACAAJ&redir_esc=y
2. Vanya Dyakova, Martina Traykovska, Nikolet Pavlova, Dimitrios Kaloudas, Robert Penchovsky, Rational Design of Chimeric Antisense Oligonucleotides that Target FMN Riboswitch mRNAs and Inhibit the Growth of Methicillin-Resistant Staphylococcus aureus, ACS Infectious Diseases, 2025, ISSN (print):2373-8227, doi:10.1021/acsinfecdis.5c00779, Ref, Web of Science, IF (3.8 - 2025), Web of Science Quartile: Q1 (2025), SCOPUS, SJR (1.241 - 2025), SCOPUS Quartile: Q1 (2025) https://pubs.acs.org/doi/10.1021/acsinfecdis.5c00779
3. Lozena A. Otcheva, Martina Traykovska, Robert Penchovsky, Targeting Bacterial Adenylate Kinase mRNA with a Chimeric Antisense Oligonucleotide for Rational Antibacterial Drug Development, Molecules, vol:30, 2025, ISSN (online): 1420-3049, doi:10.3390/molecules30163425, Ref, IF (4.6 - 2025), Web of Science Quartile: Q1 (2025), SCOPUS, SJR (0.865 - 2025), SCOPUS Quartile: Q1 (2025) https://www.mdpi.com/1420-3049/30/16/3425
4. Nikolet Pavlova, Vanya Dyakova, Martina Traykovska, Dimitrios Kaloudas, Robert Penchovsky, The Application of Aptamers in Pharmacological Drug Development and Therapeutic, ChemistrySelect, vol:10, issue:28, 2025, ISSN (print):2365-6549, ISSN (online):2365-6549, doi:10.1002/slct.202502954, Ref, Web of Science, IF (1.9 - 2024), SCOPUS, SJR (0.366 - 2024), SCOPUS Quartile: Q3 (2025)https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/slct.202502954
5. Martina Traykovska, Robert Penchovsky, Дизайн на антисенс олигонуклеотиди и приложението им като антибактериални агенти: принципи, механизми на действие и предизвикателства, монография ISBN:978-954-07-6132-9, Университетско издателство „Св. Климент Охридски“, София, Ref, Рецензирано, 2025https://penchovsky.atwebpages.com/publications.php?page=3220 Купи от тук: https://unipress.bg/dizayn-na-antisens-oligonukleotidi-i-prilozhenieto-im-kato-antibakterialni-agenti-printsipi-mehanizmi-na-deystvie-i-predizvikatelstva
6. Dimitrios Kaloudas, Nikolet Pavlova, and Robert Penchovsky. Computational Design of Allosteric Ribozymes via Genetic Algorithms, 2024, Methods in Molecular Biology, MIMB, volume 2822, RNA Amplification and Analysis, https://link.springer.com/protocol/10.1007/978-1-0716-3918-4_28
7. Robert Penchovsky, Antoniya V. Georgieva, Vanya Dyakova, Martina Traykovska, and Nikolet Pavlova, Antisense and Functional Nucleic Acids in Rational Drug Development, Antibiotics 2024, IF: 4.3, https://doi.org/10.3390/antibiotics13030221, https://penchovsky.atwebpages.com/publications.php?page=3199
8. Katya B. Popova and Robert Penchovsky, General and Specific Cytotoxicity of Chimeric Antisense Oligonucleotides in Bacterial Cells and Human Cell Lines, Antibiotics 2024, IF: 4.3, https://doi.org/10.3390/antibiotics13020122https://pubmed.ncbi.nlm.nih.gov/38391508/
9. Nikolet Pavlova, Martina Traykovska, Robert Penchovsky, “Targeting FMN, TPP, SAM-I, and glmS Riboswitches with Chimeric Antisense Oligonucleotides for Completely Rational Antibacterial Drug Development”, Antibiotics, 2023. https://pubmed.ncbi.nlm.nih.gov/37998809/
10. Dimitrios Kaloudas, Nikolet Pavlova, Robert Penchovsky, „GHOST-NOT and GHOST-YES: Two programs for generating high-speed biosensors with randomized oligonucleotide binding sites with NOT or YES Boolean logic functions based on experimentally validated algorithms“, Journal of Biotechnology Volume 373, 20 August 2023, Pages 82-89, doi:https://doi.org/10.1016/j.jbiotec.2023.07.005 https://www.sciencedirect.com/science/article/pii/S0168165623001323
11. Robert Penchovsky, Dimitrios Kaloudas, “Molecular factors affecting tomato fruit size”, Plant Gene Volume 33, March 2023, 100395, https://doi.org/10.1016/j.plgene.2022.100395 https://www.sciencedirect.com/science/article/abs/pii/S2352407322000452
12. Martina Traykovska, Robert Penchovsky, “Engineering antisense oligonucleotides as antibacterial agents that target FMN riboswitches and inhibit the growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli”, ACS Synthetic Biology, 2022, ISSN: 2161-5063, doi: 10.1021/acssynbio.2c00013, Q1, IF 5 https://pubmed.ncbi.nlm.nih.gov/35440139/
13. Martina Traykovska, Robert Penchovsky, “Targeting SAM-I Riboswitch Using Antisense Oligonucleotide Technology for Inhibiting the Growth of Staphylococcus aureus and Listeria monocytogenes”, Antibiotics, 2022, IF 5.0 https://www.mdpi.com/2079-6382/11/11/1662/pdf https://pubmed.ncbi.nlm.nih.gov/35440139/
14. Martina Traykovska, Lozena A. Otcheva, Robert Penchovsky, “Targeting TPP riboswitches using chimeric antisense oligonucleotide technology for antibacterial drug development“, ACS Applied Bio Materials, 2022, Q1, IF 4.5, doi: 10.1021/acsabm.2c00628 https://pubmed.ncbi.nlm.nih.gov/36170638/
15. Dimitrios Kaloudas, Robert Penchovsky, “An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms”, Computers in Biology and Medicine Volume 145, June 2022, 105469, https://doi.org/10.1016/j.compbiomed.2022.105469 https://www.sciencedirect.com/science/article/abs/pii/S001048252200261X
16. Robert Penchovsky, Nikolet Pavlova, Georgi Miloshev, Antoniya Georgieva, Martina Traykovska, “Versatile Tools of Synthetic Biology applied for Drug Discovery and Production”, Future Medicinal Chemistry, Q2, IF 4.75, 2022 https://pubmed.ncbi.nlm.nih.gov/35975897/
17. Georgi Y. Miloshev, Martina Traykovska, Dimitrios Kaloudas, Robert Penchovsky, “ENGINEERING A PLASMID AS A REPORTER SYSTEM FOR QUANTIFYING GENE EXPRESSION IN ESCHERICHIA COLI” Proceedings of the Bulgarian Academy of Sciences, 2022 https://www.proceedings.bas.bg/index.php/cr/article/view/7/7
18. Aikaterini Valsamatzi, Martina Traykovska, Robert Penchovsky, “Coronavirus SARS-CoV-2: Where do we stand?“, Acta Microbiologica Bulgarica, ISSN: 26033755, 2022, SJR 0.115, Q4 https://penchovsky.atwebpages.com/publications.php?page=3155
19. Nikolet Pavlova and Robert Penchovsky, “Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets”, Antibiotics 2022, Impact Factor: 4.8 (2022); 5-Year Impact Factor: 4.9 (2022) https://pubmed.ncbi.nlm.nih.gov/36139956/
20. Robert Penchovsky, Georgi Miloshev, Nikolet Pavlova, Katya Popova, Lozena Otcheva, Aikaterini Valsamatzi, Martina Traykovska, Book: New Frontiers and Applications of Synthetic Biology; chapter 8. Small RNA-based systems for sensing and therapeutic applications, Elsevier, 2022, ISBN: 9780128244692 https://www.sciencedirect.com/book/edited-volume/9780128244692/new-frontiers-and-applications-of-synthetic-biology
21. Aikaterini Valsamatzi, Robert Penchovsky, “Environmental factors influencing the transmission of the coronavirus 2019”: a review, Environmental Chemistry Letters volume 20, pages1603–1610 (2022) https://pmc.ncbi.nlm.nih.gov/articles/PMC8859930/
22. Martina Traykovska, Katya B. Popova, Robert Penchovsky, “Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development”, ACS Synthetic Biology, 2021, doi: https://pubs.acs.org/doi/10.1021/acssynbio.1c00443, SJR 5.5, Q1 https://pubmed.ncbi.nlm.nih.gov/34734706/
23. Dimitrios Kaloudas, Nikolet Pavlova & Robert Penchovsky, “Lignocellulose, algal biomass, biofuels and biohydrogen”: a review, Environmental Chemistry Letters volume 19, pages2809–2824 (2021) https://link.springer.com/article/10.1007/s10311-021-01213-y
24. Dimitrios Kaloudas, Nikolet Pavlova & Robert Penchovsky, ”Phycoremediation of wastewater by microalgae”: a review, Environmental Chemistry Letters volume 19, pages 2905–2920 (2021), Published: 28 March 2021 https://link.springer.com/article/10.1007/s10311-021-01203-0
25. Robert Penchovsky, “Nucleic Acids-Based Nanotechnology: Engineering Principles and Applications”, Biomedical Engineering: Concepts, Methodologies, Tools and Applications, DOI: 10.4018/978-1-5225-3158-6.ch006 https://penchovsky.atwebpages.com/publications.php?page=131
26. Aikaterini Valsamatzi-Panagiotou, Katya B. Popova & Robert Penchovsky, „Methods for prevention and constraint of antimicrobial resistance“: a review, Environmental Chemistry Letters volume 19, pages 2005–2012 (2021), Published: 18 February 2021 https://link.springer.com/article/10.1007/s10311-021-01206-x
27. Aikaterini Valsamatzi-Panagiotou, Katya B. Popova & Robert Penchovsky, “Chapter: Strategies for Prevention and Containment of Antimicrobial Resistance,” January 2021, Sustainable Agriculture Reviews book series https://link.springer.com/chapter/10.1007/978-3-030-58259-3_1
28. Katya B. Popova, Aikaterini Valsamatzi-Panagiotou & Robert Penchovsky, „New drug discovery strategies for targeting drug-resistant bacteria“, Environmental Chemistry Letters volume 19, pages 1995–2004 (2021), Published: 13 February 2021 https://link.springer.com/article/10.1007/s10311-021-01181-3
29. Katya B Popova, Robert Penchovsky, „Current Activators of the glmS Riboswitch” Biomedical Journal of Scientific and Technical Research, January 22, 2021, DOI: 10.26717/BJSTR.2021.33.005348chromeextension://efaidnbmnnnibpcajpcglclefindmkaj/https://biomedres.us/pdfs/BJSTR.MS.ID.005348.pdf
30. Lozena A Otcheva, Nikolet Pavlova, Katya B Popova, Martina Traykovska, Robert Penchovsky, “Why some Riboswitches are Suitable Targets for Antibacterial Drug Discovery”, EC Microbiology, 2020 https://www.researchgate.net/publication/349699835_EC_MICROBIOLOGY_EC_MICROBIOLOGY_Mini_Review_Why_Some_Riboswitches_are_Suitable_Targets_for_Antibacterial_Drug_Discovery