Publication Records

KHAN, Rayyan Tariq, Petra POKORNÁ, Jan DVORSKÝ, Simeon BORKO, Ihor AREFIEV, Joan PLANAS IGLESIAS, Adam DOBIÁŠ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Veronika SZOTKOWSKÁ, Jaroslav ŠTĚRBA, Ondřej SLABÝ, Jiří DAMBORSKÝ, Stanislav MAZURENKO and David BEDNÁŘ. A computational workflow for analysis of missense mutations in precision oncology. JOURNAL OF CHEMINFORMATICS. ENGLAND: BMC, 2024, vol. 16, No 1, p. 1-10. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-024-00876-3.

KHAN, Rayyan Tariq, Petra POKORNÁ, Jan DVORSKÝ, Simeon BORKO, Adam DOBIÁŠ, Joan PLANAS IGLESIAS, Stanislav MAZURENKO, Ihor AREFIEV, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Veronika SZOTKOWSKÁ, Jaroslav ŠTĚRBA, Jiří DAMBORSKÝ, Ondřej SLABÝ and David BEDNÁŘ. Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO. Computational and Structural Biotechnology Journal. AMSTERDAM: Elsevier, 2024, vol. 24, December 2024, p. 734-738. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2024.11.026.

VELECKÝ, Jan, Matej BEREZNÝ, Miloš MUSIL, Jiří DAMBORSKÝ, David BEDNÁŘ and Stanislav MAZURENKO. BenchStab: A tool for automated querying of web-based stability predictors. BIOINFORMATICS. ENGLAND: OXFORD UNIV PRESS, 2024, vol. 40, No 9, p. 1-5. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btae553.

KUNKA, Antonín, Dávid LACKO, Jan DVORSKÝ, Jiří DAMBORSKÝ, Zbyněk PROKOP and Stanislav MAZURENKO. Calfitter 2.0. 2024.

MARQUES, Sérgio Manuel, Petr KOUBA, Anthony Thomas P LEGRAND, Jiri SEDLAR, Lucas DISSON, Joan PLANAS IGLESIAS, Zainab Kemi SANUSI, Antonín KUNKA, Jiří DAMBORSKÝ, Tomas PAJDLA, Zbyněk PROKOP, Stanislav MAZURENKO, Josef SIVIC and David BEDNÁŘ. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2024, vol. 4, No 6, p. 2228-2245. ISSN 2691-3704. Available from: https://dx.doi.org/10.1021/jacsau.4c00182.

ATTAFI, Omar Abdelghani, Damiano CLEMENTEL, Konstantinos KYRITSIS, Emidio CAPRIOTTI, Gavin FARRELL, Styliani-Christina FRAGKOULI, Leyla Jael CASTRO, Andras HATOS, Tom LENAERTS, Stanislav MAZURENKO, Soroush MOZAFFARI, Franco PRADELLI, Patrick RUCH, Castrense SAVOJARDO, Paola TURINA, Federico ZAMBELLI, Damiano PIOVESAN, Alexander Miguel MONZON, Fotis PSOMOPOULOS and Silvio C. E. TOSATTO. DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology. GigaScience. OXFORD: Oxford University Press, 2024, vol. 13, December 2024, p. 1-8. ISSN 2047-217X. Available from: https://dx.doi.org/10.1093/gigascience/giae094.

MIČAN, Jan, Da 'san M. M. JARADAT, Weidong LIU, Gert WEBER, Stanislav MAZURENKO, Uwe T. BORNSCHEUER, Jiří DAMBORSKÝ, Ren WEI and David BEDNÁŘ. Exploring new galaxies: Perspectives on the discovery of novel PET-degrading enzymes. Applied Catalysis B: Environment and Energy. Amsterdam: Elsevier, 2024, vol. 342, March 2024, p. 1-16. ISSN 0926-3373. Available from: https://dx.doi.org/10.1016/j.apcatb.2023.123404.

HARDING-LARSEN, David, Christian Degnbol MADSEN, David TEZE, Tiia KITTILA, Mads Rosander LANGHORN, Hani GHARABLI, Mandy HOBUSCH, Felipe Mejia OTALVARO, Onur KIRTEL, Gonzalo Nahuel BIDART, Stanislav MAZURENKO, Evelyn TRAVNIK and Ditte Hededam WELNER. GASP: A Pan-Specific Predictor of Family 1 Glycosyltransferase Acceptor Specificity Enabled by a Pipeline for Substrate Feature Generation and Large-Scale Experimental Screening. ACS Omega. WASHINGTON: American Chemical Society, 2024, vol. 9, No 25, p. 27278-27288. ISSN 2470-1343. Available from: https://dx.doi.org/10.1021/acsomega.4c01583.

HADDADI, Faraneh, Ondřej VÁVRA, David BEDNÁŘ, Stanislav MAZURENKO and Jiří DAMBORSKÝ. Klasifikátor vazebných kapes v proteinech založený na strojovém učení (A machine learning-based classifier of binding pockets in proteins). 2024.

DOMÍNGUEZ-ROMERO, Elena, Stanislav MAZURENKO, Martin SCHERINGER, Vítor A.P. MARTINS DOS SANTOS, Chris T. EVELO, Mihail ANTON, John M HANCOCK, Anže ŽUPANIČ and Maria SUAREZ-DIEZ. Kód fyziologického farmakokinetického modelu (PBPK) v MatLabu pro simulaci časově závislých koncentrací chemických látek v lidském těle (Physiologically Based Pharmacokinetic (PBPK) model code in MatLab for simulating time-dependent concentrations of a chemical in a human body). 2024.

VÁVRA, Ondřej, J. TYZACK, Faraneh HADDADI, Jan DVORSKÝ, Jiří DAMBORSKÝ, Stanislav MAZURENKO, J.M. THORNTON and David BEDNÁŘ. Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2024, vol. 16, No 1, p. 1-14. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-024-00907-z.

BUSHUIEV, Anton, Roman BUSHUIEV, Petr KOUBA, Anatolii FILKIN, Marketa GABRIELOVA, Michal GABRIEL, Jiri SEDLAR, Tomas PLUSKAL4, Jiří DAMBORSKÝ, Stanislav MAZURENKO and Josef SIVIC. Learning to design protein-protein interactions with enhanced generalization. Online. In 12th International Conference on Learning Representations 2024. 2024, 26 pp.

DOMINGUEZ ROMERO, Elena, Stanislav MAZURENKO, Martin SCHERINGER, Martins Vitor A. P. DOS SANTOS, Chris T. EVELO, Mihail ANTON, John M. HANCOCK, Anze ZUPANIC and Maria SUAREZ-DIEZ. Making PBPK models more reproducible in practice. Briefings in Bioinformatics. Oxford (UK): Oxford University Press, 2024, vol. 25, No 6, p. 1-13. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbae569.

ŠTOURAČ, Jan, Simeon BORKO, Rayyan Tariq KHAN, Petra POKORNÁ, Adam DOBIÁŠ, Joan PLANAS IGLESIAS, Stanislav MAZURENKO, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Veronika SZOTKOWSKÁ, Jaroslav ŠTĚRBA, Ondřej SLABÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Briefings in Bioinformatics. Oxford University Press, 2024, vol. 25, No 1, p. 1-10. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbad441.

HARDING-LARSEN, David, Jonathan FUNK, Niklas Gesmar MADSEN, Hani GHARABLI, Carlos G. ACEVEDO-ROCHA, Stanislav MAZURENKO and Ditte Hededam WELNER. Protein representations: Encoding biological information for machine learning in biocatalysis. Biotechnology Advances. OXFORD: Elsevier, 2024, vol. 77, December 2024, p. 1-20. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2024.108459.

BUSHUIEV, Anton, Roman BUSHUIEV, Jiri SEDLAR, Tomas PLUSKAL, Jiří DAMBORSKÝ, Stanislav MAZURENKO and Josef SIVIC. Revealing data leakage in protein interaction benchmarks. In ICLR 2024 Workshop on Generative and Experimental Perspectives for Biomolecular Design. 2024, 13 pp.

MARTIN, Hector Garcia, Stanislav MAZURENKO and Huimin ZHAO. Special Issue on Artificial Intelligence for Synthetic Biology. ACS Synthetic Biology. American Chemical Society, 2024, vol. 13, No 2, p. 408-410. ISSN 2161-5063. Available from: https://dx.doi.org/10.1021/acssynbio.3c00760.

KHAN, Rayyan Tariq, Pavel KOHOUT, Miloš MUSIL, Monika ROSÍNSKÁ, Jiří DAMBORSKÝ, Stanislav MAZURENKO, David BEDNÁŘ and Jan VILÍM. Successor Sequence Predictor (SSP). 2024.

VAŠINA, Michal, David KOVÁŘ, Jiří DAMBORSKÝ, Ding YUN, Tianjin YANG, Andrew DE MELLO, Stanislav MAZURENKO, Stavros STAVRAKIS and Zbyněk PROKOP. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnology Advances. OXFORD: Elsevier, 2023, vol. 66, September 2023, p. 1-22. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2023.108171.

KOUBA, Petr, Pavel KOHOUT, Faraneh HADDADI, Anton BUSHUIEV, Raman SAMUSEVICH, Jiri SEDLAR, Jiří DAMBORSKÝ, Tomáš PLUSKAL, Josef SIVIC and Stanislav MAZURENKO. Machine Learning-Guided Protein Engineering. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2023, vol. 13, No 21, p. 13863-13895. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.3c02743.

VAŠINA, Michal, Pavel VAŇÁČEK, Jiri HON, David KOVÁŘ, Hana FALDYNOVÁ, Antonín KUNKA, Tomáš BURYŠKA, Christoffel P. S. BADENHORST, Stanislav MAZURENKO, David BEDNÁŘ, Stavros STAVRAKIS, Uwe T. BORNSCHEUER, Andrew DEMELLO, Jiří DAMBORSKÝ and Zbyněk PROKOP. Advanced database mining of efficient haloalkane dehalogenases by sequence and structure bioinformatics and microfluidics. Chem Catalysis. Elsevier, 2022, vol. 2, No 10, p. 2704-2725. ISSN 2667-1093. Available from: https://dx.doi.org/10.1016/j.checat.2022.09.011.

KUNKA, Antonín, David LACKO, Jan ŠTOURAČ, Jiří DAMBORSKÝ, Zbyněk PROKOP and Stanislav MAZURENKO. CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic acids research. Oxford: Oxford University Press, 2022, vol. 50, W1, p. "W145"-"W151", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkac378.

KOVÁŘ, David, Stanislav MAZURENKO, Jiří DAMBORSKÝ and Zbyněk PROKOP. MAPityser 2.1 - Analyzátor dat pro mikrofluidní platformu MAPit (MAPityser 2.1 - Data Analyser for the microfluidic platform MAPit). 2022.

KOVÁŘ, David, Stanislav MAZURENKO, Michal VAŠINA, Jiří DAMBORSKÝ and Zbyněk PROKOP. MicroPEX Data Analyser 1.0* (MicroPEX Data Analyser 1.0). 2022.

VELECKÝ, Jan, Marie HAMŠÍKOVÁ, Jan ŠTOURAČ, Miloš MUSIL, Jiří DAMBORSKÝ, David BEDNÁŘ and Stanislav MAZURENKO. SoluProtMutDB: A manually curated database of protein solubility changes upon mutations. Computational and Structural Biotechnology Journal. Elsevier, 2022, vol. 20, November 2022, p. 6339-6347. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2022.11.009.

VAŠINA, Michal, Jan VELECKÝ, Joan PLANAS IGLESIAS, Sérgio Manuel MARQUES, Jana ŠKAŘUPOVÁ, Jiří DAMBORSKÝ, David BEDNÁŘ, Stanislav MAZURENKO and Zbyněk PROKOP. Tools for computational design and high-throughput screening of therapeutic enzymes. ADVANCED DRUG DELIVERY REVIEWS. NETHERLANDS: ELSEVIER, 2022, vol. 183, April 2022, p. 1-16. ISSN 0169-409X. Available from: https://dx.doi.org/10.1016/j.addr.2022.114143.

DAMBORSKÝ, Jiří, David BEDNÁŘ, Zbyněk PROKOP, Martin MAREK, Stanislav MAZURENKO, Jan ŠTOURAČ, Sérgio Manuel MARQUES, Gabriela Filipa FONSECA PINTO, Joan PLANAS IGLESIAS, Miloš MUSIL, Jiří HON, Ondřej VÁVRA, Rayyan Tariq KHAN, Jiří FILIPOVIČ and Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

ŠTOURAČ, Jan, Juraj DUBRAVA, Miloš MUSIL, Jana HORÁČKOVÁ, Jiří DAMBORSKÝ, Stanislav MAZURENKO and David BEDNÁŘ. FireProt(DB): database of manually curated protein stability data. Nucleic acids research. Oxford: Oxford University Press, 2021, vol. 49, D1, p. "D319"-"D324", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkaa981.

CLASON, Christian, Stanislav MAZURENKO and Tuomo VALKONEN. Primal-Dual Proximal Splitting and Generalized Conjugation in Non-smooth Non-convex Optimization. Applied Mathematics and Optimization. New York: Springer, 2021, vol. 84, No 2, p. 1239-1284. ISSN 0095-4616. Available from: https://dx.doi.org/10.1007/s00245-020-09676-1.

KOKKONEN, Piia Pauliina, Andy BEIER, Stanislav MAZURENKO, Jiří DAMBORSKÝ, David BEDNÁŘ and Zbyněk PROKOP. Substrate inhibition by the blockage of product release and its control by tunnel engineering. RSC Chemical Biology. Cambridge: Royal Society of Chemistry, 2021, vol. 2, No 2, p. 645-655. ISSN 2633-0679. Available from: https://dx.doi.org/10.1039/d0cb00171f.

MAZURENKO, Stanislav, Zbyněk PROKOP and Jiří DAMBORSKÝ. Machine Learning in Enzyme Engineering. ACS Catalysis. Washington, D.C.: American Chemical Society, 2020, vol. 10, No 2, p. 1210-1223. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.9b04321.

MAZURENKO, Stanislav. Predicting protein stability and solubility changes upon mutations: data perspective. ChemCatChem. Weinheim: Wiley-VCH GmbH, 2020, vol. 12, No 22, p. 5590-5598. ISSN 1867-3880. Available from: https://dx.doi.org/10.1002/cctc.202000933.

MAZURENKO, Stanislav, Jyrki JAUHIAINEN and Tuomo VALKONEN. Primal-dual block-proximal splitting for a class of non-convex problems. Electronic Transactions on Numerical Analysis. Kent: Kent State University, 2020, vol. 52, No 2020, p. 509-552. ISSN 1068-9613. Available from: https://dx.doi.org/10.1553/etna_vol52s509.

CLASON, Christian, Stanislav MAZURENKO and Tuomo VALKONEN. ACCELERATION AND GLOBAL CONVERGENCE OF A FIRST-ORDER PRIMAL-DUAL METHOD FOR NONCONVEX PROBLEMS. SIAM JOURNAL ON OPTIMIZATION. PHILADELPHIA: SIAM PUBLICATIONS, 2019, vol. 29, No 1, p. 933-963. ISSN 1052-6234. Available from: https://dx.doi.org/10.1137/18M1170194.

NEVOLOVÁ, Šárka, Elisabet MAŇÁSKOVÁ, Stanislav MAZURENKO, Jiří DAMBORSKÝ and Zbyněk PROKOP. Development of Fluorescent Assay for Monitoring of Dehalogenase Activity. Biotechnology Journal. WEINHEIM: WILEY-V C H VERLAG GMBH, 2019, vol. 14, No 3, p. 1-6. ISSN 1860-6768. Available from: https://dx.doi.org/10.1002/biot.201800144.