Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. - Stanislav Mazurenko; Jirí Damborský; Zbynek Prokop (PACBB, 2017)

CalFitter: a web server for analysis of protein thermal denaturation data. - Stanislav Mazurenko; Jan Stourac; Antonin Kunka; Sava Nedeljkovic; David Bednar; Zbynek Prokop; Jirí Damborský (Nucleic Acids Res., 2018)

Primal-dual block-proximal splitting for a class of non-convex problems. - Stanislav Mazurenko; Jyrki Jauhiainen; Tuomo Valkonen (CoRR, 2019)

Acceleration and Global Convergence of a First-Order Primal-Dual Method for Nonconvex Problems. - Christian Clason; Stanislav Mazurenko; Tuomo Valkonen (SIAM J. Optim., 2019)

FireProtDB: database of manually curated protein stability data. - Jan Stourac; Juraj Dubrava; Milos Musil; Jana Horackova; Jirí Damborský; Stanislav Mazurenko; David Bednar (Nucleic Acids Res., 2021)

CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. - Antonin Kunka; David Lacko; Jan Stourac; Jirí Damborský; Zbynek Prokop; Stanislav Mazurenko (Nucleic Acids Res., 2022)

PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. - Jan Stourac; Simeon Borko; Rayyan T. Khan; Petra Pokorna; Adam Dobias; Joan Planas-Iglesias; Stanislav Mazurenko; Gaspar R. P. Pinto; Veronika Szotkowska; Jaroslav Sterba; Ondrej Slaby; Jirí Damborský; et al. (Briefings Bioinform., 2023)

Learning to design protein-protein interactions with enhanced generalization. - Anton Bushuiev; Roman Bushuiev; Petr Kouba; Anatolii Filkin; Marketa Gabrielova; Michal Gabriel; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (ICLR, 2024)

Making PBPK models more reproducible in practice. - Elena Domínguez Romero; Stanislav Mazurenko; Martin Scheringer; Vítor A. P. Martins dos Santos; Chris T. A. Evelo; Mihail Anton; John M. Hancock; Anze Zupanic; María Suárez-Diez (Briefings Bioinform., 2024)

Response to Letter to Editor by A. Derbalah et al.: the role of automation in enhancing reproducibility and interoperability of PBPK models. - Elena Domínguez Romero; Stanislav Mazurenko; Martin Scheringer; Vítor A. P. Martins dos Santos; Chris T. A. Evelo; Mihail Anton; John M. Hancock; Anze Zupanic; María Suárez-Diez (Briefings Bioinform., 2024)

Revealing data leakage in protein interaction benchmarks. - Anton Bushuiev; Roman Bushuiev; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (CoRR, 2024)

A computational workflow for analysis of missense mutations in precision oncology. - Rayyan T. Khan; Petra Pokorna; Jan Stourac; Simeon Borko; Ihor Arefiev; Joan Planas-Iglesias; Adam Dobias; Gaspar R. P. Pinto; Veronika Szotkowska; Jaroslav Sterba; Ondrej Slaby; Jirí Damborský; et al. (J. Cheminformatics, 2024)

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. - Ondrej Vavra; Jonathan D. Tyzack; Farzan Haddadi; Jan Stourac; Jirí Damborský; Stanislav Mazurenko; Janet M. Thornton; David Bednar (J. Cheminformatics, 2024)

Learning to engineer protein flexibility. - Petr Kouba; Joan Planas-Iglesias; Jirí Damborský; Jirí Sedlár; Stanislav Mazurenko; Josef Sivic (ICLR, 2025)

Anticipating protein evolution with successor sequence predictor. - Rayyan T. Khan; Pavel Kohout; Milos Musil; Monika Rosinska; Jirí Damborský; Stanislav Mazurenko; David Bednar (J. Cheminformatics, 2025)