Selected Publications

CLARA researchers actively publish their results in leading scientific journals and present them at top international conferences, contributing to advances in artificial intelligence, neuroscience, medical imaging and computational biology.

77 scientific publications, conference papers and monographs
20 articles published in JCR Q1/Q2 journals

Open Science: publications are made openly available through the CLARA Zenodo Community, following the FAIR principles (Findable, Accessible, Interoperable and Reusable) to maximize their visibility, accessibility and long-term impact.

Follow the CLARA Zenodo Community to access the complete collection of publications and stay up to date with the latest CLARA research outputs.

Below is a selection of recent publications (by June 2026).

The publications are organised to highlight research with the greatest scientific impact and relevance to CLARA. While publications in Q1 and Q2 journals represent the primary indicator of scientific excellence within CLARA’s KPIs, the order within each category also considers the journal’s standing and reputation in its research field, the publication’s relevance to CLARA’s scientific focus, and the type of scientific contribution.

2026 2025 2024

2026

In 2026, CLARA researchers published in leading international journals, including Communications Chemistry (Nature Portfolio),ACS Catalysis and Scientific Reports (Nature Portfolio). The highlighted publications, incl. a presentation awarded at HDX-MS 2026, represent advances in AI-driven research, computational methods, and data-driven life sciences.

Cima, V., Kunka, A., Planas-Iglesias, J., Grakova, E., Havlasek, M., Subramanian, M., Beloch, M., Marek, M., Slaninova, K., Damborsky, J., Prokop, Z., Bednar, D., & Martinovic, J. (2026). Experimentally validated deep learning control of protein aggregation. Communications Chemistry, 9(1). https://doi.org/10.1038/s42004-026-02007-5 (ICRC, VSB-TUO)
Marques, S. M., Planas-Iglesias, J., Velecký, J., Musil, M., Asano, Y., Borowski, T., Brissos, V., Cespugli, M., Chorozian, K., Dadashipour, M., Erdem, E., Ferrandi, E. E., Grigorakis, K., Kluza, A., Lawniczek, J., Makryniotis, K., Monti, D., Nestl, B., Ngo, A. C., … Bednar, D. (2026). Mobilizing the Biocatalysis Community for Reproducible and Reusable Data Collection. ACS Catalysis. https://doi.org/10.1021/acscatal.5c07904 (ICRC)
Radvanský, M., Vašinková, M., Kudělka, M., Kriegová, E., & Gajdoš, P. (2026). A deterministic method for quantifying spindle-shaped cells in noisy bright-field microscopy. Scientific Reports. https://doi.org/10.1038/s41598-026-51592-x (VSB-TUO)
Majerova, M., Horackova, J., Sedlackova, K., Sulova, M., Kovar, D., Damborsky, J., Prokop, Z., Bednar, D., & Marek, M. (2026). Structural insights into the evolution of alpha/beta-hydrolase fold luciferases. International Journal of Biological Macromolecules, 361, 151870. https://doi.org/10.1016/j.ijbiomac.2026.151870 (ICRC)
Nemergut, M., Štulajterová, M., Škrabana, R., Hovan, A., Ambro, L., Strunga, A., Prokop, Z., Damborský, J., Tomková, M., & Sedlák, E. (2026). Concentration‐dependent dimerization of staphylokinase variants with engineered surface charges. Protein Science, 35(3). https://doi.org/10.1002/pro.70494 (ICRC)
de Boer, R. M., Harding-Larsen, D., Mazurenko, S., & Welner, D. H. (2026). Tryptophanase Mining and Characterization toward the Biological Production of Indole Derivatives. ACS Omega, 11(9), 14909–14918. https://doi.org/10.1021/acsomega.5c11382 (ICRC)
Jochymek, L., Vašinková, M., Doleží, V., & Gajdoš, P. (2026). GAN-based bone suppression using a combined loss function. Frontiers in Artificial Intelligence, 9. https://doi.org/10.3389/frai.2026.1761336 (VSB-TUO)
Verma, N., Kučera, J., Henek, T., Vanacek, P., Legrand, A., Kašiarová, L., Mičan, J., Strunga, A., Planas-Iglesias, J., Mazurenko, S., Bednar, D., Marek, M., Prokop, Z., Damborsky, J., & Hernychova, L. (2026). HDX-MS Unveils Structure-Function Relationships in Engineered Thrombolytic Drug: Staphylokinas. Zenodo. https://doi.org/10.5281/ZENODO.20757951 (ICRC) - Note: This paper received the Award for Best Presentation at the 5th Annual International Conference on Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS 2026), which took place from March 9 to 13, 2026, at the Hilton Strasbourg in Strasbourg, France.

JCR Q1

2025

In 2025, CLARA researchers achieved strong scientific visibility with publications in leading Q1 journals, including several of the most prestigious medical and AI journals worldwide, such as Medical Image Analysis, Information Fusion, Annals of Neurology, Alzheimer’s & Dementia, Nucleic Acids Research, ACS Catalysis or JACS Au, reflecting CLARA’s contributions to brain research, medical imaging, neuroscience, and molecular biology.

El Jurdi, R., Varoquaux, G., & Colliot, O. (2025). Confidence intervals for performance estimates in brain MRI segmentation. Medical Image Analysis, 103, 103565. https://doi.org/10.1016/j.media.2025.103565 (PBI)
Kong, L., Velasquez, J. D., Snášel, V., Pant, M., Pan, J.-S., & Nowakova, J. (2025). Enhancing skin cancer detection through category representation and fusion of pre-trained models. Information Fusion, 124, 103369. https://doi.org/10.1016/j.inffus.2025.103369 (VSB-TUO)
Gregg, N. M., Ojeda Valencia, G., Pridalova, T., Huang, H., Kremen, V., Lundstrom, B. N., Van Gompel, J. J., Miller, K. J., Worrell, G. A., & Hermes, D. (2025). Thalamic Stimulation Induced Changes in Network Connectivity and Excitability in Epilepsy. Annals of Neurology, 99(3), 748–760. https://doi.org/10.1002/ana.78087 (CIIRC CTU)
Marques, S. M., Borko, S., Vavra, O., Dvorsky, J., Kohout, P., Kabourek, P., Hejtmanek, L., Damborsky, J., & Bednar, D. (2025). Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins. Nucleic Acids Research, 53(W1), W132–W142. https://doi.org/10.1093/nar/gkaf399 (ICRC)
Kohout, P., Vasina, M., Majerova, M., Novakova, V., Damborsky, J., Bednar, D., Marek, M., Prokop, Z., & Mazurenko, S. (2025). Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics. JACS Au, 5(2), 838–850. https://doi.org/10.1021/jacsau.4c01101 (ICRC)
Planas-Iglesias, J., Majerova, M., Pluskal, D., Vasina, M., Damborsky, J., Prokop, Z., Marek, M., & Bednar, D. (2025). Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis. ACS Catalysis, 15(4), 3391–3404. https://doi.org/10.1021/acscatal.4c06207 (ICRC)
Musil, M., Borko, S., Planas-Iglesias, J., Lacko, D., Rosinska, M., Kabourek, P., Martins, L. O., Tataruch, M., Damborsky, J., Mazurenko, S., & Bednar, D. (2025). FireProtDB 2.0: large-scale manually curated database of the protein stability data. Nucleic Acids Research, 54(D1), D409–D418. https://doi.org/10.1093/nar/gkaf1211 (ICRC)
Saracino, D., Cipriano, L., Houot, M., Querin, G., Rinaldi, D., Rametti‐Lacroux, A., Wallon, D., Gerardin, E., Couratier, P., Boncoeur, M., Lebouvier, T., Colliot, O., Pradat, P., Migliaccio, R., & Le Ber, I. (2025). Quantifying multimodal longitudinal brain changes in presymptomatic C9orf72 disease.Alzheimer’s & Dementia, 21(12). https://doi.org/10.1002/alz.70902 (PBI)
Khachaturian, Z., Carrillo, M. C., & Khachaturian, A. S. (2025). Perspective: Emerging challenges for a future ADNI. Alzheimer’s & Dementia, 21(2). https://doi.org/10.1002/alz.14534 (INDRC)
Fu, G., Nichelli, L., Herrán de la Gala, D., Loizillon, S., Bousfiha, C., Valabregue, R., Alentorn, A., Hoang-Xuan, K., Mathon, B., Soussain, C., Marolleau, J. P., Paillassa, J., Taillandier, L., Agapé, P., Schmitt, A., Chinot, O., Ahle, G., Dormont, D., Houillier, C., … Gastinne, T. (2025). Automatic Segmentation of Primary Central Nervous System Lymphoma at Clinical Routine Postcontrast T1-weighted MRI. Radiology: Imaging Cancer, 7(5). https://doi.org/10.1148/rycan.240446 (PBI)
Khan, R. T., Kohout, P., Musil, M., Rosinska, M., Damborsky, J., Mazurenko, S., & Bednar, D. (2025). Anticipating protein evolution with successor sequence predictor. Journal of Cheminformatics, 17(1). https://doi.org/10.1186/s13321-025-00971-z (ICRC)
Halfar, R., Damborský, J., Marques, S. M., & Martinovič, J. (2025). Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands. Journal of Cheminformatics, 17(1). https://doi.org/10.1186/s13321-025-01005-4 (ICRC, VSB-TUO)
Abualigah, L., Alomari, S. A., Almomani, M. H., Zitar, R. A., Saleem, K., Migdady, H., Snasel, V., Smerat, A., & Ezugwu, A. E. (2025). Artificial intelligence-driven translational medicine: a machine learning framework for predicting disease outcomes and optimizing patient-centric care. Journal of Translational Medicine, 23(1). https://doi.org/10.1186/s12967-025-06308-6 (VSB-TUO)
Abualigah, L., Al-Okbi, N. K., Alomari, S. A., Almomani, M. H., Moneam, S., Yousif, M. A., Snasel, V., Saleem, K., Smerat, A., & Ezugwu, A. E. (2025). Optimized image segmentation using an improved reptile search algorithm with Gbest operator for multi-level thresholding. Scientific Reports, 15(1). https://doi.org/10.1038/s41598-025-96429-1 (VSB-TUO)

JCR Q1/Q2

2025

Additional Q1/Q2 publications in 2025 covered diverse research areas, including medical imaging, computational neuroscience, biomedical AI, and molecular biology, reflecting the interdisciplinary scope of CLARA’s scientific activities.

Havlásek, M., Marques, S. M., Szotkowská, V., Kunka, A., Babková, P., Damborský, J., Prokop, Z., & Bednář, D. (2025). Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms. Journal of Chemical Information and Modeling, 65(16), 8688–8701. https://doi.org/10.1021/acs.jcim.5c00611 (ICRC)
Phan, A., Pesce, E., Baumann, L., Polakovičová, P., Bednář, D., Smutná, M., Novák, J., & Hilscherová, K. (2025). Refining the AOP for retinoid-induced teratogenicity: Insights into RAR/RXR overactivation and RXR cross-talk with retinoic acid and thyroid hormone signaling. Aquatic Toxicology, 289, 107608. https://doi.org/10.1016/j.aquatox.2025.107608 (ICRC)
Hassanaly, R., Solal, M., Colliot, O., Burgos, N., & Disease Neuroimaging Initiative, for the A. (2025). Benchmarking 3D generative autoencoders for pseudo-healthy reconstruction of brain 18F-fluorodeoxyglucose positron emission tomography. Journal of Medical Imaging, 12(05). https://doi.org/10.1117/1.jmi.12.5.054005 (PBI)
Kremen, V., Sladky, V., Mivalt, F., Gregg, N. M., Brinkmann, B. H., Balzekas, I., Marks, V., Kucewicz, M., Lundstrom, B. N., Cui, J., St Louis, E. K., Croarkin, P., Alden, E. C., Joseph, B., Fields, J., Crockett, K., Adolf, J., Bilderbeek, J., Hermes, D., … Worrell, G. A. (2025). Modulating limbic circuits in temporal lobe epilepsy: impacts on seizures, memory, mood and sleep. Brain Communications, 7(2). https://doi.org/10.1093/braincomms/fcaf106 (CIIRC CTU)
Maidenbaum, S., Kremen, V., Sladky, V., Miller, K., Gompel, J. V., Worrell, G. A., & Jacobs, J. (2025). Improved spatial memory for physical versus virtual navigation. Journal of Neural Engineering, 22(4), 046014. https://doi.org/10.1088/1741-2552/ade6aa (CIIRC CTU)
Sejak, M., Mivalt, F., Sladky, V., Vsiansky, V., Carvalho, D. Z., St. Louis, E. K., Worrell, G. A., & Kremen, V. (2025). OpenSpindleNet: An open-source deep learning network for reliable sleep spindle detection in scalp and intracranial EEG. Computers in Biology and Medicine, 197, 110854. https://doi.org/10.1016/j.compbiomed.2025.110854 (CIIRC CTU)
Štulajterová, M., Ambro, Ľ., Sedláková, D., Nemergut, M., Kohout, P., Mazurenko, S., Varhač, R., Strunga, A., Toul, M., Prokop, Z., Damborský, J., Tomková, M., & Sedlák, E. (2025). Assessing the impact of His-tags on activity and stability of staphylokinase variants. International Journal of Biological Macromolecules, 328, 147655. https://doi.org/10.1016/j.ijbiomac.2025.147655 (ICRC)
Franko, O., Čižmáriková, M., Kello, M., Michalková, R., Wesołowska, O., Środa-Pomianek, K., Marques, S. M., Bednář, D., Háziková, V., Liška, T. J., & Habalová, V. (2025). Acridine-Based Chalcone 1C and ABC Transporters. International Journal of Molecular Sciences, 26(9), 4138. https://doi.org/10.3390/ijms26094138 (ICRC)
Srutova, M., Kremen, V., & Lhotska, L. (2025). Electrocardiographic Discrimination of Long QT Syndrome Genotypes: A Comparative Analysis and Machine Learning Approach. Sensors, 25(7), 2253. https://doi.org/10.3390/s25072253 (CIIRC CTU)
Joshi, S., Pant, M., Malhotra, A., Deep, K., & Snasel, V. (2025). A nnU-Net-based automatic segmentation of FCD type II lesions in 3D FLAIR MRI images. Frontiers in Artificial Intelligence, 8. https://doi.org/10.3389/frai.2025.1601815 (INDRC)
Abualigah, L., Almomani, M. H., Alomari, S. A., Zitar, R. A., Snasel, V., Saleem, K., Smerat, A., & Ezugwu, A. E. (2025). A control-driven transition strategy for enhanced multi-level threshold image segmentation optimization. Egyptian Informatics Journal, 30, 100646. https://doi.org/10.1016/j.eij.2025.100646 (VSB-TUO)

Other Interesting Papers

2025

Beyond the selected Q1/Q2 highlights, these papers demonstrate the diversity of research activities connected to CLARA, exploring innovative methods and applications across AI, healthcare, and life sciences.

Soulier, T., Burgos, N., Hassanaly, R., Pitombeira, M., Solal, M., Roy, H., Hamzaoui, M., Yazdan-Panah, A., de Paula Faria, D., Louapre, C., Bodini, B., Bottlaender, M., Ayache, N., Colliot, O., & Stankoff, B. (2025). Artificial intelligence in presymptomatic neurological diseases: Bridging normal variation and prodromal signatures. Revue Neurologique, 181(9), 944–950. https://doi.org/10.1016/j.neurol.2025.07.011 (PBI)
Khachaturian, A. S. (2025). Building a brain watch. The Journal of Aging Research & Lifestyle, 14, 100013. https://doi.org/10.1016/j.jarlif.2025.100013 (INDRC)
Christodoulou, E., Reinke, A., Andrè, P., Godau, P., Kalinowski, P., Houhou, R., Erkan, S., Sudre, C. H., Burgos, N., Boutaj, S., Loizillon, S., Solal, M., Cheplygina, V., Heitz, C., Kozubek, M., Antonelli, M., Rieke, N., Gilson, A., Mayer, L. D., … Maier-Hein, L. (2025). False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims (Version 2). arXiv. https://doi.org/10.48550/ARXIV.2505.04720 (PBI)
Roy, H., Dorent, R., & Burgos, N. (2025). Unsupervised Anomaly Detection Using Bayesian Flow Networks: Application to Brain FDG PET in the Context of Alzheimer’s Disease. In Lecture Notes in Computer Science (pp. 254–264). Springer Nature Switzerland. https://doi.org/10.1007/978-3-032-05472-2_25 (PBI)
Reinke, A., Li, Z. O., Tizabi, M. D., André, P., Knopp, M., Rother, M. M., Machado, I. P., Altieri, M. S., Alapatt, D., Bano, S., Bodenstedt, S., Burgert, O., Chen, E. C. S., Collins, J. W., Colliot, O., Christodoulou, E., Czempiel, T., Das, A., Docea, R., … Maier-Hein, L. (2025). Current validation practice undermines surgical AI development (Version 2). arXiv. https://doi.org/10.48550/ARXIV.2511.03769 (PBI)
Fu, G., Nichelli, L., Herran, D., Valabregue, R., Alentorn, A., Hoang-Xuan, K., Houillier, C., Dormont, D., Lehéricy, S., & Colliot, O. (2025). Comparing foundation models and nnU-Net for segmentation of primary brain lymphoma on clinical routine post-contrast T1-weighted MRI. In B. S. Gimi & A. Krol (Eds.), Medical Imaging 2025: Clinical and Biomedical Imaging (p. 45). SPIE. Clinical and Biomedical Imaging. https://doi.org/10.1117/12.3044679 (PBI)
Kazakos, E., Schmid, C., & Sivic, J. (2025). Large-scale Pre-training for Grounded Video Caption Generation (Version 3). arXiv. https://doi.org/10.48550/ARXIV.2503.10781 (CIIRC CTU)

2024

Since the launch of CLARA in autumn 2024, researchers have already achieved notable scientific outputs, including publications in internationally recognised journals such as Angewandte Chemie International Edition. These early results highlight the strong foundations of CLARA’s interdisciplinary research spanning computational biology, protein design, and AI-supported life sciences.

Buller, R., Damborsky, J., Hilvert, D., & Bornscheuer, U. T. (2024). Structure Prediction and Computational Protein Design for Efficient Biocatalysts and Bioactive Proteins. Angewandte Chemie International Edition, 64(2). https://doi.org/10.1002/anie.202421686 (ICRC)
Khan, R. T., Pokorna, P., Stourac, J., Borko, S., Dobias, A., Planas-Iglesias, J., Mazurenko, S., Arefiev, I., Pinto, G., Szotkowska, V., Sterba, J., Damborsky, J., Slaby, O., & Bednar, D. (2024). Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO. Computational and Structural Biotechnology Journal, 24, 734–738. https://doi.org/10.1016/j.csbj.2024.11.026 (ICRC)
Kouba, P., Planas-Iglesias, J., Damborsky, J., Sedlar, J., Mazurenko, S., & Sivic, J. (2024). Learning to engineer protein flexibility (Version 2). arXiv. https://doi.org/10.48550/ARXIV.2412.18275 (CIIRC CTU, ICRC)
Bushuiev, A., Bushuiev, R., Pimenova, O., Zadorozhny, N., Samusevich, R., Manaskova, E., Kim, R. S., Stärk, H., Sedlar, J., Steinegger, M., Pluskal, T., & Sivic, J. (2024). One protein is all you need (Version 3). arXiv. https://doi.org/10.48550/ARXIV.2411.02109 (CIIRC CTU)