selected-publications

Selected Publications


Nemergut, M. et al. (2026)

Concentration-dependent dimerization of staphylokinase variants with engineered surface charges

Protein Science 35 (3): e70494. 

Jochymek, L. et al. (2026) 

GAN-based bone suppression using a combined loss function

Frontiers in Artificial Intelligence 9: 1761336

 

Marques, S. et al. (2025)

Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins

Nucleic Acids Research 53: W132–W142. 

 

Khan, R. et al. (2025)

Anticipating protein evolution with successor sequence predictor

Journal of Cheminformatics 17(1):34

 

Kohout, P. et al. (2025)

Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics 

JACS Au 5 :838-850. 

 

Planas-Iglesias, J. et al. (2025)

Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis

ACS Catalysis 15: 3391-3404.

 

Havlásek, M. et al. (2025)

Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms

Journal of Chemical Information and Modeling 65 (16): 8688-8701. 

 

Štulajterová, M. et al. (2025)

Assessing the impact of His-tags on activity and stability of staphylokinase variants

International Journal of Biological Macromolecules 328: 147655. 

 

Franko, O. et al. (2025)

Acridine-Based Chalcone 1C and ABC Transporters

International Journal Of Molecular Sciences 26: 4138. 

 

Musil, M. et al. (2025)

FireProtDB 2.0: large-scale manually curated database of the protein stability data

Nucleic Acids Research 54: D409–D418. 

Phan, A. et al. (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. 

 

Gregg, N.M. et al. (2025)

Thalamic Stimulation Induced Changes in Network Connectivity and Excitability in Epilepsy

Annals of Neurology 99:748–760. 

Buller, R. et al. (2024) 

Structure Prediction and Computational Protein Design for Efficient Biocatalysts and Bioactive Proteins 

Angewandte Chemie International Edition 64: e202421686. 

Maidenbaum, S. et al. (2025)

Improved spatial memory for physical versus virtual navigation

J. Neural Eng. 22: 046014. DOI 10.1088/1741-2552/ade6aa


A notable scientific result in 2025 came from a collaborative study published in the Journal of Neural Engineering, demonstrating that physical movement significantly enhances spatial memory compared with virtual navigation alone. The study showed that participants navigating through real physical space using augmented reality performed better on memory tasks, reported greater ease of navigation, and exhibited stronger hippocampal theta activity — providing new evidence that the brainʼs spatial memory circuits respond differently during real movement.

 

The study was led by Shachar Maidenbaum, Ph.D. (Ben-Gurion University of the Negev), in collaboration with Associate Professor Václav Křemen (CIIRC CTU; CLARA RP2 Co-Leader; Mayo Clinic College of Medicine and Science) and his Ph.D. student Ing. Vladimír Sladký (CIIRC CTU and CLARA collaborator), together with Kai Miller, M.D., Ph.D., Jamie Van Gompel, M.D., Gregory A. Worrell, M.D., Ph.D. (Mayo Clinic), and Josh Jacobs, Ph.D. (Columbia University). This interdisciplinary collaboration highlights the strength of combining neuroscience, immersive technologies, and computational approaches to better understand memory processes in ecologically realistic conditions.

 

Beyond its scientific significance, the result opens promising avenues for studying spatial cognition and may contribute to future approaches that support people affected by memory and orientation impairments, including in neurodegenerative disease research.