Publications

Hudák, A., Letoha, A., & Letoha, T. (2025). Peripheral leukocyte syndecan-3 is elevated in Alzheimer’s disease: Evidence from a human study. International Journal of Molecular Sciences, 26(14), 6587. 
https://doi.org/10.3390/ijms26146587

Hudák, A., Pettko-Szandtner, A., Letoha, A., & Letoha, T. (2025). Clinical and proteomic associations of SARS-CoV-2 infection and COVID-19 vaccination in multimorbid patients: A cross-sectional observational study. International Journal of Molecular Sciences, 26(16), 8007.
https://doi.org/10.3390/ijms26168007

Urda-García, B., Sánchez-Valle, J., Lepore, R., & Valencia, A. (2025). Patient stratification reveals the molecular basis of disease co-occurrences. Proceedings of the National Academy of Sciences of the United States of America, 122(35), e2421060122. 
https://doi.org/10.1073/pnas.2421060122

Babaiha, N. S., Geissler, S., Nibart, V., Güvenilir, H. A., Bharadhwaj, V. S., Kodamullil, A. T., Klein, J., Jacobs, M., & Hofmann-Apitius, M. (2025). Unraveling the co-morbidity between COVID-19 and neurodegenerative diseases through multi-scale graph analysis: A systematic investigation of biological databases and text mining. Artificial Intelligence in the Life Sciences, 5, 100138.
https://doi.org/10.1016/j.ailsci.2025.100138

Popova, E., Jacobs, M., Hofmann-Apitius, M., & Babaiha, N. S. (2025). Leveraging multimodal large language models to extract mechanistic insights from biomedical visuals: A case study on COVID-19 and neurodegenerative diseases. Machine Learning with Applications, 18, 100816.
https://doi.org/10.1016/j.mlwa.2025.100816

Martins Conde, P., Bulaev, D., Rauschenberger, A., Ohnmacht, J., Fritz, J. V., O’Sullivan, M. P., … Krüger, R. (2025). Co-occurrence of memory impairment and fatigue distinguishes post COVID from pandemic-related 
https://doi.org/10.1038/s41598-025-19984-7

Mazein, I., Rougny, A., Mazein, A., Henkel, R., Gütebier, L., Michaelis, L., Ostaszewski, M., Schneider, R., Satagopam, V., Jensen, L. J., Waltemath, D., Wodke, J. A. H., & Balaur, I. (2024). Graph databases in systems biology: A systematic review. Briefings in Bioinformatics, 25(6), bbae561. 
https://doi.org/10.1093/bib/bbae561

Pogorelov, D., Bode, S. F. N., He, X., et al. (2024). Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: An observational study. Nature Communications, 15, 10266. 
https://doi.org/10.1038/s41467-024-54684-2

Anand, A., Babaiha, N. S., Hofmann-Apitius, M., & Jacobs, M. (n.d.). Let me cypher that for you: A multi-graph agent for deciphering biomedical knowledge. SSRN. 
https://ssrn.com/abstract=6028742

Rougny, A., Ostaszewski, M., & Sagatopam, V. (2026). momapy: A Python library to work with molecular maps. Preprints.
https://www.preprints.org/frontend/manuscript/90a38d7809eb075ad7c168fb26d3bec6/download_pub

Guvenilir, H. A., Sethumadhavan, P., Kaladharan, A., de Sa, R. V., Sridhar, A., Haferkamp, U., … Kodamullil, A. T. (2025). CBM KG: A comorbidity-centric knowledge graph uncovering causal pathomechanisms between COVID-19 and neurodegenerative diseases. bioRxiv.
https://doi.org/10.1101/2025.08.18.670790

Guski, J., Aborageh, M., & Fröhlich, H. (2025). PyTMLE: A flexible Python library for targeted estimation of survival and competing risks using causal machine learning. medRxiv.
https://doi.org/10.1101/2025.07.02.25330730

Sánchez-Valle, J., Flores-Rodero, M., Costa, F. X., Carbonell-Caballero, J., Núñez-Carpintero, I., Tabarés-Seisdedos, R., … Valencia, A. (2025). Sex-specific transcriptome similarity networks elucidate comorbidity relationships. bioRxiv.
https://doi.org/10.1101/2025.01.22.634077

Urda-García, B., Cirillo, D., & Valencia, A. (2025). Disentangling the genetic and non-genetic origin of disease co-occurrences. medRxiv.
https://doi.org/10.1101/2025.10.16.25338165