Tan, J., Shenker-Tauris, N., Rodriguez-Hernaez, J., Wang, E., Sakellaropoulos, T., Boccalatte, F., ... Xia, B. & Tsirigos, A. (2023). Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nature biotechnology, 41(8), 1140-1150.

Tan, J., Le, H., Deng, J., Liu, Y., Hao, Y., Hollenberg, M., ... & Fenyö, D. "Characterization of tumour heterogeneity through segmentation-free representation learning on multiplexed imaging data." Nature Biomedical Engineering 9.3 (2025): 405-419.

Tan, J., Fu, X., Ling, X., Mo, S., Bai, J., Rabadán, R., Fenyö, D., Boeke, J.D., Tsirigos, A. and Xia, B., "Multimodal learning decodes the global binding landscape of chromatin-associated proteins." Biorxiv (2025).

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Sterling, S., Tan, J., Le, H., Share, D., Ban, Y., Snuderl, M. and Tsirigos, A., "A multi-scale segmentation-free self-supervised AI model to characterize the heterogeneity of the brain tumor microenvironment." BioRxiv (2025).

Fu, X., Mo, S., Buendia, A., Laurent, A.P., Shao, A., del Mar Alvarez-Torres, M., Yu, T., Tan, J., Su, J., Sagatelian, R. and Ferrando, A.A., … & Rabadan, R. A foundation model of transcription across human cell types. Nature, 637.8047 (2025): 965-973.

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Gambi, G., Boccalatte, F., Hernaez, J.R., Lin, Z., Nadorp, B., Polyzos, A., Tan, J., Avrampou, K., Inghirami, G., Kentsis, A. and Apostolou, E., … & Tsirigos, A. "3D chromatin hubs as regulatory units of identity and survival in human acute leukemia." Molecular cell 85.1 (2025): 42-60.

Wang, J.M., Hong, R., Demicco, E.G., Tan, J., Lazcano, R., Moreira, A.L., Li, Y., Calinawan, A., Razavian, N., Schraink, T. and Gillette, M.A., … & Fenyö, D. "Deep learning integrates histopathology and proteogenomics at a pan-cancer level." Cell Reports Medicine 4.9 (2023).

Leung, K., Zhang, B., Tan, J., Shen, Y., Geras, K.J., Babb, J.S., Cho, K., Chang, G. and Deniz, C.M., "Prediction of total knee replacement and diagnosis of osteoarthritis by using deep learning on knee radiographs: data from the osteoarthritis initiative." Radiology 296.3 (2020): 584-593.

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