• gene regulation
• deep learning

Recent publications

• launch Johansen, N.J., Kempynck, N., Zemke, N.R., Somasundaram, S., De Winter, S., Hooper, M., Dwivedi, D., Lohia, R., Wehbe, F., Li, B., Abaffyova, D., Armand, E.J., De Man, J., Eksi, E.C., Hecker, N., Hulselmans, G., Konstantakos, V., Mauduit, D., Mich, J.K., Partel, G., Daigle, T.L., Levi, B.P., Zhang, K., Tanaka, Y., Gillis, J., Ting, J.T., Ben-Simon, Y., Miller, J., Ecker, J.R., Ren, B., Aerts, S., Lein, E.S., Tasic, B., Bakken, T.E. with Bakken, T.E. (corresp. author) (2025). Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex. CELL GENOMICS, 5 (6), Art.No. ARTN 100879. doi: 10.1016/j.xgen.2025.100879 via repository
• launch Johansen, N.J., Kempynck, N., Zemke, N.R., Somasundaram, S., De Winter, S., Hooper, M., Dwivedi, D., Lohia, R., Wehbe, F., Li, B., Abaffyová, D., Armand, E.J., De Man, J., Eksi, E.C., Hecker, N., Hulselmans, G., Konstantakos, V., Mauduit, D., Mich, J.K., Partel, G., Daigle, T.L., Levi, B.P., Zhang, K., Tanaka, Y., Gillis, J., Ting, J.T., Ben-Simon, Y., Miller, J., Ecker, J.R., Ren, B., Aerts, S., Lein, E.S., Tasic, B., Bakken, T.E. (2025). Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex.. doi: 10.1101/2024.08.21.609075
• launch Hecker, N., Kempynck, N., Mauduit, D., Abaffyova, D., Vandepoel, R., Dieltiens, S., Borm, L., Sarropoulos, I., Gonzalez-Blas, C.B., De Man, J., Davie, K., Leysen, E., Vandensteen, J., Moors, R., Hulselmans, G., Lim, L., De Wit, J., Christiaens, V., Poovathingal, S., Aerts, S. with Aerts, S. (corresp. author) (2025). Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium. SCIENCE, 387 (6735), Art.No. ARTN eadp3957, 734-+. doi: 10.1126/science.adp3957 via repository
• launch Kempynck, N., De Winter, S., Blaauw, C., Konstantakos, V., Dieltiens, S., Ekşi, E.C., Bercier, V., Taskiran, I., Hulselmans, G., Spanier, K., Christiaens, V., Van Den Bosch, L., Mahieu, L., Aerts, S. (2025). CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species. bioRxiv. doi: 10.1101/2025.04.02.646812
• launch Dickmänken, H., Wojno, M., Theunis, K., Ekşi, E.C., Mahieu, L., Christiaens, V., Kempynck, N., De Rop, F., Roels, N., Spanier, K., Vandepoel, R., Hulselmans, G., Poovathingal, S., Aerts, S. (2025). HyDrop v2: Scalable atlas construction for training sequence-to-function models. bioRxiv. doi: 10.1101/2025.04.02.646792
• launch Taskiran, I.I., Spanier, K.I., Dickmanken, H., Kempynck, N., Pancikova, A., Eksi, E.C., Hulselmans, G., Ismail, J.N., Theunis, K., Vandepoel, R., Christiaens, V., Mauduit, D., Aerts, S. with Aerts, S. (corresp. author) (2024). Cell-type-directed design of synthetic enhancers. NATURE, 626 (7997). doi: 10.1038/s41586-023-06936-2 via repository
• launch Hecker, N., Kempynck, N., Mauduit, D., Abaffyová, D., Vandepoel, R., Dieltiens, S., Sarropoulos, I., Bravo González-Blas, C., Leysen, E., Moors, R., Hulselmans, G., Lim, L., De Wit, J., Christiaens, V., Poovathingal, S., Aerts, S. (2024). Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium. bioRxiv. doi: 10.1101/2024.04.17.589795
• launch Filtjens, B., Yang, P-K., Goris, M., Gilat, M., Kempynck, N., Ginis, P., Nieuwboer, A., Slaets, P., Vanrumste, B. with Filtjens, B. (joint first author), Yang, P-K. (joint first author) (2023). Automated freezing of gait assessment with deep learning and data augmentation from simulated inertial measurement unit data. In: 2023 IEEE 19th International Conference on Body Sensor Networks (BSN). Presented at the 2023 IEEE 19th International Conference on Body Sensor Networks (BSN), Boston MA USA, 09 Oct 2023-11 Oct 2023. ISBN: 979-8-3503-3841-6. doi: 10.1109/BSN58485.2023.10330987