Publications

• Catalina Rozalen et al. TIM3+ breast cancer cells license immune evasion during micrometastasis outbreak. Cancer Cell (2025) 

• Martínez Mir, C., Pisterzi, P., De Poorter, I., Rilou, M., van Kranenburg, M., Heijs, B., Alemany, A., Sage, F. & Geijsen, N. Spatial multi-omics in whole skeletal muscle reveals complex tissue architecture. Communications Biology volume 7, Article number: 1272 (2024) 

• van Beijnum, H., Koopmans, T., Tomasso, A., Disela, V., Te Lindert, S.,  Bakkers ,J. , Alemany, A., Berezikov, E., & Bartscherer, K.. Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear. Genome research 33, no. 8 (2023): 1424-1437.

• Salmen, F., De Jonghe, J., Kaminski, T. S., Alemany, A., Parada, G. E., Verity-Legg, J., ... & van Oudenaarden, A. (2022). High-throughput total RNA sequencing in single cells using VASA-seq. Nature Biotechnology, 1-14.

• Hita, A., Brocart, G., Fernandez, A., Rehmsmeier, M., Alemany, A. & Shvartzman, S. (2022). MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. BMC Bioinformatics 23: 23-39. 

• Alemany, A. (2020). Cell differentiation unravelled by single-cell RNA sequencing. Europhysics News, 51(5), 31-34.

• van den Brink, S. C., Alemany, A., van Batenburg, V., Moris, N., Blotenburg, M., Vivié, J., ... & van Oudenaarden, A. (2020). Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids. Nature, 582(7812), 405-409.

• Moris, N., Anlas, K., van den Brink, S. C., Alemany, A., Schröder, J., Ghimire, S., Balayo, T., van Oudenaarden, A. & Arias, A. M. (2020). An in vitro model of early anteroposterior organization during human development. Nature, 582(7812), 410-415.

• Ashoti, A., Limone, F., van Kranenburg, M., Alemany, A., Baak, M., Vivie, J., Piccioni, F., Creyghton, M., Eggan, K. and Geijsen, N. (2020). A genome-wide CRISPR/Cas phenotypic screen for modulators of DUX4 cytotoxicity reveals screen complications. bioRxiv.

• Pepe-Mooney, B. J., Dill, M. T., Alemany, A., Ordovas-Montanes, J., Matsushita, Y., Rao, A., ... & Camargo, F. D. (2019). Single-cell analysis of the liver epithelium reveals dynamic heterogeneity and an essential role for YAP in homeostasis and regeneration. Cell stem cell, 25(1), pp.23-38.

• Alemany, A., Florescu, M., Baron, C. S., Peterson-Maduro, J., & Van Oudenaarden, A. (2018). Whole-organism clone tracing using single-cell sequencing. Nature, 556(7699), 108-112. 

previous work on Single-molecule physics

(Selected publications)