Publications

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)

Design by J. Alemany

Camunas-Soler, J., Alemany, A., & Ritort, F. (2017). Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems. Science, 355(6323), 412-415.
Bizarro, C. V., Alemany, A., & Ritort, F. (2012). Non-specific binding of Na+ and Mg 2+ to RNA determined by force spectroscopy methods. Nucleic acids research, 40(14), 6922-6935.
Alemany, A., Mossa, A., Junier, I., & Ritort, F. (2012). Experimental free-energy measurements of kinetic molecular states using fluctuation theorems. Nature Physics, 8(9), 688-694.
Alemany, A., Ribezzi, M., & Ritort, F. (2011). Recent progress in fluctuation theorems and free energy recovery. AIP Conference Proceedings (Vol. 1332, No. 1, pp. 96-110). American Institute of Physics.