Publications

2026                                        

• Amel, A., & Alemany, A. (2026). What’s in a niche? Elucidating the role of the ECM in cell fate commitment. Current Opinion in Genetics & Development, 100, 102528.

• Yildiz, M., Dommann, N., Hasdemir, T. K., de Vries, E., Alemany, A., Dijkers, P. F., & Geijsen, N. (2026). Retinoic acid and FGF signaling interact to control elongation and lineage specification in a mouse gastruloid model. Development, dev-205153.

• Blanch-Asensio, A., Ploessl, D. S., Johnson, B. B., Cascione, S., Berndsen, M. R., Wang, N. B., ... & Davis, R. P. (2026). STRAIGHT-IN Dual: a platform for dual single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cells. Nature Biomedical Engineering, 1-18.

• Bessler, N., Wezenaar, A. K., Ariese, H. C., Honhoff, C., Dommann, N., Wehrens, E. J., ... & Rios, A. C. (2026). De novo H3. 3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function. Nature cancer, 7(2), 316-333.

• Mir, C. M., Boers, R., Gribnay, J., Alemany, A., Sage, F., & Geijsen, N. (2026). Sex-specific DNA methylation in adult skeletal muscle. bioRxiv, 2026-03.

2025                                        

• Rozalén, C., Sangrador, I., Avalle, S., Blasco-Benito, S., Tzortzi, P., Sanz-Flores, M., ... & Celià-Terrassa, T. (2025). TIM3+ breast cancer cells license immune evasion during micrometastasis outbreak. Cancer Cell, 43(8), 1549-1567.

• Baron, C. S., & Alemany, A. (2025). Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace. In Lineage Tracing: Methods and Protocols (pp. 221-241). New York, NY: Springer US.

• de Winter, T. J., Sovrovic, M., Dekker, E., de Graaf, N., Sun, H., Johnson, J. D., ... & Alemany, A. (2025). Cell type-specific eQTL detection from single-cell RNA-seq reveals post-transcriptional regulatory mechanisms in human islets. bioRxiv, 2025-01.

• Wezenaar, A. K., Pandey, U., Keramati, F., Hernandez-Roca, M., Brazda, P., Barrera Román, M., ... & Rios, A. C. (2025). Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics. Nature protocols, 20(9), 2453-2480.

• Cao, X., Mircea, M., Cascione, S., Amel, A., Tsikari, T., van den Hil, F. E., ... & Orlova, V. V. (2025). Tissue microenvironment dictates the state of human iPSC-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues. Iscience, 28(10).

2024                                        

• 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) 

• Seubert, A. C., Krafft, M., Bopp, S., Helal, M., Bhandare, P., Wolf, E., ... & Kretzschmar, K. (2024). Spatial transcriptomics reveals molecular cues underlying the site specificity of the adult mouse oral mucosa and its stem cell niches. Stem Cell Reports, 19(12), 1706-1719.

• Andersson-Rolf, A., Groot, K., Korving, J., Begthel, H., Hanegraaf, M. A., VanInsberghe, M., ... & Clevers, H. (2024). Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages. Cell, 187(26), 7394-7413.

2023                                        

• 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.

2022                                        

• 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. 

• Kester, L., de Barbanson, B., Lyubimova, A., Chen, L. T., van der Schrier, V., Alemany, A., ... & van Oudenaarden, A. (2022). Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution. Cell Genomics, 2(2).

• Ashoti, A., Limone, F., van Kranenburg, M., Alemany, A., Baak, M., Vivié, J., ... & Geijsen, N. (2022). Considerations and practical implications of performing a phenotypic CRISPR/Cas survival screen. PLoS One, 17(2), e0263262.

• Seong, J., Frias-Aldeguer, J., Holzmann, V., Kagawa, H., Sestini, G., Khoei, H. H., ... & Rivron, N. C. (2022). Epiblast inducers capture mouse trophectoderm stem cells in vitro and pattern blastoids for implantation in utero. Cell stem cell, 29(7), 1102-1118.

Before 2020                                        

• 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)