Publications

ZORA Publication List

Publications

• 2025

  • Journal Article

    • McIntyre, A. B. R., Tschan, A. B., Meyer, K., Walser, S., Rai, A. K., Fujita, K., & Pelkmans, L. (2025). Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention Nature Communications, 16, 390. https://doi.org/10.1038/s41467-024-55469-3

• 2024

  • Journal Article

    • Yin, J.-A., Frick, L., Scheidmann, M. C., Liu, T., Trevisan, C., Dhingra, A., Spinelli, A., Wu, Y., Yao, L., Vena, D. L., Knapp, B., Guo, J., De Cecco, E., Ging, K., Armani, A., Oakeley, E. J., Nigsch, F., Jenzer, J., Haegele, J., … et al. (2024). Arrayed CRISPR libraries for the genome-wide activation, deletion and silencing of human protein-coding genes Nature Biomedical Engineering, 9, 127–148. https://doi.org/10.1038/s41551-024-01278-4
    • Rutowicz, K., Lüthi, J., de Groot, R., Holtackers, R., Yakimovich, Y., Pazmiño, D. M., Gandrillon, O., Pelkmans, L., & Baroux, C. (2024). Multiscale chromatin dynamics and high entropy in plant iPSC ancestors Journal of Cell Science, 137, jcs261703. https://doi.org/10.1242/jcs.261703
    • Immer, A., Stark, S. G., Jacob, F., Bonilla, X., Thomas, T., Kahles, A., Goetze, S., Milani, E. S., Wollscheid, B., Aebersold, R., Ak, M., Al-Quaddoomi, F. S., Albert, S. I., Albinus, J., Alborelli, I., Andani, S., Attinger, P.-O., Bacac, M., Baumhoer, D., … Pelkmans, L. (2024). Probabilistic pathway-based multimodal factor analysis Bioinformatics, 40, i189–i198. https://doi.org/10.1093/bioinformatics/btae216
    • Ramella, M., Ribolla, L. M., Surini, S., Sala, K., Tonoli, D., Cioni, J.-M., Rai, A. K., Pelkmans, L., & de Curtis, I. (2024). Dual specificity kinase DYRK3 regulates cell migration by influencing the stability of protrusions IScience, 27, 109440. https://doi.org/10.1016/j.isci.2024.109440

• 2023

  • Journal Article

    • Bunne, C., Stark, S. G., Gut, G., del Castillo, J. S., Levesque, M., Lehmann, K.-V., Pelkmans, L., Krause, A., & Rätsch, G. (2023). Learning single-cell perturbation responses using neural optimal transport Nature Methods, 20, 1759–1768. https://doi.org/10.1038/s41592-023-01969-x
    • Gallo, R., Rai, A. K., McIntyre, A. B. R., Meyer, K., & Pelkmans, L. (2023). DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites Developmental Cell, 58, 1880-1897.e11. https://doi.org/10.1016/j.devcel.2023.08.005
    • Moore, J., Basurto-Lozada, D., Besson, S., Bogovic, J., Bragantini, J., Brown, E. M., Burel, J.-M., Casas Moreno, X., de Medeiros, G., Diel, E. E., Gault, D., Ghosh, S. S., Gold, I., Halchenko, Y. O., Hartley, M., Horsfall, D., Keller, M. S., Kittisopikul, M., Kovacs, G., … Pelkmans, L. (2023). OME-Zarr: a cloud-optimized bioimaging file format with international community support Histochemistry and Cell Biology, 160, 223–251. https://doi.org/10.1007/s00418-023-02209-1
    • Kramer, B. A., del Castillo, J. S., Pelkmans, L., & Gut, G. (2023). Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections Bio-Protocol, 13, e4712. https://doi.org/10.21769/bioprotoc.4712
    • Spitzer, H., Berry, S., Donoghoe, M., Pelkmans, L., & Theis, F. J. (2023). Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps Nature Methods, 20, 1058–1069. https://doi.org/10.1038/s41592-023-01894-z

• 2022

  • Journal Article

    • Kramer, B. A., del Castillo, J. S., & Pelkmans, L. (2022). Multimodal perception links cellular state to decision-making in single cells Science, 377, 642–648. https://doi.org/10.1126/science.abf4062
    • Berry, S., & Pelkmans, L. (2022). Mechanisms of cellular mRNA transcript homeostasis Trends in Cell Biology, 32, 655–668. https://doi.org/10.1016/j.tcb.2022.05.003
    • Berry, S., Müller, M., Rai, A., & Pelkmans, L. (2022). Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells Cell Systems, 13, 454-470.e15. https://doi.org/10.1016/j.cels.2022.04.005
    • Böddeker, T. J., Rosowski, K. A., Berchtold, D., Emmanouilidis, L., Han, Y., Allain, F. H. T., Style, R. W., Pelkmans, L., & Dufresne, E. R. (2022). Non-specific adhesive forces between filaments and membraneless organelles Nature Physics, 18, 571–578. https://doi.org/10.1038/s41567-022-01537-8
    • Böddeker, T. J., Rosowski, K. A., Berchtold, D., Emmanouilidis, L., Han, Y., Allain, F. H. T., Style, R. W., Pelkmans, L., & Dufresne, E. R. (2022). Publisher Correction: Non-specific adhesive forces between filaments and membraneless organelles Nature Physics, 18, 601–601. https://doi.org/10.1038/s41567-022-01600-4
    • Cole, J. D., del Castillo, J. S., Gut, G., Gonzalez-Bohorquez, D., Pelkmans, L., & Jessberger, S. (2022). Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging ELife, 11, e68000. https://doi.org/10.7554/elife.68000

• 2021

  • Journal Article

    • Irmisch, A., Bonilla, X., Chevrier, S., Lehmann, K.-V., Singer, F., Toussaint, N. C., Esposito, C., Mena, J., Milani, E. S., Casanova, R., Stekhoven, D. J., Wegmann, R., Jacob, F., Sobottka-Brillout, B., Goetze, S., Kuipers, J., Sarabia del Castillo, J., Prummer, M., Tuncel, M. A., … Levesque, M. P. (2021). The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support Cancer Cell, 39, 288–293. https://doi.org/10.1016/j.ccell.2021.01.004

• 2020

  • Journal Article

    • Rai, A., & Pelkmans, L. (2020). Liquid droplets in the skin Science, 367, 1193–1194. https://doi.org/10.1126/science.abb0060

• 2019

  • Working Paper

    • Kramer, B. A., & Pelkmans, L. (2019). Cellular state determines the multimodal signaling response of single cells (No. 880930; BioRxiv). https://doi.org/10.1101/2019.12.18.880930

• 2018

  • Journal Article

    • Berchtold, D., Battich, N., & Pelkmans, L. (2018). A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells Molecular Cell, 72, 1035–1049. https://doi.org/10.1016/j.molcel.2018.10.036
    • Popovic, D., Koch, B., Kueblbeck, M., Ellenberg, J., & Pelkmans, L. (2018). Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells Cell Systems, 7, 398–411. https://doi.org/10.1016/j.cels.2018.09.001
    • Gut, G., Herrmann, M. D., & Pelkmans, L. (2018). Multiplexed protein maps link subcellular organization to cellular state Science, 361, eaar7042. https://doi.org/10.1126/science.aar7042
    • de Groot, R., Lüthi, J., Lindsay, H., Holtackers, R., & Pelkmans, L. (2018). Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens Molecular Systems Biology, 14, e8064. https://doi.org/10.15252/msb.20178064

• 2015

  • Journal Article

    • Liberali, P., Snijder, B., & Pelkmans, L. (2015). Single-cell and multivariate approaches in genetic perturbation screens Nature Reviews. Genetics, 16, 18–32. https://doi.org/10.1038/nrg3768