Publications

ZORA Publication List

Publications

• 2024

  • Journal Article

    • Yin, Jiang-An; Frick, Lukas; Scheidmann, Manuel C; Liu, Tingting; Trevisan, Chiara; Dhingra, Ashutosh; Spinelli, Anna; Wu, Yancheng; Yao, Longping; Vena, Dalila Laura; Knapp, Britta; Guo, Jingjing; De Cecco, Elena; Ging, Kathi; Armani, Andrea; Oakeley, Edward J; Nigsch, Florian; Jenzer, Joel; Haegele, Jasmin; Pikusa, Michal; Täger, Joachim; Rodriguez-Nieto, Salvador; Bouris, Vangelis; Ribeiro, Rafaela; Baroni, Federico; Berry, Scott; Losa, Marco; Hornemann, Simone; Pelkmans, Lucas; Aguzzi, Adriano; et al (2024). Arrayed CRISPR libraries for the genome-wide activation, deletion and silencing of human protein-coding genes. Nature Biomedical Engineering:Epub ahead of print.
    • Rutowicz, Kinga; Lüthi, Joel; de Groot, Reinoud; Holtackers, René; Yakimovich, Yauhen; Pazmiño, Diana M; Gandrillon, Olivier; Pelkmans, Lucas; Baroux, Célia (2024). Multiscale chromatin dynamics and high entropy in plant iPSC ancestors. Journal of Cell Science, 137(20):jcs261703.
    • Immer, Alexander; Stark, Stefan G; Jacob, Francis; Bonilla, Ximena; Thomas, Tinu; Kahles, André; Goetze, Sandra; Milani, Emanuela S; Wollscheid, Bernd; Aebersold, Rudolf; Ak, Melike; Al-Quaddoomi, Faisal S; Albert, Silvana I; Albinus, Jonas; Alborelli, Ilaria; Andani, Sonali; Attinger, Per-Olof; Bacac, Marina; Baumhoer, Daniel; Beck-Schimmer, Beatrice; Beerenwinkel, Niko; Beisel, Christian; Bernasconi, Lara; Bertolini, Anne; Bodenmiller, Bernd; Bonilla, Ximena; Bosshard, Lars; Calgua, Byron; Casanova, Ruben; et al; Pelkmans, Lucas (2024). Probabilistic pathway-based multimodal factor analysis. Bioinformatics, 40(Suppl 1):i189-i198.
    • Ramella, Martina; Ribolla, Lucrezia Maria; Surini, Sara; Sala, Kristyna; Tonoli, Diletta; Cioni, Jean-Michel; Rai, Arpan Kumar; Pelkmans, Lucas; de Curtis, Ivan (2024). Dual specificity kinase DYRK3 regulates cell migration by influencing the stability of protrusions. iScience, 27(4):109440.

• 2023

  • Journal Article

    • Bunne, Charlotte; Stark, Stefan G; Gut, Gabriele; del Castillo, Jacobo Sarabia; Levesque, Mitch; Lehmann, Kjong-Van; Pelkmans, Lucas; Krause, Andreas; Rätsch, Gunnar (2023). Learning single-cell perturbation responses using neural optimal transport. Nature Methods, 20(11):1759-1768.
    • Gallo, Raffaella; Rai, Arpan Kumar; McIntyre, Alexa B R; Meyer, Katrina; Pelkmans, Lucas (2023). DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Developmental Cell, 58(19):1880-1897.e11.
    • Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hartley, Matthew; Horsfall, Dave; Keller, Mark S; Kittisopikul, Mark; Kovacs, Gabor; Küpcü Yoldaş, Aybüke; Kyoda, Koji; le Tournoulx de la Villegeorges, Albane; Li, Tong; Liberali, Prisca; Lindner, Dominik; Linkert, Melissa; Lüthi, Joel; Maitin-Shepard, Jeremy; Manz, Trevor; Marconato, Luca; et al; Pelkmans, Lucas (2023). OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and Cell Biology, 160(3):223-251.
    • Kramer, Bernhard; Castillo, Jacobo; Pelkmans, Lucas; Gut, Gabriele (2023). Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections. Bio-protocol, 13(13):e4712.
    • Spitzer, Hannah; Berry, Scott; Donoghoe, Mark; Pelkmans, Lucas; Theis, Fabian J (2023). Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps. Nature Methods, 20(7):1058-1069.

• 2022

  • Journal Article

    • Kramer, Bernhard A; del Castillo, Jacobo Sarabia; Pelkmans, Lucas (2022). Multimodal perception links cellular state to decision-making in single cells. Science, 377(6606):642-648.
    • Berry, Scott; Pelkmans, Lucas (2022). Mechanisms of cellular mRNA transcript homeostasis. Trends in Cell Biology, 32(8):655-668.
    • Berry, Scott; Müller, Micha; Rai, Arpan; Pelkmans, Lucas (2022). Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells. Cell Systems, 13(6):454-470.e15.
    • Böddeker, Thomas J; Rosowski, Kathryn A; Berchtold, Doris; Emmanouilidis, Leonidas; Han, Yaning; Allain, Frédéric H T; Style, Robert W; Pelkmans, Lucas; Dufresne, Eric R (2022). Non-specific adhesive forces between filaments and membraneless organelles. Nature Physics, 18(5):571-578.
    • Böddeker, Thomas J; Rosowski, Kathryn A; Berchtold, Doris; Emmanouilidis, Leonidas; Han, Yaning; Allain, Frédéric H T; Style, Robert W; Pelkmans, Lucas; Dufresne, Eric R (2022). Publisher Correction: Non-specific adhesive forces between filaments and membraneless organelles. Nature Physics, 18(5):601.
    • Cole, John Darby; del Castillo, Jacobo Sarabia; Gut, Gabriele; Gonzalez-Bohorquez, Daniel; Pelkmans, Lucas; Jessberger, Sebastian (2022). Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging. eLife, 11:e68000.

• 2021

  • Journal Article

    • Irmisch, Anja; Bonilla, Ximena; Chevrier, Stéphane; Lehmann, Kjong-Van; Singer, Franziska; Toussaint, Nora C; Esposito, Cinzia; Mena, Julien; Milani, Emanuela S; Casanova, Ruben; Stekhoven, Daniel J; Wegmann, Rebekka; Jacob, Francis; Sobottka-Brillout, Bettina; Goetze, Sandra; Kuipers, Jack; Sarabia del Castillo, Jacobo; Prummer, Michael; Tuncel, Mustafa A; Menzel, Ulrike; Jacobs, Andrea; Engler, Stefanie; Sivapatham, Sujana; Frei, Anja L; Gut, Gabriele; Ficek, Joanna; Miglino, Nicola; Aebersold, Rudolf; Bacac, Marina; Beerenwinkel, Niko; Moch, Holger; Beisel, Christian; Bodenmiller, Bernd; Dummer, Reinhard; Heinzelmann-Schwarz, Viola; Koelzer, Viktor H; Manz, Markus G; Pelkmans, Lucas; Snijder, Berend; Theocharides, Alexandre P A; Tolnay, Markus; Wicki, Andreas; Wollscheid, Bernd; Rätsch, Gunnar; Levesque, Mitchell Paul (2021). The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell, 39(3):288-293.

• 2020

  • Journal Article

    • Rai, Arpan; Pelkmans, Lucas (2020). Liquid droplets in the skin. Science, 367(6483):1193-1194.

• 2019

  • Working Paper

    • Kramer, Bernhard A; Pelkmans, Lucas (2019). Cellular state determines the multimodal signaling response of single cells. bioRxiv 880930, Cold Spring Harbor Laboratory.

• 2018

  • Journal Article

    • Berchtold, Doris; Battich, Nico; Pelkmans, Lucas (2018). A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells. Molecular Cell, 72(6):1035-1049.
    • Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, Lucas (2018). Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. Cell Systems, 7(4):398-411.
    • Gut, Gabriele; Herrmann, Markus D; Pelkmans, Lucas (2018). Multiplexed protein maps link subcellular organization to cellular state. Science, 361(6401):eaar7042.
    • de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas (2018). Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens. Molecular Systems Biology, 14(1):e8064.

• 2015

  • Journal Article

    • Liberali, Prisca; Snijder, Berend; Pelkmans, Lucas (2015). Single-cell and multivariate approaches in genetic perturbation screens. Nature Reviews. Genetics, 16(1):18-32.