Publications

ZORA Publication List

Publications

• 2026

  • Journal Article

    • Moro, G., Brunner, E., & Basler, K. (2026). A practical guide to targeted single-cell RNA sequencing technologies Communications Biology, 9, 250. https://doi.org/10.1038/s42003-026-09675-y
    • Little, J. C., Debrunner, M., de Hoog, T., Tadjik, F., Kehl, C. J., Hausmann, G., Brunner, E., & Basler, K. (2026). Systematic generation of Wnt transgenes enables the characterization of canonical Wnt signaling Fly, 20, 2624185. https://doi.org/10.1080/19336934.2026.2624185

• 2025

  • Journal Article

    • Moro, G. A., Mallona, I., Barz, M. J., Maillard Joel, Brügger, M. D., Fazilaty, H., Szabo Quentin, Valenta Tomas, Handler Kristina, Kerlin Fiona, Bastian Lorenz, Baldus Claudia D, Moor Andreas E, Zinzen Robert, Robinson Mark, Brunner Erich, & Basler, K. (2025). RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing Nature Communications, 16, 10991. https://doi.org/10.1038/s41467-025-66248-z
    • Brutscher, F., Germani, F., Hausmann, G., Jutz, L., & Basler, K. (2025). Activation of the Drosophila innate immune system accelerates growth in cooperation with oncogenic Ras PLoS Biology, 23, e3003068. https://doi.org/10.1371/journal.pbio.3003068
    • Janeckova, L., Stastna, M., Hrckulak, D., Berkova, L., Kubovciak, J., Onhajzer, J., Kriz, V., Dostalikova, S., Mullerova, T., Vecerkova, K., Tenglerova, M., Coufal, S., Kostovcikova, K., Blumberg, R. S., Filipp, D., Basler, K., Valenta, T., Kolar, M., & Korinek, V. (2025). Tcf4 regulates secretory cell fate decisions in the small intestine and colon tumors: insights from transcriptomic, histological, and microbiome analyses Stem Cell Research & Therapy, 16, 170. https://doi.org/10.1186/s13287-025-04280-y
    • Brutscher, F., & Basler, K. (2025). Functions of Drosophila Toll/NF-κB signaling in imaginal tissue homeostasis and cancer Frontiers in Cell and Developmental Biology, 13, 1559753. https://doi.org/10.3389/fcell.2025.1559753

• 2024

  • Journal Article

    • Oliveira-Paula, G. H., Liu, S., Maira, A., Ressa, G., Ferreira, G. C., Quintar, A., Jayakumar, S., Almonte, V., Parikh, D., Valenta, T., Basler, K., Hla, T., Riascos-Bernal, D. F., & Sibinga, N. E. S. (2024). The β-catenin C terminus links Wnt and sphingosine-1-phosphate signaling pathways to promote vascular remodeling and atherosclerosis Science Advances, 10, eadg9278. https://doi.org/10.1126/sciadv.adg9278

• 2023

  • Journal Article

    • He, J., Nascakova, Z., Leary, P., Papa, G., Valenta, T., Basler, K., & Müller, A. (2023). Inactivation of the tumor suppressor gene Apc synergizes with H. pylori to induce DNA damage in murine gastric stem and progenitor cells Science Advances, 9, eadh0322. https://doi.org/10.1126/sciadv.adh0322
    • Berková, L., Fazilaty, H., Yang, Q., Kubovčiak, J., Stastna, M., Hrckulak, D., Vojtechova, M., Dalessi, T., Brügger, M. D., Hausmann, G., Liberali, P., Korinek, V., Basler, K., & Valenta, T. (2023). Terminal differentiation of villus tip enterocytes is governed by distinct Tgfβ superfamily members EMBO Reports, 24, e56454. https://doi.org/10.15252/embr.202256454
    • Kim, J.-M., Min, K. W., Kim, Y.-J., Smits, R., Basler, K., & Kim, J. W. (2023). Wnt/β-Catenin Signaling Pathway Is Necessary for the Specification but Not the Maintenance of the Mouse Retinal Pigment Epithelium Molecules and Cells, 46, 441–450. https://doi.org/10.14348/molcells.2023.0029
    • Gurtner, A., Borrelli, C., Gonzalez-Perez, I., Bach, K., Acar, I. E., Núñez, N. G., Crepaz, D., Handler, K., Vu, V. P., Lafzi, A., Stirm, K., Raju, D., Gschwend, J., Basler, K., Schneider, C., Slack, E., Valenta, T., Becher, B., Krebs, P., … Arnold, I. C. (2023). Active eosinophils regulate host defense and immune responses in colitis Nature, 615, 151–157. https://doi.org/10.1038/s41586-022-05628-7
    • Häfliger, J., Schwarzfischer, M., Atrott, K., Stanzel, C., Morsy, Y., Wawrzyniak, M., Lang, S., Valenta, T., Basler, K., Rogler, G., Scharl, M., & Spalinger, M. R. (2023). Glycoprotein (GP)96 is essential for maintaining intestinal epithelial architecture by supporting its self-renewal capacity Cellular and Molecular Gastroenterology and Hepatology, 15, 717–739. https://doi.org/10.1016/j.jcmgh.2022.12.004
    • Fazilaty, H., & Basler, K. (2023). Reactivation of embryonic genetic programs in tissue regeneration and disease Nature Genetics, 55, 1792–1806. https://doi.org/10.1038/s41588-023-01526-4
    • Brügger, M. D., & Basler, K. (2023). The diverse nature of intestinal fibroblasts in development, homeostasis, and disease Trends in Cell Biology, 33, 834–849. https://doi.org/10.1016/j.tcb.2023.03.007

• 2022

  • Journal Article

    • Maruyama, T., Hasegawa, D., Valenta, T., Haigh, J., Bouchard, M., Basler, K., & Hsu, W. (2022). GATA3 mediates nonclassical β-catenin signaling in skeletal cell fate determination and ectopic chondrogenesis Science Advances, 8, eadd6172. https://doi.org/10.1126/sciadv.add6172

• 2021

  • Journal Article

    • Degirmenci, B., Dincer, C., Demirel, H. C., Berkova, L., Moor, A. E., Kahraman, A., Hausmann, G., Aguet, M., Tuncbag, N., Valenta, T., & Basler, K. (2021). Epithelial Wnt secretion drives the progression of inflammation-induced colon carcinoma in murine model IScience, 24, 103369. https://doi.org/10.1016/j.isci.2021.103369
    • Borrelli, C., Valenta, T., Handler, K., Vélez, K., Gurtner, A., Moro, G., Lafzi, A., De Vargas Roditi, L., Hausmann, G., Arnold, I. C., Moor, A. E., & Basler, K. (2021). Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells Nature Communications, 12, 1368. https://doi.org/10.1038/s41467-021-21591-9
    • Doumpas, N., Söderholm, S., Narula, S., Moreira, S., Doble, B. W., Cantù, C., & Basler, K. (2021). TCF/LEF regulation of the topologically associated domain ADI promotes mESCs to exit the pluripotent ground state Cell Reports, 36, 109705. https://doi.org/10.1016/j.celrep.2021.109705
    • Fazilaty, H., Brügger, M. D., Valenta, T., Szczerba, B. M., Berkova, L., Doumpas, N., Hausmann, G., Scharl, M., & Basler, K. (2021). Tracing colonic embryonic transcriptional profiles and their reactivation upon intestinal damage Cell Reports, 36, 109484. https://doi.org/10.1016/j.celrep.2021.109484
    • Diener, J., Baggiolini, A., Pernebrink, M., Dalcher, D., Lerra, L., Cheng, P. F., Varum, S., Häusel, J., Stierli, S., Treier, M., Studer, L., Basler, K., Levesque, M. P., Dummer, R., Santoro, R., Cantù, C., & Sommer, L. (2021). Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4 Nature Communications, 12, 5056. https://doi.org/10.1038/s41467-021-25326-8

• 2020

  • Journal Article

    • Brügger, M. D., Valenta, T., Fazilaty, H., Hausmann, G., & Basler, K. (2020). Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis PLoS Biology, 18, e3001032. https://doi.org/10.1371/journal.pbio.3001032
    • Saxena, M., Kalathur, R. K., Rubinstein, N., Vettiger, A., Sugiyama, N., Neutzner, M., Coto-Llerena, M., Kancherla, V., Ercan, C., Piscuoglio, S., Fischer, J., Fagiani, E., Cantù, C., Basler, K., & Christofori, G. (2020). A Pygopus 2-histone interaction is critical for cancer cell de-differentiation and progression in malignant breast cancer Cancer Research, 80, 3631–3648. https://doi.org/10.1158/0008-5472.can-19-2910
    • Bosch, P. S., Pepperl, J., & Basler, K. (2020). Anchor away – A fast, reliable and reversible technique to inhibit proteins in Drosophila melanogaster G3 : Genes, Genomes, Genetics, 10, 1745–1752. https://doi.org/10.1534/g3.120.401055
    • Cannac, F., Qi, C., Falschlunger, J., Hausmann, G., Basler, K., & Korkhov, V. M. (2020). Cryo-EM structure of the hedgehog release protein dispatched Science Advances, 6, eaay7928. https://doi.org/10.1126/sciadv.aay7928

  • Working Paper

    • Borrelli, C., Valenta, T., Handler, K., Vélez, K., Moro, G., Lafzi, A., de Vargas Roditi, L., Hausmann, G., Moor, A. E., & Basler, K. (2020). Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells (No. 103499; BioRxiv). https://doi.org/10.1101/2020.05.19.103499
    • Zimmerli, D., Borrelli, C., Jauregi-Miguel, A., Söderholm, S., Brütsch, S., Doumpas, N., Reichmuth, J., Murphy-Seiler, F., Aguet, M., Basler, K., Moor, A. E., & Cantù, C. (2020). TBX3 acts as tissue-specific component of the Wnt/β-catenin enhanceosome (No. 053561; BioRxiv). https://doi.org/10.1101/2020.04.22.053561

• 2019

  • Journal Article

    • Kabakci, Z., Käppeli, S., Cantù, C., Jensen, L. D., König, C., Toggweiler, J., Gentili, C., Ribaudo, G., Zagotto, G., Basler, K., Pinna, L. A., Cozza, G., & Ferrari, S. (2019). Pharmacophore-guided discovery of CDC25 inhibitors causing cell cycle arrest and tumor regression Scientific Reports, 9, 1335. https://doi.org/10.1038/s41598-019-38579-7
    • Brunner, E., Yagi, R., Debrunner, M., Beck-Schneider, D., Burger, A., Escher, E., Mosimann, C., Hausmann, G., & Basler, K. (2019). CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms Life Science Alliance, 2, e201800267. https://doi.org/10.26508/lsa.201800267
    • Zurkirchen, L., Varum, S., Giger, S., Klug, A., Häusel, J., Bossart, R., Zemke, M., Cantù, C., Atak, Z. K., Zamboni, N., Basler, K., & Sommer, L. (2019). Yin Yang 1 sustains biosynthetic demands during brain development in a stage-specific manner Nature Communications, 10, 2192. https://doi.org/10.1038/s41467-019-09823-5
    • Varum, S., Baggiolini, A., Zurkirchen, L., Atak, Z. K., Cantù, C., Marzorati, E., Bossart, R., Wouters, J., Häusel, J., Tuncer, E., Zingg, D., Veen, D., John, N., Balz, M., Levesque, M. P., Basler, K., Aerts, S., Zamboni, N., Dummer, R., & Sommer, L. (2019). Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation Cell Stem Cell, 24, 637-653.e9. https://doi.org/10.1016/j.stem.2019.03.011
    • Shokri, L., Inukai, S., Hafner, A., Weinand, K., Hens, K., Vedenko, A., Gisselbrecht, S. S., Dainese, R., Bischof, J., Furger, E., Feuz, J.-D., Basler, K., Deplancke, B., & Bulyk, M. L. (2019). A Comprehensive Drosophila melanogaster Transcription Factor Interactome Cell Reports, 27, 955-970.e7. https://doi.org/10.1016/j.celrep.2019.03.071
    • Doumpas, N., Lampart, F., Robinson, M. D., Lentini, A., Nestor, C. E., Cantù, C., & Basler, K. (2019). TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes The EMBO Journal, 38, e98873. https://doi.org/10.15252/embj.201798873

• 2018

  • Journal Article

    • Baillon, L., Germani, F., Rockel, C., Hilchenbach, J., & Basler, K. (2018). Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells Scientific Reports, 8, 17712. https://doi.org/10.1038/s41598-018-36277-4
    • Germani, F., Hain, D., Sternlicht, D., Moreno, E., & Basler, K. (2018). The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner ELife, 7, e39939. https://doi.org/10.7554/eLife.39939
    • Cantù, C., Felker, A., Zimmerli, D., Prummel, K. D., Cabello, E. M., Chiavacci, E., Méndez-Acevedo, K. M., Kirchgeorg, L., Burger, S., Ripoll, J., Valenta, T., Hausmann, G., Vilain, N., Aguet, M., Burger, A., Panáková, D., Basler, K., & Mosimann, C. (2018). Mutations in and genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling Genes and Development, 32, 1443–1458. https://doi.org/10.1101/gad.315531.118
    • Wang, Y., Lu, P., Wu, B., Riascos-Bernal, D. F., Sibinga, N. E. S., Valenta, T., Basler, K., & Zhou, B. (2018). Myocardial β-Catenin-BMP2 signaling promotes mesenchymal cell proliferation during endocardial cushion formation Journal of Molecular and Cellular Cardiology, 123, 150–158. https://doi.org/10.1016/j.yjmcc.2018.09.001
    • Bischof, J., Duffraisse, M., Furger, E., Ajuria, L., Giraud, G., Vanderperre, S., Paul, R., Björklund, M., Ahr, D., Ahmed, A. W., Spinelli, L., Brun, C., Basler, K., & Merabet, S. (2018). Generation of a versatile BiFC ORFeome library for analyzing protein-protein interactions in live ELife, 7, e38853. https://doi.org/10.7554/eLife.38853
    • Zingg, D., Debbache, J., Peña-Hernández, R., Antunes, A. T., Schaefer, S. M., Cheng, P. F., Zimmerli, D., Haeusel, J., Calçada, R. R., Tuncer, E., Zhang, Y., Bossart, R., Wong, K.-K., Basler, K., Dummer, R., Santoro, R., Levesque, M. P., & Sommer, L. (2018). EZH2-mediated primary cilium deconstruction drives metastatic melanoma formation Cancer Cell, 34, 69–84. https://doi.org/10.1016/j.ccell.2018.06.001
    • Degirmenci, B., Valenta, T., Dimitrieva, S., Hausmann, G., & Basler, K. (2018). GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells Nature, 558, 449–453. https://doi.org/10.1038/s41586-018-0190-3
    • Spletter, M. L., Barz, C., Yeroslaviz, A., Zhang, X., Lemke, S. B., Bonnard, A., Brunner, E., Cardone, G., Basler, K., Habermann, B. H., & Schnorrer, F. (2018). A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle ELife, 7, e34058. https://doi.org/10.7554/eLife.34058
    • Zimmerli, D., Cecconi, V., Valenta, T., Hausmann, G., Cantù, C., Restivo, G., Hafner, J., Basler, K., & van den Broek, M. (2018). WNT ligands control initiation and progression of human papillomavirus-driven squamous cell carcinoma Oncogene, 37, 3753–3762. https://doi.org/10.1038/s41388-018-0244-x
    • Degirmenci, B., Hausmann, G., Valenta, T., & Basler, K. (2018). Wnt Ligands as a Part of the Stem Cell Niche in the Intestine and the Liver Progress in Molecular Biology and Translational Science, 153, 1–19. https://doi.org/10.1016/bs.pmbts.2017.11.011

• 2017

  • Journal Article

    • Franz, A., Brunner, E., & Basler, K. (2017). Generation of genome-modified Drosophila cell lines using SwAP Fly, 11, 303–311. https://doi.org/10.1080/19336934.2017.1372068
    • Marty, F., Rago, G., Smith, D. F., Gao, X., Eijkel, G. B., MacAleese, L., Bonn, M., Brunner, E., Basler, K., & Heeren, R. M. A. (2017). Combining ToF-SIMS imaging mass spectrometry and CARS microspectroscopy reveals lipid patterns reminiscent of gene expression patterns in the wing imaginal disc of Drosophila melanogaster Analytical Chemistry, 89, 9664–9670. https://doi.org/10.1021/acs.analchem.7b00125
    • Sanchez Bosch, P., Ziukaite, R., Alexandre, C., Basler, K., & Vincent, J.-P. (2017). Dpp controls growth and patterning in Drosophila wing precursors through distinct modes of action ELife, 6, e22546. https://doi.org/10.7554/eLife.22546
    • Zimmerli, D., Hausmann, G., Cantù, C., & Basler, K. (2017). Pharmacological interventions in the Wnt pathway: Inhibition of Wnt secretion versus disrupting the protein-protein interfaces of nuclear factors British Journal of Pharmacology, 174, 4600–4610. https://doi.org/10.1111/bph.13864
    • Blyszczuk, P., Müller-Edenborn, B., Valenta, T., Osto, E., Stellato, M., Behnke, S., Glatz, K., Basler, K., Lüscher, T. F., Distler, O., Eriksson, U., & Kania, G. (2017). Transforming growth factor-β-dependent Wnt secretion controls myofibroblast formation and myocardial fibrosis progression in experimental autoimmune myocarditis European Heart Journal, 38, 1413–1425. https://doi.org/10.1093/eurheartj/ehw116
    • Cantù, C., Pagella, P., Shajiei, T. D., Zimmerli, D., Valenta, T., Hausmann, G., Basler, K., & Mitsiadis, T. A. (2017). A cytoplasmic role of Wnt/β-catenin transcriptional cofactors Bcl9, Bcl9l, and Pygopus in tooth enamel formation Science Signaling, 10, eaah4598. https://doi.org/10.1126/scisignal.aah4598
    • Franz, A., Shlyueva, D., Brunner, E., Stark, A., & Basler, K. (2017). Probing the canonicity of the Wnt/Wingless signaling pathway PLoS Genetics, 13, e1006700. https://doi.org/10.1371/journal.pgen.1006700
    • Eder, D., Aegerter, C., & Basler, K. (2017). Forces controlling organ growth and size Mechanisms of Development, 144, 53–61. https://doi.org/10.1016/j.mod.2016.11.005

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