Prof. Dr. Patrick Tschopp

Wang, M., Di Pietro-Torres, A., Feregrino, C., Luxey, M., Moreau, C., Fischer, S., Fages, A., Ritz, D., & Tschopp, P. (2025). Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis [Journal-article]. Nature Communications , 16(1). https://doi.org/10.1038/s41467-025-57480-8

Herrera-Castillo, C. M., Brechbühl, T., Fages, A., Tschopp, P., MacColl, A., & Berner, D. (2025). Developmental genetic basis of dorsal spine reduction in acidic-adapted threespine stickleback fish [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.08.04.667941

Huyghe, C. E. T., Fages, A., Ronco, F., Indermaur, A., Schedel, F. D. B., Kimirei, I., Makasa, L., Tschopp, P., & Salzburger, W. (2025). Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika [Journal-article]. Molecular Ecology, 34(9). https://doi.org/10.1111/mec.17743

Fages, A., Luxey, M., Ronco, F., Huyghe, C. E. T., Menon, P. N. K., Indermaur, A., Salzburger, W., & Tschopp, P. (2024). Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishes [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.11.28.625862

Clark, Bethan, Sommer-Trembo, Carolin, Santos, M. Emília, Werner, Marco, Fages, Antoine, Matschiner, Michael, Hornung, Simon, Ronco, Fabrizia, Oliver, Chantal, Garcia, Cody, Tschopp, Patrick, Malinsky, Milan, & Salzburger, Walter. (2024). The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes [Journal-article]. Science, 384(6694), 470–475. https://doi.org/10.1126/science.adj9228

Wang, M., Di Pietro-Torres, A., Feregrino, C., Luxey, M., Moreau, C., Fischer, S., Fages, A., & Tschopp, P. (2024). Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.03.26.586769

Atsuta, Yuji, Lee, ChangHee, Rodrigues, Alan R., Colle, Charlotte, Tomizawa, Reiko R., Lujan, Ernesto G., Tschopp, Patrick, Galan, Laura, Zhu, Meng, Gorham, Joshua M., Vannier, Jean-Pierre, Seidman, Christine E., Seidman, Jonathan G., Ros, Marian A., Pourquié, Olivier, & Tabin, Clifford J. (2024). Direct reprogramming of non-limb fibroblasts to cells with properties of limb progenitors [Journal-article]. Developmental Cell, 59(3), 415–430. https://doi.org/10.1016/j.devcel.2023.12.010

Grall, E., Feregrino, C., Fischer, S., De Courten, A., Sacher, F., Hiscock, T. W., & Tschopp, P. (2024). Self-organized BMP signaling dynamics underlie the development and evolution of digit segmentation patterns in birds and mammals. Proceedings of the National Academy of Sciences of the United States of America, 121(2). https://doi.org/10.1073/pnas.2304470121

Luxey, Maëva, Stieger, Gabriela, Berki, Bianka, & Tschopp, Patrick. (2023). Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies [Journal-article]. Frontiers in Cell and Developmental Biology, 11. https://doi.org/10.3389/fcell.2023.1154205

Grall, E., Feregrino, C., Fischer, S., De Courten, A., Hiscock, T. W., & Tschopp, P. (2023). Self-organized BMP signaling dynamics underlie the development and evolution of tetrapod digit patterns [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.03.28.534660

Berki, Bianka, Sacher, Fabio, Fages, Antoine, Tschopp, Patrick, & Luxey, Maëva. (2023). A method to investigate muscle target-specific transcriptional signatures of single motor neurons. Developmental Dynamics, 252(1), 208–219. https://doi.org/10.1002/dvdy.507

Atsuta, Y., Lee, C., Rodrigues, A. R., Colle, C., Tomizawa, R. R., Lujan, E. G., Tschopp, P., Gorham, J. M., Vannier, J.-P., Seidman, C. E., Seidman, J. G., Pourquié, O., & Tabin, C. J. (2021). Direct Reprogramming of Non-limb Fibroblasts to Cells with Properties of Limb Progenitors [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.01.462632

Feregrino, Christian, & Tschopp, Patrick. (2021). Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Developmental Dynamics, 1–18. https://doi.org/10.1002/dvdy.384

Sacher, Fabio, Feregrino, Christian, Tschopp, Patrick, & Ewald, Collin. (2021). Extracellular matrix gene expression signatures as cell type and cell state identifiers. Matrix Biol Plus, 10, 100069. https://doi.org/10.1016/j.mbplus.2021.100069

Luxey, Maëva, Berki, Bianka, Heusermann, Wolf, Fischer, Sabrina, & Tschopp, Patrick. (2020). Development of the chick wing and leg neuromuscular systems and their plasticity in response to changes in digit numbers. Developmental Biology, 458(2), 133–140. https://doi.org/10.1016/j.ydbio.2019.10.035

Darbellay, F., Bochaton, C., Lopez-Delisle, L., Mascrez, B., Tschopp, P., Delpretti, S., Zakany, J., & Duboule, D. (2019). Constrained Transcriptional Polarity in the Organization of Mammalian Hox Gene Clusters [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/572875

Darbellay, Fabrice, Bochaton, Célia, Lopez-Delisle, Lucille, Mascrez, Bénédicte, Tschopp, Patrick, Delpretti, Saskia, Zakany, Jozsef, & Duboule, Denis. (2019). The constrained architecture of mammalian Hox gene clusters. Proceedings of the National Academy of Sciences, 116(27), 13424–13433. https://doi.org/10.1073/pnas.1904602116

Feregrino, Christian, Sacher, Fabio, Parnas, Oren, & Tschopp, Patrick. (2019). A single-cell transcriptomic atlas of the developing chicken limb. BMC Genomics, 20(1), 401. https://doi.org/10.1186/s12864-019-5802-2

Grall, Emmanuelle, & Tschopp, Patrick. (2019). A sense of place, many times over - pattern formation and evolution of repetitive morphological structures. Developmental Dynamics, 249(3), 313–327. https://doi.org/10.1002/dvdy.131

Tschopp, Patrick. (2017). Wie wird der Hals der Giraffe so lang? In Füglister, Kurt M.; Hicklin, Martin; Mäser, Pascal (Ed.), natura obscura. 200 Naturforschende - 200 Naturphänomene - 200 Jahre Naturforschende Gesellschaft in Basel (pp. 205). Schwabe.

Hiscock, Tom W., Tschopp, Patrick, & Tabin, Clifford J. (2017). On the Formation of Digits and Joints during Limb Development. Developmental Cell, 41(5), 459–465. https://doi.org/10.1016/j.devcel.2017.04.021

Marin, Ray, Cortez, Diego, Lamanna, Francesco, Pradeepa, Madapura M., Leushkin, Evgeny, Julien, Philippe, Liechti, Angélica, Halbert, Jean, Brüning, Thoomke, Mössinger, Katharina, Trefzer, Timo, Conrad, Christian, Kerver, Halie N., Wade, Juli, Tschopp, Patrick, & Kaessmann, Henrik. (2017). Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage. Genome Research, 27(12), 1974–1987. https://doi.org/10.1101/gr.223727.117

Tschopp, Patrick, & Tabin, Clifford J. (2017). Deep homology in the age of next-generation sequencing. Philosophical Transactions B: Biological Sciences, 372(1713), 1–7. https://doi.org/10.1098/rstb.2015.0475

Groner, A. C., Cato, L., de Tribolet-Hardy, J., Bernasocchi, T., Janouskova, H., Melchers, D., Houtman, R., Cato, A. C. B., Tschopp, P., Gu, L., Corsinotti, A., Zhong, Q., Fankhauser, C., Fritz, C., Poyet, C., Wagner, U., Guo, T., Aebersold, R., Garraway, L. A., et al. (2016). TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer. Cancer Cell, 29(6), 846–858. https://doi.org/10.1016/j.ccell.2016.04.012

Tschopp, P., Sherratt, E., Sanger, T. J., Groner, A. C., Aspiras, A. C., Hu, J. K., Pourquié, O., Gros, J., & Tabin, C. J. (2014). A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature, 516(7531), 391–394. https://doi.org/10.1038/nature13819

Rohner, N., Tschopp, P., & Tabin, C. (2014). Development: Facial makeup enhancing our looks. Current Biology, 24(1). https://doi.org/10.1016/j.cub.2013.11.026

Tschopp, P., & Duboule, D. (2014). The genetics of murine Hox Loci: TAMERE, STRING, and PANTHERE to engineer chromosome variants. Methods in Molecular Biology, 1196, 89–102. https://doi.org/10.1007/978-1-4939-1242-1_6

Schorderet, P., Lonfat, N., Darbellay, F., Tschopp, P., Gitto, S., Soshnikova, N., & Duboule, D. (2013). A Genetic Approach to the Recruitment of PRC2 at the HoxD Locus. PLoS Genetics, 9(11). https://doi.org/10.1371/journal.pgen.1003951

Mosimann, C., Puller, A.-C., Lawson, K. L., Tschopp, P., Amsterdam, A., & Zon, L. I. (2013). Site-directed zebrafish transgenesis into single landing sites with the phiC31 integrase system. Developmental Dynamics, 242(8), 949–963. https://doi.org/10.1002/dvdy.23989

Lonfat, N., Montavon, T., Jebb, D., Tschopp, P., Huynh, T. H. N., Zakany, J., & Duboule, D. (2013). Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations. Proceedings of the National Academy of Sciences of the United States of America, 110(29), 11946–11951. https://doi.org/10.1073/pnas.1310704110

Groner, A. C., Tschopp, P., Challet, L., Dietrich, J.-E., Verp, S., Offner, S., Barde, I., Rodriguez, I., Hiiragi, T., & Trono, D. (2012). The Krüppel-associated box repressor domain can induce reversible heterochromatization of a mouse locus in vivo. Journal of Biological Chemistry, 287(30), 25361–25369. https://doi.org/10.1074/jbc.M112.350884

Tschopp, P., Christen, A. J., & Duboule, D. (2012). Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters. Development, 139(5), 929–939. https://doi.org/10.1242/dev.076794

Tschopp, P., & Duboule, D. (2011). A genetic approach to the transcriptional regulation of Hox gene clusters. Annual Review of Genetics, 45, 145–166. https://doi.org/10.1146/annurev-genet-102209-163429

Tschopp, P., Fraudeau, N., Béna, F., & Duboule, D. (2011). Reshuffling genomic landscapes to study the regulatory evolution of Hox gene clusters. Proceedings of the National Academy of Sciences of the United States of America, 108(26), 10632–10637. https://doi.org/10.1073/pnas.1102985108

Tschopp, P., & Duboule, D. (2011). A regulatory ‘landscape effect’ over the HoxD cluster. Developmental Biology, 351(2), 288–296. https://doi.org/10.1016/j.ydbio.2010.12.034

Suga, Hiroshi, Tschopp, Patrick, Graziussi, Daria F, Stierwald, Michael, Schmid, Volker, & Gehring, Walter J. (2010). Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish. Proceedings of the National Academy of Sciences of the United States of America, 107(32), 8–14263. https://doi.org/10.1073/pnas.1008389107

Tschopp, P., Tarchini, B., Spitz, F., Zakany, J., & Duboule, D. (2009). Uncoupling time and space in the collinear regulation of Hox genes. PLoS Genetics, 5(3). https://doi.org/10.1371/journal.pgen.1000398