Publications

ZORA Publication List

Publications

• 2026

  • Halstead-Nussloch, G., Okada, M., Haberer, G., Lux, T., Islam, A. S. M. F., Hatakeyama, M., Briskine, R., White, B., Hall, A., Pozniak, C., Walkowiak, S., Klymiuk, V., Byrns, B., Nilsen, K., Ens, J., Wiebe, K., Diaye, A. N., Hucl, P. J., Fu, B. X., … Shimizu, K. K. (2026). Purifying selection on deleterious variants affected by the combination of subgenomes and gene expression in bread wheat Cell Reports, 116785. https://doi.org/10.1016/j.celrep.2025.116785

• 2025

  • Jung, K., Akiyama, R., Nie, J., Nitta, M., Hamaya, N.-B., Qureshi, N., Bhavani, S., Wicker, T., Keller, B., Kishii, M., Nasuda, S., & Shimizu, K. K. (2025). Unveiling yellow rust resistance in the near-Himalayan region: insights from a nested association mapping study TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 138, 135. https://doi.org/10.1007/s00122-025-04886-z
  • Guérin, A., Levasseur, C., Herger, A., Renggli, D., Sotiropoulos, A. G., Kadler, G., Hou, X., Schaufelberger, M., Meyer, C., Wicker, T., Bigler, L., & Ringli, C. (2025). Histidine limitation alters plant development and influences the TOR network Journal of Experimental Botany, 76, 1085–1098. https://doi.org/10.1093/jxb/erae479

• 2024

  • Sotiropoulos, A. G., Sánchez-Martín, J., Widrig, V., Isaksson, J., Bernasconi, Z., Koller, T., Bearth, G., Herren, G., Wicker, T., & Keller, B. (2024). A fictional field case study to understand the genetic basis of host-fungal pathogen interactions using the wheat powdery mildew-wheat pathosystem Journal of Biological Education, 58, 1022–1034. https://doi.org/10.1080/00219266.2022.2147574
  • Bernasconi, Z. M. L. B. (2024). Race-Specific Resistance Mechanisms and Evasion from Recognition: Insights from the Wheat-Powdery Mildew Pathosystem (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-263214
  • Russo, A., Alessandrini, M., El Baidouri, M., Frei, D., Galise, T. R., Gaidusch, L., Oertel, H. F., Garcia Morales, S. E., Potente, G., Tian, Q., Smetanin, D., Bertrand, J. A. M., Onstein, R. E., Panaud, O., Frey, J. E., Cozzolino, S., Wicker, T., Xu, S., Grossniklaus, U., & Schlüter, P. M. (2024). Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation Nature Communications, 15, 6308. https://doi.org/10.1038/s41467-024-50622-4
  • Leber, R. (2024). Genetic Diversity and Powdery Mildew Resistance of Bread Wheat Landraces (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-261321
  • Gupta, S., Guérin, A., Herger, A., Hou, X., Schaufelberger, M., Roulard, R., Diet, A., Roffler, S., Lefebvre, V., Wicker, T., Pelloux, J., & Ringli, C. (2024). Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module PLoS Genetics, 20, e1011087. https://doi.org/10.1371/journal.pgen.1011087

• 2023

  • Manser, B., Zbinden, H., Herren, G., Steger, J., Isaksson, J., Bräunlich, S., Wicker, T., & Keller, B. (2023). Wheat zinc finger protein TaZF interacts with both the powdery mildew AvrPm2 protein and the corresponding wheat Pm2a immune receptor Plant Communications, online. https://doi.org/10.1016/j.xplc.2023.100769
  • Sharma, P. K., Ahmed, H. I., Heuberger, M., Koo, D.-H., Quiroz-Chavez, J., Adhikari, L., Raupp, J., Cauet, S., Rodde, N., Cravero, C., Callot, C., Yadav, I. S., Kathiresan, N., Athiyannan, N., Ramirez-Gonzalez, R. H., Uauy, C., Wicker, T., Abrouk, M., Gu, Y. Q., … Tiwari, V. K. (2023). An online database for einkorn wheat to aid in gene discovery and functional genomics studies Database, 2023, baad079. https://doi.org/10.1093/database/baad079
  • Saripalli, G., Adhikari, L., Amos, C., Kibriya, A., Ahmed, H. I., Heuberger, M., Raupp, J., Athiyannan, N., Wicker, T., Abrouk, M., Wallace, S., Hosseinirad, S., Chhuneja, P., Livesay, J., Rawat, N., Krattinger, S. G., Poland, J., & Tiwari, V. (2023). Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits Communications Biology, 6, online. https://doi.org/10.1038/s42003-023-05189-z
  • Ahmed, H. I., Heuberger, M., Schoen, A., Koo, D.-H., Quiroz-Chavez, J., Adhikari, L., Raupp, J., Cauet, S., Rodde, N., Cravero, C., Callot, C., Lazo, G. R., Kathiresan, N., Sharma, P. K., Moot, I., Yadav, I. S., Singh, L., Saripalli, G., Rawat, N., … Krattinger, S. G. (2023). Einkorn genomics sheds light on history of the oldest domesticated wheat Nature, 620, 830–838. https://doi.org/10.1038/s41586-023-06389-7
  • Poretti, M., Praz, C. R., Sotiropoulos, A. G., & Wicker, T. (2023). A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material Plant Direct, 7, e484. https://doi.org/10.1002/pld3.484
  • Russo, A. (2023). The genome assembly of Ophrys sphegodes to explore the genomic basis of rapid evolution in a mediterranean orchid (Dissertation, University of Zurich)

• 2022

  • Sotiropoulos, A. G., Arango-Isaza, E., Ban, T., Barbieri, C., Bourras, S., Cowger, C., Czembor, P. C., Ben-David, R., Dinoor, A., Ellwood, S. R., Graf, J., Hatta, K., Helguera, M., Sánchez-Martín, J., McDonald, B. A., Morgounov, A. I., Müller, M. C., Shamanin, V., Shimizu, K. K., … Wicker, T. (2022). Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade Nature Communications, 13, 4315. https://doi.org/10.1038/s41467-022-31975-0
  • Wicker, T., Stritt, C., Sotiropoulos, A. G., Poretti, M., Pozniak, C. J., Walkowiak, S., Gundlach, H., & Stein, N. (2022). Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons Advanced Genetics, 3, 2100022. https://doi.org/10.1002/ggn2.202100022
  • Sotiropoulos, A. G. (2022). Global population analyses of wheat powdery mildew using whole genome sequencing data (Dissertation, University of Zurich)

• 2021

  • Kolodziej, M. C., Singla, J., Sánchez-Martín, J., Zbinden, H., Šimková, H., Karafiátová, M., Doležel, J., Gronnier, J., Poretti, M., Glauser, G., Zhu, W., Köster, P., Zipfel, C., Wicker, T., Krattinger, S. G., & Keller, B. (2021). A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat Nature Communications, 12, 956. https://doi.org/10.1038/s41467-020-20777-x
  • Poretti, M., Sotiropoulos, A. G., Graf, J., Jung, E., Bourras, S., Krattinger, S. G., & Wicker, T. (2021). Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens Frontiers in Plant Science, 12, 720462. https://doi.org/10.3389/fpls.2021.720462
  • Oggenfuss, U., Badet, T., Wicker, T., Hartmann, F. E., Singh, N. K., Abraham, L., Karisto, P., Vonlanthen, T., Mundt, C., McDonald, B. A., & Croll, D. (2021). A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen ELife, 10, e69249. https://doi.org/10.7554/elife.69249
  • Mascher, M., Wicker, T., Jenkins, J., Plott, C., Lux, T., Koh, C. S., Ens, J., Gundlach, H., Boston, L. B., Tulpová, Z., Holden, S., Hernández-Pinzón, I., Scholz, U., Mayer, K. F. X., Spannagl, M., Pozniak, C. J., Sharpe, A. G., Šimková, H., Moscou, M. J., … Stein, N. (2021). Long-read sequence assembly: a technical evaluation in barley Plant Cell, 33, 1888–1906. https://doi.org/10.1093/plcell/koab077
  • Rabanus-Wallace, M. T., Hackauf, B., Mascher, M., Lux, T., Wicker, T., Gundlach, H., Baez, M., Houben, A., et al, Praz, C. R., & Keller, B. (2021). Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential Nature Genetics, 53, 564–573. https://doi.org/10.1038/s41588-021-00807-0
  • Yang, P., Scheuermann, D., Kessel, B., Koller, T., Greenwood, J. R., Hurni, S., Herren, G., Zhou, S., Marande, W., Wicker, T., Krattinger, S. G., Ouzunova, M., & Keller, B. (2021). Alleles of a wall‐associated kinase gene account for three of the major northern corn leaf blight resistance loci in maize The Plant Journal, 106, 526–535. https://doi.org/10.1111/tpj.15183
  • Sánchez-Martín, J., Widrig, V., Herren, G., Wicker, T., Zbinden, H., Gronnier, J., Spörri, L., Praz, C. R., Heuberger, M., Kolodziej, M. C., Isaksson, J., Steuernagel, B., Karafiátová, M., Doležel, J., Zipfel, C., & Keller, B. (2021). Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins Nature Plants, 7, 327–341. https://doi.org/10.1038/s41477-021-00869-2
  • Poretti, M. (2021). Comparative genomics and transcriptomics of Triticeae (Dissertation, University of Zurich)
  • Kolodziej, M. C. (2021). The use of a high-quality genome from the Swiss winter wheat line ArinaLrFor: genomic structure and isolation of leaf rust resistance genes (Dissertation, University of Zurich)
  • Müller, M. C. (2021). Genomic and genetic analysis of host and cultivar adaption in the cereal powdery mildew pathosystem (Dissertation, University of Zurich)

• 2020

  • Walkowiak, S., Gao, L., Monat, C., et al, Kolodziej, M. C., Copetti, D., Krattinger, S. G., Keller, B., Wicker, T., Halstead-Nussloch, G., Paape, T., Shimizu-Inatsugi, R., & Shimizu, K. K. (2020). Multiple wheat genomes reveal global variation in modern breeding Nature, 588, 277–283. https://doi.org/10.1038/s41586-020-2961-x
  • Abrouk, M., Ahmed, H. I., Cubry, P., Šimoníková, D., Cauet, S., Pailles, Y., Bettgenhaeuser, J., Gapa, L., Scarcelli, N., Couderc, M., Zekraoui, L., Kathiresan, N., Čížková, J., Hřibová, E., Doležel, J., Arribat, S., Bergès, H., Wieringa, J. J., Gueye, M., … Krattinger, S. G. (2020). Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate Nature Communications, 11, 4488. https://doi.org/10.1038/s41467-020-18329-4
  • Schaefer, L. K., Parlange, F., Buchmann, G., Jung, E., Wehrli, A., Herren, G., Müller, M. C., Stehlin, J., Schmid, R., Wicker, T., Keller, B., & Bourras, S. (2020). Cross-kingdom RNAi of pathogen effectors leads to quantitative adult plant resistance in wheat Frontiers in Plant Science, 11, 253. https://doi.org/10.3389/fpls.2020.00253

• 2019

  • Müller, M. C., Praz, C. R., Sotiropoulos, A. G., Menardo, F., Kunz, L., Schudel, S., Oberhänsli, S., Poretti, M., Wehrli, A., Bourras, S., Keller, B., & Wicker, T. (2019). A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew New Phytologist, 221, 2176–2189. https://doi.org/10.1111/nph.15529
  • Thalmann, M., Coiro, M., Meier, T., Wicker, T., Zeeman, S. C., & Santelia, D. (2019). The evolution of functional complexity within the β-amylase gene family in land plants BMC Evolutionary Biology, 19:66. https://doi.org/10.1186/s12862-019-1395-2

• 2013

  • Oberhänsli, S. (2013). A reference sequence for Blumeria graminis f. sp. tritici (wheat powdery mildew) and its application for comparative and evolutionary genomics (Dissertation, University of Zurich) https://doi.org/10.5167/uzh-89957