Publications

ZORA Publication List

Publications

• 2025

  • Jung, Katharina; Akiyama, Reiko; Nie, Jilu; Nitta, Miyuki; Hamaya, Naoto-Benjamin; Qureshi, Naeela; Bhavani, Sridhar; Wicker, Thomas; Keller, Beat; Kishii, Masahiro; Nasuda, Shuhei; Shimizu, Kentaro 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(7):135.
  • Guérin, Amandine; Levasseur, Caroline; Herger, Aline; Renggli, Dominik; Sotiropoulos, Alexandros Georgios; Kadler, Gabor; Hou, Xiaoyu; Schaufelberger, Myriam; Meyer, Christian; Wicker, Thomas; Bigler, Laurent; Ringli, Christoph (2025). Histidine limitation alters plant development and influences the TOR network Journal of Experimental Botany, 76(4):1085-1098.

• 2024

  • Sotiropoulos, Alexandros G; Sánchez-Martín, Javier; Widrig, Victoria; Isaksson, Jonatan; Bernasconi, Zoe; Koller, Teresa; Bearth, Giulia; Herren, Gerhard; Wicker, Thomas; Keller, Beat (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(5):1022-1034.
  • Bernasconi, Zoe Maria Luisa Bartolomea . Race-Specific Resistance Mechanisms and Evasion from Recognition: Insights from the Wheat-Powdery Mildew Pathosystem 2024, University of Zurich, Faculty of Science.
  • Russo, Alessia; Alessandrini, Mattia; El Baidouri, Moaine; Frei, Daniel; Galise, Teresa Rosa; Gaidusch, Lara; Oertel, Hannah F; Garcia Morales, Sara E; Potente, Giacomo; Tian, Qin; Smetanin, Dmitry; Bertrand, Joris A M; Onstein, Renske E; Panaud, Olivier; Frey, Jürg E; Cozzolino, Salvatore; Wicker, Thomas; Xu, Shuqing; Grossniklaus, Ueli; Schlüter, Philipp M (2024). Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation Nature Communications, 15(1):6308.
  • Leber, Rebecca . Genetic Diversity and Powdery Mildew Resistance of Bread Wheat Landraces 2024, University of Zurich, Faculty of Science.
  • Gupta, Shibu; Guérin, Amandine; Herger, Aline; Hou, Xiaoyu; Schaufelberger, Myriam; Roulard, Romain; Diet, Anouck; Roffler, Stefan; Lefebvre, Valérie; Wicker, Thomas; Pelloux, Jérôme; Ringli, Christoph (2024). Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module PLoS Genetics, 20(1):e1011087.

• 2023

  • Manser, Beatrice; Zbinden, Helen; Herren, Gerhard; Steger, Joel; Isaksson, Jonatan; Bräunlich, Stephanie; Wicker, Thomas; Keller, Beat (2023). Wheat zinc finger protein TaZF interacts with both the powdery mildew AvrPm2 protein and the corresponding wheat Pm2a immune receptor Plant Communications:online.
  • Sharma, Parva Kumar; Ahmed, Hanin Ibrahim; Heuberger, Matthias; Koo, Dal-Hoe; Quiroz-Chavez, Jesus; Adhikari, Laxman; Raupp, John; Cauet, Stéphane; Rodde, Nathalie; Cravero, Charlotte; Callot, Caroline; Yadav, Inderjit Singh; Kathiresan, Nagarajan; Athiyannan, Naveenkumar; Ramirez-Gonzalez, Ricardo H; Uauy, Cristobal; Wicker, Thomas; Abrouk, Michael; Gu, Yong Q; Poland, Jesse; Krattinger, Simon G; Lazo, Gerard R; Tiwari, Vijay K (2023). An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database, 2023:baad079.
  • Saripalli, Gautam; Adhikari, Laxman; Amos, Cameron; Kibriya, Ashraf; Ahmed, Hanin Ibrahim; Heuberger, Matthias; Raupp, John; Athiyannan, Naveenkumar; Wicker, Thomas; Abrouk, Michael; Wallace, Sydney; Hosseinirad, Seyedali; Chhuneja, Parveen; Livesay, Janelle; Rawat, Nidhi; Krattinger, Simon G; Poland, Jesse; Tiwari, Vijay (2023). Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits Communications Biology, 6(1):online.
  • Ahmed, Hanin Ibrahim; Heuberger, Matthias; Schoen, Adam; Koo, Dal-Hoe; Quiroz-Chavez, Jesus; Adhikari, Laxman; Raupp, John; Cauet, Stéphane; Rodde, Nathalie; Cravero, Charlotte; Callot, Caroline; Lazo, Gerard R; Kathiresan, Nagarajan; Sharma, Parva K; Moot, Ian; Yadav, Inderjit Singh; Singh, Lovepreet; Saripalli, Gautam; Rawat, Nidhi; Datla, Raju; Athiyannan, Naveenkumar; Ramirez-Gonzalez, Ricardo H; Uauy, Cristobal; Wicker, Thomas; Tiwari, Vijay K; Abrouk, Michael; Poland, Jesse; Krattinger, Simon G (2023). Einkorn genomics sheds light on history of the oldest domesticated wheat Nature, 620(7975):830-838.
  • Poretti, Manuel; Praz, Coraline R; Sotiropoulos, Alexandros G; Wicker, Thomas (2023). A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material Plant Direct, 7(3):e484.
  • Russo, Alessia . The genome assembly of Ophrys sphegodes to explore the genomic basis of rapid evolution in a mediterranean orchid 2023, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2022

  • Sotiropoulos, Alexandros G; Arango-Isaza, Epifanía; Ban, Tomohiro; Barbieri, Chiara; Bourras, Salim; Cowger, Christina; Czembor, Paweł C; Ben-David, Roi; Dinoor, Amos; Ellwood, Simon R; Graf, Johannes; Hatta, Koichi; Helguera, Marcelo; Sánchez-Martín, Javier; McDonald, Bruce A; Morgounov, Alexey I; Müller, Marion C; Shamanin, Vladimir; Shimizu, Kentaro K; Yoshihira, Taiki; Zbinden, Helen; Keller, Beat; Wicker, Thomas (2022). Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade Nature Communications, 13(1):4315.
  • Wicker, Thomas; Stritt, Christoph; Sotiropoulos, Alexandros G; Poretti, Manuel; Pozniak, Curtis J; Walkowiak, Sean; Gundlach, Heidrun; Stein, Nils (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(1):2100022.
  • Sotiropoulos, Alexandros Georgios . Global population analyses of wheat powdery mildew using whole genome sequencing data 2022, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2021

  • Kolodziej, Markus C; Singla, Jyoti; Sánchez-Martín, Javier; Zbinden, Helen; Šimková, Hana; Karafiátová, Miroslava; Doležel, Jaroslav; Gronnier, Julien; Poretti, Manuel; Glauser, Gaétan; Zhu, Wangsheng; Köster, Philipp; Zipfel, Cyril; Wicker, Thomas; Krattinger, Simon G; Keller, Beat (2021). A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat Nature Communications, 12:956.
  • Poretti, Manuel; Sotiropoulos, Alexandros G; Graf, Johannes; Jung, Esther; Bourras, Salim; Krattinger, Simon G; Wicker, Thomas (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.
  • Oggenfuss, Ursula; Badet, Thomas; Wicker, Thomas; Hartmann, Fanny E; Singh, Nikhil Kumar; Abraham, Leen; Karisto, Petteri; Vonlanthen, Tiziana; Mundt, Christopher; McDonald, Bruce A; Croll, Daniel (2021). A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen eLife, 10:e69249.
  • Mascher, Martin; Wicker, Thomas; Jenkins, Jerry; Plott, Christopher; Lux, Thomas; Koh, Chu Shin; Ens, Jennifer; Gundlach, Heidrun; Boston, Lori B; Tulpová, Zuzana; Holden, Samuel; Hernández-Pinzón, Inmaculada; Scholz, Uwe; Mayer, Klaus F X; Spannagl, Manuel; Pozniak, Curtis J; Sharpe, Andrew G; Šimková, Hana; Moscou, Matthew J; Grimwood, Jane; Schmutz, Jeremy; Stein, Nils (2021). Long-read sequence assembly: a technical evaluation in barley Plant Cell, 33(6):1888-1906.
  • Rabanus-Wallace, M Timothy; Hackauf, Bernd; Mascher, Martin; Lux, Thomas; Wicker, Thomas; Gundlach, Heidrun; Baez, Mariana; Houben, Andreas; et al; Praz, Coraline R; Keller, Beat (2021). Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential Nature Genetics, 53(4):564-573.
  • Yang, Ping; Scheuermann, Daniela; Kessel, Bettina; Koller, Teresa; Greenwood, Julian R; Hurni, Severine; Herren, Gerhard; Zhou, Shenghui; Marande, William; Wicker, Thomas; Krattinger, Simon G; Ouzunova, Milena; Keller, Beat (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(2):526-535.
  • Sánchez-Martín, Javier; Widrig, Victoria; Herren, Gerhard; Wicker, Thomas; Zbinden, Helen; Gronnier, Julien; Spörri, Laurin; Praz, Coraline R; Heuberger, Matthias; Kolodziej, Markus C; Isaksson, Jonatan; Steuernagel, Burkhard; Karafiátová, Miroslava; Doležel, Jaroslav; Zipfel, Cyril; Keller, Beat (2021). Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins Nature Plants, 7(3):327-341.
  • Müller, Marion Claudia . Genomic and genetic analysis of host and cultivar adaption in the cereal powdery mildew pathosystem 2021, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Kolodziej, Markus C . The use of a high-quality genome from the Swiss winter wheat line ArinaLrFor: genomic structure and isolation of leaf rust resistance genes 2021, University of Zurich, Faculty of Science.
  • Poretti, Manuel . Comparative genomics and transcriptomics of Triticeae 2021, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2020

  • Walkowiak, Sean; Gao, Liangliang; Monat, Cecile; et al; Kolodziej, Markus C; Copetti, Dario; Krattinger, Simon G; Keller, Beat; Wicker, Thomas; Halstead-Nussloch, Gwyneth; Paape, Timothy; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K (2020). Multiple wheat genomes reveal global variation in modern breeding Nature, 588(7837):277-283.
  • Abrouk, Michael; Ahmed, Hanin Ibrahim; Cubry, Philippe; Šimoníková, Denisa; Cauet, Stéphane; Pailles, Yveline; Bettgenhaeuser, Jan; Gapa, Liubov; Scarcelli, Nora; Couderc, Marie; Zekraoui, Leila; Kathiresan, Nagarajan; Čížková, Jana; Hřibová, Eva; Doležel, Jaroslav; Arribat, Sandrine; Bergès, Hélène; Wieringa, Jan J; Gueye, Mathieu; Kane, Ndjido A; Leclerc, Christian; Causse, Sandrine; Vancoppenolle, Sylvie; Billot, Claire; Wicker, Thomas; Vigouroux, Yves; Barnaud, Adeline; Krattinger, Simon G (2020). Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate Nature Communications, 11(1):4488.
  • Schaefer, Luisa Katharina; Parlange, Francis; Buchmann, Gabriele; Jung, Esther; Wehrli, Andreas; Herren, Gerhard; Müller, Marion Claudia; Stehlin, Jonas; Schmid, Roman; Wicker, Thomas; Keller, Beat; Bourras, Salim (2020). Cross-kingdom RNAi of pathogen effectors leads to quantitative adult plant resistance in wheat Frontiers in Plant Science, 11:253.

• 2019

  • Müller, Marion C; Praz, Coraline R; Sotiropoulos, Alexandros G; Menardo, Fabrizio; Kunz, Lukas; Schudel, Seraina; Oberhänsli, Simone; Poretti, Manuel; Wehrli, Andreas; Bourras, Salim; Keller, Beat; Wicker, Thomas (2019). A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew New Phytologist, 221(4):2176-2189.
  • Thalmann, Matthias; Coiro, Mario; Meier, Tiago; Wicker, Thomas; Zeeman, Samuel C; Santelia, Diana (2019). The evolution of functional complexity within the β-amylase gene family in land plants BMC Evolutionary Biology:19:66.

• 2013

  • Oberhänsli, Simone . A reference sequence for Blumeria graminis f. sp. tritici (wheat powdery mildew) and its application for comparative and evolutionary genomics 2013, University of Zurich, Faculty of Science.