Publications

ZORA Publication List

Publications

• 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.
  • 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.
  • 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.

• 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.
  • Müller, Marion C; Kunz, Lukas; Schudel, Seraina; Lawson, Aaron W; Kammerecker, Sandrine; Isaksson, Jonatan; Wyler, Michele; Graf, Johannes; Sotiropoulos, Alexandros G; Praz, Coraline R; Manser, Beatrice; Wicker, Thomas; Bourras, Salim; Keller, Beat (2022). Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat. Proceedings of the National Academy of Sciences of the United States of America, 119(30):e2108808119.
  • 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.

• 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.
  • 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.
  • 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.
  • Shimizu, Kentaro K; Copetti, Dario; Okada, Moeko; Wicker, Thomas; Tameshige, Toshiaki; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Aquino, Catharine; et al (2021). De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes. Plant & Cell Physiology, 62(1):8-27.
  • Schumacher, Isabel; Ndinyanka Fabrice, Tohnyui; Abdou, Marie-Therese; Kuhn, Benjamin M; Voxeur, Aline; Herger, Aline; Roffler, Stefan; Bigler, Laurent; Wicker, Thomas; Ringli, Christoph (2021). Defects in Cell Wall Differentiation of the Arabidopsis Mutant rol1-2 Is Dependent on Cyclin-Dependent Kinase CDK8. Cells, 10(3):685.
  • 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.

• 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.
  • Poretti, Manuel; Praz, Coraline Rosalie; Meile, Lukas; Kälin, Carol; Schaefer, Luisa Katharina; Schläfli, Michael; Widrig, Victoria; Sanchez-Vallet, Andrea; Wicker, Thomas; Bourras, Salim (2020). Domestication of high-copy transposons underlays the wheat small RNA response to an obligate pathogen. Molecular Biology and Evolution, 37(3):839-848.

• 2019

  • Monat, Cécile; Padmarasu, Sudharsan; Lux, Thomas; Wicker, Thomas; Gundlach, Heidrun; Himmelbach, Axel; Ens, Jennifer; Li, Chengdao; Muehlbauer, Gary J; Schulman, Alan H; Waugh, Robbie; Braumann, Ilka; Pozniak, Curtis; Scholz, Uwe; Mayer, Klaus F X; Spannagl, Manuel; Stein, Nils; Mascher, Martin (2019). TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biology, 20:284.
  • Bourras, Salim; Kunz, Lukas; Xue, Minfeng; Praz, Coraline Rosalie; Müller, Marion Claudia; Kälin, Carol; Schläfli, Michael; Ackermann, Patrick; Flückiger, Simon; Parlange, Francis; Menardo, Fabrizio; Schaefer, Luisa Katharina; Ben-David, Roi; Roffler, Stefan; Oberhaensli, Simone; Widrig, Victoria; Lindner, Stefan; Isaksson, Jonatan; Wicker, Thomas; Yu, Dazhao; Keller, Beat (2019). The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nature Communications, 10(1):2292-2308.
  • Izuno, Ayako; Wicker, Thomas; Hatakeyama, Masaomi; Copetti, Dario; Shimizu, Kentaro K (2019). Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence. G3 : Genes, Genomes, Genetics, 9(11):3513-3520.
  • Schaufelberger, Myriam; Galbier, Florian; Herger, Aline; de Brito Francisco, Rita; Roffler, Stefan; Clement, Gilles; Diet, Anouck; Hörtensteiner, Stefan; Wicker, Thomas; Ringli, Christoph (2019). Mutations in the Arabidopsis ROL17/isopropylmalate synthase 1 locus alter amino acid content, modify the TOR network, and suppress the root hair cell development mutant lrx1. Journal of Experimental Botany, 70(8):2313-2323.
  • 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.

• 2018

  • Thind, Anupriya Kaur; Wicker, Thomas; Müller, Thomas; Ackermann, Patrick M; Steuernagel, Burkhard; Wulff, Brande B H; Spannagl, Manuel; Twardziok, Sven O; Felder, Marius; Lux, Thomas; Mayer, Klaus F X; Keller, Beat; Krattinger, Simon G (2018). Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars. Genome Biology, 19:104.
  • Keller, Beat; Wicker, Thomas; Krattinger, Simon G (2018). Advances in Wheat and Pathogen Genomics: Implications for Disease Control. Annual Review of Phytopathology, 56(1):67-87.
  • Praz, Coraline R; Menardo, Fabrizio; Robinson, Mark D; Müller, Marion C; Wicker, Thomas; Bourras, Salim; Keller, Beat (2018). Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. Frontiers in Plant Science, 9:49.
  • Stritt, Christoph; Gordon, Sean P; Wicker, Thomas; Vogel, John P; Roulin, Anne C (2018). Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the mediterranean grass brachypodium distachyon. Genome Biology and Evolution, 10(1):304-318.
  • Ma, Xin; Keller, Beat; McDonald, Bruce A; Palma-Guerrero, Javier; Wicker, Thomas (2018). Comparative transcriptomics reveals how wheat responds to infection by Zymoseptoria tritici. Molecular Plant-Microbe Interactions, 31(4):420-431.

• 2017

  • Wicker, Thomas; Schulman, Alan H; Tanskanen, Jaakko; Spannagl, Manuel; Twardziok, Sven; Mascher, Martin; Springer, Nathan M; Li, Qing; Waugh, Robbie; Li, Chengdao; Zhang, Guoping; Stein, Nils; Mayer, Klaus F. X; Gundlach, Heidrun (2017). The repetitive landscape of the 5100 Mbp barley genome. Mobile DNA:8:22.
  • Praz, Coraline R; Bourras, Salim; Zeng, Fansong; Sánchez-Martín, Javier; Menardo, Fabrizio; Xue, Minfeng; Yang, Lijun; Roffler, Stefan; Böni, Rainer; Herren, Gerard; McNally, Kaitlin E; Ben-David, Roi; Parlange, Francis; Oberhaensli, Simone; Flückiger, Simon; Schäfer, Luisa K; Wicker, Thomas; Yu, Dazhao; Keller, Beat (2017). AvrPm2 encodes an RNase-like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. New Phytologist, 213(3):1301-1314.
  • Luo, Ming-Cheng; Gu, Yong Q; et al; Wicker, Thomas; Dvořák, Jan (2017). Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature:498-502.
  • Menardo, Fabrizio; Praz, Coraline R; Wicker, Thomas; Keller, Beat (2017). Rapid turnover of effectors in grass powdery mildew (Blumeria graminis). BMC Evolutionary Biology, 17(1):223.
  • Thind, Anupriya K; Wicker, Thomas; Krattinger, Simon G (2017). Rapid identification of rust resistance genes through cultivar-specific de novo chromosome assemblies. In: Periyannan, Sam. Wheat Rust Diseases. New York, NY: Springer, 245-255.
  • Baumgartner, Michael; Roffler, Stefan; Wicker, Thomas; Pernthaler, Jakob (2017). Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment. The ISME journal, 11(10):2258-2266.
  • Thind, Anupriya Kaur; Wicker, Thomas; Šimková, Hana; Fossati, Dario; Moullet, Odile; Brabant, Cécile; Vrána, Jan; Doležel, Jaroslav; Krattinger, Simon G (2017). Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nature Biotechnology, 35(8):793-796.
  • Mascher, Martin; Gundlach, Heidrun; et al; Wicker, Thomas; Stein, Nils (2017). A chromosome conformation capture ordered sequence of the barley genome. Nature, 544(7651):427-433.
  • Hyles, J; Vautrin, S; Pettolino, F; MacMillan, C; Stachurski, Z; Breen, J; Berges, H; Wicker, T; Spielmeyer, W (2017). Repeat-length variation in a wheat cellulose synthase-like gene is associated with altered tiller number and stem cell wall composition. Journal of Experimental Botany, 68(7):1519-1529.
  • Menardo, Fabrizio; Wicker, Thomas; Keller, Beat (2017). Reconstructing the evolutionary history of powdery mildew lineages (Blumeria graminis) at different evolutionary time scales with NGS data. Genome Biology and Evolution, 9(2):446-456.
  • Qureshi, Naeela; Bariana, Harbans; Forrest, Kerrie; Hayden, Matthew; Keller, Beat; Wicker, Thomas; Faris, Justin; Salina, Elena; Bansal, Urmil (2017). Fine mapping of the chromosome 5B region carrying closely linked rust resistance genes Yr47 and Lr52 in wheat. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 130(3):495-504.
  • Singla, Jyoti; Lüthi, Linda; Wicker, Thomas; Bansal, Urmil; Krattinger, Simon G; Keller, Beat (2017). Characterization of Lr75: a partial, broad-spectrum leaf rust resistance gene in wheat. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 130(1):1-12.

• 2016

  • Sánchez-Martín, Javier; Steuernagel, Burkhard; Ghosh, Sreya; Herren, Gerhard; Hurni, Severine; Adamski, Nikolai; Vrána, Jan; Kubaláková, Marie; Krattinger, Simon G; Wicker, Thomas; Doležel, Jaroslav; Keller, Beat; Wulff, Brande B H (2016). Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biology, 17(1):221.
  • Ben-David, Roi; Parks, Ryan; Dinoor, Amos; Kosman, Evsey; Wicker, Thomas; Keller, Beat; Cowger, Christina (2016). Differentiation among blumeria graminis f. sp.tritici isolates originating from wild versus domesticated triticum species in Israel. Phytopathology, 106(8):861-870.
  • Bourras, Salim; McNally, Kaitlin E; Müller, Marion C; Wicker, Thomas; Keller, Beat (2016). Avirulence Genes in Cereal Powdery Mildews: The Gene-for-Gene Hypothesis 2.0. Frontiers in Plant Science:7:241.
  • Kamber, Tim; Buchmann, Jan P; Pothier, Joël F; Smits, Theo H M; Wicker, Thomas; Duffy, Brion (2016). Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection. Scientific Reports, 6:21600.
  • Wicker, Thomas; Yu, Yeisoo; Haberer, Georg; Mayer, Klaus F X; Marri, Pradeep Reddy; Rounsley, Steve; Chen, Mingsheng; Zuccolo, Andrea; Panaud, Olivier; Wing, Rod A; Roffler, Stefan (2016). DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nature Communications, 7:12790.
  • Pinto-Carbó, Marta; Sieber, Simon; Dessein, Steven; Wicker, Thomas; Verstraete, Brecht; Gademann, Karl; Eberl, Leo; Carlier, Aurelien (2016). Evidence of horizontal gene transfer between obligate leaf nodule symbionts. The ISME journal, 10(9):2092-2105.
  • Shi, Gongjun; Zhang, Zengcui; Friesen, Timothy L; Bansal, Urmil; Cloutier, Sylvie; Wicker, Thomas; Rasmussen, Jack B; Faris, Justin D (2016). Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Molecular Genetics and Genomics, 291(1):107-119.
  • Menardo, Fabrizio; Praz, Coraline R; Wyder, Stefan; Ben-David, Roi; Bourras, Salim; Matsumae, Hiromi; McNally, Kaitlin E; Parlange, Francis; Riba, Andrea; Roffler, Stefan; Schaefer, Luisa K; Shimizu, Kentaro K; Valenti, Luca; Zbinden, Helen; Wicker, Thomas; Keller, Beat (2016). Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nature Genetics, 48(2):201-205.

• 2015

  • Roffler, Stefan; Menardo, Fabrizio; Wicker, Thomas (2015). The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants. Mobile DNA:6:23.
  • Roffler, Stefan; Wicker, Thomas (2015). Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons. Mobile DNA, 6(8):online.
  • Hurni, Severine; Scheuermann, Daniela; Krattinger, Simon G; Kessel, Bettina; Wicker, Thomas; Herren, Gerhard; Fitze, Mirjam N; Breen, James; Presterl, Thomas; Ouzunova, Milena; Keller, Beat (2015). The maize disease resistance geneHtn1against northern corn leaf blight encodes a wall-associated receptor-like kinase. Proceedings of the National Academy of Sciences of the United States of America, 112(28):8780-8785.
  • Chhuneja, Parveen; Yadav, Bharat; Stirnweis, Daniel; Hurni, Severine; Kaur, Satinder; Elkot, Ahmed Fawzy; Keller, Beat; Wicker, Thomas; Sehgal, Sunish; Gill, Bikram S; Singh, Kuldeep (2015). Fine mapping of powdery mildew resistance genes PmTb7A.1 and PmTb7A.2 in Triticum boeoticum (Boiss.) using the shotgun sequence assembly of chromosome 7AL. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 128(10):2099-2111.
  • Parlange, Francis; Roffler, Stefan; Menardo, Fabrizio; Ben-David, Roi; Bourras, Salim; McNally, Kaitlin E; Oberhaensli, Simone; Stirnweis, Daniel; Buchmann, Gabriele; Wicker, Thomas; Keller, Beat (2015). Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles. Fungal Genetics and Biology, 82:181-192.
  • Copetti, Dario; Zhang, Jianwei; El Baidouri, Moaine; Gao, Dongying; Wang, Jun; Barghini, Elena; Cossu, Rosa M; Angelova, Angelina; Maldonado L, Carlos E; Roffler, Stefan; Ohyanagi, Hajime; Wicker, Thomas; Fan, Chuanzhu; Zuccolo, Andrea; Chen, Mingsheng; Costa de Oliveira, Antonio; Han, Bin; Henry, Robert; Hsing, Yue-ie; Kurata, Nori; Wang, Wen; Jackson, Scott A; Panaud, Olivier; Wing, Rod A (2015). RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16(538):online.
  • Pourkheirandish, Mohammad; Hensel, Goetz; Kilian, Benjamin; Senthil, Natesan; Chen, Guoxiong; Sameri, Mohammad; Azhaguvel, Perumal; Sakuma, Shun; Dhanagond, Sidram; Sharma, Rajiv; Mascher, Martin; Himmelbach, Axel; Gottwald, Sven; Nair, Sudha K; Tagiri, Akemi; Yukuhiro, Fumiko; Nagamura, Yoshiaki; Kanamori, Hiroyuki; Matsumoto, Takashi; Willcox, George; Middleton, Christopher P; Wicker, Thomas; Walther, Alexander; Waugh, Robbie; Fincher, Geoffrey B; Stein, Nils; Kumlehn, Jochen; Sato, Kazuhiro; Komatsuda, Takao (2015). Evolution of the Grain Dispersal System in Barley. Cell, 162(3):527-539.
  • Wicker, Thomas; Wing, Rod A; Schubert, Ingo (2015). Recurrent sequence exchange between homeologous grass chromosomes. The Plant Journal, 84(4):747-759.
  • Bourras, Salim; McNally, Kaitlin Elyse; Ben-David, Roi; Parlange, Francis; Roffler, Stefan; Praz, Coraline Rosalie; Oberhaensli, Simone; Menardo, Fabrizio; Stirnweis, Daniel; Frenkel, Zeev; Schaefer, Luisa Katharina; Flückiger, Simon; Treier, Georges; Herren, Gerhard; Korol, Abraham B; Wicker, Thomas; Keller, Beat (2015). Multiple Avirulence Loci and Allele-Specific Effector Recognition Control thePm3Race-Specific Resistance of Wheat to Powdery Mildew. Plant Cell, 27(10):2991-3012.
  • Amselem, Joelle; Vigouroux, Marielle; Oberhaensli, Simone; Brown, James K M; Bindschedler, Laurence V; Skamnioti, Pari; Wicker, Thomas; Spanu, Pietro D; Quesneville, Hadi; Sacristán, Soledad (2015). Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics, 16(917):online.
  • Chauhan, Harsh; Boni, Rainer; Bucher, Rahel; Kuhn, Benjamin; Buchmann, Gabriele; Sucher, Justine; Selter, Liselotte L; Hensel, Goetz; Kumlehn, Jochen; Bigler, Laurent; Glauser, Gaëtan; Wicker, Thomas; Krattinger, Simon G; Keller, Beat (2015). The wheat resistance gene Lr34 results in the constitutive induction of multiple defense pathways in transgenic barley. The Plant Journal, 84(1):202-215.

• 2014

  • Song, Won-Yong; Mendoza-Cózatl, David G; Lee, Youngsook; Schroeder, Julian I; Ahn, Sang-Nag; Lee, Hyun-Sook; Wicker, Thomas; Martinoia, Enrico (2014). Phytochelatin-metal(loid) transport into vacuoles shows different substrate preferences in barley and Arabidopsis. Plant, Cell & Environment, 37(5):1192-1201.
  • Wang, Muhua; Yu, Yeisoo; Haberer, Georg; Marri, Pradeep Reddy; Fan, Chuanzhu; Goicoechea, Jose Luis; Zuccolo, Andrea; Song, Xiang; Kudrna, Dave; Ammiraju, Jetty S S; Cossu, Rosa Maria; Maldonado, Carlos; Chen, Jinfeng; Lee, Seunghee; Sisneros, Nick; de Baynast, Kristi; Golser, Wolfgang; Wissotski, Marina; Kim, Woojin; Sanchez, Paul; Ndjiondjop, Marie-Noelle; Sanni, Kayode; Long, Manyuan; Carney, Judith; Panaud, Olivier; Wicker, Thomas; Machado, Carlos A; Chen, Mingsheng; Mayer, Klaus F X; Rounsley, Steve; Wing, Rod A (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46(9):982-988.
  • Buchmann, Jan P; Löytynoja, Ari; Wicker, Thomas; Schulman, Alan H (2014). Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts. Mobile DNA, 5:24.
  • Bansal, Urmil; Bariana, Harbans; Wong, Debbie; Randhawa, Mandeep; Wicker, Thomas; Hayden, Matthew; Keller, Beat (2014). Molecular mapping of an adult plant stem rust resistance gene Sr56 in winter wheat cultivar Arina. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 127(6):1441-1448.
  • Shatalina, Margarita; Messmer, Monika; Feuillet, Catherine; Mascher, Fabio; Paux, Etienne; Choulet, Frédéric; Wicker, Thomas; Keller, Beat (2014). High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 127(3):573-586.
  • Middleton, Christopher P; Senerchia, Natacha; Stein, Nils; Akhunov, Eduard D; Keller, Beat; Wicker, Thomas; Kilian, Benjamin (2014). Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe. PLoS ONE, 9(3):e85761.

• 2013

  • Middleton, Christopher P; Stein, Nils; Keller, Beat; Kilian, Benjamin; Wicker, Thomas (2013). Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity. The Plant Journal, 73(2):347-356.
  • Grob, Stefan; Schmid, Marc W; Luedtke, Nathan W; Wicker, Thomas; Grossniklaus, Ueli (2013). Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biology, 14:R129.
  • Buchmann, J P; Wicker, T; Keller, B (2013). Transposons in cereals: shaping genomes and driving their evolution. In: Gupta, P K; Varshney, P K. Cereal Genomics II. Dordrecht: Springer Science+Business Media Dordrecht, 127-154.
  • Raats, Dina; Frenkel, Zeev; Krugman, Tamar; Dodek, Itay; Sela, Hanan; Šimková, Hana; Magni, Federica; Cattonaro, Federica; Vautrin, Sonia; Bergès, Hélène; Wicker, Thomas; Keller, Beat; Leroy, Philippe; Philippe, Romain; Paux, Etienne; Doležel, Jaroslav; Feuillet, Catherine; Korol, Abraham; Fahima, Tzion (2013). The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biology, 14(12):R138.
  • Breen, James; Wicker, Thomas; Shatalina, Margarita; Frenkel, Zeev; Bertin, Isabelle; Philippe, Romain; Spielmeyer, Wolfgang; Šimková, Hana; Šafář, Jan; Cattonaro, Federica; Scalabrin, Simone; Magni, Federica; Vautrin, Sonia; Bergès, Hélène; Paux, Etienne; Fahima, Tzion; Doležel, Jaroslav; Korol, Abraham; Feuillet, Catherine; Keller, Beat (2013). A physical map of the short arm of wheat chromosome 1A. PLoS ONE, 8(11):e80272.
  • Hurni, Severine; Brunner, Susanne; Buchmann, Gabriele; Herren, Gerhard; Jordan, Tina; Krukowski, Patricia; Wicker, Thomas; Yahiaoui, Nabila; Mago, Rohit; Keller, Beat (2013). RyePm8and wheatPm3are orthologous genes and show evolutionary conservation of resistance function against powdery mildew. The Plant Journal, 76(6):957-969.
  • Wicker, Thomas; Oberhaensli, Simone; Parlange, Francis; Buchmann, Jan P; Shatalina, Margarita; Roffler, Stefan; Ben-David, Roi; Doležel, Jaroslav; Šimkova, Hana; Schulze-Lefert, Paul; Spanu, Pietro D; Bruggmann, Rémy; Amselem, Joelle; Quesneville, Hadi; van Themaat, Emiel Ver Loren; Paape, Timothy; Shimizu, Kentaro K; Keller, Beat (2013). The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature Genetics, 45(9):1092-1096.
  • Shatalina, Margarita; Wicker, Thomas; Buchmann, Jan P; Oberhaensli, Simone; Simková, Hana; Doležel, Jaroslav; Keller, Beat (2013). Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno. Plant biotechnology journal, 11(1):23-32.

• 2012

  • D'Hont, Angélique; Denoeud, France; Aury, Jean-Marc; Baurens, Franc-Christophe; Carreel, Françoise; Garsmeur, Olivier; Noel, Benjamin; Bocs, Stéphanie; Droc, Gaëtan; Rouard, Mathieu; Da Silva, Corinne; Jabbari, Kamel; Cardi, Céline; Poulain, Julie; Souquet, Marlène; Labadie, Karine; Jourda, Cyril; Lengellé, Juliette; Rodier-Goud, Marguerite; Alberti, Adriana; Bernard, Maria; Correa, Margot; Ayyampalayam, Saravanaraj; Mckain, Michael R; Leebens-Mack, Jim; Burgess, Diane; Freeling, Mike; Mbéguié-A-Mbéguié, Didier; Chabannes, Matthieu; Wicker, Thomas; Panaud, Olivier; Barbosa, Jose; Hribova, Eva; Heslop-Harrison, Pat; Habas, Rémy; Rivallan, Ronan; Francois, Philippe; Poiron, Claire; Kilian, Andrzej; Burthia, Dheema; Jenny, Christophe; Bakry, Frédéric; Brown, Spencer; Guignon, Valentin; Kema, Gert; Dita, Miguel; Waalwijk, Cees; Joseph, Steeve; Dievart, Anne; Jaillon, Olivier; Leclercq, Julie; Argout, Xavier; Lyons, Eric; Almeida, Ana; Jeridi, Mouna; Dolezel, Jaroslav; Roux, Nicolas; Risterucci, Ange-Marie; Weissenbach, Jean; Ruiz, Manuel; Glaszmann, Jean-Christophe; Quétier, Francis; Yahiaoui, Nabila; Wincker, Patrick (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410):213-217.
  • Buchmann, Jan P; Matsumoto, Takashi; Stein, Nils; Keller, Beat; Wicker, Thomas (2012). Inter-species sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity. The Plant Journal, 71(4):550-563.
  • Martis, M M; Klemme, S; Banaei-Moghaddam, A M; Blattner, F R; Macas, J; Schmutzer, T; Scholz, Uwe; Gundlach, H; Wicker, T; Simkova, H; Novak, P; Neumann, P; Kubalakova, M; Bauer, E; Haseneyer, G; Fuchs, J; Dolezel, J; Stein, N; Mayer, K F X; Houben, A (2012). Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proceedings of the National Academy of Sciences of the United States of America, 109(33):13343-13346.
  • Kritsas, Konstantinos; Wuest, Samuel E; Hupalo, Daniel; Kern, Andrew D; Wicker, Thomas; Grossniklaus, Ueli (2012). Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Research, 22(12):2455-2466.

• 2011

  • John, F; Roffler, S; Wicker, T; Ringli, C (2011). Plant TOR signaling components. Plant Signaling & Behavior, 6(11):1700-1705.
  • Mago, R; Tabe, L; McIntosh, R A; Pretorius, Z; Kota, R; Paux, E; Wicker, T; Breen, J; Lagudah, E S; Ellis, J G; Spielmeyer, W (2011). A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew. Theoretical and Applied Genetics, 123(4):615-623.
  • Krattinger, S G; Lagudah, E S; Wicker, T; Risk, J M; Ashton, A R; Selter, L L; Matsumoto, T; Keller, B (2011). Lr34 multi-pathogen resistance ABC transporter: molecular analysis of homoeologous and orthologous genes in hexaploid wheat and other grass species. The Plant Journal, 65(3):392-403.
  • Wicker, Thomas; Mayer, K F X; Gundlach, H; Martis, M; Steuernagel, B; Scholz, Uwe; Simková, H; Kubaláková, M; Choulet, F; Taudien, S; Platzer, M; Feuillet, C; Fahima, T; Budak, H; Dolezel, J; Keller, B; Stein, N (2011). Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. The Plant Cell, 23(5):1706-1718.
  • Oberhaensli, S; Parlange, F; Buchmann, J P; Jenny, F H; Abbott, J C; Burgis, T A; Spanu, P D; Keller, B; Wicker, T (2011). Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution. Fungal Genetics And Biology, 48(3):327 - 334.
  • Parlange, F; Oberhaensli, S; Breen, J; Platzer, M; Taudien, S; Šimková, H; Wicker, T; Doležel, J; Keller, B (2011). A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome. Functional & Integrative Genomics, 11(4):671-677.

• 2010

  • Choulet, F; Wicker, T; Rustenholz, C; Paux, E; Salse, J; Leroy, P; Schlub, S; Le Paslier, M C; Magdelenat, G; Gonthier, C; Couloux, A; Budak, H; Breen, J; Pumphrey, M; Liu, S; Kong, X; Jia, J; Gut, M; Brunel, D; Anderson, J A; Gill, B S; Appels, R; Keller, B; Feuillet, C (2010). Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell, 22(6):1686-1701.
  • Wicker, Thomas. Unravelling the mechanisms of genome evolution in plants. 2010, University of Zurich, Faculty of Science.
  • Vu, G T H; Wicker, T; Buchmann, J P; Chandler, P M; Matsumoto, T; Graner, A; Stein, N (2010). Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Functional & Integrative Genomics, 10(4):509-521.
  • Spanu, P D; Abbott, J C; Amselem, J; Burgis, T A; Soanes, D M; Stüber, K; van Themaat, E Ver Loren; Brown, J K M; Butcher, S A; Gurr, S J; Lebrun, M H; Ridout, C J; Schulze-Lefert, P; Talbot, N J; Ahmadinejad, N; Ametz, C; Barton, G R; Benjdia, M; Bidzinski, P; Bindschedler, L V; Both, M; Brewer, M T; Cadle-Davidson, L; Cadle-Davidson, M M; Collemare, J; Cramer, R; Frenkel, O; Godfrey, D; Harriman, J; Hoede, C; King, B C; Klages, S; Kleemann, J; Knoll, D; Koti, P S; Kreplak, J; López-Ruiz, F J; Lu, X; Maekawa, T; Mahanil, S; Micali, C; Milgroom, M G; Montana, G; Noir, S; O'Connell, R J; Oberhaensli, S; Parlange, F; Pedersen, C; Quesneville, H; Reinhardt, R; Rott, M; Sacristán, S; Schmidt, S M; Schön, M; Skamnioti, P; Sommer, H; Stephens, A; Takahara, H; Thordal-Christensen, H; Vigouroux, M; Wessling, R; Wicker, T; Panstruga, R (2010). Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science, 330(6010):1543-1546.
  • Breen, J; Li, D; Dunn, D S; Békés, F; Xiuying, K; Zhang, J; Jia, J; Wicker, T; Mago, R; Ma, W; Bellgard, M; Appels, R (2010). Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain. BMC Plant Biology, 10:99.
  • Wicker, T; Buchmann, J P; Keller, B (2010). Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Research, 20(9):1229-1237.
  • Breen, J; Wicker, T; Kong, X; Juncheng, Z; Ma, W; Feuillet, C; Paux, E; Appels, R; Bellgard, M (2010). A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. BMC Plant Biology, 10:98.
  • Bhullar, N K; Zhang, Z; Wicker, T; Keller, B (2010). Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project. BMC Plant Biology, 10:88.
  • International Brachypodium Initiative; Vogel, J P; Wicker, T; Buchmann, J P; et al (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463(7282):763-768.
  • Nair, S K; Wang, N; Turuspekov, Y; Pourkheirandish, M; Sinsuwongwat, S; Chen, G; Sameri, M; Tagiri, A; Honda, I; Watanabe, Y; Kanamori, H; Wicker, T; Stein, N; Nagamura, Y; Matsumoto, T; Komatsuda, T (2010). Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(1):490-495.

• 2009

  • Paterson, A H; Bowers, J E; Bruggmann, R; Dubchak, I; Grimwood, J; Gundlach, H; Haberer, G; Hellsten, U; Mitros, T; Poliakov, A; Schmutz, J; Spannagl, M; Tang, H; Wang, X; Wicker, T; Bharti, A K; Chapman, J; Feltus, F A; Gowik, Udo; Grigoriev, Igor V; Lyons, Eric; Maher, C A; Martis, M; Narechania, A; Otillar, R P; Penning, B W; Salamov, A A; Wang, Y; Zhang, L; Carpita, N C; Freeling, M; Gingle, A R; Hash, C T; Keller, B; Klein, P; Kresovich, S; McCann, M C; Ming, R; Peterson, D G; Mehboob-ur-Rahman, M; Ware, D; Westhoff, P; Mayer, K F X; Messing, J; Rokhsar, D S (2009). The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229):551-556.
  • Wicker, T; Krattinger, S G; Lagudah, E; Komatsuda, T; Pourkheirandish, M; Matsumoto, T; Cloutier, S; Reiser, L; Kanamori, H; Sato, K; Perovic, D; Stein, N; Keller, B (2009). Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight into the structure of diploid and hexaploid triticeae gene pools. Plant Physiology, 149(1):258-270.
  • Wicker, T; Buell, C R (2009). Gene and repetitive sequence annotation in the Triticeae. In: Feuillet, C; Muehlbauer, G J. Genetics and Genomics of the Triticeae. New York, US: Springer, 407-426.
  • Loutre, C; Wicker, T; Travella, S; Galli, P; Scofield, S; Fahima, T; Feuillet, C; Keller, B (2009). Two different CC-NBS-LRR genes are required for Lr10-mediated leaf rust resistance in tetraploid and hexaploid wheat. The Plant Journal, 60(6):1043-1054.
  • Wicker, T; Taudien, S; Houben, A; Keller, B; Graner, A; Platzer, M; Stein, N (2009). A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. The Plant Journal, 59(5):712-722.
  • Hanemann, A; Schweizer, G F; Cossu, R; Wicker, T; Röder, M S (2009). Fine mapping, physical mapping and development of diagnostic markers for the Rrs2 scald resistance gene in barley. Theoretical and Applied Genetics, 119(8):1507-1522.
  • Mayer, K F X; Taudien, S; Martis, M; Simková, H; Suchánková, P; Gundlach, H; Wicker, T; Petzold, A; Felder, M; Steuernagel, B; Scholz, Uwe; Graner, A; Platzer, M; Dolezel, J; Stein, N (2009). Gene content and virtual gene order of barley chromosome 1H. Plant Physiology, 151(2):496-505.

• 2008

  • Wicker, T; Narechania, A; Sabot, F; Stein, J; Vu, G T H; Graner, A; Ware, D; Stein, N (2008). Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics, 9:518.

• 2006

  • Wicker, T; Schlagenhauf, E; Graner, A; Close, T J; Keller, B; Stein, N (2006). 454 sequencing put to the test using the complex genome of barley. BMC Genomics, 7:275.