Publications
_{Molecular Biology}

Cheng, L.; Wang, N.; Bao, Z.; Zhou, Q.; Guarracino, A.; Yang, Y.; Wang, P.; Zhang, Z.; Tang, D.; Zhang, P. et al.; Wu, Y.; Zhou, Y.; Zheng, Y.; Hu, Y.; Liang, Q.; Ma, Z.; Lassois, L.; Zhang, C.; Lucas, W.; Garrison, E.; Stein, N.; Städler, T.; Zhou, Y.; Huang, S.: Leveraging a phased pangenome for haplotype design of hybrid potato. Nature 640 (8058), pp. 408 - 417 (2025)

Du, K.; Deusch, O.; Bezrukov, I.; Lanz, C.; Guiguen, Y.; Hoffmann, M.; Habring, A.; Weigel, D.; Schartl, M.; Dreyer, C.: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly. Genome Research 35 (3), pp. 489 - 498 (2025)

Morales-Díaz, N.; Sushko, S.; Campos-Dominguez, L.; Kopalli, V.; Golicz, A.; Castanera, J.; Casacuberta, M.: Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes. Mobile DNA 16 (1), 10 (2025)

Wang, H.; Caetano-Andrade, V.; Boivin, N.; da Silva Costa, F.; Weigel, D.; Roberts, P.: Long-term human influence on the demography and genetic diversity of the hyperdominant Bertholletia excelsa in the Amazon Basin. Current Biology 35 (3), pp. 629 - 639 (2025)

Chen, H.; Xiong, F.; Wangler, A.-M.; Bischoff, T.; Wang, K.; Miao, Y.; Slane, D.; Schwab, R.; Laux, T.; Bayer, M.: Phosphorylation-Dependent Activation of the bHLH Transcription Factor ICE1/SCRM Promotes Polarization of the Arabidopsis Zygote. New Phytologist 245 (3), pp. 1029 - 1039 (2025)

Mencia, R.; Arce, A.; Houriet, C.; Xian, W.; Contreras, A.; Shirsekar, G.; Weigel, D.; Manavella, P.: Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response. Nature Structural & Molecular Biology 32 (1), pp. 199 - 211 (2025)

Xian, W.; Bezrukov, I.; Bao, Z.; Vorbrugg, S.; Gautam, A.; Weigel, D.: TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data. Molecular Biology and Evolution 42 (1), msae247 (2025)

Vasseur, F.; Baldrich, P.; Jiménez-Góngora, T.; Villar-Martin, L.; Weigel, D.; Rubio-Somoza, I.: miR472 deficiency enhances Arabidopsis thaliana defense without reducing seed production. Molecular Plant-Microbe Interactions 37 (12), pp. 819 - 827 (2024)

Vorbrugg, S.; Bezrukov, I.; Bao, Z.; Weigel, D.: Gretl: Variation GRaph Evaluation TooLkit. Bioinformatics 41 (1), btae755 (2024)

Garrison, E.; Guarracino, A.; Heumos, S.; Villani, F.; Bao, Z.; Tattini, T.; Hagmann, J.; Vorbrugg, S.; Marco-Sola, S.; Kubica, C. et al.; Ashbrook, G.; Thorell, K.; Rusholme-Pilcher, R.; Liti, G.; Rudbeck, E.; Golicz, A.; Nahnsen, S.; Yang, Z.; Mwaniki, M.; Nobrega, F.; Wu, Y.; Chen, H.; de Ligt, J.; Sudmant, P.; Huang, S.; Weigel, D.; Soranzo, N.; Colonna, V.; Williams, R.; Prins, P.: Building pangenome graphs. Nature Methods 21 (11), pp. 2008 - 2012 (2024)

Koren, S.; Bao, Z.; Guarracino, A.; Ou, S.; Goodwin, S.; Jenike, K.; Lucas, J.; McNulty, B.; Park, J.; Rautiainen, M. et al.; Rhie, A.; Roelofs, D.; Schneiders, H.; Vrijenhoek, I.; Nijbroek, K.; Nordesjo, O.; Nurk, S.; Vella, M.; Lawrence, K.; Ware, D.; Schatz, M.; Garrison, E.; Huang, S.; McCombie, W.; Miga, K.; Wittenberg, A.; Phillippy, A.: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Genome Research 34 (11), pp. 1919 - 1930 (2024)

Lotharukpong, J.; Zheng, M.; Luthringer, R.; Liesner, D.; Drost, H.-G.; Coelho, S.: A Transcriptomic Hourglass In Brown Algae. Nature 635 (8037), pp. 129 - 135 (2024)

Karasov, T.; Neumann, M.; Leventhal, L.; Symeonidi, E.; Shirsekar, G.; Hawks, A.; Monroe, G.; Pathodopsis Team; Exposito-Alonso, M.; Borgelsen, J. et al.; Weigel, D.; Schwab, R.: Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought. Nature Microbiology 9 (10), pp. 2748 - 2758 (2024)

Liu, T.; Liu, H.; Xian, W.; Liu, Z.; Yuan, Y.; Fan, J.; Xiang, S.; Yang, X.; Liu, Y.; Liu, S. et al.; Zhang, M.; Shen, Y.; Jiao, Y.; Cheng, S.; Doyle, J.; Xie, F.; Li, J.; Tian, Z.: Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution. Journal of Integrative Plant Biology 66 (10), pp. 2191 - 2207 (2024)

Sunil, S.; Beeh, S.; Stöbbe, E.; Fischer, K.; Wilhelm, F.; Meral, A.; Paris, C.; Teasdale, L.; Jiang, Z.; Zhang, L. et al.; Urban, M.; Aguilar Parras, E.; Nürnberger, T.; Weigel, D.; Lozano-Duran, R.; El Kasmi, F.: Activation of an atypical plant NLR with an N-terminal deletion initiates cell death at the vacuole. EMBO Reports 25 (10), pp. 4358 - 4386 (2024)

Voichek, Y.; Hristova, G.; Mollá-Morales, A.; Weigel, D.; Nordborg, M.: Widespread position-dependent transcriptional regulatory sequences in plants. Nature Genetics 56 (10), pp. 2238 - 2246 (2024)

Wegner, H.; Roitman, S.; Kupczok, A.; Braun, V.; Woodhouse, J.; Grossart, H.-P.; Zehner, S.; Béjà, O.; Frankenberg-Dinkel, N.: Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments. Nature Communications 15 (1), 8713 (2024)

Whiting, J.; Booker, T.; Rougeux , C.; Lind, B.; Singh, P.; Lu, M.; Huang, K.; Whitlock , M.; Aitken, S.; Andrew, R. et al.; Borevitz, J.; Bruhl, J.; Collins, T.; Fischer, M.; Hodgins, K.; Holliday, J.; Ingvarsson, P.; Janes, J.; Khandaker, M.; Koenig, D.; Kreiner, J.; Kremer, A.; Lascoux, M.; Leroy, T.; Milesi, P.; Murray, K.; Pyhäjärvi, T.; Rellstab, C.; Rieseberg, L.; Roux, F.; Stinchcombe, J.; Telford, I.; Todesco, M.; Tyrmi , J.; Wang, B.; Weigel, D.; Willi, Y.; Wright, S.; Zhou, L.; Yeaman, S.: The genetic architecture of repeated local adaptation to climate in distantly related plants. Nature Ecology & Evolution 8 (10), pp. 1933 - 1947 (2024)

Cury, J.; Haudiquet, M.; Hernandez Trejo, V.; Mordret, E.; Hanouna, A.; Rotival, M.; Tesson, F.; Bonhomme, D.; Ofir, G.; Quintana-Murci, L. et al.; Benaroch, P.; Poirier, E.; Bernheim, A.: Conservation of antiviral systems across domains of life reveals immune genes in humans. Cell Host & Microbe 32 (9), pp. 1594 - 1607 (2024)

Huang, G.; Bao, Z.; Feng, L.; Zhai, J.; Wendel, J.; Cao, X.; Zhu, Y.: A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development. Nature Genetics 56 (9), pp. 1953 - 1963 (2024)