Publications of J Hagmann

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)

Hüther, P.; Hagmann, J.; Nunn, A.; Kakoulidou, I.; Pisupati, R.; Langenberger, D.; Weigel, D.; Johannes, F.; Schultheiss, S.; Becker, C.: MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data. Quantitative Plant Biology 3, e19 (2022)

Zacharaki, V.; Ponnu, J.; Crepin, N.; Langenecker, T.; Hagmann, J.; Skorzinski, N.; Musialak-Lange, M.; Wahl, V.; Rolland, F.; Schmid, M.: Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant. New Phytologist 235 (1), pp. 220 - 233 (2022)

Fertey, J.; Hagmann, J.; Ruscheweyh, H.-J.; Munk, C.; Kjaer, S.; Huson, D.; Haedicke-Jarboui, J.; Stubenrauch, F.; Iftner, T.: Methylation of CpG 5962 in L1 of the human papillomavirus 16 genome as a potential predictive marker for viral persistence: A prospective large cohort study using cervical swab samples. Cancer Medicine 9 (3), pp. 1058 - 1068 (2020)

Barragan, C.; Wu, R.; Kim, S.-T.; Xi, W.; Habring, A.; Hagmann, J.; Van de Weyer, A.-L.; Zaidem, M.; Ho, W.; Wang, G. et al.; Bezrukov, I.; Weigel, D.; Chae, E.: RPW8/HR repeats control NLR activation in Arabidopsis thaliana. PLoS Genetics 15 (7), e1008313 (2019)

Koenig, D.; Hagmann, J.; Li, R.; Bemm, F.; Slotte, T.; Neuffer, B.; Wright, S.; Weigel, D.: Long-term balancing selection drives evolution of immunity genes in Capsella. eLife 8, e43606 (2019)

Exposito-Alonso, M.; Becker, C.; Schuenemann, V.; Reiter, E.; Setzer, C.; Slovak, R.; Brachi, B.; Hagmann, J.; Grimm, D.; Chen, J. et al.; Busch, W.; Bergelson, J.; Ness, R.; Krause, J.; Burbano, H.; Weigel, D.: The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genetics 14 (2), e1007155 (2018)

Lang, P.; Christie, M.; Dogan, E.; Schwab, R.; Hagmann, J.; Van de Weyer, A.-L.; Scacchi, E.; Weigel, D.: A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function. Plant Physiology 176 (1), pp. 730 - 741 (2018)

Mao, H.; Aryal, B.; Langenecker, T.; Hagmann, J.; Geisler, M.; Grebe, M.: Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility. Nature Plants 3 (11), pp. 854 - 858 (2017)

Hagmann, J.; Becker, C.: Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing. Methods in Molecular Biology 1610 (2017)

Mable, B.; Hagmann, J.; Kim, S.-T.; Adam, A.; Kilbride, E.; Weigel, D.; Stift, M.: What causes mating system shifts in plants? Arabidopsis lyrata as a case study. Heredity 118 (1), pp. 52 - 63 (2017)

Li, Z.-W.; Chen, X.; Wu, Q.; Hagmann, J.; Han, T.-S.; Zou, Y.-P.; Ge, S.; Guo, Y.-L.: On the Origin of De Novo Genes in Arabidopsis thaliana Populations. Genome Biology and Evolution 8 (7), pp. 2190 - 2202 (2016)

Wibowo, A.; Becker, C.; Marconi, G.; Durr, J.; Price, J.; Hagmann, J.; Papareddy, R.; Putra, H.; Kageyama, J.; Becker, J. et al.; Weigel, D.; Gutierrez-Marcos, J.: Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. eLife 5, e1354 (2016)

Karlsson, P.; Christie, M.; Seymour, D.; Wang, H.; Wang, X.; Hagmann, J.; Kulcheski, F.; Manavella, P.: KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1. Proceedings of the National Academy of Sciences of the United States of America 112 (45), pp. 14096 - 14101 (2015)

Lutz, U.; Posé, D.; Pfeifer, M.; Gundlach, H.; Hagmann, J.; Wang, C.; Weigel, D.; Mayer, K.; Schmid, M.; Schwechheimer, C.: Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M. PLoS Genetics 11 (10), e1005588 (2015)

Kolb, C.; Nagel, M.-K.; Kalinowska, K.; Hagmann, J.; Ichikawa, M.; Anzenberger, F.; Alkofer, A.; Sato, M.; Braun, P.; Isono, E.: FYVE1 is essential for vacuole biogenesis and intracellular trafficking in Arabidopsis. Plant Physiology 167 (4), pp. 1361 - 1373 (2015)

Willing, E.-M.; Rawat, V.; Mandakova, T.; Maumus, F.; James, G.; Nordstroem, K.; Becker, C.; Warthmann, N.; Chica, C.; Szarzynska, B. et al.; Zytnicki, M.; Albani, M.; Kiefer, C.; Bergonzi, S.; Castaings, L.; Mateos, J.; Berns, M.; Bujdoso, N.; Piofczyk, T.; de Lorenzo, L.; Barrero-Sicilia, C.; Mateos, I.; Piednoel, M.; Hagmann, J.; Chen-Min-Tao, R.; Iglesias-Fernandez, R.; Schuster, S.; Alonso-Blanco, C.; Roudier, F.; Carbonero, P.; Paz-Ares, J.; Davis, S.; Pecinka, A.; Quesneville, H.; Colot, V.; Lysak, M.; Weigel, D.; Coupland, G.; Schneeberger, K.: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1 (2), 14023 (2015)

Hagmann, J.; Becker, C.; Müller, J.; Stegle, O.; Meyer, R.; Wang, G.; Schneeberger, K.; Fitz, J.; Altmann, T.; Bergelson, J. et al.; Borgwardt, K.; Weigel, D.: Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage. PLoS Genetics 11 (1), e1004920 (2015)

Lim, E.-C.; Müller, J.; Hagmann, J.; Henz, S.; Kim, S.-T.; Weigel, D.: Trowel: a fast and accurate error correction module for Illumina sequencing reads. Bioinformatics 30 (22), pp. 3264 - 3265 (2014)

Seymour, D.; Koenig, D.; Hagmann, J.; Becker, C.; Weigel, D.: Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genetics 10 (11), e1004785 (2014)