Schneeberger, K.; Hagmann, J.; Ossowski, S.; Warthmann, N.; Gesing, S.; Kohlbacher, O.; Weigel, D.: Simultaneous alignment of short reads against multiple genomes. Genome Biology 10 (9), R98 (2009)

Schneeberger, K.; Ossowski, S.; Lanz, C.; Juul, T.; Petersen, A.; Nielsen, K.; Jørgensen, J.-E.; Weigel, D.; Andersen, S.: SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nature Methods 6 (8), pp. 550 - 551 (2009)

Schultheiss, S.; Busch, W.; Lohmann, J.; Kohlbacher, O.; Rätsch, G.: KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics 25 (16), pp. 2126 - 2133 (2009)

Wang, J.-W.; Czech, B.; Weigel, D.: miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138 (4), pp. 738 - 749 (2009)

Wu, G.; Park, M.; Conway, S.; Wang, J.-W.; Weigel, D.; Poethig, R.: The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138 (4), pp. 750 - 759 (2009)

Mathieu, J.; Yant, L.; Mürdter, F.; Küttner, F.; Schmid, M.: Repression of flowering by the miR172 target SMZ. PLoS Biology 7 (7), e1000148 (2009)

McNally, K.; Childs, K.; Bohnert, R.; Davidson, R.; Zhao, K.; Ulat, V.; Zeller, G.; Clark, R.; Hoen, T.; Bureau, D. et al.; Stokowski, R.; Ballinger, D.; Frazer, K.; Cox, D.; Padhukasahasram, B.; Bustamante, C.; Weigel, D.; Mackill, D.; Bruskiewich, R.; Rätsch, G.; Buell, C.; Leung, H.; Leach, J.: Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America 106 (30), pp. 12273 - 12278 (2009)

Schweikert, G.; Behr, J.; Zien, A.; Zeller, G.; Ong, C.; Sonnenburg, S.; Rätsch, G.: mGene.web: a web service for accurate computational gene finding. Nucleic Acids Research (London) 37 (Supplement 2), pp. W312 - W316 (2009)

Weigel, D.; Glazebrook, J.: Phenotypic analysis of Arabidopsis mutants: bacterial pathogens. Cold Spring Harbor protocols 4 (7), pdb.prot4983 (2009)

Tripathi, N.; Hoffmann, M.; Willing, E.-M.; Lanz, C.; Weigel, D.; Dreyer, C.: Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation. Proceedings of the Royal Society B: Biological Sciences 276 (1665), pp. 2195 - 2208 (2009)

Zeller, G.; Henz, S.; Widmer, C.; Sachsenberg, T.; Rätsch, G.; Weigel, D.; Laubinger, S.: Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. The Plant Journal 58 (6), pp. 1068 - 1082 (2009)

Maier, A.; Stehling-Sun, S.; Wollmann, H.; Demar, M.; Hong, R.; Haubeiß, S.; Weigel, D.; Lohmann, J.: Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression. Development 136 (10), pp. 1613 - 1620 (2009)

Trigueros, M.; Navarrete-Gómez, M.; Sato, S.; Christensen, S.; Pelaz, S.; Weigel, D.; Yanofsky, M.; Ferrándiz, C.: The NGATHA genes direct style development in the Arabidopsis gynoecium. Plant Cell 21 (5), pp. 1394 - 1409 (2009)

Tripathi, N.; Hoffmann, M.; Weigel, D.; Dreyer, C.: Linkage analysis reveals the independent origin of Poeciliid sex chromosomes and a case of atypical sex inheritance in the guppy (Poecilia reticulata). Genetics 182 (1), pp. 365 - 374 (2009)

Weigel, D.; Mott, R.: The 1001 genomes project for Arabidopsis thaliana. Genome Biology 10 (5), 107 (2009)

Molnar, A.; Bassett, A.; Thuenemann, E.; Schwach, F.; Karkare, S.; Ossowski, S.; Weigel, D.; Baulcombe, D.: Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. The Plant Journal 58 (1), pp. 165 - 174 (2009)

Felippes, F.; Weigel, D.: Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. EMBO Reports 10 (3), pp. 264 - 270 (2009)

Guo, Y.-L.; Bechsgaard, J.; Slotte, T.; Neuffer, B.; Lascoux, M.; Weigel, D.; Schierup, M.: Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proceedings of the National Academy of Sciences of the United States of America 106 (13), pp. 5246 - 5251 (2009)

Stöbe, P.; Stein, S.; Habring-Müller, A.; Bezdan, D.; Fuchs, A.; Hueber, S.; Wu, H.; Lohmann, I.: Multifactorial regulation of a hox target gene. PLoS Genetics 5 (3), e1000412 (2009)

Weigel, D.; Glazebrook, J.: Dellaporta miniprep for plant DNA isolation. Cold Spring Harbor protocols 4 (3), pdb.prot5178 (2009)