Publications

2015

Steige, K. A., Reimegård, J., Koenig, D., Scofield, D. G. & Slotte, T. Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella. Mol. Biol. Evol. 32, 2501–2514 (2015).

Rawat, V. et al. Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PLoS One 10, e0137391 (2015).

Koenig, D. & Weigel, D. Beyond the thale: comparative genomics and genetics of Arabidopsis relatives. Nat. Rev. Genet. 16, 285–298 (2015).

2014

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

Bolger, A. et al. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat. Genet. 46, 1034–1038 (2014).

Agren, J. Å. et al. Mating system shifts and transposable element evolution in the plant genus Capsella. BMC Genomics 15, 602 (2014).

Garcês, H. M. P., Koenig, D., Townsley, B. T., Kim, M. & Sinha, N. R. Truncation of LEAFY COTYLEDON1 protein is required for asexual reproduction in Kalanchoë daigremontiana. Plant Physiol. 165, 196–206 (2014).

2013

Koenig, D. et al. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc. Natl. Acad. Sci. U. S. A. 110, E2655–62 (2013).

Slotte, T. et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat. Genet. 45, 831–835 (2013).


Sharlach, M. et al. Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Theor. Appl. Genet. 126, 601–609 (2013).

Grimm, D., Hagmann, J., Koenig, D., Weigel, D. & Borgwardt, K. Accurate indel prediction using paired-end short reads. BMC Genomics 14, 132 (2013).

Manavella, P. A. et al. Tissue-specific silencing of Arabidopsis SU (VAR) 3-9 HOMOLOG8 by miR171a*. Plant Physiol. 161, 805–812 (2013).

2012

Alakonya, A. et al. Interspecific RNA interference of SHOOT MERISTEMLESS-like disrupts Cuscuta pentagona plant parasitism. Plant Cell 24, 3153–3166 (2012).

Chitwood, D. H. et al. Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. Plant Cell 24, 2318–2327 (2012).

Zoulias, N., Koenig, D., Hamidi, A., McCormick, S. & Kim, M. A role for PHANTASTICA in medio-lateral regulation of adaxial domain development in tomato and tobacco leaves. Ann. Bot. 109, 407–418 (2012).

Manavella, P. A., Koenig, D. & Weigel, D. Plant secondary siRNA production determined by microRNA-duplex structure. Proceedings of the National Academy of Sciences 109, 2461–2466 (2012).

2011

Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 (2011).

Cao, J. et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43, 956–963 (2011).

2010

Ji, J. et al. WOX4 promotes procambial development. Plant Physiol. 152, 1346–1356 (2010).

Koenig, D. & Sinha, N. Evolution of leaf shape: A pattern emerges. Curr. Top. Dev. Biol. 91, 169–183 (2010).

Uchida, N., Kimura, S., Koenig, D. & Sinha, N. Coordination of leaf development via regulation of KNOX1 genes. J. Plant Res. 123, 7–14 (2010).

2009

David-Schwartz, R., Koenig, D. & Sinha, N. R. LYRATE is a key regulator of leaflet initiation and lamina outgrowth in tomato. Plant Cell 21, 3093–3104 (2009).

Koenig, D., Bayer, E., Kang, J., Kuhlemeier, C. & Sinha, N. Auxin patterns Solanum lycopersicum leaf morphogenesis. Development 136, 2997–3006 (2009).

2008

Kimura, S., Koenig, D., Kang, J., Yoong, F. Y. & Sinha, N. Natural variation in leaf morphology results from mutation of a novel KNOX gene. Curr. Biol. 18, 672–677 (2008).