Publications

(* = contributed equally, = corresponding author, [OA] = open access)


Shirsekar, G., Devos, J., Latorre, S. M., Blaha, A., Dias, M. Q., Hernando, A. G., Lundberg, D. S., Burbano, H. A., Fenster, C. B., & Weigel, D. (2021). Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia, Molecular Biology and Evolution. Molecular Biology and Evolution, msab268, https://doi.org/10.1093/molbev/msab268 [OA]

Lundberg, D. S., Pramoj Na Ayutthaya, P., Strauß, A., Shirsekar, G., Lo, W.-S., Lahaye, T., & Weigel, D. (2021). Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 10 (2021): e66186. https://elifesciences.org/articles/66186 [OA]

Shalev O., Karasov T.L., Lundberg D.S., Ashkenazy H., Weigel D. 2021. Protective host-dependent antagonism among Pseudomonas in the Arabidopsis phyllosphere. in bioRxiv. https://doi.org/10.1101/2021.04.08.438928 [OA]

Cambiagno, D. A., Giudicatti, A. J., Arce, A. L., Gagliardi, D., Li, L., Yuan, W., Lundberg, D. S., Weigel, D., & Manavella, P. A. (2020). HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. Molecular Plant. https://doi.org/10.1016/j.molp.2020.12.019

Regalado, J.*, Lundberg, D. S.*, Deusch, O., Kersten, S., Karasov, T., Poersch, K., Shirsekar, G., & Weigel, D. (2020). Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves. The ISME Journal, 14, 2116–2130. https://doi.org/10.1038/s41396-020-0665-8 [OA]

Pramoj Na Ayutthaya, P., Lundberg, D.S., Weigel, D., & Li, L. (2020). Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for the Analysis of Protein Oligomers in Plants. Current Protocols in Plant Biology, 5(2), e20107. https://doi.org/10.1002/cppb.20107 [OA]

Karasov, T. L., Neumann, M., Duque-Jaramillo, A., Kersten, S., Bezrukov, I., Schröppel, B., Symeonidi, E., Lundberg, D. S., Regalado, J., Shirsekar, G., Bergelson, J., & Weigel, D. (2019). The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere. In bioRxiv, 828814. https://doi.org/10.1101/828814 [OA]

Karasov, T. L., Almario, J.*, Friedemann, C.*, Ding, W., Giolai, M., Heavens, D., Kersten, S., Lundberg, D. S., Neumann, M., Regalado, J., Neher, R. A., Kemen, E., & Weigel, D. (2018). Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe, 24(1), 168–179.e4. https://doi.org/10.1016/j.chom.2018.06.011 [OA]

Lundberg, D. S., & Teixeira, P. J. P. L. (2018). Root-exuded coumarin shapes the root microbiome [Commentary about “MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health” by Stringlis et al. in the same issue]. Proceedings of the National Academy of Sciences of the United States of America, 115(22), 5629–5631. https://doi.org/10.1073/pnas.1805944115 [OA]

Levy A.*, Salas Gonzalez I.*, Mittelviefhaus M., Clingenpeel S., Herrera Paredes S., Miao J., Wang K., Devescovi G., Stillman K., Monteiro F., Rangel Alvarez B., Lundberg D.S., Lu T-Y., Lebeis S., Jin Z., McDonald M., Klein A.P., Feltcher M.E., Glavina del Rio T., Grant S.R., Doty S.L., Ley R.E., Pelletier D.A., Vorholt J., Tringe S.G., Woyke T., and Dangl J.L. (2018). Genomic features of bacterial adaptation to plants. Nature Genetics, 50(1), 138–150. https://doi.org/10.1038/s41588-017-0012-9 [OA]

Rowan, B. A., Seymour, D. K., Chae, E., Lundberg, D. S., & Weigel, D. (2017). Methods for Genotyping-by-Sequencing. Methods in Molecular Biology, 1492, 221–242. https://doi.org/10.1007/978-1-4939-6442-0_16

Wagner, M. R., Lundberg, D. S., Del Rio, T. G., Tringe, S. G., Dangl, J. L., & Mitchell-Olds, T. (2016). Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications, 7, 12151. https://doi.org/10.1038/ncomms12151 [OA]

Biswas, S., Mcdonald, M., Lundberg, D. S., Dangl, J. L., & Jojic, V. (2016). Learning Microbial Interaction Networks from Metagenomic Count Data. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 23(6), 526–535. https://doi.org/10.1089/cmb.2016.0061

Johnston-Monje, D., Lundberg, D. S., Lazarovits, G., Reis, V. M., & Raizada, M. N. (2016). Bacterial populations in juvenile maize rhizospheres originate from both seed and soil. Plant and Soil, 405(1-2), 337–355. https://doi.org/10.1007/s11104-016-2826-0 [OA]

Tennessen, K., Andersen, E., Clingenpeel, S., Rinke, C., Lundberg, D. S., Han, J., Dangl, J. L., Ivanova, N., Woyke, T., Kyrpides, N., & Pati, A. (2016). ProDeGe: a computational protocol for fully automated decontamination of genomes. The ISME Journal, 10(1), 269–272. https://doi.org/10.1038/ismej.2015.100 [OA]

Lebeis, S. L.*, Paredes, S. H.*, Lundberg, D. S.*, Breakfield, N., Gehring, J., McDonald, M., Malfatti, S., Glavina del Rio, T., Jones, C. D., Tringe, S. G., & Dangl, J. L. (2015). Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science, 349(6250), 860–864. https://doi.org/10.1126/science.aaa8764 [OA]

Argüeso, C., Huot, B., Kim, P., Lundberg, D.S., Halane, M., Serrano, I., Innes, R., & Mudgett, M. B. (2014). XVI Congress on Molecular Plant-Microbe Interactions Meeting Report. Molecular Plant-Microbe Interactions: MPMI, 27(11 Suppl), S1–S5. https://doi.org/10.1094/MPMI-27-11-S1 [OA]

Yourstone, S. M., Lundberg, D. S., Dangl, J. L., & Jones, C. D. (2014). MT-Toolbox: improved amplicon sequencing using molecule tags. BMC Bioinformatics, 15, 284. https://doi.org/10.1186/1471-2105-15-284 [OA]

Wagner, M. R., Lundberg, D. S., Coleman-Derr, D., Tringe, S. G., Dangl, J. L., & Mitchell-Olds, T. (2014). Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecology Letters, 17(6), 717–726. https://doi.org/10.1111/ele.12276 [OA]

Lundberg, D. S.*, Yourstone, S.*, Mieczkowski, P., Jones, C. D., & Dangl, J. L. (2013). Practical innovations for high-throughput amplicon sequencing. Nature Methods, 10(10), 999–1002. https://doi.org/10.1038/nmeth.2634

Lundberg, D. S.*, Lebeis, S. L.*, Paredes, S. H.*, Yourstone, S.*, Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Del Rio, T. G., Edgar, R. C., Eickhorst, T., Ley, R. E., Hugenholtz, P., Tringe, S. G., & Dangl, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86–90. https://doi.org/10.1038/nature11237 [OA]

Goel, A. K., Lundberg, D.S., Torres, M. A., Matthews, R., Akimoto-Tomiyama, C., Farmer, L., Dangl, J. L., & Grant, S. R. (2008). The Pseudomonas syringae type III effector HopAM1 enhances virulence on water-stressed plants. Molecular Plant-Microbe Interactions: MPMI, 21(3), 361–370. https://doi.org/10.1094/MPMI-21-3-0361 [OA]