Devin Coleman-Derr
Plant Gene Expression Center
Director
Phone: (510) 559-5911
Fax: (510) 559-5678
(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
Publications
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will take you to the publication reprint.)
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Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates
- (Peer Reviewed Journal)
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Alvarez-Aponte, Z., Govindaraju, A., Hallberg, Z., Nicolas, A., Green, M., Mok, K.C., Fonseca-Garcia, C., Coleman-Derr, D.A., Brodie, E.L., Carlson, H.K., Taga, M.E. 2024. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. Journal of the International Society for Microbial Ecology. Article wrae068. https://doi.org/10.1093/ismejo/wrae068.
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Streptomyces umbrella toxin particles block hyphal growth of competing species
- (Peer Reviewed Journal)
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Zhao, Q., Bertolli, S., Park, Y., Tan, Y., Cutler, K., Srivivas, P., Asfahl, K., Garcia, C.F., Gallagher, L., Li, Y., Wang, Y., Coleman-Derr, D.A., DiMaio, F., Zhang, F., Peterson, S.B., Veesler, D., Mougous, J.D. 2024. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature. 629:165–173. https://doi.org/10.1038/s41586-024-07298-z.
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Drought shifts sorghum root metabolite and microbiome profiles and enriches for pipecolic acid
- (Peer Reviewed Journal)
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Caddell, D.F., Pettinga, D., Louie, K., Bowen, B.P., Sievert, J.A., Hollingsworth, J., Rubanowitz, R., Dahlberg, J., Purdom, E., Northen, T., Coleman-Derr, D.A. 2023. Drought shifts sorghum root metabolite and microbiome profiles and enriches for pipecolic acid. Phytobiomes Journal. 7(4):449-463. https://doi.org/10.1094/PBIOMES-02-23-0011-R.
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High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration
- (Peer Reviewed Journal)
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Elmore, J., Dexter, G., Baldino, H., Huenemann, J., Francis, R., Peabody, G.L., Martinez-Baird, J., Riley, L.A., Simmons, T., Coleman-Derr, D.A., Guss, A., Egbert, R. 2023. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Science Advances. 9(10). Article eade1285. https://doi.org/10.1126/sciadv.ade1285.
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Photosynthesis in rice is increased by CRISPR/Cas9-mediated transformation of two truncated light-harvesting antenna
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Caddell, D.F., Langenfeld, N.J., Zhen, S., Eckels, M., Zhen, S., Klaras, R., Mishra, L., Bugbee, B., Coleman-Derr, D.A. 2023. Photosynthesis in rice is increased by CRISPR/Cas9-mediated transformation of two truncated light-harvesting antenna. Frontiers in Plant Science. 14. Article 1050483. https://doi.org/10.3389/fpls.2023.1050483.
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Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities
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Gao, C., Xu, L., Montoya, L., Madera, M., Hollingsworth, J., Chen, L., Purdom, E., Singan, V., Vogel, J., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P., Taylor, J. 2022. Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities. Nature Communications. 13. Article 3867. https://doi.org/10.1038/s41467-022-31343-y.
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Plant microbiome-based genome-wide association studies
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Deng, S., Meier, M., Caddell, D., Yang, J., Coleman-Derr, D.A. 2022. Plant microbiome-based genome-wide association studies. In: Torkamaneh, D., Belzile, F., editors. Genome-Wide Association Studies. Methods in Molecular Biology. New York, NY: Humana. p. 353-367. https://doi.org/10.1007/978-1-0716-2237-7_20.
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Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation
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Tang, J., Wu, D., Li, X., Wang, L., Xu, L., Zhang, Y., Xu, F., Liu, H., Xie, Q., Dai, S., Coleman-Derr, D.A., Yu, F. 2022. Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation. EMBO Journal. 41(6). Article e109102. https://doi.org/10.15252/embj.2021109102.
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Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression
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Gao, C., Courty, P., Varoquaux, N., Cole, B., Montoya, L., Xu, L., Purdom, E., Vogel, J., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P., Taylor, J. 2022. Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression. Molecular Ecology. https://doi.org/10.1111/mec.16343.
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Keep your friends close: Host compartmentalisation of microbial communities facilitates decoupling from effects of habitat fragmentation
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Willing, C., Pierroz, G., Guzman, A., Anderegg, L., Gao, C., Coleman-Derr, D.A., Taylor, J., Bruns, T., Dawson, T. 2021. Keep your friends close: Host compartmentalisation of microbial communities facilitates decoupling from effects of habitat fragmentation. Ecology Letters. 24(12):2674–2686. https://doi.org/10.1111/ele.13886.
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Plant single-cell solutions for energy and the environment
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Cole, B., Bergmann, D., Blaby-Haas, C., Blaby, I., Bouchard, K., Brady, S., Ciobanu, D., Coleman-Derr, D.A., Leiboff, S., Mortimer, J., Nobori, T., Rhee, S., Schmutz, J., Simmons, B., Singh, A., Sinha, N., Vogel, J., O'Malley, R., Visel, A., Dickel, D. 2021. Plant single-cell solutions for energy and the environment. Communications Biology. 4. Article 962. https://doi.org/10.1038/s42003-021-02477-4.
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Towards a biomanufactory on Mars
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Berliner, A., Hilzinger, A., Abel, A., McNulty, M., Makrygiorgos, G., Averesch, N., Gupta, S., Benvenuti, A., Caddell, A., Coleman-Derr, D.A., et al. 2021. Towards a biomanufactory on Mars. Frontiers in Astronomy and Space Sciences. 8. Article 711550. https://doi.org/10.3389/fspas.2021.711550.
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The plastid-localized AtFtsHi3 pseudo-protease of Arabidopsis thaliana has an impact on plant growth and drought tolerance
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Mishra, L., Mishra, S., Caddell, D.F., Coleman-Derr, D.A., Funk, C. 2021. The plastid-localized AtFtsHi3 pseudo-protease of Arabidopsis thaliana has an impact on plant growth and drought tolerance. Frontiers in Plant Science. 12. Article 694727. https://doi.org/10.3389/fpls.2021.694727.
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Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
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Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H.M., Caddell, D.F., Varoquaux, N., Madera, M.A., Hutmacher, R., Deutschbauer, A., Dahlberg, J., Guerinot, M., Purdom, E., Banfield, J.F., Taylor, J.W., Lemaux, P.G., Coleman-Derr, D.A. 2021. Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications. 12. Article 3209. https://doi.org/10.1038/s41467-021-23553-7.
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Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome
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Deng, S., Caddell, D.F., Xu, G., Dahlen, L., Washington, L., Wang, J., Coleman-Derr, D.A. 2021. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. Available: https://doi.org/10.1038/s41396-021-00993-z.
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Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome
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Wipf, H., Coleman-Derr, D.A. 2021. Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome. PLoS ONE. 16(3). Article e0248030. https://doi.org/10.1371/journal.pone.0248030.
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Holo-omics for deciphering plant-microbiome interactions
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Xu, L., Pierroz, G., Wipf, E., Gao, C., Taylor, J., Lemaux, P., Coleman-Derr, D.A. 2021. Holo-omics for deciphering plant-microbiome interactions. Microbiome. 9:69. https://doi.org/10.1186/s40168-021-01014-z.
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Agricultural soil management practices differentially shape the bacterial and fungal microbiome of Sorghum bicolor
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Wipf, H., Xu, L., Gao, C., Spinner, H., Taylor, J., Lemaux, P., Mitchell, J., Coleman-Derr, D.A. 2021. Agricultural soil management practices differentially shape the bacterial and fungal microbiome of Sorghum bicolor. Applied and Environmental Microbiology. 87(5). https://doi.org/10.1128/AEM.02345-20.
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Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress
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Mishra, L., Kim, S., Caddell, D.F., Coleman-Derr, D.A., Funk, C. 2021. Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress. Physiologia Plantarum. 172(2):1045-1058. https://doi.org/10.1111/ppl.13299.
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Distinguishing between the impacts of heat and drought stress on the root microbiome of Sorghum bicolor
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Wipf, H., Bui, T., Coleman-Derr, D.A. 2021. Distinguishing between the impacts of heat and drought stress on the root microbiome of Sorghum bicolor. Applied and Environmental Microbiology. 5(2):2471-2906. https://doi.org/10.1094/PBIOMES-07-20-0052-R.
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The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots
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Willing, C., Pierroz, G., Coleman-Derr, D.A., Dawson, T. 2020. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Molecular Ecology. 29:4721–4734. https://doi.org/10.1111/mec.15666.
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Nematode-encoded RALF peptide mimics facilitate parasitism of plants through the FERONIA receptor kinase
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Zhang, X., Peng, H., Zhu, S., Xing, J., Li, X., Zhu, Z., Zheng, J., Wang, L., Wang, B., Chen, J., Ming, Z., Yao, K., Jian, J., Luan, S., Coleman-Derr, D.A., Liao, H., Peng, Y., Peng, D., Yu, F. 2020. Nematode-encoded RALF peptide mimics facilitate parasitism of plants through the FERONIA receptor kinase. Molecular Plant. 13:214-216. https://doi.org/10.1016/j.molp.2020.08.014.
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Nematode-encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase
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Zhang, X., Peng, H., Zhu, S., Xing, J., Li, X., Zhu, Z., Zheng, J., Wang, L., Wang, B., Chen, J., Ming, Z., Yao, K., Jian, J., Luan, S., Coleman-Derr, D.A., Liao, H., Peng, Y., Peng, D., Yu, F. 2020. Nematode-encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase. Molecular Plant. https://doi.org/10.1016/j.molp.2020.08.014.
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Drought drives spatial variation in the millet root microbiome
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Simmons, T., Styer, A., Pierroz, G., Goncalves, A., Pasicha, R., Hazra, A., Bubner, P., Coleman-Derr, D.A. 2020. Drought drives spatial variation in the millet root microbiome. Frontiers in Plant Science. 11. https://doi.org/10.3389/fpls.2020.00599.
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Fungal community assembly in drought-stressed sorghum shows stochasticity, selection and universal ecological dynamics
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Gao, C., Montoya, L., Xu, L., Purdom, E., Hollingsworth, J., Singan, V., Vogel, J., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P., Taylor, J. 2020. Fungal community assembly in drought-stressed sorghum shows stochasticity, selection and universal ecological dynamics. Nature Communications. 11:34. https://doi.org/10.1038/s41467-019-13913-9.
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Peanut plant growth was altered by monocropping-associated microbial enrichment of rhizosphere microbiome
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Li, X., Panke-Buisse, K., Yao, X., Coleman-Derr, D.A., Ding, C., Wang, X., Ruan, H. 2019. Peanut plant growth was altered by monocropping-associated microbial enrichment of rhizosphere microbiome. Plant and Soil. 446:655–669. https://doi.org/10.1007/s11104-019-04379-1.
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A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome
- (Peer Reviewed Journal)
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Deng, S., Wipf, H., Pierroz, G., Raab, T.K., Khanna, R., Coleman-Derr, D.A. 2019. A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome. Scientific Reports. 9:17677. https://doi.org/10.1038/s41598-019-53623-2.
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Transcriptomic analysis of field-droughted sorghum from seeding to maturity reveals biotic and metabolic responses
- (Peer Reviewed Journal)
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Varoquaux, N., Cole, B., Gao, C., Pierroz, G., Baker, C., Patel, D., Madera, M., Jeffers, T., Hollingsworth, J., Sievert, J., Yoshinaga, Y., Owiti, J., Singan, V., Degraaf, S., Xu, L., Blow, M., Harrison, M., Visel, A., Jansson, C., Niyogi, K., Hutmacher, R., Coleman-Derr, D.A., O'Malley, R., Taylor, J., Dahlberg, J., Vogel, J., Lemaux, P., Purdom, E. 2019. Transcriptomic analysis of field-droughted sorghum from seeding to maturity reveals biotic and metabolic responses. Proceedings of the National Academy of Sciences. 116(52):27124–27132. https://doi.org/10.1073/pnas.1907500116.
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Causes and consequences of a conserved bacterial root microbiome resposnse to drought stress
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Xu, L., Coleman-Derr, D.A. 2019. Causes and consequences of a conserved bacterial root microbiome resposnse to drought stress. Current Opinion in Microbiology. 49:1-6.
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OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species
- (Peer Reviewed Journal)
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Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y.Q., Coleman-Derr, D.A., Xia, Q., Wang, Y. 2019. OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 47(W1):W52-W58. https://doi.org/10.1093/nar/gkz333.
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Role of the plant root microbiome in abiotic stress tolerance
- (Book / Chapter)
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Caddell, D., Deng, S., Coleman-Derr, D. 2019. Role of the plant root microbiome in abiotic stress tolerance. In: Verma, S. and White, J. editors. Seed Endophytes 1st Edition. Sham, Switzerland: Springer Verlag. p. 273-311.
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Strong succession in arbuscular mycorrhizal fungal communities
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Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Sievert, J.A., Purdom, E., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P.G., Taylor, J.W. 2018. Strong succession in arbuscular mycorrhizal fungal communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 13:214-226. https://doi.org/10.1038/s41396-018-0264-0.
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Strong succession in arbuscular mycorrhizal fungul communities
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Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Purdom, E., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P.G., Taylor, J.W. 2018. Strong succession in arbuscular mycorrhizal fungul communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 13:214-226. https://doi.org/10.1038/s41396-018-0264-0.
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Exploring the root microbiome: extracting bacterial community data for the soil, rhizosphere, and root endosphere
- (Peer Reviewed Journal)
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Simmons, T., Caddell, D., Deng, S., Coleman-Derr, D.A. 2018. Exploring the root microbiome: extracting bacterial community data for the soil, rhizosphere, and root endosphere. Journal of Visualized Experiments. 135:1-10.
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Drought stress and root-associated bacterial communities
- (Review Article)
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Naylor, D., Coleman-Derr, D.A. 2018. Drought stress and root-associated bacterial communities. Frontiers in Plant Science. 8(2223):1-16. https://doi.org/10.3389/fpls.2017.02223.
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Drought and host selection influence microbial community dynamics in the grass root microbiome
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Naylor, D., Degraaf, S., Purdom, E., Coleman-Derr, D.A. 2017. Drought and host selection influence microbial community dynamics in the grass root microbiome. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 11:2691-2704. https://doi.org/10.1038/ismej.2017.118.
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Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria
- (Peer Reviewed Journal)
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Xu, L., Naylor, D., Dong, Z., Simmons, T., Pierroz, G., Hixson, K., Young, M., Zink, E.M., Engbrecht, K., Wang, Y., Gao, C., Degraff, S., Madera, M., Sievert, J.A., Hollingsworth, J., Birdseye, D., Scheller, H., Hutmacher, R., Dahlberg, J., Jansson, C., Taylor, J., Lemaux, P., Coleman-Derr, D.A. 2018. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proceedings of the National Academy of Sciences. 115(18):E4284-E4293.
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PIECE 2.0: an update for the plant gene structure comparison and evolution database
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Wang, Y., Xu, L., Thilmony, R.L., You, F., Gu, Y.Q., Coleman-Derr, D.A. 2016. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Research. 45(D1):1015-1020. https://doi.org/10.1093/nar/gkw935.
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Piece2.0: an update for the pant gene structure comparison and evolution database
- (Peer Reviewed Journal)
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Wang, Y., Ling, X., Thilmony, R., You, F., Gu, Y., Coleman-Derr, D.A. 2016. Piece2.0: an update for the pant gene structure comparison and evolution database. Nucleic Acids Research. 45:1015-1020.
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Drought-induced shifts in the root microbiome
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Naylor, D., Deng, S., Xu, L., Coleman-Derr, D.A. 2016. Drought-induced shifts in the root microbiome. Meeting Abstract. Plant Microbial Interactions Symposium, Joint Genome Institute
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GSP: A web-based platform for designing genome-specific primers in polyploids
- (Peer Reviewed Journal)
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Wang, Y., Tiwari, T., Coleman-Derr, D.A., Rawda, N., Gill, B., Huo, N., You, F., Gu, Y.Q. 2016. GSP: A web-based platform for designing genome-specific primers in polyploids. Bioinformatics. doi: 10.1093/bioinformatics/btw/34.
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MetaCoMET: a web platform for discovery and visualization of the core microbiome
- (Peer Reviewed Journal)
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Wang, Y., Xu, L., Gu, Y.Q., Coleman-Derr, D.A. 2016. MetaCoMET: a web platform for discovery and visualization of the core microbiome. Bioinformatics. 32(22):3469-3470. doi:10.1093/bioinformatics/btw507.
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GSP: a web-based platform for designing genome-specific primers in polyploids
- (Peer Reviewed Journal)
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Wang, Y., Tiwari, V.K., Rawat, N., Gill, B.S., Huo, N., You, F.M., Coleman-Derr, D.A., Gu, Y.Q. 2016. GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics. 32(15):2382-2383.
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The Cacti microbiome: interplay between habitat-filtering and host-specificity
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Fonseca-Garcia, C., Coleman-Derr, D.A., Garrido, E., Visel, A., Tringe, S., Partida-Martinez, L. 2016. The Cacti microbiome: interplay between habitat-filtering and host-specificity. Frontiers in Microbiology. 7:1-16.
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High-resolution phylogenic microbial community profiling
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Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.
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OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
- (Peer Reviewed Journal)
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Wang, Y., Coleman-Derr, D.A., Chen, G., Gu, Y.Q. 2015. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 43(W1):W78-W84. doi: 10.1093/nar/gkv487.
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Inferring geographic origin of barley accessions using molecular markers
- (Peer Reviewed Journal)
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Bonman, J.M., Gu, Y.Q., Coleman Derr, D., Jackson, E.W., Bockelman, H.E. 2010. Inferring geographic origin of barley accessions using molecular markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-010-9574-4.
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Origin of barley accessions with multiple disease resistance determined by SSR analysis.
- (Abstract Only)
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Bonman, J.M., Gu, Y., Coleman Derr, D., Jackson, E.W., Chao, S., Bockelman, H.E. 2008. Origin of barley accessions with multiple disease resistance determined by SSR analysis.. International Congress of Plant Pathology Abstracts and Proceedings.
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HYBSWEEPER: A RESOURCE FOR DETECTING HIGH-DENSITY PLATE COORDINATES
- (Peer Reviewed Journal)
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Lazo, G.R., Lui, N., Gu, Y.Q., Kong, X., Coleman Derr, D., Anderson, O.D. 2005. Hybsweeper: a resource for detecting high-density plate coordinates. Biotechniques. 39:320-324.
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GENOMIC ORGANIZATION OF THE COMPLEX A-GLIADIN GENE LOCI IN WHEAT
- (Peer Reviewed Journal)
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Gu, Y.Q., Crossman, C.C., Kong, X., Luo, M., You, F.M., Coleman Derr, D., Dubcovsky, J., Anderson, O.D. 2004. Genomic organization of the complex a-gliadin gene loci in wheat. Theoretical and Applied Genetics. 109:648-657.
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Rapid genome evolution as revealed by comparative sequence analysis of orthologous regions from four triticeae genomes
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Gu, Y.Q., Coleman-Derr, D., Kong, X., Anderson, O.D. 2004. Dynamics and rapid genome evolution in allopolyploid wheat as revealed by comparative sequence analysis of the complex hmw-glutenin locus regions. Plant Physiology. 135:459-470.
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ARS News Articles
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