Devin Coleman-Derr
Plant Gene Expression Center
Research Molecular Biologist
Phone: (510) 559-5911
Fax: (510) 559-5678
Room 1026
USDA, ARS, PWA, PGEC
800 BUCHANAN STREET
ALBANY, CA 94710
Publications
(Clicking on the reprint icon
will take you to the publication reprint.)
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Holo-omics for deciphering plant-microbiome interactions
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(Peer Reviewed Journal)
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Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor
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(Peer Reviewed Journal)
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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. e02345-20. 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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(Peer Reviewed Journal)
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Nematode-encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase
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(Peer Reviewed Journal)
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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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(Peer Reviewed Journal)
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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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(Peer Reviewed Journal)
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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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A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome
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(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
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(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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(Peer Reviewed Journal)
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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
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(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
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Caddell, D., Deng, S., Coleman-Derr, D.A. 2019. Role of the plant root microbiome in abiotic stress tolerance. Springer Verlag. pp273-311.
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Strong succession in arbuscular mycorrhizal fungal communities
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(Peer Reviewed Journal)
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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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(Peer Reviewed Journal)
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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
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(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
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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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(Peer Reviewed Journal)
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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
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(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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(Peer Reviewed Journal)
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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
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(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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(Abstract Only)
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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
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(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
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(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
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(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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(Peer Reviewed Journal)
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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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(Peer Reviewed Journal)
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Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.
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(Peer Reviewed Journal)
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OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
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(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
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(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.
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(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
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(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
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(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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(Peer Reviewed Journal)
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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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