Comparative genomics tool from Haney Lab PDF Ryan Melnyk!: “PyParanoid: Scalable homolog detection from large genomic databases”

Haney Lab Publications

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Song, Y., Zhang, X., Qiu, Y., Briggs, A., Millet, Y., Bartenstein, D., Mankiw, C., Cerulli, C., Bush, J., Adams, K.L., Diener, A.C., Ausubel, F.M., Haney, C.H. (2021). A screen for mutants deficient in coronatine-mediated suppression of root immunity identifies Arabidopsis SDA1 as a novel integrator of immunity and phytohormone signaling. bioRxiv 2021.09.12.459990 doi:

Wang, N.R., Melnyk, R.A., Wiesmann, C.L., Hossain, S.S., Chi, M., Martens, K., Haney, C.H. (2021). Commensal Pseudomonas fluorescens protect Arabidopsis from closely-related Pseudomonas pathogens in a colonization-dependent manner. bioRxiv 2021.09.02.458786.

Socha A.L., Song, Y., Ross, B.R., Bush, J., Ausubel, F.M., Guerinot, M., Haney, C.H. (2021). Natural variation in Arabidopsis ISR1 affects iron localization and induced systemic resistance. bioRxiv 2021.09.01.458588.

Geissmann, Q., Abram, P.K., Wu, D., Haney, C.H., and Cariillo, J. (2021). Sticky Pi, an AI-powered smart insect trap for community chronoecology. bioRxiv


Song, Y. and Haney, C.H.* (2021). Drought dampens microbiome development. Nature Plants.

Song, Y., Wilson, A., Zhang, X.C., Thoms, D., Sohrabi, R., Song, S., Geissmann, Q., Liu, Y., Walgren, L., He, S.Y. and Haney, C.H.* (2021). FERONIA restricts Pseudomonas in the rhizosphere microbiome via regulation of reactive oxygen speciesNature Plants.

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Harting, R.#, Nagel, A.#, Nesemann, K., Höfer, A.M., Kusch, H.,, Stanley, C.E., Stöckli, M., Kaever, A., Hoff, H., Stanke, M., deMello, A.J., Künzler, M., Haney, C. H., Braus-Stromeyer, S.A., and Braus, G.H.* (2021). Pseudomonas strains induce transcriptional and morphological changes and reduce root colonization of Verticillium spp. Frontiers in Microbiology.

Thoms, D., Liang, Y., and Haney, C. H.* (2021). Maintaining symbiotic homeostasis: How do plants engage with beneficial microorganisms while at the same time restricting pathogens? Molecular-plant microbe interactions.

Song, S., Liu, Y., Wang, N., and Haney, C. H.* (2021). Mechanisms in plant-microbiome interactions: lessons from model systems. Current Opinion in Plant Biology.


Wang, N., and Haney, C. H*. (2020). Harnessing the genetic potential of the plant microbiome. The Biochemist. 42 (4): 20–25. doi:

Vishwanathan, K., Zienkiewicz, K., Liu, Y., Janz, D., Feussner, I., Polle, A.*, and Haney, C. H*. (2020). Ectomycorrhizal fungi induce systemic resistance against insects on a non-mycorrhizal plant in a CERK1-dependent manner. New Phytologist. doi:

Beskrovnaya, P.#, Melnyk, R. A.#, Liu, Z., Liu, Y., Higgins, M. A., Song, Y., Ryan, K., and Haney, C. H*.  (2020) Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility.  mBIO. doi: #Equal contributions.


Yu, K., Liu, Y., Tichelaar, R., Savant, N., Lagendijk, E., van Kuijk, S.J.L., Stringlis, I.A., van Dijken, A.J.H., Pieterse, C.M.J., Bakker, P.A.H.M, Haney, C.H. and Berendsen, R.L. (2019). Plant-beneficial Pseudomonas spp. suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Current Biology. Doi: 10.1016/j.cub.2019.09.015

Melnyk, R. A., Hossain, S. S., and Haney, C. H*. (2019). Convergent gain and loss of genomic islands drive lifestyle changes in plant-associated bacteria. ISME.  In the news.


Liu, Z. X., Beskrovnaya, P., Melnyk, R. A., Hossain, S. S.,  Khorasani, S., O’Sullivan, L.R., Wiesmann, C. L., Bush, J, Richard, J. D., and Haney, C. H*. (2018). A genome-wide screen identifies genes in rhizosphere-associated Pseudomonas required to evade plant defences.  mBioDOI: 10.1128/mBio.00433-18.   Liu et al. News Release

Melnyk, R. A. and Haney, C. H*. (2018). Bacterial genomics of plant adaptation. Nature Genetics. 50 (2-4) doi:

Lang, C., Smith, L., Haney, C.H., and Long, S.R. (2018). Characterization of novel plant symbiosis mutants using a new multiple gene-expression reporter Sinorhizobium meliloti strain. Frontiers in Plant Science.

(2017 and prior)

Melnyk, R. A. and Haney, C. H*. (2017). Plant Pathology: Plasmid powered evolutionary transitions.  ELife2017;6:e33383  DOI: 10.7554/eLife.33383.

Haney, C.H*., Wiesmann, C., Shapiro, L., Melnyk, R. A., O’Sullivan, L., Khorasani, S.,  Xiao, L., Han, J., Bush, J., Carillo, J, Pierce, N., Ausubel, F.M. (2017). Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens. Molecular Ecology. Oct 31. doi: 10.1111/mec.14400 

Haney, C. H. and Aususbel, F. M. (2015). Plant microbiome blueprints. Science. 349 (6250): 788-9. doi:

Rellán-Álvarez, R., Lobet, G., Lindner, H., Pradier, P.L., Yee, M. C., Sebastian, J., Geng, Y., Trontin, C., LaRue, T., Schrager, A., Haney, C. H., Nieu, R., Maloof, J., Vogel, J., and Dinneny J. R. (2015) Multidimensional mapping of root system responses to soil environmental cues using a luminescence-based imaging system. ELife. doi: 10.7554/eLife.07597

Haney, C.H., Samuel, B. S., Bush, J and Ausubel, F.M. (2015). Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nature Plants. 1(6): 1-9. doi:

Haney, C.H., Urbach, J. and Ausubel, F.M. (2014). Innate immunity in plants and animals: Differences and similarities. The Biochemist. 36(5):1-5. doi: