Author

J. J. Doyle

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 2 Plant Biology· 2

Signature Assays, Organisms & Methods

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Organism:Arabidopsis· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Assay:DNA methylation· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Assay:bulk RNA-seq· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

J. E. Coate· 2 shared A. D. Farmer· 1 shared A. D. Grinage· 1 shared A. M. Berry· 1 shared B. I. Potter· 1 shared C. D. Specht· 1 shared C. Jelley· 1 shared C. S. Moreau· 1 shared

Activity by Year

2019-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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2 shared papersPlant Biology

J. E. Coate

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Author profile →

4 papers

Recent·Most cited

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

J. S. Suissa, G. Y. De La Cerda, L. C. Graber, C. Jelley, D. Wickell, H. R. Phillips, A. D. Grinage, C. S. Moreau, C. D. Specht, J. J. Doyle, J. B. Landis

This study compares SNP and full locus datasets in phylogenomic analyses, finding that tree topology is largely congruent but filtering missing data too strictly can reduce confidence in relationships.

bioRxiv · Sep 2, 2023 · PreprintEvolutionary Biology

Comparative Phylogenomics and Phylotranscriptomics Provide Insights into the Genetic Complexity of Nitrogen Fixing Root Nodule Symbiosis

Y. Zhang, Y. Fu, W. Xian, X. Li, Y. Feng, F. Bu, Y. Shi, S. Chen, R. v. Velzen, A. M. Berry, M. G. Salgado, H. Liu, T. Yi, P. Fournier, N. Alloisio, , S. Cheng

The paper uses phylogenomic and phylotranscriptomic analyses to study the evolution of nitrogen-fixing root nodule symbiosis across the Nitrogen-Fixing Nodulation Clade, finding no convergence at the amino acid level and highlighting the role of NIN as a master regulator.

bioRxiv · Apr 3, 2023Evolutionary Biology

Expression partitioning of duplicate genes at single cell resolution in Arabidopsis roots

J. E. Coate, A. D. Farmer, J. Schiefelbein, J. J. Doyle

The paper analyzes expression patterns of duplicate genes in Arabidopsis roots at single-cell resolution, identifying subfunctionalization and shifts in expression across cell types and states.

bioRxiv · Aug 20, 2020Plant Biology

Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana

B. I. Potter, M. J. Song, J. J. Doyle, J. E. Coate

The paper quantifies gene dosage responses in Arabidopsis thaliana after ploidy change, showing variable expression responses and coordinated changes in dosage-sensitive gene groups.

bioRxiv · Oct 7, 2019Plant Biology