Publications

Roy et al. (2025). “The PO-Driven Model”: A Basic Science Pipeline for the Bioeconomy with Solutions Inspired by Convergent Evolution for Connecting Parallel Research Ideas. Integrative and Comparative Biology.

Lee et al. (2025). A well-annotated genome of Apium graveolens var. dulce cv. Challenger, a celery with resistance to Fusarium oxysporum f. sp. apii race 2. The Plant Journal.

Groh et al. (2025). Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories. Science.

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Zhang et al. (2025). Cell layer-specific cell wall modification is associated with exo-mesocarp split in pistachio (Pistacia vera L.). Journal of Experimental Botany.

Klein et al. (2025). Climate adaptation in Populus trichocarpa: key adaptive loci identified for stomata and leaf traits. New Phytologist.

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Monroe et al. (2025). Delineating Mutation Bias and Selection during Plant Development. bioRxiv.

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Quiroz et al. (2025). Evolutionary trajectories of cohesin gatekeepers across the Tree of Life. bioRxiv.

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Davis et al. (2025). Extreme somatic mutation variation through time and space in walnut clones. bioRxiv.

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Zhao et al. (2025). Functional insights into dispensable genes using genome-wide loss-of-function burden tests in Arabidopsis. bioRxiv.

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Adaskaveg & Lee et al. (2025). In a nutshell: pistachio genome and kernel development. New Phytologist.

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Pierce et al. (2025). Intron architecture predicts chromatin features in Arabidopsis thaliana. bioRxiv.

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Rose et al. (2025). Introns increase gene expression in Caenorhabditis elegans by a mechanism that must be at least partly different than in plants. Scientific Reports.

Ebrahimi et al. (2025). Phylogenomic and comparative genome analysis of the Juglandaceae family reveals black walnut (Juglans nigra) as an ancient lineage of the Rhysocaryon section. bioRxiv.

Long et al. (2025). Protein structure and selection pressure in plants: using mutation to understand the functional importance of protein structure. BMC Genomics.

Lensink et al. (2025). Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis. Genetics.

Zhao et al. (2025). Unlocking genetic diversity in Colombian cassava landraces for accelerated breeding. New Phytologist.

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Karasov et al. (2024). Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought. Nature Microbiology.

Monroe et al. (2024). Convergent discoveries support convergent evolution of life-history strategies: the importance of summer drought.. New Phytologist.

Monroe et al. (2024). Convergent evolution of epigenome recruited DNA repair across the Tree of Life. bioRxiv.

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Waneka et al. (2024). Exploring the relationship between gene expression and low-frequency somatic mutations in Arabidopsis with duplex sequencing. Genome biology and evolution.

Quiroz et al. (2024). H3K4me1 recruits DNA repair proteins in plants. The Plant Cell.

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Sutherland et al. (2024). High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features. EMBO reports.

Monroe et al. (2023). Are Mutations Random?. Evolution.

Quiroz et al. (2023). Causes of mutation rate variability in plant genomes. Annual Review of Plant Biology.

Williams et al. (2023). Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants. Genome Biology.

Raju et al. (2023). Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs. New Phytologist.

Lee et al. (2023). PE0306 Haplotype-Resolved Genome Assemblies and a Pan-Genome of Six Pistachio Cultivars.

Monroe et al. (2023). Potential and limits of (mal) adaptive mutation rate plasticity in plants. New Phytologist.

Monroe et al. (2023). Reply to: Re-evaluating evidence for adaptive mutation rate variation. Nature.

Heckman et al. (2022). Beyond bulk: Density fractions explain heterogeneity in global soil carbon abundance and persistence. Global Change Biology.

Monroe et al. (2022). Mutation bias reflects natural selection in Arabidopsis thaliana. Nature.

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Monroe et al. (2021). Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium. G3.

Monroe et al. (2021). Evolutionary Genetics: Concepts, Analysis, and Practice by Glenn-Peter Sætre and Mark Ravinet. The Quarterly Review of Biology.

Monroe et al. (2021). The population genomics of adaptive loss of function. Heredity.

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Lawrence et al. (2020). An open-source database for the synthesis of soil radiocarbon data: International Soil Radiocarbon Database (ISRaD) version 1.0. Earth System Science Data.

Togninalli et al. (2020). AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. Nucleic acids research.

Baggs et al. (2020). Convergent loss of an EDS1/PAD4 signaling pathway in several plant lineages reveals coevolved components of plant immunity and drought response. The Plant Cell.

Mason et al. (2020). Learning from dynamic traits: seasonal shifts yield insights into ecophysiological trade-offs across scales from macroevolutionary to intraindividual. International Journal of Plant Sciences.

Monroe et al. (2020). The lowest hanging fruit: Beneficial gene knockouts in past, present, and future crop evolution. Current Plant Biology.

Keiluweit et al. (2019). An open source database for the synthesis of soil radiocarbon data: ISRaD version 1.0. (No Title).

Monroe et al. (2019). Drought regimens predict life history strategies in Heliophila. New Phytologist.

Srikant et al. (2019). The A. thaliana methylome influences chromatin accessibility after heat stress.

Endriss et al. (2019). The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours. Ecology Letters.

Price et al. (2018). Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana. Proceedings of the National Academy of Sciences.

Monroe et al. (2018). Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife.

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Monroe et al. (2018). Ecoevolutionary dynamics of carbon cycling in the anthropocene. Trends in ecology & evolution.

Dittberner et al. (2018). Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana. Molecular ecology.

Monroe et al. (2017). TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps. BioData mining.

Monroe et al. (2016). Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana. Molecular ecology.

Mojica et al. (2016). Genetics of water use physiology in locally adapted Arabidopsis thaliana. Plant Science.

Zhu et al. (2016). Molecular and systems approaches towards drought-tolerant canola crops. New Phytologist.

Rockenbach et al. (2016). Positive selection in rapidly evolving plastid--nuclear enzyme complexes. Genetics.