Yuko Yoshinaga

This study integrates multi-omic data with interpretable machine learning to identify genetic mechanisms underlying trait variation and phenotypic plasticity in switchgrass across environments.

The paper investigates DNA methylation-expression relationships in rice internode development using RNA-seq and bisulfite sequencing, finding specific methylation contexts correlate with gene expression patterns.

This study identifies hundreds of drought-responsive genes in sorghum using multi-season transcriptomic data from field experiments.

This study investigates the origins and adaptive consequences of polyploidy in the prairie grass Andropogon gerardi, finding that whole genome duplication is common and provides fitness advantages in xeric climates.

The paper identifies single-cell transcriptional responses to drought in Sorghum bicolor and highlights shared regulatory mechanisms across cell types.

The paper presents a scalable TFBS assay to create an atlas of 3,000 genome-wide binding site maps for 360 TFs across 10 flowering plant species, revealing conservation and rewiring of regulatory elements.

The paper presents an improved haplotype-resolved genome assembly for Eucalyptus grandis, increasing gene annotation completeness and revealing structural variations and tandem duplicates.

The paper analyzes 739 Thlaspi arvense accessions to uncover genetic variation and adaptation mechanisms, identifying genomic regions linked to agronomic traits and climate resilience.

This study uses multi-omics analysis to characterize Neurospora intermedia in oncom, revealing its role in byproduct conversion and potential for waste-to-food upcycling.

The paper analyzes a thousand-genome panel of Zymoseptoria tritici to trace its global spread and identify genetic changes associated with climatic adaptation.

The paper presents version 6 of the Chlamydomonas reinhardtii reference genome, improving assembly quality and revealing structural mutations in laboratory strains.

The paper maps meiotic recombination hotspots and sex-biased recombination in Populus trichocarpa using dense genetic mapping and haplotype reconstruction.

The paper develops a MAGIC population in maize to map flowering time and plant height, finding that predictive models perform better when trained on direct data rather than indirect data from hybrids.

This study uses long-read metagenomics and metatranscriptomics to analyze soil communities, revealing phylum-specific secondary metabolite dynamics during wetting events.

This study uses ChIP-Seq to profile H3K4 methylation across the Chlamydomonas cell cycle, revealing distinct patterns of mono- and trimethylation at gene promoters and their relationship to gene expression.

The paper describes a metagenome processing workflow that includes assembly, annotation, and binning, and provides tools for researchers to apply it to their data.