Nathan Johnson

SlEIL3-1 associates with a conserved EIL3/SLIM1 sulfate deficiency response core in tomato

The paper identifies SlEIL3-1 as a key regulator of sulfate deficiency response in tomato, showing its conserved function across species and its role in regulating S-related genes.

ABF2 and bZIP2 remodel root system architecture under combined phosphate deficiency and salinity in Arabidopsis

Organ-level Gene Regulatory Network models enable the identification of central transcription factors in Solanum lycopersicum

The paper constructs organ-level gene regulatory networks in tomato using RNA-seq data and validates them with DAP-seq, identifying key and novel transcription factors involved in fruit ripening and ABA response.

Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms

YASMA improves sRNA annotation accuracy and reproducibility by balancing sensitivity and specificity across diverse organisms.

Clade-wide fungal proteome analysis reveals structure-function conservation in divergent Dicer proteins

The paper analyzes fungal Dicer proteins across eight phyla, revealing structural and functional conservation despite divergence from canonical domain architectures.

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

The paper re-analyzes mi/milRNA hairpin RNAs in 40 fungal species, identifies high-quality loci, and provides a centralized resource for future research.