Amit M. Fenn

The paper analyzes transcriptomic responses of FER-RALF-LRX pathway mutants to Ecr infection, finding limited transcriptional changes but altered basal gene expression related to cell wall metabolism and immunity.

This study evaluates WGCNA's ability to recover effector genes in dual-organism RNA-seq by simulating varying library ratios and signal strengths.

The paper shows that KAI2 signaling is not essential for AM symbiosis in all angiosperms, with some species showing only quantitative effects.

This paper derives a geometric state equation for the tree of life, showing evolution embeds into 2D hyperbolic space with curvature determined by entropy, and confirms this across multiple biological systems.

The paper presents a pangenome and pantranscriptome of hexaploid oat, describing gene expression diversity and structural genome variation across 33 accessions and six tissues.

The paper investigates how alternative splicing affects miRNA regulation by analyzing six TCGA cancer datasets, finding that transcripts with miRNA target sites in coding regions better predict miRNA expression.

Spycone analyzes alternative splicing in time course data to detect isoform switches and provides downstream analysis tools.

DICAST benchmarks alternative splicing analysis tools, showing STAR and HISAT2 perform best, and proposes a reporting standard for event detection.

The paper introduces NEASE, a tool for functional analysis of alternative splicing events, showing its ability to identify pathways related to tissue identity and cell type development, and highlight splicing-related biomarkers.