Sean T. Bresnahan

The paper shows that RNA-seq quantification methods and reference annotations significantly impact eQTL analysis, colocalization, and TWAS results across multiple tissues and phenotypes.

ICONIC is an R package that integrates instrumental variable and negative-control methods for causal inference in multi-omic studies, offering diagnostics and benchmarks for mediation analysis.

The paper uses long-read RNA-seq to create a comprehensive placental transcriptome reference, revealing high transcriptional complexity and identifying novel isoforms associated with metabolic and endocrine functions in gestational diabetes.

The paper shows PFAS affect birth weight and gestational age through distinct transcriptional network architectures, with network position, not fold-change, determining mediator importance.

This study identifies genetic risk mechanisms for six cancers by analyzing isoform-level expression data, finding more associations and greater heritability explained compared to gene-level analysis.

The paper investigates parent-of-origin gene expression differences in honey bee caste determination, finding patrigenes favor queen fate and linking these to histone modifications.