Diane E. Trout

The paper uses hybrid crosses to analyze regulatory variation in mouse tissues, finding cell-type-specific trans-acting effects and highlighting the limitations of bulk tissue analysis.

The paper characterizes transcriptomes across 8 tissues in 8 mouse strains to identify expression variation linked to genetic differences and phenotypic traits.

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

The paper identifies regulatory programs in postnatal mouse development using single-nucleus data, revealing cell-type-specific and common regulatory topics across multiple tissues.

The paper introduces Topyfic, a reproducible LDA method, to identify cellular programs in single-cell data and shows sex-specific differences in microglial activation in Alzheimer's disease mouse models.

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper introduces LR-Split-seq, a long-read single-cell RNA-seq method, to study differential RNA isoform expression and validates it using mouse myoblast differentiation data.

The paper quantifies the mouse embryo transcriptome from E10.5 to birth using whole-tissue and single-cell RNA-seq, identifying key gene expression patterns and cell types.

The paper maps DNA methylation changes across 12 mouse tissues at 8 developmental stages, identifying methylation variant regions and tissue-specific enhancers linked to human genetic diseases.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

TALON annotates and counts full-length reads from PacBio or Nanopore in one framework; in mouse brain, 422 genes showed more novel-isoform reads than annotated ones.

The paper analyzes miRNA expression dynamics across mouse embryonic development, identifying tissue-specific clusters and their regulatory roles.