Barbara J. Wold

This study identifies second-order spatial features, such as ligand-receptor interactions, as predictive of glioma malignant transformation using integrated spatial DNA and RNA profiling.

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 introduces ember, an entropy-based framework to assess gene specificity in single-cell RNA sequencing data, revealing unexpected patterns in gene expression across tissues and mouse strains.

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

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

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.

This paper creates a human embryonic limb cell atlas using single-cell and spatial transcriptomics, identifying novel cell populations and developmental patterns.

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 the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

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 identifies and characterizes HOT loci with high DAP associations, finds driver motifs, and shows their regulatory importance through mutagenesis.

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.

The paper presents ChIP-seq data for 208 DNA-associated proteins in HepG2 cells, revealing occupancy patterns and DNA motifs, and distinguishing promoters from enhancers.

The paper develops a method to quantify transcriptome-wide epistasis using whole-organism RNA-seq and applies it to reconstruct genetic pathways in C. elegans.