Brian A. Williams

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 expands hematopoietic progenitors to study T cell development, identifying key regulators that control progression.

This paper shows that age-related memory CD8 T cells drive AD-like neurodegeneration upstream of Aβ/pTau in mice and are elevated in human AD patients.

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.

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 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.

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.