Andrew Oldfield

Malignant epithelial diversification and inflammatory neutrophil remodeling define a transitional stage between tumor cell dissemination and overt metastatic outgrowth in breast cancer

The paper identifies a transitional stage in breast cancer metastasis characterized by malignant epithelial diversification and inflammatory neutrophil remodeling, linking these to poor clinical outcomes.

Bivalent chromatin protects reversibly repressed genes from irreversible silencing

The paper shows that bivalent chromatin protects reversibly repressed genes from irreversible silencing by maintaining H3K4me3 at promoters, which prevents de novo DNA methylation in adult cancers.

Histone marks are drivers of the splicing changes necessary for an epithelial-to-mesenchymal transition

The paper shows that histone marks H3K27ac and H3K27me3 drive splicing changes during epithelial-to-mesenchymal transition by modulating splicing factor recruitment.

Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing

The paper shows LSD1 associates with RNA polymerase II pausing at gene promoters in mouse ESCs and influences gene expression patterns.

TALC: Transcript-level Aware Long Read Correction

TALC improves long-read transcriptome correction by modeling RNA expression and isoform representation, enhancing downstream RNA-seq accuracy.

NF-Y Controls Fidelity of Transcription Initiation at Gene Promoters Through Maintenance of the Nucleosome-Depleted Region

This study shows NF-Y maintains nucleosome-depleted regions at promoters to ensure accurate transcription initiation, preventing aberrant gene expression.

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

The paper maps multi-omic changes during mouse pluripotency transition, showing phosphoproteome dynamics precede epigenome and transcriptome changes.