Martin Hirst

Cell-of-origin epigenome underlies SS18::SSX-mediated transformation

This study identifies the cell-of-origin of synovial sarcoma as a rare fibroblastic population and shows that SS18::SSX induces an embryonic-like mesenchymal stem cell phenotype.

Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi

The paper discovers that haploid chromosomes in two pathogenic fungi are segregated into separate nuclei, challenging the traditional view of nuclear chromosome content.

Cell type-specific epigenomic variation and its association with genotype in the human breast

The paper quantifies cell type-specific epigenomic variation in human breast epithelial cells and links it to genetic variants, showing most regulatory variants act in a single cell type.

tp53 R217H and R242H Mutant Zebrafish Exhibit Dysfunctional p53 Hallmarks and Recapitulate Li-Fraumeni Syndrome Phenotypes

This study characterizes zebrafish models of Li-Fraumeni syndrome with TP53 mutations, showing dysfunctional p53 pathways, tumor development, and mutation-specific phenotypes.

Synovial Sarcoma Chromatin Dynamics Reveal a Continuum in SS18:SSX Reprograming

This study examines the epigenomic states of synovial sarcoma using multi-omics analysis, revealing a continuum of epigenomic states and identifying H3K4me3 inhibition as a potential therapeutic strategy.

SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription

This paper shows SS18::SSX fusion protein alters BAF chromatin remodeler distribution, leading to transcriptional activation and repression by changing histone modifications at regulatory regions.

The ENCODE Uniform Analysis Pipelines

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.

Genome-Wide Detection of Imprinted Differentially Methylated Regions Using Nanopore Sequencing

The paper uses nanopore sequencing to detect imprinted differentially methylated regions in human B-lymphocyte cell lines, identifying known and novel DMRs and showing conservation across species.

Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

The paper optimizes a magnetic bead-based nucleic acid extraction protocol for SARS-CoV-2 testing to reduce cross-well contamination while maintaining sensitivity.

Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data

Epiclomal clusters sparse single-cell DNA methylation data and imputes missing values, outperforming non-probabilistic methods and revealing sub-clonal methylation patterns in tumour genomes.

Genetic dissection of the redundant and divergent functions of histone chaperone paralogs in yeast

This study investigates the redundant and divergent functions of histone chaperone paralogs Fpr3 and Fpr4 in yeast using a refined synthetic genetic array approach.