Josie Gleeson

GenomeProt: User friendly proteogenomics for canonical and non-canonical proteoform characterisation

GenomeProt integrates genomics, transcriptomics, and proteomics to characterise proteoforms, discovering novel proteins and variant-containing peptides in human brain and melanoma samples.

Isoform-level resolution in single-cell CRISPR screens reveals hidden functional consequences of gene perturbation

This paper evaluates isoform-level resolution in single-cell CRISPR screens using long-read sequencing, finding that it captures splicing changes missed by gene-level analysis.

Alternative promoters used during myeloid differentiation and upon activation change the gene products available for innate immune programs.

The paper identifies new gene products and transcript isoforms in macrophage differentiation and activation, revealing how alternative promoters influence innate immune functions.

Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain

The paper uses long-read sequencing to identify novel RNA isoforms in neuropsychiatric risk genes, revealing previously undetected exons and isoforms that may contribute to disease mechanisms.

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

LongBench benchmarks long-read RNA-sequencing technologies using a cross-platform dataset of cancer cell lines, showing high gene-level concordance but reduced transcript-level consistency across platforms.

Isoform-level profiling of m6A epitranscriptomic signatures in human brain

The paper uses Oxford Nanopore DRS to profile m6A modifications at the isoform level in human brain regions, identifying thousands of m6A sites and region-specific patterns.

Discovery of NRG1-VII: a novel myeloid-derived class of NRG1 isoforms

The paper identifies a new class of NRG1 isoforms, NRG1-VII, expressed in myeloid cells and suggests it may be the most common NRG1 class in adult tissues outside the brain.

Nanopore direct RNA sequencing detects differential expression between human cell populations

This study uses nanopore direct RNA sequencing to accurately detect differential gene and isoform expression between human cell populations during differentiation.