Paul G. Ekert

METTL1 gene dosage and catalytic activity define a targetable vulnerability in pediatric cancers

This study identifies METTL1 gene dosage and catalytic activity as therapeutic targets in pediatric cancers, showing that inhibiting METTL1 synergizes with BCL-xL inhibitors.

Closing the fusion-detection gap in single-cell RNA-seq with a scalable, probe-based workflow

The paper introduces a probe-based workflow to detect oncogenic gene fusions in single-cell RNA-seq, validated in cancer cell lines and pediatric B-ALL cohorts.

Single-cell RNA-sequencing of cerebral spinal fluid identifies circulating tumour cells in children with brain cancer

This study uses single-cell RNA-sequencing of cerebrospinal fluid to identify circulating tumour cells in children with brain cancer, revealing their dynamics and potential as biomarkers.

CBL mutations in pediatric solid and CNS tumors are a marker of receptor tyrosine kinase activation and a potential therapeutic target

Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology

This paper shows RNA-seq can detect most mutations found by WGS in pediatric tumors and provides additional insights into their pathogenicity.

Systematic silencing of oncogenic fusion transcripts with ultra-precise CRISPR-Cas13b

This paper introduces CRISPR-PspCas13b as a method to systematically silence oncogenic fusion transcripts, showing effectiveness against drug-resistant cancer drivers.

TALLSorts: a T-cell acute lymphoblastic leukaemia subtype classifier using RNA-seq expression data

TALLSorts classifies T-ALL samples using bulk RNA-seq data with high accuracy across four international cohorts.

Molecular principles of CRISPR-Cas13 mismatch intolerance enable selective silencing of point-mutated oncogenic RNA with single-base precision

This paper develops CRISPR-Cas13 crRNAs that selectively silence oncogenic SNV transcripts with single-base precision by exploiting mismatch intolerance in target-spacer interactions.

Toblerone: detecting exon deletion events in cancer using RNA-seq

Toblerone detects exon deletions in RNA-seq data, specifically applied to IKZF1 in B-ALL samples, identifying deletions associated with poor prognosis.

Single-base precision design of CRISPR-Cas13b enables systematic silencing of oncogenic fusions

This study designs CRISPR-Cas13b crRNAs with single-base precision to silence oncogenic gene fusions, enhancing targeting efficacy and selectivity.

JAFFAL: Detecting fusion genes with long read transcriptome sequencing

JAFFAL detects fusion genes from long-read transcriptome sequencing with high accuracy, outperforming existing methods and enabling single-cell resolution.

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

MINTIE identifies novel structural and splice variants in transcriptomes using RNA-seq data, outperforming existing methods in detecting a wide range of variants.

ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia.

ALLSorts classifies B-ALL samples into 18 subtypes and five meta-subtypes using RNA-Seq data with high accuracy.

Clinker: visualising fusion genes detected in RNA-seq data

Clinker visualizes fusion genes detected in RNA-seq data, enabling interpretable analysis of fusion transcripts and breakpoints in B-ALL.