Rebecca Claire Fitzgerald

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

This study uses spatial transcriptomic and proteomic profiling to identify cell interaction patterns that predict progression of Barrett's esophagus.

The paper uses single cell RNA-sequencing and genome-wide association study data to identify cell types and processes involved in Barrett's esophagus and esophageal adenocarcinoma risk.

This study uses long-read nanopore sequencing of cell-free RNA to detect early-stage cancer and discover novel biomarkers, identifying 270,679 intergenic RNAs and potential therapeutic targets.

The paper investigates how CDKN2A and other 9p21 gene losses influence oesophageal cancer progression, finding context-dependent effects on survival and immune infiltration.

The paper develops CliPP to estimate subclonal mutation load (sML) and shows it predicts survival and immunotherapy response in cancers with low to moderate TMB.

The paper introduces a dual-modality imaging method combining high-resolution immunofluorescence and imaging mass cytometry to generate whole-slide IMC images with accurate single-cell segmentation.

This study compares mutational landscapes in somatic and germline cells across 29 anatomical structures, identifying key mutational signatures and their contributions to different cell types.

The paper investigates the development and evolution of extrachromosomal DNA (ecDNA) in Barrett's esophagus patients progressing to esophageal adenocarcinoma, finding ecDNA is strongly associated with cancer progression and enriched for oncogenes and immunomodulatory genes.

This study identifies genomic features associated with response to neoadjuvant chemotherapy in esophageal adenocarcinoma, finding lower mutation burden and specific copy number alterations linked to resistance.

The paper reconstructs phylogenies of human development using whole-genome sequencing to show variable embryonic patterns and lineage asymmetries across individuals and tissues.

This study shows genomic copy number changes can predict oesophageal cancer up to 10 years before diagnosis, enabling earlier treatment and reduced unnecessary monitoring.

The paper uses whole genome sequencing and phylogenetic analysis to show that metastases in esophageal adenocarcinoma spread rapidly through a clonal diaspora model.

This study evaluates the impact of cold storage on scRNAseq data quality for lung, spleen, and oesophagus tissues, finding minimal effects within 24 hours but increased stress markers at 72 hours.

The paper examines how somatic mutation distributions vary across chromatin folding domains in cancer genomes, revealing distinct patterns associated with different mutational processes.

The paper analyzes somatic retrotransposition events in 2,954 cancer genomes, identifying L1 insertions as significant contributors to structural variations and oncogenesis.

The paper introduces conliga, a method for inferring high-resolution SCNA profiles from a low-cost and simple assay, addressing the need for affordable SCNA analysis in clinical settings.