Rebecca Claire Fitzgerald

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

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.

Spatially resolved transcriptomic and proteomic profiling reveals cell interaction programs that predict Barrett's esophagus progression

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

Single cell analysis of Barrett's esophagus and carcinoma reveals cell types conferring risk via genetic predisposition

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.

RNA liquid biopsy via nanopore sequencing for novel biomarker discovery and cancer early detection

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.

Subclonal mutation load predicts survival and response to immunotherapy in cancers with low to moderate tumor mutation burden

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.

Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

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.

The mutational landscape of human somatic and germline cells

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.

Extrachromosomal DNA in the cancerous transformation of Barrett's esophagus

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.

Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma

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.

Extensive phylogenies of human development reveal variable embryonic patterns

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

Genomic copy number predicts oesophageal cancer years before transformation

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

Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma

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

Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation

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.

Process-specific somatic mutation distributions vary with three-dimensional genome structure

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

Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

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

Low-cost and clinically applicable copy number profiling using repeat DNA

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.