Nicola Waddell

Genomic alterations enable BRCA1 methylation loss and promoter bypass to drive resistance in high-grade serous ovarian cancer

This study identifies genomic mechanisms enabling BRCA1 methylation loss and promoter bypass in ovarian cancer, leading to PARP inhibitor resistance.

Mapping Functional Tumor Suppressor Networks in Esophageal Adenocarcinoma Using In Vivo CRISPR Screening and Perturb-sequencing

The paper identifies tumor suppressors and their functional roles in esophageal adenocarcinoma progression using CRISPR screening and Perturb-seq.

Explainable machine learning identifies features and thresholds predictive of immunotherapy response

The paper develops a multi-omic random forest model to predict immunotherapy response in melanoma using SHAP for feature threshold identification.

Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS-chemokine-myeloid axis

This study shows that chromosomal instability in esophageal adenocarcinoma drives an inflammatory tumor microenvironment through a cGAS-chemokine-myeloid axis, with CXCL8 as a key mediator.

Cancer genomic profiling predicts pathogenicity of BRCA1 and BRCA2 variants

The paper develops machine learning models to predict pathogenicity of BRCA1 and BRCA2 variants using cancer genomic profiles, improving classification of variants of uncertain significance.

Agent SPI-WSI: In context learning for computationally spatial pathwayinferring on whole slide histopathology images conditioned on bulk RNAsequencing using pathologist in the loop.

The paper introduces an AI agent that localizes bulk RNA-seq pathway activity in histopathology images using pathologist feedback and large language models.

Integrating breast tumor homologous recombination deficiency status to aid germline BRCA1 and BRCA2 variant classification

This paper integrates tumor homologous recombination deficiency status with germline BRCA1 and BRCA2 variant classification to improve pathogenicity prediction.

Demethylating agents drive PARP inhibitor resistance in ovarian carcinomas with BRCA1 gene silencing

This study shows that DNMT1 inhibitors reduce BRCA1 promoter methylation in HGSOC, leading to BRCA1 re-expression and PARP inhibitor resistance.

Generation of a PARPi-sensitive homozygous BRCA1-methylated OVCAR8 cell line using targeted CRISPR gene editing

The paper generates a homozygous BRCA1-methylated OVCAR8 cell line using CRISPR editing to study meBRCA1 stability and PARPi resistance.

Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology

This paper benchmarks Bayesian deep learning models for predicting cancer of unknown primary, showing improved uncertainty generalisation and accuracy under distributional shifts.

Genomic analysis of patient-derived xenograft models reveals intra-tumor heterogeneity in endometrial cancer and can predict tumor growth inhibition with talazoparib

The paper develops endometrial cancer PDX models that capture tumor heterogeneity and predict response to talazoparib.

CRISPR/Cas9-mediated genome editing of Schistosoma mansoni acetylcholinesterase

This paper uses CRISPR/Cas9 to edit the acetylcholinesterase gene in Schistosoma mansoni eggs, resulting in reduced AChE activity and decreased granuloma size in mice.

Genomic footprints of activated telomere maintenance mechanisms in cancer

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

Chromatin interactome mapping at 139 independent breast cancer risk signals

The paper maps chromatin interactions at 139 breast cancer risk signals using Capture Hi-C and identifies candidate target genes and functional mechanisms.

Genome Scale Epigenetic Profiling Reveals Five Distinct Subtypes of Colorectal Cancer

The paper identifies five distinct subtypes of colorectal cancer using DNA methylation profiling and links them to specific mutations and gene body methylation patterns.

Profiling copy number alterations in cell-free tumour DNA using a single-reference

This paper introduces qCNV and sCNA-seq tools to profile somatic copy number alterations in cell-free DNA without a reference panel, showing effectiveness in detecting clinically relevant mutations from plasma samples.