Daniel Lai

G4SCOPE predicts chromatin G-quadruplex occupancy from DNA sequence, revealing epigenetic differences in BRCA1 and BRCA2 deficient cells.

Serval is a modular framework for decoding spatial transcriptomics data that introduces Cosine, a method improving transcript recovery and correlation with expression references.

This paper develops a framework to analyze chromosomal mutational patterns at single-cell resolution, revealing drug-induced mutational signatures in human tissues.

The paper investigates the mutational signature of CX5461, a photosensitiser, when combined with UVA light, showing increased SNV burden only in co-exposed cells.

This study shows that somatic copy number mutations (CNA) influence metastatic fitness in breast cancer by mediating transcriptional changes and affecting clone survival in different sites.

The paper analyzes copy number alterations in breast epithelial cells from BRCA mutation carriers and wildtype individuals, finding lineage-specific CNAs that mirror cancer genomes.

The paper identifies genomic and non-genomic contributions to drug resistance in triple negative breast cancer using single cell transcriptomics and copy number data.

This paper introduces MRD-EDGE, a machine learning platform for ultrasensitive ctDNA detection in plasma WGS, showing improved sensitivity and broader applicability for MRD monitoring.

The paper introduces a scalable Bayesian method for phylogenetic tree inference from single-cell whole genome sequencing data, demonstrating its application on three datasets.

The paper uses single-cell sequencing to study the evolution of follicular lymphoma and its microenvironment during transformation, finding gene programs and TME changes associated with progression.

Epiclomal clusters sparse single-cell DNA methylation data and imputes missing values, outperforming non-probabilistic methods and revealing sub-clonal methylation patterns in tumour genomes.

This study identifies transcriptional stress responses in single-cell RNA-seq data from dissociated tumour tissues, showing that collagenase digestion induces a conserved stress response minimized by cold active protease.

clonealign integrates single-cell RNA and DNA sequencing data from cancer samples to identify clone-specific gene expression patterns and dysregulated pathways.

CellAssign probabilistically assigns cell types to scRNA-seq data, revealing spatiotemporal dynamics in human cancers like ovarian and follicular lymphoma.

This study identifies somatic coding and regulatory variants in DLBCL, revealing novel mechanisms of oncogene deregulation and potential therapeutic targets.

The paper analyzes the interaction between tumor and immune clones in ovarian cancer, finding that immune contexture patterns mirror malignant spread and that foldback inversions correlate with poor outcomes.