Weini Huang

Inferring ecDNA Evolution from Allele Frequency Spectra

This paper introduces ecEvol, a method to infer ecDNA emergence time and other parameters from bulk whole-genome sequencing data, finding that ecDNA typically emerges early and is associated with poorer survival.

Mathematical Modelling of Stochastic Gene Expression Quantifies mRNA Heterogeneity in Cancer Cell Populations with Extrachromosomal DNA

This study uses a stochastic gene expression model to quantify mRNA heterogeneity in cancer cells with extrachromosomal DNA and shows similar transcriptional parameters across different cell lines and amplification types.

Biodiversity dynamics with complex genotype-to-phenotype architecture in multilayer networks

This study investigates how genotype-to-phenotype architecture influences biodiversity dynamics in multilayer networks, showing that correlated and modular architectures affect diversity under different ecological conditions.

Stochastic modelling of prostate progenitor architecture

This study models prostate cancer emergence using compartmental stochastic simulations to show how luminal compartment dynamics drive rapid tumor growth, while basal compartment tumors are more aggressive and persistent.

Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

Extrachromosomal DNA micronucleation constrains tumour fitness andimproves patient survival

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

The maintenance and de-mixing of extrachromosomal DNA variants in single cells

This study develops computational models to show that mixed ecDNA subpopulations in tumour cells require variant switching and a positive fitness of ecDNA+ cells, not direct co-selection.

Accumulating waves of random mutations before fixation

The paper quantifies joint fixation events of neutral mutations in constant populations, introducing the concept of mutation waves and deriving the Wave Frequency Distribution.

Cancer-immune coevolution dictated by antigenic mutation accumulation

This study presents an individual-based model of cancer-immune coevolution, showing how mutation accumulation and immune interactions influence tumour progression outcomes.

LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

LiquidCNA tracks subclonal evolution from liquid biopsies using somatic copy number alterations, revealing new subpopulations in metastatic lung cancer.

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

This paper shows that spatial tumour structure affects mutation patterns in sequencing data and introduces a framework to account for these effects in cancer genomic analysis.