Alexandre Bouchard‐Côté

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

bayesReact infers microRNA regulatory activities from single-cell and bulk data, showing strong correlation with expression and improved performance over existing methods.

PhyClone is a Bayesian method that reconstructs cancer phylogenies from bulk sequencing data, showing improved accuracy and scalability over existing methods.

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

SpatialSort is a Bayesian clustering method for spatial proteomics data that integrates spatial information and prior knowledge to improve cell population annotation.

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

MuClone improves somatic mutation detection and classification by integrating clonal structure information across multiple tumor samples.