Simon Tavaré

Serval: A modular framework for decoding imaging based spatial transcriptomics data

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

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.

Accurate detection of tumor clonality and ongoing expansion mode from genomic data

DECODE improves tumor clonality and expansion mode detection by accounting for sequencing biases and neutral tail in SFS, showing better performance on synthetic data and clinical relevance in glioma.

Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer

This study shows that ongoing whole-genome doubling in ovarian cancer promotes cell diversity and immune dysregulation through chromosomal instability and quiescent states.

CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution

CINner models chromosomal instability in cancer, showing how selection parameters and WGD influence tumor progression and heterogeneity.

Spatial regulation of Drosophila ovarian Follicle Stem Cell division rates and cell cycle transitions

The paper measures division rates and cell cycle transitions in Drosophila ovarian Follicle Stem Cells, finding spatial differences and roles for JAK-STAT, Yorkie, and PI3 kinase signaling.

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.

Division-independent differentiation mandates proliferative competition among stem cells

The paper shows that faster-proliferating stem cell mutants outcompete others only when division and differentiation are independent, using Drosophila Follicle Stem Cells as a model.