Anna Trigos

ATAClone: Cancer Clone Identification and Copy Number Estimation from Single-cell ATAC-seq

ATAClone identifies cancer clones and estimates copy numbers from scATAC-seq data, improving accuracy over existing methods.

SMAD4 loss drives chromosomal instability during tumourigenesis via translational reprogramming

This study shows SMAD4 loss reprograms translation to induce chromosomal instability, driving tumourigenesis, and identifies CDK11B-p58 as a key mediator.

2D spatial tissue analysis often misrepresents true biological patterns of 3D tissues

This study shows that 2D spatial analysis of tissues often leads to spurious associations and misrepresentation of 3D biological patterns.

Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins

The paper shows cancer disrupts gene regulatory networks by altering co-expression between genes of unicellular and multicellular origins, with changes more pronounced in advanced tumors.

SPIAT: An R package for the Spatial Image Analysis of Cells in Tissues

SPIAT is an R package designed for spatial analysis of cells in tissues, offering tools for data processing, visualization, and analysis of spatially resolved single-cell data.