Lisa Barros de Andrade e Sousa

Probe set selection for targeted spatial transcriptomics

Spapros selects optimal probe sets for targeted spatial transcriptomics to improve cell type identification and spatial variation detection across multiple datasets.

Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes

This study benchmarks six sequencing-based and two array-based cell-type deconvolution methods for bulk DNA methylomes, identifying the best-performing method and factors affecting performance.

Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect modeling and data integration

The paper develops a mixed-effect random forest model to predict CRISPRi guide efficiency using data from depletion screens and gene-specific features, outperforming existing methods.

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features

The paper predicts Xist-induced gene silencing kinetics using a Random Forest model based on epigenetic and genomic features, identifying key factors like distance to Xist and promoter pre-marking.