Tiago C. Silva

MethReg identifies CpG sites with high regulatory potential by integrating DNA methylation, gene expression, and TF binding data to uncover TF-target gene associations in specific methylation contexts.

This study shows that DNA methylation and gene expression patterns are preserved in recurrent high grade serous ovarian cancers, with BRCA1/2 carriers showing more shared methylation changes and improved survival.

The paper introduces new features in the TCGAbiolinks R/Bioconductor package to improve cancer data analysis, including better differential expression analysis, tumor purity estimation, and integration of normal samples from GTEx.

ELMER v.2 reconstructs gene regulatory networks from DNA methylation and transcriptome data to identify Master Regulators in diseases like breast cancer.

HiCAGE provides an R package for annotating and visualizing 3C-based genomic data, integrating with RNA-seq and gene ontologies.

TCGAbiolinksGUI provides a graphical interface for analyzing GDC cancer data, making the TCGAbiolinks package more accessible to non-R users.

Moonlight identifies cancer driver genes and their roles by integrating functional analysis and gene regulatory networks from expression data, distinguishing tumor suppressors, oncogenes, and moonlight genes.