Rodrigo I. Castro

Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

Functional dissection of complex and molecular trait variants at single nucleotide resolution

This study functionally characterizes 221,412 trait-associated variants using MPRA in 5 cell types, identifying 12,025 regulatory variants and revealing widespread epistasis and non-TF mechanisms.

Global cis-regulatory landscape of double-stranded DNA viruses

The paper identifies ~2,000 cis-regulatory elements (CREs) across 27 dsDNA viruses using reporter assays and machine learning, revealing their regulatory features and associated transcription factors.

Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays

This study introduces MPAC, a machine learning model that predicts the cis-regulatory impact of non-coding variants, demonstrating its accuracy across diverse applications and datasets.

Machine-guided design of synthetic cell type-specific cis-regulatory elements

This paper designs synthetic cis-regulatory elements (CREs) that outperform natural ones in driving cell type-specific gene expression using deep learning and experimental validation.