Denis Torre

The paper identifies pre-established chromatin regions in human ESCs that enable rapid activation of lineage-specific genes during differentiation.

This paper develops a human organoid model of early PDAC that identifies genetic and epigenetic barriers to lineage plasticity, showing CDKN2A loss is essential with KRAS/TP53 mutations and TET1 suppression links ERK signaling to transcription factor silencing.

The paper presents a LINCS Microenvironment perturbation dataset cataloging transcriptional, proteomic, epigenomic, and phenotypic responses of MCF10A cells to six ligands, enabling integrative analysis of molecular and phenotypic changes.

The paper identifies a risk variant for liver disease in Puerto Ricans by integrating EHR and genomic data, showing a dose-dependent association with disease severity.

This study links genomic data with EHRs to identify health outcomes enriched in sub-populations, revealing both known and novel associations.

The paper predicts PKMYT1 as a potential therapeutic target for kidney cancer using bioinformatics tools.

FAIRshake evaluates the FAIRness of research digital resources through community-driven metrics, automated assessments, and visualization tools, revealing opportunities for improvement.

BioJupies automates the creation of interactive Jupyter Notebooks for RNA-seq analysis, enabling users to generate reproducible reports from raw data to visualizations and differential expression analyses.

The paper develops ARCHS4, a resource that provides uniformly processed RNA-seq data from human and mouse, enabling easier integration and analysis.