Ignacio J. Tripodi

The paper introduces MechSpy, a framework that generates mechanistic hypotheses of toxicity by combining gene expression data with biological knowledge, and validates predictions experimentally.

The paper introduces PheKnowLator, a framework for constructing large-scale biomedical knowledge graphs, and evaluates its performance on human disease mechanisms.

The paper uses ATAC-seq signal processing and recurrent neural networks to classify transcriptional activity from chromatin accessibility data.

The paper demonstrates a method to detect differential transcription factor activity using ATAC-seq data by analyzing TF recognition motifs relative to open chromatin regions.