Nicolò Stranieri

CREP: Cis-Regulatory Element Predictor Based on Fine-Tuned Enformer

CREP predicts cis-regulatory element identity from DNA sequence using a fine-tuned Enformer model trained on cell-type-specific annotations.

Expert-Guided Supervised Annotation of Erythroid Differentiation in Single-Cell RNA-seq

This paper develops a supervised framework for annotating erythroid differentiation stages in scRNA-seq using expert-curated data, achieving high accuracy across cell states and transferability to bulk RNA-seq and external datasets.

Enformer-Based Phylogenetic Tree Reconstruction

The paper uses Enformer to reconstruct phylogenetic trees across multiple species by analyzing regulatory signals from orthologous genes, showing strong correlation with known evolutionary relationships.

REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sites

REnformer predicts chromatin accessibility from single-cell ATAC-seq data, outperforming Enformer in accuracy and error rates, and validates its utility with a known thalassemia variant.

CREST-GV: Cell types Ranking and Enrichment Score for selecTive Genetic Variants

CREST-GV prioritizes disease-relevant cell types by analyzing genetic variants intersecting open chromatin regions across hundreds of cell types.