Nathan J. LeRoy

Atacformer is a transformer-based model for scATAC-seq data analysis that improves clustering, cell-type annotation, and cross-modal alignment with RNA-seq data.

BEDMS standardizes genomic interval metadata by predicting standardized attributes using trained models and supports custom schemas for improved data interoperability.

The paper introduces methods to construct and evaluate consensus genomic interval sets, showing how to minimize loss of resolution while enabling interoperability of interval data.

The paper introduces scEmbed, a framework for fast clustering and cell-type annotation of scATAC-seq data using pre-trained embeddings, showing improved performance and transferability.

The paper introduces four metrics to evaluate unsupervised embeddings of genomic regions and provides guidelines for reliable embedding learning.

DeepGSEA provides an explainable deep learning approach for gene set enrichment analysis in single-cell RNA sequencing data, improving sensitivity and specificity over traditional methods.

The paper develops a system for fast and flexible genomic interval retrieval using joint representation learning of region sets and metadata.

PEPhub is a database and web interface for sharing, editing, and validating biological sample metadata, enabling fast semantic search and interoperability.

Optipyzer provides a fast, flexible, and extensible codon optimization server for multi-species gene expression, with a web interface and Python package.