Selected Publications

Some publications that I have written or contributed to. For a full list, see my Google Scholar profile. My research focuses on developing powerful representation learning methods for single-cell epigenomic data. These methods leverage techniques in natural language processing and interpretable machine learning to study gene regulation and single-cell epigenetic datasets.

Fast clustering and cell-type annotation of scATAC data using pre-trained region embeddings

Nathan J. LeRoy, Jason P. Smith, Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Donald E. Brown, Aidong Zhang, Nathan C. Sheffield

Nuceic Acids Research Genomics and Bioinformatics

(2024)

DOI: https://doi.org/10.1093/nargab/lqae073

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

Nathan J. LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafal Stepien, Alip Arslan, Nathan C. Sheffield

GigaScience

(2024)

DOI: https://doi.org/10.1093/gigascience/giae033

Optipyzer: A Fast and Flexible Multi-Species Codon Optimization Server

Nathan J. LeRoy, Caleigh Roleck

bioRxiv

(2023)

DOI: https://doi.org/10.1101/2023.05.22.541759

Joint representation learning for retrieval and annotation of genomic interval sets

Erfaneh Gharavi, Nathan J. LeRoy, Guangtao Zheng, Aidong Zhang, Donald E. Brown, Nathan C. Sheffield

Bioengineering

(2024)

DOI: https://doi.org/10.3390/bioengineering11030263

DeepGSEA: Explainable Deep Gene Set Enrichment Analysis for Single-cell Transcriptomic Data

Guangzhi Xiong, Nathan J. LeRoy, Stefan Bekiranov, Aidong Zhang

Bioinformatics

(2024)

DOI: https://doi.org/10.1101/2023.11.03.565235

Methods for constructing and evaluating consensus genomic interval sets

Julia Rymuza, Yuchen Sun, Guangtao Zheng, Nathan J. LeRoy, Maria Murach, Neil Phan, Aidong Zhang, Nathan C. Sheffield

bioRxiv

(2023)

DOI: https://doi.org/10.1101/2023.08.03.551899

Challenges to Sharing Sample Metadata in Computational Genomics

Nathan Sheffield, Nathan J. LeRoy, Oleksandr Khoroshevskyi

Frontiers in Genetics

(2023)

DOI: https://doi.org/10.3389/fgene.2023.1155809

GEOfetch: A Command-Line Tool for Downloading Data and Standardized Metadata from GEO and SRA

Oleksandr Khoroshevskyi, Nathan J. LeRoy, Vincent P Reuter, Nathan C Sheffield

Bioinformatics

(2023)

DOI: https://doi.org/10.1093/bioinformatics/btad069

Neuron Activity Dependent Redox Compartmentation Revealed with a Second Generation Red-Shifted Ratiometric Sensor

Saranya Radhakrishnan, Jacob Norley, Stefan Wendt, Nathan J. LeRoy, Hana Hall, Stevie Norcross, Sara Doan, Jordan Snaider, Brian A MacVicar, Vikki M Weake, Libai Huang, Mathew Tantama

ACS Chemical Neuroscience

(2020)

DOI: https://doi.org/10.1021/acschemneuro.0c00342