Selected Publications

Some publications that I have written or contributed to. For a full list, see my Google Scholar profile.

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

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

bioRxiv

(2023)

DOI: https://doi.org/10.1101/2023.08.01.551452

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

bioRxiv

(2023)

DOI: https://doi.org/10.1101/2023.08.15.551388

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

bioRxiv

(2023)

DOI: https://doi.org/10.1101/2023.08.21.554131

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