Nathan J LeRoy (Nathan LeRoy)

Publication Activity (10 Years)

Years Active: 2022-2024
Publications (10 Years): 22

Top Topics

Gene Expression

Top Venues

NAR genomics and bioinformatics

Bioinformatics (Oxford, England)

Bioengineering (Basel, Switzerland)

This page only lists publications with an associated author ORCID identifier.

Publications

Nathan J LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafał Stępień, Alip Arslan, Nathan C Sheffield
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. GigaScience 13 (2024)
Nathan J LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafał Stępień, Alip Arslan, Nathan C Sheffield
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. GigaScience 13 (2024)
Erfaneh Gharavi, Nathan J LeRoy, Guangtao Zheng, Aidong Zhang, Donald E Brown, Nathan C Sheffield
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets. Bioengineering (Basel, Switzerland) 11 (3) (2024)
Guangzhi Xiong, Nathan J LeRoy, Stefan Bekiranov, Nathan C Sheffield, Aidong Zhang
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. Bioinformatics (Oxford, England) 40 (7) (2024)
Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Nathan J LeRoy, Aidong Zhang, Nathan C Sheffield
Methods for evaluating unsupervised vector representations of genomic regions. NAR genomics and bioinformatics 6 (3) (2024)
Nathan J LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafał Stępień, Alip Arslan, Nathan C Sheffield
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. GigaScience 13 (2024)
Nathan J LeRoy, Jason P Smith, Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Donald E Brown, Aidong Zhang, Nathan C Sheffield
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings. NAR genomics and bioinformatics 6 (3) (2024)
Erfaneh Gharavi, Nathan J LeRoy, Guangtao Zheng, Aidong Zhang, Donald E Brown, Nathan C Sheffield
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets. Bioengineering (Basel, Switzerland) 11 (3) (2024)
Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Nathan J LeRoy, Aidong Zhang, Nathan C Sheffield
Methods for evaluating unsupervised vector representations of genomic regions. NAR genomics and bioinformatics 6 (3) (2024)
Erfaneh Gharavi, Nathan J LeRoy, Guangtao Zheng, Aidong Zhang, Donald E Brown, Nathan C Sheffield
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets. Bioengineering (Basel, Switzerland) 11 (3) (2024)
Nathan J LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafał Stępień, Alip Arslan, Nathan C Sheffield
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. GigaScience 13 (2024)
Erfaneh Gharavi, Nathan J LeRoy, Guangtao Zheng, Aidong Zhang, Donald E Brown, Nathan C Sheffield
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets. Bioengineering (Basel, Switzerland) 11 (3) (2024)
Julia Rymuza, Yuchen Sun, Guangtao Zheng, Nathan J LeRoy, Maria Murach, Neil Phan, Aidong Zhang, Nathan C Sheffield
Methods for constructing and evaluating consensus genomic interval sets. Nucleic acids research (2024)
Nathan J LeRoy, Jason P Smith, Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Donald E Brown, Aidong Zhang, Nathan C Sheffield
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings. NAR genomics and bioinformatics 6 (3) (2024)
Guangzhi Xiong, Nathan J LeRoy, Stefan Bekiranov, Nathan C Sheffield, Aidong Zhang
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. Bioinformatics (Oxford, England) 40 (7) (2024)
Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Nathan J LeRoy, Aidong Zhang, Nathan C Sheffield
Methods for evaluating unsupervised vector representations of genomic regions. NAR genomics and bioinformatics 6 (3) (2024)
Nathan J LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafał Stępień, Alip Arslan, Nathan C Sheffield
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. GigaScience 13 (2024)
Oleksandr Khoroshevskyi, Nathan J LeRoy, Vincent P Reuter, Nathan C Sheffield
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA. Bioinformatics (Oxford, England) 39 (3) (2023)
Oleksandr Khoroshevskyi, Nathan J LeRoy, Vincent P Reuter, Nathan C Sheffield
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA. Bioinformatics (Oxford, England) 39 (3) (2023)
Oleksandr Khoroshevskyi, Nathan J LeRoy, Vincent P Reuter, Nathan C Sheffield
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA. Bioinformatics (Oxford, England) 39 (3) (2023)
Nathan J LeRoy, Oleksandr Khoroshevskyi, Aaron O'Brien, Rafał Stepień, Alip Arslan, Nathan C Sheffield
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. bioRxiv : the preprint server for biology (2023)
Kristyna Kupkova, Jose Verdezoto Mosquera, Jason P Smith, Michał Stolarczyk, Tessa L Danehy, John T Lawson, Bingjie Xue, John T Stubbs, Nathan J LeRoy, Nathan C Sheffield
GenomicDistributions: fast analysis of genomic intervals with Bioconductor. BMC genomics 23 (1) (2022)