Nathan C Sheffield

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 35

Top Venues

NAR genomics and bioinformatics

GigaScience

Bioinformatics (Oxford, England)

Bioengineering (Basel, Switzerland)

Duke University (PHD)

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

Education History

Duke University

United States

PHD :: Program in Computational Biology and Bioinformatics

Brigham Young University

United States

BSC :: Biology

Publications

Jason P Smith, Robert Paxton, Silvia Medrano, Nathan C Sheffield, Maria Luisa S Sequeira-Lopez, R Ariel Gomez
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension (Dallas, Tex. : 1979) 81 (9) (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, 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)
Jason P Smith, Robert Paxton, Silvia Medrano, Nathan C Sheffield, Maria Luisa S Sequeira-Lopez, R Ariel Gomez
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension (Dallas, Tex. : 1979) 81 (9) (2024)
Jason P Smith, Robert Paxton, Silvia Medrano, Nathan C Sheffield, Maria Luisa S Sequeira-Lopez, R Ariel Gomez
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension (Dallas, Tex. : 1979) 81 (9) (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)
Jason P Smith, Robert Paxton, Silvia Medrano, Nathan C Sheffield, Maria Luisa S Sequeira-Lopez, R Ariel Gomez
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. Hypertension (Dallas, Tex. : 1979) (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)
Alexandre G Martini, Jason P Smith, Silvia Medrano, Gal Finer, Nathan C Sheffield, Maria Luisa Soledad Sequeira-Lopez, Roberto Ariel Gomez
Renin Cell Development: Insights From Chromatin Accessibility and Single-Cell Transcriptomics. Circulation research (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)
Nathan C Sheffield, Michał Stolarczyk, Vincent P Reuter, André Figueiredo Rendeiro
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. GigaScience 10 (12) (2022)
Nathan C Sheffield, Vivien R Bonazzi, Philip E Bourne, Tony Burdett, Timothy W Clark, Robert L Grossman, Ola Spjuth, Andrew D Yates
From biomedical cloud platforms to microservices: next steps in FAIR data and analysis. Scientific data 9 (1) (2022)
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)
Aaron Gu, Hyun Jae Cho, Nathan C Sheffield
Bedshift: perturbation of genomic interval sets. Genome biology 22 (1) (2021)
Jason P Smith, Arun B Dutta, Kizhakke Mattada Sathyan, Michael J Guertin, Nathan C Sheffield
PEPPRO: quality control and processing of nascent RNA profiling data. Genome biology 22 (1) (2021)
Jason P Smith, M Ryan Corces, Jin Xu, Vincent P Reuter, Howard Y Chang, Nathan C Sheffield
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments. NAR genomics and bioinformatics 3 (4) (2021)
Michał Stolarczyk, Bingjie Xue, Nathan C Sheffield
Identity and compatibility of reference genome resources. NAR genomics and bioinformatics 3 (2) (2021)
John T Lawson, Jason P Smith, Stefan Bekiranov, Francine E Garrett-Bakelman, Nathan C Sheffield
COCOA: coordinate covariation analysis of epigenetic heterogeneity. Genome biology 21 (1) (2020)
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, José A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho, Ansuman T Satpathy, Maxwell R Mumbach, Katherine A Hoadley, A Gordon Robertson, Nathan C Sheffield, Ina Felau, Mauro A A Castro, Benjamin P Berman, Louis M Staudt, Jean C Zenklusen, Peter W Laird, Christina Curtis, null null, William J Greenleaf, Howard Y Chang
The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.) 362 (6413) (2018)

Nathan C Sheffield.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Nathan C Sheffield