| GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA O Khoroshevskyi, N LeRoy, VP Reuter, NC Sheffield Bioinformatics 39 (3), btad069, 2023 | 11 | 2023 |
| GenomicDistributions: fast analysis of genomic intervals with Bioconductor K Kupkova, JV Mosquera, JP Smith, M Stolarczyk, TL Danehy, JT Lawson, ... BMC genomics 23 (1), 299, 2022 | 10 | 2022 |
| Methods for constructing and evaluating consensus genomic interval sets J Rymuza, Y Sun, G Zheng, NJ LeRoy, M Murach, N Phan, A Zhang, ... Nucleic Acids Research 52 (17), 10119-10131, 2024 | 4 | 2024 |
| Neuron activity dependent redox compartmentation revealed with a second generation red-shifted ratiometric sensor S Radhakrishnan, J Norley, S Wendt, N LeRoy, H Hall, S Norcross, ... ACS chemical neuroscience 11 (17), 2666-2678, 2020 | 4 | 2020 |
| Methods for evaluating unsupervised vector representations of genomic regions G Zheng, J Rymuza, E Gharavi, NJ LeRoy, A Zhang, NC Sheffield NAR Genomics and Bioinformatics 6 (3), lqae086, 2024 | 3 | 2024 |
| Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings NJ LeRoy, JP Smith, G Zheng, J Rymuza, E Gharavi, DE Brown, A Zhang, ... NAR Genomics and Bioinformatics 6 (3), lqae073, 2024 | 3 | 2024 |
| Joint representation learning for retrieval and annotation of genomic interval sets E Gharavi, NJ LeRoy, G Zheng, A Zhang, DE Brown, NC Sheffield Bioengineering 11 (3), 263, 2024 | 3 | 2024 |
| Challenges to sharing sample metadata in computational genomics NC Sheffield, NJ LeRoy, O Khoroshevskyi Frontiers in Genetics 14, 1154198, 2023 | 3 | 2023 |
| PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata NJ LeRoy, O Khoroshevskyi, A O’Brien, R Stępień, A Arslan, NC Sheffield GigaScience 13, giae033, 2024 | 1 | 2024 |
| Optipyzer: A fast and flexible multi-species codon optimization server N LeRoy, C Roleck bioRxiv, 2023.05. 22.541759, 2023 | 1 | 2023 |
| DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data G Xiong, NJ LeRoy, S Bekiranov, NC Sheffield, A Zhang Bioinformatics 40 (7), btae434, 2024 | | 2024 |
| BEDMS: A metadata standardizer for genomic region attributes S Tambe, O Khoroshevskyi, SH Park, NJ LeRoy, DR Campbell Jr, ... bioRxiv, 2024.09. 18.613791, 2024 | | 2024 |
| FRET Biosensors: Engineering Fluorescent Proteins as Biological Tools for Studying Parkinson’s Disease NJ LeRoy, JR Norley, S Radhakrishnan, M Tantama | | 2017 |
