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For: Xue B, Khoroshevskyi O, Gomez RA, Sheffield NC. Opportunities and challenges in sharing and reusing genomic interval data. Front Genet 2023;14:1155809. [PMID: 37020996 PMCID: PMC10067617 DOI: 10.3389/fgene.2023.1155809] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/07/2023] [Indexed: 03/22/2023]  Open
Number Cited by Other Article(s)
1
Guimarães PAS, Carvalho MGR, Ruiz JC. A computational framework for extracting biological insights from SRA cancer data. Sci Rep 2025;15:8117. [PMID: 40057525 PMCID: PMC11890766 DOI: 10.1038/s41598-025-91781-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 02/24/2025] [Indexed: 05/13/2025]  Open
2
Rymuza J, Sun Y, Zheng G, LeRoy N, Murach M, Phan N, Zhang A, Sheffield N. Methods for constructing and evaluating consensus genomic interval sets. Nucleic Acids Res 2024;52:10119-10131. [PMID: 39180401 PMCID: PMC11417377 DOI: 10.1093/nar/gkae685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 07/05/2024] [Accepted: 07/29/2024] [Indexed: 08/26/2024]  Open
3
Zheng G, Rymuza J, Gharavi E, LeRoy N, Zhang A, Sheffield N. Methods for evaluating unsupervised vector representations of genomic regions. NAR Genom Bioinform 2024;6:lqae086. [PMID: 39131817 PMCID: PMC11316252 DOI: 10.1093/nargab/lqae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 06/14/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]  Open
4
LeRoy N, Smith J, Zheng G, Rymuza J, Gharavi E, Brown D, Zhang A, Sheffield N. Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings. NAR Genom Bioinform 2024;6:lqae073. [PMID: 38974799 PMCID: PMC11224678 DOI: 10.1093/nargab/lqae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 04/29/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024]  Open
5
Lott MJ, Frankham GJ, Eldridge MDB, Alquezar‐Planas DE, Donnelly L, Zenger KR, Leigh KA, Kjeldsen SR, Field MA, Lemon J, Lunney D, Crowther MS, Krockenberger MB, Fisher M, Neaves LE. Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 2024;14:e11700. [PMID: 39091325 PMCID: PMC11289790 DOI: 10.1002/ece3.11700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024]  Open
6
LeRoy NJ, Khoroshevskyi O, O’Brien A, Stepień R, Arslan A, Sheffield NC. PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.15.551388. [PMID: 37645717 PMCID: PMC10462087 DOI: 10.1101/2023.08.15.551388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
7
Gharavi E, LeRoy NJ, Zheng G, Zhang A, Brown DE, Sheffield NC. Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets. Bioengineering (Basel) 2024;11:263. [PMID: 38534537 PMCID: PMC10967841 DOI: 10.3390/bioengineering11030263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/28/2024]  Open
8
LeRoy NJ, Khoroshevskyi O, O’Brien A, Stępień R, Arslan A, Sheffield NC. PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata. Gigascience 2024;13:giae033. [PMID: 38991851 PMCID: PMC11238423 DOI: 10.1093/gigascience/giae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/07/2024] [Accepted: 05/21/2024] [Indexed: 07/13/2024]  Open
9
Sheffield NC, LeRoy NJ, Khoroshevskyi O. Challenges to sharing sample metadata in computational genomics. Front Genet 2023;14:1154198. [PMID: 37287537 PMCID: PMC10243526 DOI: 10.3389/fgene.2023.1154198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023]  Open
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