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For: Guo Z, Tzvetkova B, Bassik JM, Bodziak T, Wojnar BM, Qiao W, Obaida MA, Nelson SB, Hu BH, Yu P. RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets. Bioinformatics 2015;31:4038-40. [PMID: 26323714 DOI: 10.1093/bioinformatics/btv503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 08/23/2015] [Indexed: 01/24/2023]  Open
Number Cited by Other Article(s)
1
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]
2
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
3
Yu P, Li J, Deng SP, Zhang F, Grozdanov PN, Chin EWM, Martin SD, Vergnes L, Islam MS, Sun D, LaSalle JM, McGee SL, Goh E, MacDonald CC, Jin P. Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. Sci Data 2020;7:178. [PMID: 32546682 PMCID: PMC7297722 DOI: 10.1038/s41597-020-0514-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/13/2020] [Indexed: 02/05/2023]  Open
4
Li J, Deng SP, Vieira J, Thomas J, Costa V, Tseng CS, Ivankovic F, Ciccodicola A, Yu P. RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018;2018:5040291. [PMID: 29931156 PMCID: PMC6009576 DOI: 10.1093/database/bay054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/17/2018] [Indexed: 01/03/2023]
5
Li Z, Li J, Yu P. GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018;2018:4953404. [PMID: 29688376 PMCID: PMC5868185 DOI: 10.1093/database/bay019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/30/2018] [Indexed: 01/15/2023]
6
Li J, Tseng CS, Federico A, Ivankovic F, Huang YS, Ciccodicola A, Swanson MS, Yu P. SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018;2017:4161772. [PMID: 29220461 PMCID: PMC5737203 DOI: 10.1093/database/bax071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023]
7
Li J, Zheng L, Uchiyama A, Bin L, Mauro TM, Elias PM, Pawelczyk T, Sakowicz-Burkiewicz M, Trzeciak M, Leung DYM, Morasso MI, Yu P. A data mining paradigm for identifying key factors in biological processes using gene expression data. Sci Rep 2018;8:9083. [PMID: 29899432 PMCID: PMC5998123 DOI: 10.1038/s41598-018-27258-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 05/21/2018] [Indexed: 12/15/2022]  Open
8
Bernstein MN, Doan A, Dewey CN. MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bioinformatics 2018;33:2914-2923. [PMID: 28535296 PMCID: PMC5870770 DOI: 10.1093/bioinformatics/btx334] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/21/2017] [Indexed: 01/31/2023]  Open
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