杨用三 -华西生物医学大数据中心 - 华西生物医学大数据中心

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杨用三

简介

四川大学华西医院华西生物医学大数据研究院工程师，数据分析师。入职四川大学华西医院以来从事于生物信息学领域研究。近年来，参与国家自然科学基金、四川省科技厅等科研项目3项，发表论文9篇

研究方向：

基因组区域富集分析、单细胞数据分析等研究。主要研究兴趣包括超级增强子、增强子、开放染色质区域等DNA调控元件的功能研究；生物信息数据库和平台的开发

文章发表

(1) Yang Y, Qian F, Li X, Li Y, Zhou L, Wang Q, Zhou X, Zhang J, Song C, Yu Z, Cui T, Feng C, Zhu J, Shang D, Liu J, Sun M, Zhang Y, Tang H, Li C. GREAP: a comprehensive enrichment analysis software for human genomic regions. Brief Bioinform. 2022 Sep 20;23(5):bbac329. doi: 10.1093/bib/bbac329. PMID: 35959979

(2) Li Y, Li X, Yang Y, Li M, Qian F, Tang Z, Zhao J, Zhang J, Bai X, Jiang Y, Zhou J, Zhang Y, Zhou L, Xie J, Li E, Wang Q, Li C. TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs. Brief Bioinform. 2021 Mar 22;22(2):1929-1939. doi: 10.1093/bib/bbaa011. PMID: 32047897

(3) Yang Y, Dong L, Li Y, Huang Y, Zeng X. Summary data-based Mendelian randomization and single-cell RNA sequencing analyses identify immune associations with low-level LGALS9 in sepsis. J Cell Mol Med. 2024 Jul;28(14):e18559. doi: 10.1111/jcmm.18559. PMID: 39044269; PMCID: PMC11265992

(4) Zhou X, Qin Y, Li J, Fan L, Zhang S, Zhang B, Wu L, Gao A, Yang Y, Lv X, Guo B, Sun L. LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNAs. Nucleic Acids Res. 2025 Jan 6;53(D1):D468-D476. doi: 10.1093/nar/gkae905. Erratum in: Nucleic Acids Res. 2025 Feb 27;53(5):gkaf186. doi: 10.1093/nar/gkaf186. PMID: 39435995; PMCID: PMC11701525

(5) Xu M, Bai X, Ai B, Zhang G, Song C, Zhao J, Wang Y, Wei L, Qian F, Li Y, Zhou X, Zhou L, Yang Y, Chen J, Liu J, Shang D, Wang X, Zhao Y, Huang X, Zheng Y, Zhang J, Wang Q, Li C. TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human. Nucleic Acids Res. 2022 Jan 7;50(D1):D402-D412. doi: 10.1093/nar/gkab1114. PMID: 34986601; PMCID: PMC8728118

(6) Zhang Y, Song C, Zhang Y, Wang Y, Feng C, Chen J, Wei L, Pan Q, Shang D, Zhu Y, Zhu J, Fang S, Zhao J, Yang Y, Zhao X, Xu X, Wang Q, Guo J, Li C. TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. Nucleic Acids Res. 2022 Jan 7;50(D1):D391-D401. doi: 10.1093/nar/gkab950. PMID: 34718747; PMCID: PMC8728270

(7) Chen J, Zhang J, Gao Y, Li Y, Feng C, Song C, Ning Z, Zhou X, Zhao J, Feng M, Zhang Y, Wei L, Pan Q, Jiang Y, Qian F, Han J, Yang Y, Wang Q, Li C. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. Nucleic Acids Res. 2021 Jan 8;49(D1):D969-D980. doi: 10.1093/nar/gkaa806. PMID: 33045741; PMCID: PMC7778898

(8) Tang Z, Li X, Zhao J, Qian F, Feng C, Li Y, Zhang J, Jiang Y, Yang Y, Wang Q, Li C. TRCirc: a resource for transcriptional regulation information of circRNAs. Brief Bioinform. 2019 Nov 27;20(6):2327-2333. doi: 10.1093/bib/bby083. PMID: 30184150

(9) Zhao J, Qian F, Li X, Yu Z, Zhu J, Yu R, Zhao Y, Ding K, Li Y, Yang Y, Pan Q, Chen J, Song C, Wang Q, Zhang J, Wang G, Li C. CanMethdb: a database for genome-wide DNA methylation annotation in cancers. Bioinformatics. 2022 Dec 7:btac783. doi: 10.1093/bioinformatics/btac783. Epub ahead of print. PMID: 36477791

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