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Jingyao Zeng
Jingyao Zeng

Associate Professor

Precision Medicine

Email: zengjy (AT) big.ac.cn

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PROFESSIONAL EXPERIENCE

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (CNCB), China, 2023−present

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (CNCB), China, 2019−2023

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2016−2019

EDUCATION

  • Ph.D. in Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2016

  • B.S. in Biological Sciences, Minzu University of China, China, 2010

RESEARCH INTERESTS

  • Tumor Data Integration and Curation

  • Omics Database Construction

PROJECTS & RESOURCES

  • CancerSCEM (integration, analysis and visualization of single-cell RNA-seq data across various human cancers)

  • CancerSCEM 2.0 (an updated data resource of single-cell expression map across various human cancers)

  • TWAS Atlas (a curated knowledgebase of transcriptome-wide association studies)

  • scTWAS Atlas (catalogue and integration of transcriptome-wide associations at the cellular level)

  • PlantPan (a comprehensive database that encompasses pan-genome analysis results of 195 sub-species from 11 species)

  • CVD Atlas (a comprehensive database of cardiovascular disease)

SOFTWARE COPYRIGHT

  • 肿瘤单细胞表达图谱数据库系统 [简称：CancerSCEM] V1.0, 2021SR1971134

  • 全转录组关联研究知识库系统 [简称：TWAS Atlas] V1.0, 2023SR0620716

  • 基因型填补参考集重构软件 [简称：RefRGim] V1.0, 2021SR2039215

  • 肿瘤体细胞变异检测软件 [简称：TSomVar] V1.0, 2023SR0619909

  • 癌症细胞系鉴定软件 [简称：CCLHunter] V1.0, 2024SR0524877

FUNDING

  • The Youth Innovation Promotion Association, CAS (No. 2022098), 80w RMB, 2022.01-2025.12

  • National Natural Science Foundation of China (No. 32300542): The study of metabolic reprogramming and pathological accurate staging of lung cancer based on scRNA-seq data, 30w RMB, 2024.01-2026.12

ACADEMIC ACTIVITIES

  • 口头报告：大规模人群多组学数据智能解析与应用，第九届中国科学数据大会，成都，2024.9.20

  • 口头报告：高性能计算在生命科学领域的研究应用，科学计算技术与应用会议，三亚，2023.12.5

  • 口头报告：癌症转录组学数据的整合分析与知识库体系建设，第十二届全国生物信息学与系统生物学学术大会，青岛，2023.10.28

  • 口头报告：癌症多维组学数据整合分析与知识库体系建设，第八届大数据论坛，北京，2023.10.20

  • 口头报告：CancerSCEM: 癌症单细胞表达谱数据库，第八届中国科学数据大会，青岛，2023.4.27

  • 口头报告：CGVD: A genomic variation database for Chinese populations，第四届大数据论坛，2019.10.16

  • 墙报交流：CancerSCEM 2.0: an updated database of single-cell expression map across various human cancers（三等奖），第十三届全国生物信息学与系统生物学学术大会，海口，2024.10.20-2024.10.22

  • 中国科学院继续教育网课程录制：癌症转录组学数据的整合分析与知识库体系建设

SCIENCE POPULARIZATION

  • 科普报告：从基因/基因组到人类健康与行为，中科院青促会北京分会2024年“爱科学小课题”第21期“DNA与心灵对话”科普活动，中科院心理所，2024.6.30

PUBLICATIONS

  1. Zeng J#, Zhang Y#, Shang Y#, Mai J, Shi S, Lu M, Bu C, Zhang Z, Zhang Z, Li Y, Du Z, Xiao J*. CancerSCEM: a database of single-cell expression map across various human cancers. Nucleic Acids Research, 2022, 50(D1):D1147-D1155. [PMID=34643725]

  2. Zeng J#, Nie Z#, Shang Y#, Mai J#, Zhang Y, Yang Y, Xu C, Zhao J, Xiao J*, et al. CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers. Nucleic Acids Research, 2024, Online ahead of print. [PMID=39460627]

  3. Shang Y#, Zeng J#,*, Mai J, Xiao J*. Metabolic reprogramming landscape of pan-cancer by single-cell transcriptome data integration. Science Bulletin, 2024, DOI: https://doi.org/10.1016/j.scib.2024.10.026.

  4. Xie J#, Li M#, Zeng J#, Li X, Zhang D*. Single-cell RNA sequencing profiles of stem-differentiating xylem in poplar. Plant Biotechnology Journal, 2023, 20(3):417-419. [PMID=34882927]

  5. Mai J#, Qian Q#, Gao H#, Fan Z, Zeng J*, Xiao J*. scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies. Nucleic Acids Research, 2024, Online ahead of print. [PMID=39420631]

  6. Mai J#, Lu M#, Gao Q#, Zeng J*, Xiao J*. Transcriptome-wide association studies: recent advances in methods, applications and available databases. Communications Biology, 2023, 6(1):899. [PMID=37658226]

  7. Lu M#, Zhang Y#, Yang F#, Mai J#, Gao Q, Xu X, Kang H, Hou L, Shang Y, Qian Q, Liu J, Jiang M, Zhang H, Bu C, Wang J, Zhang Z, Zhang Z, Zeng J*, Li J*, Xiao JF*, et al. TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. Nucleic Acids Research, 2023,51(D1):D1179-D1187. [PMID=36243959]

  8. Zeng J#, Liu S#, Zhao Y#, Tan X, Hasan A, Liu W*, Hu S*. Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq datasets across 15 mouse tissues. Gene, 2016, 576(1 Pt 3):560-70. [PMID=26551299]

  9. Zhao Y#, Liu W#, Zeng J#, Liu SC, Tan XY, Hu SN*. Identification and analysis of mouse non-coding RNA using transcriptome data. SCIENCE CHINA Life Sciences, 2016, 59(6):589-603. [PMID=26944582]

  10. Zeng J# as co-first author in CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Research, 2023, 51(D1):D18-D28. [PMID=36420893] 

  11. Zeng J# as co-first author in CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research, 2022, 50(D1):D27-D38. [PMID=34718731]

  12. Zeng J# as co-first author in BIG Data Center Members. Database Resources of the BIG Data Center in 2019. Nucleic Acids Research, 2019. [PMID=30365034]

  13. Jiang M, Chen M, Zeng J, Du Z, Xiao J*. A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence. Frontiers in Plant Science, 2024, 15:1371222. [PMID=38567138]

  14. Qian Q#, Xue R#, Xu C, Wang F, Zeng J, Xiao J*. CVD Atlas: a multi-omics database of cardiovascular disease. Nucleic Acids Research, 2024, Online ahead of print. [PMID=39351894]

  15. Bu C#, Zheng X#, Mai J, Nie Z, Zeng J, Qian Q, Xu T, Sun Y, Bao Y*, Xiao J*. CCLHunter: An efficient toolkit for cancer cell line authentication. Computational and Structural Biotechnology Journal, 2023, 21:4675–4682. [PMID=37841327]

  16. Luo J#, Li H#, Xiu J, Zeng J, Feng Z, Zhao H, Li Y*, Wei W*. Elevated ZNF704 expression is associated with poor prognosis of uveal melanoma and promotes cancer cell growth by regulating AKT/mTOR signaling. Biomarker Research, 2023, 11(1):38. [PMID=37038184]

  17. Shi S#, Wang Q#, Shang Y#, Bu C, Lu M, Jiang M, Zhang H, Yu S, Zeng J, Zhang Z, Du Z, Xiao J*. TSomVar: a tumor-only somatic and germline variant identification method with random forest. Briefings in Bioinformatics, 2022, 23(5):bbac381. [PMID=36088550]

  18. Jiang M#, Bu C#, Zeng J, Du Z*, Xiao J*, Applications and challenges of high performance computing in genomics. CCF Transactions on High Performance Computing, 2021, 3:344-352.

  19. Shi S, Qian Q, Yu S, Wang Q, Wang J, Zeng J, Du Z, Xiao J*. RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks. Briefings in Bioinformatics, 2021, 22(6):bbab326. [PMID=34402866]

  20. Song S#, Ma L#, Zou D#, Tian D#, Li C#, Zhu J#, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z, Zhao W*, Xue Y*, Bao Y*. The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. Genomics Proteomics & Bioinformatics, 2020, 18(6):749–759. [PMID=33704069]

  21. Du Z#, Ma L#, Qu H#, Chen W#, Zhang B#, Lu X, Zhai W, Sheng X, Sun Y, Li W, Lei M, Qi Q, Yuan N, Shi S, Zeng J, Wang J, Zhang Y, Liu Q, Hong Y, Dong L, Zhang Z, Zou D, Wang Y, Song S, Liu F, Fang X, Chen H, Liu X, Xiao J*, Zeng C*. Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. Genomics Proteomics & Bioinformatics, 2019, 17(3):229–247. [PMID=31494266]

  22. Aljohi H#, Liu W#, Lin Q#, Zhao Y, Zeng J, Alamer A, Alanazi I, Alawad A, AI-sadi A, Hu S*, Yu J*. Complete Sequence and Analysis of Coconut Palm (Cocos nucifera) Mitochondrial Genome. PLoS One, 2016, 11(10):e0163990. [PMID=27736909]

  23. Zeng J as co-author in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Research, 2024, 52(D1):D18-D32. [PMID=38018256]

  24. Zeng J as co-author in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021, Nucleic Acids Research, 2021, 49(D1):D18-D28. [PMID=33175170]

  25. Zeng J as co-author in National Genomics Data Center Members and Partners, Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research, 2020, 48(D1):D24-D33. [PMID=31702008]

  26. Zeng J as co-author in BIG Data Center Members, Database Resources of the BIG Data Center in 2018. Nucleic Acids Research, 2018, 46(D1):D14-D20. [PMID=29036542]

  27. Zeng J as co-author in BIG Data Center Members, The BIG Data Center: from deposition to integration to translation. Nucleic Acids Research, 2017, 45(D1):D18-D24. [PMID=27899658]

  28. 曾瀞瑶#，苑娜#，魏文娟，李根，杜政霖*，高通量计算在大规模人群队列基因组数据解析应用中的挑战，数据与计算发展前沿，2020，DOI: 10.11871/jfdc.issn.2096-742X.2020.01.010.

  29. 刘万飞，王西亮，赵宇慧，曾瀞瑶，耿佳宁，胡松年*，基于第二代测序技术的细菌基因组与转录组研究策略简介，微生物学通报，2011.