基本信息

张金阳  男  硕导  中国科学院动物研究所

电子邮件： zhangjinyang@ioz.ac.cn
通信地址： 北京市朝阳区奥运村街道中国科学院遗传与发育研究所1号楼三层
邮政编码： 100101

研究领域

张金阳，博士，副研究员。主要研究方向为非编码RNA相关计算方法学开发，利用生物组学大数据探索非编码RNA的组成结构及调控功能。以第一/通讯（含共同）作者在 Nature Biotechnology (2021, 2025), Nature Genetics (2025), Nature Cell Biology (2024), Nature Communications (2020, 2022, 2026), Nucleic Acids Research (2023), Nature Protocols (2023), Advanced Science (2022, 2024), Trends in Biochemical Sciences (2021) 等学术期刊发表论文15篇，多个工作入选ESI高被引论文。研究成果入选2019与2021年度中国生物信息学十大进展。获得中国科学院院长特别奖、北京市优秀毕业生、中国科学院优秀博士学位论文。作为项目负责人，主持国家自然科学基金优秀青年科学基金 (2024)、重点研发课题、博士后创新人才支持计划 (2022)等多项基金。

招生信息

招生专业

0710Z1-基因组学 / 非编码RNA生物信息学 （学术硕士）

086000-生物与医药 / 非编码RNA组学 （工程硕士）

招生信息

2026年度拟招收工程硕士1名

教育背景

2015-09--2021-07   中国科学院大学   博士学位
2011-09--2015-07   北京大学   学士学位

工作经历

2023-07~至今, 中国科学院动物研究所, 副研究员

2021-08~2023-07,中国科学院动物研究所, 博士后（特别研究助理）

出版信息

代表论著

(#第一作者, *通讯作者)

1. Dong, H., Gao, Y., Cai, Z., Li, Y., Li, X.*, Zhao, F.* & Zhang, J.* (2026). Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing. Nature Communications doi: 10.1038/s41467-026-68419-y (最后通讯作者)

2. Zhang, J.* & Zhao, F*. (2025). Circular RNA discovery with emerging sequencing and deep learning technologies. Nature Genetics 57, 1089–1102 (第一作者&共同通讯作者)

3. Zhang, J.#, Hou, L.#, Ma, L.#, Cai, Z., Ye, S., Liu, Y., Ji, P., Zuo, Z., & Zhao, F. (2024) Real-time and programmable transcriptome sequencing with PROFIT-seq. Nature Cell Biology, 26, 2183-2194 (第一作者)

4. Wu, W., Zhao, F.*, Zhang, J.* (2023). circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs through a standardized nomenclature scheme. Nucleic Acids Research, 52, D52-D60 (最后通讯作者)

5. Zhang, J.#, Hou, L.#, Zuo, Z.#, Ji, P., Zhang, X., Xue, Y. & Zhao, F. (2021). Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nature Biotechnology, 39, 836–845. (第一作者)

6. Zhang, J., Chen, S., Yang, J., & Zhao, F. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications, 11(1), 90. (第一作者)


所有已发表论著

Web of Science: AFS-9879-2022


2026

  • Dong, H., Gao, Y., Cai, Z., Li, Y., Li, X.*, Zhao, F.* & Zhang, J.* (2026). Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing. Nature Communications. [DOI] [PDF] [Citation] [GitHub]

2025

  • Zheng, X.#, Zhang, J.#, Song, L.#, Li, XJ., Zhao, F.*, & Gao, Y*. (2025). CIRI3: scalable and accurate detection and quantification of circular RNAs in extremely large RNA-seq datasets. Nature Biotechnology. [DOI] [PDF] [Citation]
  • Chen, Z.#, Jiang, H.#, Yuan, L., Yao, T., Rong, X., Gao, W., Zeng, C., He, L., Yin, Y., Jaffrey, S., Zhao, F., Zhang, J.*, Xu, P.* & Li, X.* (2025). Photoactivatable RNA Tags for Subcellular Photolabeling of RNA. Journal of the American Chemical Society. [DOI] [PDF] [Citation]
  • Zhang, J.* & Zhao, F*. (2025) Circular RNA discovery with emerging sequencing and deep learning technologies. Nature Genetics, 57, 1089–1102 [DOI] [PDF] [Citation]
  • Hu, B.#, He, R.#, Pang, K.#, Wang, G.#, Wang, N., Zhu, W., Sui, X., Teng, H., Liu, T., Zhu, J., Jiang, Z., Zhang, J., Zuo, Z., Wang, W., Ji, P.*, Zhao, F.* (2025). High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning. Cell, 188, 1-15 [DOI] [PDF] [Citation]

2024

  • Cao, X.#, Cai, Z.#, Zhang, J. & Zhao, F. (2024). Engineering circular RNA medicines. Nature Reviews Bioengineering, 3, 270–287 [DOI] [PDF] [Citation]
  • Zhang, J.#, Hou, L.#, Ma, L.#, Cai, Z., Ye, S., Liu, Y., Ji, P., Zuo, Z., & Zhao, F. (2024) Real-time and programmable transcriptome sequencing with PROFIT-seq. Nature Cell Biology, 26, 2183-2194 [DOI] [PDF] [Citation] [GitHub] [Protocols.io] [Source data]
  • Zhou, Z.#, Zhang, J.#, Zheng, X., Pan, Z., Zhao, F.*, Gao, Y.* (2024) CIRI-deep Enables Single-cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. Advanced Science, 11, e2308115 [DOI] [PDF] [Citation] [GitHub] [Website]

2023

  • Wu, W., Zhao, F.*, Zhang, J.* (2023). circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs through a standardized nomenclature scheme. Nucleic Acids Research, 52(D1), D52-D60 [DOI] [PDF] [Citation] [Source Data] [Nature Work/Technology &Tools]
  • Wu, W.#, Zhang, J.#*, Zhao, F.* (2023). CIRI-hub: an integrated and visual analytics platform for circular RNAs in cancers. bioRxiv. 10.1101/2023.08.09.552604 [DOI]
  • Vromman, M.#, Anckaert, J., Bortoluzzi, S, Buratin, A., Chen, C., Chu, Q., Chuang, T., Dehghannasiri, R., Dieterich, C., Dong, X., Flicek, P., Gaffo, E., Gu, W., He, C., Hoffmann, S., Izuogu, O., Jackson, M., Jakobi, T., Lai, E., Nuytens, J., Salzman, J., Santibanez-Koref, M., Stadler, P., Thas, O., Eynde, E., Verniers, K., Wen, G., Westholm, J., Yang, L., Ye, C., Yigit, N., Yuan, G., Zhang, J., Zhao, F., Volders, P.*, Vandesompele, J.* (2023) Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nature Methods 20, 1159–1169 [DOI] [PDF] [Citation] [Nature Methods]
  • Hou, L.#, Zhang, J.#* & Zhao, F.* (2023). Full-length circular RNA profiling by nanopore sequencing with CIRI-long. Nature Protocols, 18, 1795–1813 [DOI] [PDF] [Citation]
  • Deshpande, D.#, Chhugani, K.#, Chang, Y., Karlsberg, A., Loeffler, C., Zhang, J., Muszynska, A., Rotman, J., Tao, L., Martin, L. S., Balliu, B., Tseng, E., Eskin, E., Zhao, F., Mohammadi, P., Labaj, P. P., & Mangul, S. (2023). RNA-seq data science: From raw data to effective interpretation. Frontiers in Genetics, 14, 997383 [DOI] [PDF] [Citation]

2022

  • Wu. W.#, Zhang, J.#, & Zhao, F. (2022). Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing. Nature Communications, 13, 3242. [DOI] [PDF] [Citation] [GitHub] [Source Data]
  • Yang, J.#, Hou, L.#, Wang, J.#, Xiao, L., Zhang, J., Yin, N., Wei, Y., Yao, Su., Cheng, K., Zhang, W., Shi, Z., Wang, J., Jiang, H., Huang, N., You, Y., Lin, M., Shang, R., Zhao, Y.* & Zhao, F.* (2022). Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins. Gut, 71:2451-2462. [DOI] [PDF] [Citation]
  • Chen, S.#, Cao, X.#, Zhang, J.#, Wu, W., Zhang, B. & Zhao, F. (2022). circVAMP3 drives CAPRIN1 phase separation and inhibits hepatocellular carcinoma by suppressing c-Myc translation. Advanced Science, 9(8): e2103817. [DOI] [PDF] [Citation]
  • Chen, S.#, Zhang, J.#, & Zhao, F. (2022). Screening linear and circular RNA transcripts from stress granules. Genomics, Proteomics & Bioinformatics, 21, 886-893 [DOI] [PDF] [Citation]

2021

  • Zhang, J. & Zhao, F. (2021). Characterizing circular RNAs using nanopore sequencing. Trends in Biochemical Sciences. 46, 785–786 [DOI] [PDF] [Citation]
  • Zhang, J. & Zhao, F. (2021). Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets. Methods 196, 17–22 [DOI] [PDF] [Citation]
  • Zhang, J.#, Hou, L.#, Zuo, Z.#, Ji, P., Zhang, X., Xue, Y. & Zhao, F. (2021). Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nature Biotechnology, 39, 836–845. [DOI] [PDF] [Citation] [GitHub] [Nature Biotechnology News & Views] [2021 Top 10 Advances in Bioinformatics in China]
  • Li, X.#, Zheng, J.#, Ma, X.#, Zhang, B., Zhang, J., Wang, W., Sun, C., Wang, Y., Zheng, J., Chen, H., Tao, J., Wang, H., Zhang, F., Wang, J., & Zhang, H. (2021). The Oral Microbiome of Pregnant Women Facilitates Gestational Diabetes Discrimination. Journal of Genetics and Genomics, 48, 32–39 [DOI] [PDF] [Citation]

2020

2019

  • Ji, P.#, Wu, W.#, Chen, S.#, Zheng, Y., Zhou, L., Zhang, J., Cheng, H., Yan, J., Zhang, S., Yang, P., & Zhao, F. (2019). Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals. Cell Reports, 26(12), 3444–3460.e5. [DOI][PDF] [Citation]

2018

  • Gao, Y., Zhang, J., & Zhao, F. (2018). Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics, 19(5), 803–810. [DOI][PDF] [Citation]

2016

  • Gao, Y.#, Wang, J.#, Zheng, Y.#, Zhang, J., Chen, S., & Zhao, F. (2016). Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nature Communications, 7, 12060. [DOI][PDF] [Citation]