Omics & AI Lab

Interdisciplinary Science Center, State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management,

Institute of Zoology, Chinese Academy of Sciences

No.1 Beichen West Road

Chaoyang District, Beijing, 100101, P.R. China

2015-2021, Ph.D., Genetics, Beijing Institutes of Life Science (College of Life Science), CAS, China

2011-2015, B.S., Life Science, School of Life Science, Peking University, China

2023- , Research Associate, Institute of Zoology, CAS, China

2021-2023, Post-Doctoral Associate, Beijing Institutes of Life Science, CAS, China

Selected Publications

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 17, 1722 (Last corresponding author)
2. Zhang, J.* & Zhao, F*. (2025). Circular RNA discovery with emerging sequencing and deep learning technologies. Nature Genetics 57, 1089–1102 (First Author & co-corresponding author)
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 (First author)
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 (Last corresponding author)
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 (First author)
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 (First author)

All Publications

Web of Science: AFS-9879-2022

2025

• 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. 17, 1722 [DOI] [PDF] [Citation] [GitHub]
• 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]
• 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] [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

• Zhang, J., Chen, S., Yang, J., & Zhao, F. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications, 11, 90. [DOI] [PDF] [Citation] [GitHub] [2020 Top 10 Advances in Bioinformatics in China]

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]

2022, China National Postdoctoral Program for Innovative Talents

2022, Excellent Doctoral Thesis, Beijing

2022, Excellent Doctoral Thesis, CAS

2021, Special Research Assistant funded projects, CAS

2021, CAS President Scholarship (Special Prize), CAS

2019, Zhuliyuehua Outstanding Doctoral Award, CAS