Personal information
- Computational Genomics Lab, Beijing Institutes of Life Science (BIOLS)
- Chinese Academy of Sciences
- No.1 Beichen West Road
- Chaoyang District, Beijing, 100101, P.R. China
Education
- 09/2011-06/2015 B.S., Life Science
- School of Life Science
- Peking University, P.R. China
- 09/2015-06/2021 Ph.D., Genetics (with honors),
- Beijing Institutes of Life Science (College of Life Science)
- Chinese Academy of Sciences, P.R. China
- Supervisor: Prof. Fangqing Zhao
- Dissertion: Accurate quantification and reconstruction of circular RNAs using high-throughput sequencing data
Work experience
- 09/2021-07/2023 Post-Doctoral Associate
- Computational Genomics Lab, Beijing Institutes of Life Science
- Chinese Academy of Sciences, P.R. China
- Supervisor: Prof. Fangqing Zhao
- Special Research Assistant funded projects, Chinese Academy of Sciences
- China National Postdoctoral Program for Innovative Talents
- 07/2023-now Associate Research Fellow
- Computational Genomics Lab, Beijing Institutes of Life Science
- Chinese Academy of Sciences, P.R. China
Awards & Honors
- 2022 Excellent Doctoral Thesis, Beijing
- 2022 Excellent Doctoral Thesis, Chinese Academy of Sciences
- 2021 CAS President Scholarship (Special Prize), Chinese Academy of Sciences
- 2021 Pacemaker to Merit Student, University of Chinese Academy of Sciences
- 2019 Zhuliyuehua Outstanding Doctoral Award, Chinese Academy of Sciences
- 2019 Merit Student, University of Chinese Academy of Sciences
- 2017 Merit Student, University of Chinese Academy of Sciences
Selected Publications
(# indicates co first authors, *corresponding authors)
- 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. (IF=46.9)
- Featured in Nature Biotechnology, 39, 811–812 (2021).
- Featured in 2021 Top 10 Advances in Bioinformatics in China, Genomics, Proteomics & Bioinformatics
- 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. (IF=16.6)
- Zhang, J.#, Hou, L.#, Ma, L.#, Ye, S., Liu, Y., Ji, P., Zuo, Z., & Zhao, F. (2023) Real-time and programmable transcriptome sequencing with PROFIT-seq. (Submitted)
- 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 (IF=14.9)
- Zhang J & Zhao F. (2021). Characterizing circular RNAs using nanopore sequencing. Trends in Biochemical Sciences, 46, 785–786 (IF=13.8)
Publications
Web of Science: AFS-9879-2022
2024
- 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, 10.1002/advs.202308115 (IF=15.1) [DOI] [PDF] [Citation] [GitHub]
2021-2023
- 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 (IF=14.9) [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 (IF=48.0) [DOI] [SharedIt] [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 (IF=14.8) [DOI] [SharedIt] [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 (IF=3.7) [DOI] [PDF] [Citation]
- 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. (IF=16.6) [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. (IF=24.5) [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. (IF=15.1) [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 (IF=9.5) [DOI] [PDF] [Citation]
2015-2021
- Zhang, J. & Zhao, F. (2021). Characterizing circular RNAs using nanopore sequencing. Trends in Biochemical Sciences. 46, 785–786 (IF=13.8) [DOI] [Citation]
- Zhang, J. & Zhao, F. (2021). Reconstruction of circular RNAs using Illumina and Nanopore RNA-seq datasets. Methods 196, 17–22 (IF=4.8) [DOI] [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. (IF=46.9) [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 (IF=5.9) [DOI] [PDF] [Citation]
- Zhang, J., Chen, S., Yang, J., & Zhao, F. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications, 11, 90. (IF=16.6) [DOI] [PDF] [Citation] [GitHub] [2020 Top 10 Advances in Bioinformatics in China]
- 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. (IF=8.8) [DOI][PDF] [Citation]
- Gao, Y., Zhang, J., & Zhao, F. (2018). Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics, 19(5), 803–810. (IF=9.5) [DOI][PDF] [Citation]
- 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. (IF=16.6) [DOI][PDF] [Citation]
Invited Talks & Conference Presentations
- 2023 The 10th forum of Young Bioinformatics PI (YBP). Dec 13-14th. Shanghai, China (Invited talk)
- 2021 The 11th youth forum of national symposium of Chinese RNA society. July 2-5th. Dalian, China (Invited talk)
- 2019 The 1st National Postgraduate Forum of Basic Medicine held by the Savaid Medical School, University of Chinese Academy of Sciences. November 30th. Beijing, China (Invited talk)
Journal Reviewer
Reviewers of Nucleic Acids Research, RNA Biology, Briefings in Bioinformatics, Genomics Proteomics and Bioinformatics, mLife