Personal information

• Omics Technology & Artificial Intelligence Lab, Institute of Zoology
• Chinese Academy of Sciences
• No.1 Beichen West Road
• Chaoyang District, Beijing, 100101, P.R. China

Work experience

• 2023.07 - now Associate Research Fellow
  • Omics Technology & Artificial Intelligence Lab, Institute of Zoology
  • Chinese Academy of Sciences, P.R. China
• 2021.09 - 2023.07 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

Education

• 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
• 09/2011-06/2015 B.S., Life Science
  • School of Life Science
  • Peking University, 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
• 2019 Zhuliyuehua Outstanding Doctoral Award, Chinese Academy of Sciences

Selected Publications

(# indicates co first authors, *corresponding authors)

1. 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
2. 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, https://doi.org/10.1038/s41556-024-01537-1 (IF=17.3)
3. 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)
   • Featured in 2020 Top 10 Advances in Bioinformatics in China, Genomics, Proteomics & Bioinformatics
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 (IF=14.9)
5. Zhang J & Zhao F. (2021). Characterizing circular RNAs using nanopore sequencing. Trends in Biochemical Sciences, 46, 785–786 (IF=13.8)

All Publications

Web of Science: AFS-9879-2022

2024

• 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, https://doi.org/10.1038/s41556-024-01537-1 (IF=17.3) [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 (IF=14.3) [DOI] [PDF] [Citation] [GitHub] [Website]

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=16.6) [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=36.1) [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 (IF=13.1) [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 (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=14.7) [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] [PDF] [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] [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. (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]