ZHANG, Jilin (張繼林)

Prof. Zhang received his BSc in Bioengineering at Beijing Institute of Technology in 2008, MSc in Biophysics at Beijing Jiaotong University in 2010, and PhD in Medical Science at Karolinska Institutet in 2020. During his PhD study, he successfully delivered a valuable resource of structural binding specificities recognised by human RBPs and demonstrated that RBPs exhibit potentially multi-facet functions in gene regulation. Between September 2020 and September 2021, he worked as a post-doctoral researcher with Björn Reinius at Karolinska Institutet to study the fundamental molecular basis of dosage compensation in the ZW sex-determining system using state-of-art single-cell sequencing technologies. In March 2022, Prof. Zhang was appointed as an assistant professor at the Department of Biomedical Sciences. His research focuses on dissecting the functional roles of regulatory elements encrypted in the genome.

Research Interests

Our overarching goal is to uncover the principles governing the complex regulome—particularly processes driven by RNA-binding proteins (RBPs) and non-coding RNAs—by combining computational approaches, cutting-edge high-throughput assays, and interdisciplinary methodologies. Our research falls within the following four lines:

1. RBP-RNA Interactome
   • Identify the functional modules of RNA-binding proteins and RNAs.
   • Elucidate mechanisms that determine the binding between RNAs and RBPs.
   • Develop novel strategies to understand and target the dysregulated RNA-RBP interactome in human diseases.
2. Single-cell Multi-omics
   • Integrate single-cell transcriptomic and epigenetic profiles to address biological questions.
3. Comparative Genomics
   • Use comparative genomics to tackle evolutionary questions.
4. Tools and Methods
   • Develop Bioinformatics tools and methods.
   • Apply artificial intelligence for RNA structure dynamics.

Position Availability

PhD program position is available all year round. Please send an email for inquiry with your updated CV. Candidates should obtain valid English test scores before admission.

News

RNA modifications are widely associated with RNA structures

Evolution of the smallest vertebrate genomes

Publication List (Since 2021)

• Zhou, X., Zhang, Y., Sun, L., Kwok, C. K. & Zhang, J.# Dysregulated RNA G-quadruplex binding proteins reveal shifted stress responses in Alzheimer’s Disease. biorxiv (2026). https://doi.org:10.64898/2026.01.20.700564
• Sun, W., Wu, N., Xia, M., Pan, Y., Liu, M., Fan, S., Wang, J., Zeng, Y., Fan, L., Chen, J., Liu, G., Yan, H., Qiu, Y., Xie, Y., Jiang, Z., Chen, F., Yin, Y., Zhang, J., Li, L., Xie, W., Wang, H., Zhang, L., Yu, M., Wang, X. & Yan, J. NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architecture. Mol Cell 86, 2617-2634 e2611 (2026). https://doi.org:10.1016/j.molcel.2026.05.010
• Kabbe, M., Agirre, E., Carlstrom, K. E., Dumral, O., Lor, Y. K., Pohl, F. B., Ruffin, N., van Bruggen, D., Meijer, M., Seeker, L. A., Bestard-Cuche, N., Lederer, A. R., Zhang, J., Ahola, V., Goldman, S. A., Edstrom, E., Arvidsson, L., Moreira, T. H., Bartosovic, M., Jagodic, M., Williams, A. & Castelo-Branco, G. Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs. Nat Neurosci 29, 992-1006 (2026). https://doi.org:10.1038/s41593-026-02208-0
• He, J., Zhou, T., Hu, L. F., Jiao, Y., Wang, J., Yan, S., Jia, S., Chen, Q., Zhu, W., Zhang, J., Jia, M., Li, Y., Wang, X., Wang, Y., Yang, Y. T. & Sun, L. Augmented prediction of multi-species protein-RNA interactions using evolutionary conservation of RNA-binding proteins. Nat Commun 17 (2026). https://doi.org:10.1038/s41467-026-72351-6
• Zhou, Y., Lyu, S., Liew, S. W., Mou, X., Hoffecker, I., Yan, J., Li, Y., Kwok, C. K. & Zhang, J.# MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics. Genomics Proteomics Bioinformatics (2025). https://doi.org:10.1093/gpbjnl/qzaf106
• Sur, I., Zhao, W., Zhang, J., Kling Pilstrom, M., Webb, A. T., Cheng, H., Ristimaki, A., Katajisto, P., Enge, M., Rannikmae, H., de la Roche, M. & Taipale, J. Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer. Life Sci Alliance 8 (2025). https://doi.org:10.26508/lsa.202403090
• Papanicolaou, N., Lentini, A., Wettersten, S., Hagemann-Jensen, M., Kruger, A., Zhang, J., Coucoravas, C., Petrosian, I., Xin, X., Ceyhan, I., Rorbach, J., Wright, D. & Reinius, B. Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates. Nat Commun 16, 9088 (2025). https://doi.org:10.1038/s41467-025-64817-w
• Liu, K., Wang, Q., Wang, N., Meng, L., Li, S., Wang, H. Y., Liu, Y., Liu, Q., Zhang, Y., Doretto, L. B., Zhang, M., Qin, Y., Pan, S., Han, S., Li, W., Liu, S., Gao, F., Meyer, A., Taipale, J., Fan, G., Schartl, M., Zhang, J.# & Shao, C. Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes. Adv Sci (Weinh) 12, e17251 (2025). https://doi.org:10.1002/advs.202417251
• Li, T., Chen, H., Ma, N., Jiang, D., Wu, J., Zhang, X., Li, H., Su, J., Chen, P., Liu, Q., Guan, Y., Zhu, X., Lin, J., Zhang, J., Wang, Q., Guo, H. & Zhu, F. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding. Imeta 4, e70009 (2025). https://doi.org:10.1002/imt2.70009
• Wang, X., Li, X., Pu, A., Shun, H. B., Chen, C., Ai, L., Tan, Z., Zhang, J., Liu, K., Gao, J., Ban, K. & Yao, X. On-chip droplet analysis and cell spheroid screening by capillary wrapping enabled shape-adaptive ferrofluid transporters. Lab Chip 24, 1782-1793 (2024). https://doi.org:10.1039/d3lc00906h
• Rimoldi, M., Wang, N., Zhang, J., Villar, D., Odom, D. T., Taipale, J., Flicek, P. & Roller, M. DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts. Genome Biol 25, 146 (2024). https://doi.org:10.1186/s13059-024-03218-6
• Yang, L., Lin, Z., Gao, Y., Zhang, J., Peng, H., Li, Y., Che, J., Zhao, L. & Zhang, J. Populational pan-ethnic screening panel enabled by deep whole genome sequencing. NPJ Genom Med 8, 38 (2023). https://doi.org:10.1038/s41525-023-00383-8
• Fan, S., Sun, W., Fan, L., Wu, N., Sun, W., Ma, H., Chen, S., Li, Z., Li, Y., Zhang, J. & Yan, J. The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity. Comput Struct Biotechnol J 20, 5040-5044 (2022). https://doi.org:10.1016/j.csbj.2022.09.007
• Wang, Z., Zhang, J.*, Xu, X., Witt, C., Deng, Y., Chen, G., Meng, G., Feng, S., Xu, L., Szekely, T., Zhang, G. & Zhou, Q. Phylogeny and sex chromosome evolution of Palaeognathae. J Genet Genomics 49, 109-119 (2022). https://doi.org:10.1016/j.jgg.2021.06.013

Selected Publication (Before 2021)

1. Li, J., Zhang, J., Liu, J., Zhou, Y., Cai, C., Xu, L., Dai, X., Feng, S., Guo, C., Rao, J., Wei, K., Jarvis, E.D., Jiang, Y., Zhou, Z., Zhang, G., and Zhou, Q. (2021). A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. Gigascience 10.
2. Jolma, A.*, Zhang, J.*, Mondragon*, E., Morgunova, E., Kivioja, T., Laverty, K.U., Yin, Y., Zhu, F., Bourenkov, G., Morris, Q., Hughes, T.R., Maher, L.J., 3rd, and Taipale, J. (2020). Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences. Genome Res 30, 962-973.
3. Yi, W., Li, J., Zhu, X., Wang, X., Fan, L., Sun, W., Liao, L., Zhang, J., Li, X., Ye, J., Chen, F., Taipale, J., Chan, K.M., Zhang, L., and Yan, J. (2020). CRISPR-assisted detection of RNA-protein interactions in living cells. Nat Methods 17, 685-688.
4. Schmierer, B., Botla, S.K., Zhang, J., Turunen, M., Kivioja, T., and Taipale, J. (2017). CRISPR/Cas9 screening using unique molecular identifiers. Mol Syst Biol 13, 945.
5. Dave, K., Sur, I., Yan, J., Zhang, J., Kaasinen, E., Zhong, F., Blaas, L., Li, X., Kharazi, S., Gustafsson, C., De Paepe, A., Mansson, R., and Taipale, J. (2017). Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. eLife 6.
6. Zhang, J*., Li, C., Zhou, Q., and Zhang, G. (2015). Improving the ostrich genome assembly using optical mapping data. GigaScience 4, 4-6.
7. Zhou, Q.*, Zhang, J.*, Bachtrog, D.*, An, N., Huang, Q., Jarvis, E.D., Gilbert, M.T.P., and Zhang, G. (2014). Complex evolutionary trajectories of sex chromosomes across bird taxa. Science (New York, NY) 346, 1246338-1246338.

* First/co-first author

Complete publication list: https://orcid.org/0000-0002-9976-1605

17 June 2026