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

Tens of thousands of non-coding regulatory elements are encoded in the genome. However, their regulatory roles have not been comprehensively unveiled. The revolution of sequencing techniques has now offered many powerful tools to interrogate the functional roles of these regulatory elements. Our over-arching goal is to expose the principles that dictate the complex regulome, particularly biological processes mediated or driven by non-coding RNAs, by combining computational approaches, cutting-edge high-throughput assays and interdisciplinary methodologies. The current research topics in the lab include:

1. RBP-lncRNA Interactome

• Study the evolution of functional modules of lncRNAs and RNA binding proteins.
• Elucidate the underlying mechanisms that determine the interaction between lncRNAs and RBPs.
• Investigate the impact of dysregulated regulome on pathogenesis and identify potential targets for therapeutic purposes.

2. Single-cell Multi-omics

• Apply single-cell transcriptomic and epigenetic profiles to understand the roles of different cells.
• Reveal underlying molecular mechanisms that confer functional characteristics.

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.

Selected Publication List

1. Wang, Z.*, Zhang, J.*, Xu, X., Witt, C., Deng Y., Chen, G., et al. (2021). Phylogeny and sex chromosome evolution of palaeognathae. J Genet Genomics.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. Zhang, J*., Li, C., Zhou, Q., and Zhang, G. (2015). Improving the ostrich genome assembly using optical mapping data. GigaScience 4, 4-6.
8. 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

5 February 2023