About Myself

I earned my BSc in Biological Sciences from Tsinghua University and my PhD in Medical Science from Karolinska Institutet in 2014, where I studied transcriptional regulatory mechanisms in colorectal cancer under the supervision of Prof. Jussi Taipale. From 2015 to 2018, I performed postdoctoral research with Prof. Bing Ren at the University of California, San Diego, focusing on epigenetic regulation and 3D genome organization. In 2018, I joined CityU Hong Kong as a tenure‑track Assistant Professor and was promoted to Associate Professor with tenure in 2023. In 2021, I received the university’s prestigious Outstanding Research Award for Junior Faculty in recognition of my research contributions.

Beyond research, I strongly believe in maintaining a healthy work–life balance. I enjoy hiking, scuba diving, traveling, and alpine skiing in my spare time, and I always encourage my lab members to pursue their interests and cultivate a fulfilling, balanced life alongside their academic work.

Research Interests

The noncoding genome makes up ~98% of the human genome and harbors the vast majority of disease associated genetic variants. It encodes critical regulatory elements and noncoding RNAs that precisely control gene transcription, and its dysregulation is a central driver of human diseases. However, the functional mechanisms of most noncoding regions remain poorly understood.

Our lab focuses on two synergistic core directions: (1) developing high throughput experimental methods to dissect interactions of protein–nucleic acid (both RNA and DNA, as well as their epigenetic modifications), and (2) building deep learning models (CNN, LLM, etc) to decode the functional logic of the noncoding genome in transcriptional regulation and disease. The major research projects include:

1. Systems biology study on function of noncoding variants
   1. How genetic variants affect binding of transcription factors (^ref. Nature 2021; Nature Communications 2020)
   2. How (epi)genetic variants alter enhancer activity (^ref. Science Advances 2026)
2. RNA-RBP interactions
   1. Developing new method to identify RNA’s RBPs (^ref. Nature Methods 2020)
   2. Developing high throughput method to study how RNA structures (e.g. G-quadruplex) & RNA modifications (m⁶A, Ψ, etc.) affect protein binding
   3. Applying the tools to study the function of transposable elements (TE) and long noncoding RNA (^ref. Journal of Translational Medicine 2025)
3. Epigenetic-/Epitranscriptomic-modifications
   1. Leveraging multi-omics strategy to identify the key oncogenic pathways (^ref. Advanced Science 2025; International Journal of Biological Sciences 2025; Nucleic Acids Research 2019)
   2. Developing new tools to identify chromatin associated RNA (^ref. Science Advances 2024)

Students with diverse backgrounds are strongly welcome:

• Students with biology & chemistry background
• Students with computer science, mathematics, or engineering backgrounds
• Students interested in both experiments & computation are especially encouraged.

But no worries if you lack cross disciplinary experience: We will provide full guidance through internal collaboration and training to you to support your growth and success.

The PhD programme position is available all year round. Should you have any interest, please send an email for inquiry with your updated CV enclosed. Note that a valid English language test score fulfilling the university minimum requirement (TOEFL iBT 79 or IELTS 6.5) should be obtained before admission.

Publications

(^# corresponding authors; * co-first author)

2026

• E. Chen, Q. Yang*, H. Dai*, Y. Chen*, Y. Zhang*, Q. Wang, R. Hou, M. Chen, J. Wang, Q. Xie, W. Sun, Y. Ning, L. Fan, J. Yan^#, Systematic analysis of functional genetic and epigenetic variants in colorectal cancer, Science Advances 12 (8) (2026) aeb2473.
• Y. Ning*, L. Liao*, L.J. Zhang*, X. Yang, J. Wang, Q. Xie, Y. Zhang, R. Li, Q. Liu, X. Zhao, N. Wu, S. Zhao, J. He, E. Chen, P. Gao, G.H. Wei, K. Dong, W. Sun, J. Ye^#, J. Yan^#, CEBPB binding at rs2643219 modulates insulin sensitivity via RASGRP1–GLUT4 axis, Genes & Diseases (2026) 102042.
• J. Liu, D.L.S. Chung, L.K.Y. Chow, S. Han, W. Yi, C.J. Cremin, Y. Liao, P. Wang, B.W.Y. Mok, M. Ji, J. Yan, W. Dai, H. Chen^#, Epstein‐Barr Virus Expressed Long Non‐Coding RNA (lncBARTs) Regulate EBV Latent Genome Replication, Advanced Science 13 (8) (2026) e07286

2025

• Y. Zhou*, S. Lyu*, S.W. Liew, X. Mou, I. Hoffecker, J. Yan, Y. Li, C.K. Kwok^#, J. Zhang^#, MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics, Genomics, Proteomics & Bioinformatics (2025) qzaf106.
• J. Wang*, X. Yang*, X. Su*, W. Yi, W. Sun, J. Wei, Y.Q. Ning^#, J. Yan^#, Targeting PURPL RNA enabled rejuvenation of senescence cells via epigenetic reprogramming, Journal of Translational Medicine 23 (1) (2025) 1127.
• Z. Wang, X. Xie, Y. Zhou, H. He, Z. Guo, Z. Zhou, B. Liu, J. Sun, W. Li, Q. Nie, J. Dai, W. Yi, X. Zhou, J. Yan, M. Yang^#, 3D Nanofibrillar Matrix Stiffness Modulates Extracellular Vesicle Cargo and Pro-Tumour Functions, Journal of Extracellular Vesicles 14 (10) (2025) e70165.
• Y.Q. Ning*, J. Wang*, Y. Zhang*, H. Li*, Z. Jiang*, X. Su, X. Yang, X. Wu, B. Wei, J. Ying, J. Yan^#, W. Li^#, Enhancer Reprogramming Reveals the Tumorigenic Role of PTPRZ1 in Lung Squamous Cell Carcinoma, Advanced Science 12 (44) (2025) e09344
• W. Yi, J. Yan^#, Decoding RNA–Protein Interactions: Methodological Advances and Emerging Challenges, Advanced Genetics (2025) 2500011.
• X. Li*, Y. Zhou*, J. Wei, W. Sun, L. Fan, J. Yan^#, Unlocking the Puzzle of Mammalian Transfection: The Role of the RNA-sensing-Mediated Interferon Response in the Cellular Defense Against Foreign DNA Intrusion, International Journal of Biological Sciences 21 (9) (2025) 3886-3900.

2024

• Y. Gao, D.S. Tan, M. Girbig, H. Hu, X. Zhou, Q. Xie, S.W. Yeung, K.S. Lee, S.Y. Ho, V. Cojocaru, J. Yan, G.K.A. Hochberg, A. de Mendoza, R. Jauch#, The emergence of Sox and POU transcription factors predates the origins of animal stem cells, Nature Communications 15 (1) (2024) 9868.
• L. Fan*, W. Sun*, Y. Lyu, F. Ju, W. Sun, J. Chen, H. Ma, S. Yang, X. Zhou, N. Wu, W. Yi, E. Chen, R. Villaseñor, T. Baubec, J. Yan^#, Chrom-seq identifies RNAs at chromatin marks, Science Advances 10 (31) (2024) eadn1397.

2022

• X. Yue, Z. Xie, M. Li, K. Wang, X. Li, X. Zhang, J. Yan, Y. Yin^#, Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing, Nature Communications 13 (1) (2022) 1-14.
• P. Benaglio*, H. Zhu*, M.L. Okino*, J. Yan, R. Elgamal, N. Nariai, E. Beebe, K. Korgaonkar, Y. Qiu, M.K.R. Donovan, J. Chiou, G. Wang, J. Newsome, J. Kaur, M. Miller, S. Preissl, S. Corban, A. Aylward, J. Taipale, B. Ren, K.A. Frazer, M. Sander, K.J. Gaulton^#, Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines, Cell Genomics (2022) 100214.
• S. Fan*, W. Sun*, L. Fan*, N. Wu, W. Sun, H. Ma, S. Chen, Z. Li, Y. Li, J. Zhang, J. Yan^#, The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity, Computational and Structural Biotechnology Journal 20 (2022) 5040-5044.
• P. Gao^#,*, J.L. Hao*, Q.W. Xie*, G.Q. Han, B.B. Xu, H. Hu, N.E. Sa, X.W. Du, H.L. Tang, J. Yan, X.M. Dong^#, PELO facilitates PLK1-induced the ubiquitination and degradation of Smad4 and promotes the progression of prostate cancer, Oncogene 41 (21) (2022) 2945-2957.
• W. Zhang, J. Lin, P. Shi, D. Su, X. Cheng, W. Yi, J. Yan, H. Chen, F. Cheng^#, Small Extracellular Vesicles Derived From MSCs Have Immunomodulatory Effects to Enhance Delivery of ASO-210 for Psoriasis Treatment, Frontiers in Cell and Developmental Biology 10 (2022) 842813-842813.

2021

• J. Yan^#,*, Y. Qiu*, A. dos Santos*, Y. Yin, Yang E. Li, N. Vinckier, N. Nariai, P. Benaglio, A. Raman, X. Li, S. Fan, J. Chiou, F. Chen, K.A. Frazer, K.J. Gaulton, M. Sander, J. Taipale^#, B. Ren^#, Systematic analysis of binding of transcription factors to noncoding variants, Nature 591 (2021) 147-151.
• T. Wang*, W. Sun*, L. Fan*, C. Hua*, N. Wu, S. Fan, J. Zhang, X. Deng^#, J. Yan^#, An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence, eLife 10 (2021) e61885.
• D.S. Tan*, Y. Chen*, Y. Gao, A. Bednarz, Y. Wei, V. Malik, D. HH Ho, M. Weng, S. Y. Ho, Y. Srivastava, S. Velychko, X. Yang, L. Fan, J. Kim, J. Graumann, G. D Stormo, T. Braun, J. Yan, H. R Schöler, R. Jauch^#. Directed evolution of an enhanced POU reprogramming factor for cell fate engineering, Molecular Biology and Evolution 38(7) (2021) 2854-2868.
• R.J. Geusz*, A. Wang*, J. Chiou*, J.J. Lancman*, N. Wetton, S. Kefalopoulou, J. Wang, Y. Qiu, J. Yan, A. Aylward, B. Ren, P. DS Dong, K. J Gaulton^#, M. Sander^#, Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development, eLife 10 (2021) e59067.

2020

• W. Yi*, J. Li*, X. Zhu*, X. Wang*, L. Fan, W. Sun, L. Liao, J. Zhang, X. Li, J. Ye, F. Chen, J. Taipale, K.M. Chan^#, L. Zhang^#, J. Yan^#, CRISPR-assisted detection of RNA-protein interactions in living cells, Nature Methods 17(7) (2020) 685-688.
• L. Fan, T*. Wang*, C. Hua*, W. Sun*, X. Li, L. Grunwald, J. Liu, N. Wu, X. Shao, Y. Yin, J. Yan^#, X. Deng^#, A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae, Nature Communications 11(1) (2020) 4947.
• J. Yan^#, X. Wang, Detection of Disease-associated Mutations and Biomarkers Using Next-generation Sequencing, Detection Methods Precision Medicine 18, (2021) 119. (book chapter)
• Z. Wang*, Y. Li*, B. Hou*, M.I. Pronobis*, M. Wang, Y. Wang, G. Cheng, W. Weng, Y. Wang, Y. Tang, X. Xu, R. Pan, F. Lin, N. Wang, Z. Chen, S. Wang, L. z Ma, Y. Li, D. Huang, L. Jiang, Z. Wang, W. Zeng, Y. Zhang, X. Du, Y. Lin, Z. Li, Q. Xia, J. Geng, H. Dai, Y. Yu, X. Zhao, Z. Yuan, J. Yan, Q. Nie, X. Zhang, K. Wang, F. Chen, Q. Zhang, Y. Zhu, S. Zheng, K. D Poss, S. Tao^#, X. Meng^#, An array of 60,000 antibodies for proteome-scale antibody generation and target discovery, Science Advances 6 (11) (2020) eaax2271.

2019

• X. Wang^#, M.J. Cairns, J. Yan^#, Super-enhancers in transcriptional regulation and genome organization, Nucleic Acids Research 47(22) (2019) 11481-11496.
• W.W. Greenwald*, J. Chiou*, J. Yan*, Y. Qiu*, N. Dai*, A. Wang, N. Nariai, A. Aylward, J.Y. Han, N. Kadakia, N. Barrufet, M. Okino, F. Drees, N. Vinckier, L. Minichiello, D. Gorkin, J. Avruch, K. Frazer, M. Sander, B. Ren, K.J. Gaulton^#, Pancreatic islet chromatin accessibility and conformation defines distal enhancer networks of type 2 diabetes risk, Nature Communications 10 (2019) 2078.

2018 and Earlier (representative)

• J. Yan*, S.A. Chen*, A. Local, T. Liu, Y. Qiu, K.M. Dorighi, S. Preissl, C.M. Rivera, C. Wang, Z. Ye, K. Ge, M. Hu, J. Wysocka, B. Ren^#, Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers, Cell Research 28(2) (2018) 204-220.
• Y. Yin, E. Morgunova, A. Jolma, E. Kaasinen, B. Sahu, S. Khund-Sayeed, P.K. Das, T. Kivioja, K. Dave, F. Zhong, K.R. Nitta, M. Taipale, A. Popov, P.A. Ginno, S. Domcke, J. Yan, D. Schubeler, C. Vinson, J. Taipale^#, Impact of cytosine methylation on DNA binding specificities of human transcription factors, Science 356 (6337) (2017).
• J. Yan*, M. Enge*, T. Whitington, K. Dave, J. Liu, I. Sur, B. Schmierer, A. Jolma, T. Kivioja, M. Taipale, J. Taipale^#, Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites, Cell 154(4) (2013) 801-813.
• A. Jolma*, J. Yan*, T. Whitington, J. Toivonen, K.R. Nitta, P. Rastas, E. Morgunova, M. Enge, M. Taipale, G. Wei, K. Palin, J.M. Vaquerizas, R. Vincentelli, N.M. Luscombe, T.R. Hughes, P. Lemaire, E. Ukkonen, T. Kivioja, J. Taipale^#, DNA-binding specificities of human transcription factors, Cell 152 (1-2) (2013) 327-339.
• I.K. Sur, O. Hallikas, A. Vaharautio, J. Yan, M. Turunen, M. Enge, M. Taipale, A. Karhu, L.A. Aaltonen, J. Taipale^#, Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors, Science 338(6112) (2012) 1360-3.

22 April 2026