Prof. Yan received his BSc in biological sciences at Tsinghua University (in 2005) and PhD in Medical Science at Karolinska Institutet (in 2014), investigating molecular mechanism of transcriptional regulation in colorectal cancer cells (Mentor: Prof. Jussi Taipale). Prof. Yan obtained postdoc training with Prof. Bing Ren at UC San Diego to study 3D genome organisation and gene regulation (2015–2018). In 2018, Prof. Yan joined Department of Biomedical Sciences as a tenure-track assistant professor. In 2021, Prof. Yan received the university’s prestigious prize of “Outstanding Research Award for Junior Faculty”.

Research Interests

Due to high mutation burden in regulatory elements, affected cells develop aberrant gene transcription compared with surrounding normal cells that could device them with growth advantage. Some noncoding RNA transcripts have been used as clinical diagnostic markers for some diseases whereas the molecular mechanism of their relevance largely elusive. Our research goal is to unveil molecular mechanism of how transcriptional aberration affects cellular function and human health issues, using high throughput, state-of-the-art tools. My current interest focuses on developing genomic tools to:

1. Dissect of lncRNA function and mechanism in disease
2. Identify of genetic variations that contribute to disease pathogenesis
3. Study protein-nucleic acid interaction with high throughput pipeline

The Ph.D. program 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)

2025

• 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 Sch?ler, 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.

21 June 2025