I am a molecular biologist with a long-standing interest in transcription regulation and epigenetic control of cell fate decisions, particularly during hematopoietic development. My training across Taiwan, the UK, and the US has shaped a multidisciplinary perspective that bridges chromatin biology, developmental hematopoiesis, and computational analysis.
My research focuses on how chromatin states and transcription factors work together to guide lineage transitions, with a current emphasis on the endothelial-to-hematopoietic transition (EHT). I have developed several bioinformatics tools, including BiasFreeATAC, HomologySeeker, and SEM, to better interpret single-cell and epigenomic data. These methods, combined with experimental approaches, have enabled me to uncover conserved regulatory axes, such as SPI1–KLF1/LYL1, and chromatin features, including H3K18ac, that influence transcription factor (TF) binding specificity in both normal and leukemic contexts.
I have published in Cell, Nature, Genome Research, and Communications Biology, and my work has helped clarify how chromatin remodeling underlies transcriptional specificity during development and transformation. I was selected for China’s National High-Level Talent Program in 2015 and received the Tianjin Youth Leading Talent Award in 2024. Currently, I lead a research group at the Institute of Hematology, Chinese Academy of Medical Sciences.
PhD, Molecular Biology, The University of Manchester, Manchester, UK, 2001–2005
Scientist, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 2022–
PRINCIPAL HONORS, AWARDS:
2015 National High-Level Talent Program (11th cohort)
2024 Tianjin Youth Leading Talent Award
SELECTED PUBLICATIONS:
1. Jianyu Yang, Kuangyu Yen#, Shaun Mahony#. (2024) Size-based expectation maximization for characterizing nucleosome positions and subtypes. Genome Research. DOI: 10.1101/gr.279138.124
2. Shaokang Mo*, Kengyuan Qu*, Junfeng Huang*,#, Qiwei Li, Wenqing Zhang, Kuangyu Yen#. (2023) Cross-species transcriptomics reveals bifurcation point during the arterial-to-hemogenic transition. Commun Biol. 6(1):827
3. Wang, Yajie*; Lu, Ting*; Sun, Guohuan; Zheng, Yawei; Yang, Shangda; Zhang, Hongyan; Hao, Sha; Liu, Yanfeng; Ma, Shihui; Zhang, Houyu; Ru, Yongxin; Gao, Shaorong; Yen, Kuangyu#; Cheng, Hui#; Cheng, Tao# (2019) Targeting of apoptosis gene loci by reprogramming factors leads to selective eradication of leukemia cells. Nature Communications. 10(1): 0-5594.
4. de Dieuleveult, M*, Yen K*#, Hmitou I*, Depaux A*, Boussouar F, Dargham DB, Jounier S, Humbertclaude H, Ribierre F, Baulard C, Farrell NP, Park B, Keime C, Carriere L, Merlivet S, Gut M, Gut I, Werner M, Deleuze JF, Olaso R, Aude JC, Chantalat S, Pugh BF and Gerard M. (2016) Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 530(7588): 113-116.
5. Yen K, Vinayachandran V and Pugh BF. (2013) Genome-wide structural integration of SWR-C and INO80 chromatin remodelers at +1 nucleosomes. Cell. 154(6):1246-56.
6. Yen K, Vinayachandran V, Batta K. Koerber RT and Pugh BF. (2012) Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell. 149(7):1461-73