Ye Liu Ph.D.

Ye Liu, Ph.D.
Postdoctoral fellow, Yang Laboratory



Dr. Ye Liu earned a B.S. in biology and food sciences from University of Dalian Polytechnic University (China), an M.Sc. in life and environmental sciences from AIST Biomedical Research Institute and University of Tsukuba (Japan) and a Ph.D. in biological sciences from RIKEN Center for Integrative Medical Sciences and University of Tsukuba (Japan). During his graduate work, Dr. Liu focused on articular knee cartilage in relation to osteoarthritis doing genome-wide accessible chromatin mapping. His research is possible through his extensive laboratory skills, including molecular cloning and human clinical sample section, along with his next-generation sequencing data analysis skills. In 2019, he joined the laboratory of Dr. Tao Yang at Van Andel Research Institute as a postdoctoral fellow.


Current research focus

Osteoarthritis (OA) is a common joint disorder of thinning cartilage that becomes increasingly more common with age. It is a large and growing global health burden that represents one of the most common causes of chronic disabilities in the world. There is no effective cure except for joint replacement surgery. Inflammatory and catabolic environment in the joints accelerates OA development. Senescent articular chondrocytes (ACs), which accumulate in aging or injured joints, are a major source of inflammatory and catabolic factors. I apply ATAC-seq (assay for transposase accessible chromatin with high-throughput sequencing) on OA patient samples. ATAC-seq determines open chromatin regions, mainly enhancer regions. Integrative analyses of ATAC-seq data with publicly available datasets such as the GWAS, DNA methylation and RNA-seq have revealed potential pathways that may be contributing towards its pathogenesis. We will apply in vivo and in vitro genetic models to validate the molecular mechanisms underlying the disease. Sumoylation is an enzymatic pathway that has been associated with both the stress response and the aging process. Uncovering mechanisms that connect the sumoylation pathways to stress response, epigenetic alterations, cell senescence, joint aging and OA will enable a basis for developing new OA treatment strategies by inhibiting AC senescence.

Education & Training

Ph.D. in biological Sciences, RIKEN Center for Integrative Medical Sciences and University of Tsukuba (Japan) (Advisors: Dr. Aki Minoda, Dr. Ming Ta Michael Lee and Dr. Zhenya Zhang)
Thesis: Genome-wide accessible chromatin mapping for articular knee cartilage reveals abnormal endochondral ossification in the primary osteoarthritis

M.Sc. in life and environmental sciences, AIST Biomedical Research Institute and University of Tsukuba (Japan) (Advisors: Dr. Renu Wadhwa and Dr. Zhenya Zhang)

B.S. in biology and food sciences, University of Dalian Polytechnic University (China) (Advisor: Dr. Beiwei Zhu)

Awards & External Funding

RIKEN funded Ph.D. student fellowship, Junior Research Associate (JRA) program (2015–2018)


To view a list of selected publications click below.

Read More

Liu Y, Chang JC, Hon CC, Fukui N, Zhang Y, Zhang Z, Ikegawa S, Ta M, Lee M, Minoda A. 2018.  Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis. Sci Rep 8(1):15499.

Bhargava P, Malik V, Liu Y, Ryu J, Kaul SC, Sundar D, Wadhwa R. 2019. Molecular insights to Withaferin-A induced senescence: bioinformatics and experimental evidence to the role of NF-kappa B and CARF. J Gerontol 74(2):183–191.

Kojo S, Tanaka H, Endo T, Muroi S, Liu Y, Seo W, Tenno M, Kakugawa K, Naoe Y, Nair K, Moro K, Katsuragi Y, Kanai A, Inaba T, Egawa T, Venkatesh B, Minoda A, Kominami R, Taniuchi I. 2017. Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes. Nat Commun 207(8).

Li K, Yu Y, Sun S, Liu Y, Garg S, Kaul SC, Lei Z, Gao R, Wadhwa R, Zhang Z. 2016. Functional characterization of anticancer activity in the aqueous extract of Helicteres angustifolia L. roots. PLoS One 11(3).

Ryu J, Kaul Z, Yoon AR, Liu Y, Yaguchi T, Na Y, Ahn HM, Gao R, Choi IK, Yun CO, Kaul SC, Wadhwa R. 2014. Identification and functional characterization of nuclear mortalin in human carcinogenesis. J Biol Chem 289(36):24832–24844.

Saxena N, Katiyar SP, Liu Y, Grover A, Gao R, Sundar D, Kaul SC, Wadhwa R. 2013. Molecular interactions of Bcl-2 and Bcl-Xl with mortalin: Identification and functional characterization. Biosci Rep 33:5.