Xun Chen

Xun Chen

Researcher (Bourque-G)

Program-Specific Researcher
Research Field
Bioinformatics, Systems Biology, Comparative Epigenomics

Research Overview

Developing new analytical methodologies to dissect the functional role of human non-coding DNA during evolution and human diseases development

Transposable elements (TEs) occupy nearly half of numerous mammalian genomes. Many studies have shown that TEs play various roles in genome evolution. They are also the causative factors of various human diseases. However, their functions involved in mammalian genome evolution and disease occurrence are still poorly understood. Many TEs have gained promoter and enhancer activities during evolution and have been pervasively co-opted into gene regulatory elements. I aim to develop new bioinformatic methodologies to study the functional roles of human non-coding DNA including TE-derived enhancers and promoters, during primate genome evolution and human disease development. Additionally, I am also interested in using omics approach to systematically interpret the viral etiology during tumorigenesis, and to interpret the diseases causative factors of complex structural variants, TE insertions and others in human and other primate species. We have developed multiple bioinformatic tools to assist the field of human genomics, evolutionary epigenomics, and viral etiology. We have recently developed “VIcaller” to study viral etiology in cancers. We have also studied the association between transposable element insertions and various human diseases using newly developed bioinformatics tool “ERVcaller”, which can be applied to in other primate species.

Fig 1 of Dr Chen's Research

Fig 1: The illustration of interpreting TE-derived regulatory elements in primate species. (A) The evolution of HERVs within the primate lineage (from Marina et al., 2016). (B) The gain of activation and repression activities of the ERV-derived regulatory elements.

Fig 2 of Dr Chen's Research

Fig 2: A bioinformatic platform “VIcaller” developed to discover oncovirus candidates through identification of clonal viral integrations (from Chen et al., 2019)


Xun Chen obtained his PhD from Huazhong Agricultural University in 2014 and he was trained as a postdoctoral researcher at the University of Vermont in U.S. (2014-2019). He currently works as a Program Specific Researcher in Bourque Lab at Kyoto University (2020-).


Chen X, Li D: ERVcaller: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data. Bioinformatics. 2019 Mar. DOI: 10.1093/bioinformatics/btz205

Chen X, Jason Kost, Sulovari A, Wong N, Liang WS, Cao J, and Li D: A virome-wide clonal integration analysis platform for discovering cancer viral etiologies. Genome Research. 2019 Mar. DOI: 10.1101/gr.242529.118

Shi L, Song J, Guo C, Wang B, Yang P, Chen X, King GJ, Wang J, Liu K: A CACTA-like transposable element in upstream of CYP78A9 acts as an enhancer to increase silique length and seed weight in rapeseed. The Plant Journal. 2019 Jan. 98:524-539

Chen X, Kost J, Li D: Comprehensive comparative analysis of methods and software for identifying viral integrations. Briefings in Bioinformatics. 2018 Aug. DOI: 10.1093/bib/bby070

Chen X, Ge X, Wang J, Tan C, King GJ, Liu K: Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. Frontiers in Plant Science. 2015 Oct. 6:836


ASHG/Charles J. Epstein Trainee Award for Excellence in Human Genetics Research – Semifinalist (2017), ACGA/The Association of Chinese Geneticists in America Trainee Awardees (2017)

Research Group

Bourque Group
Contact X.Chen

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