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Gene co-expression analysis for functional classification and gene–disease predictions. Brief Bioinform. 2017.

H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity. Genome Biology. 2017, 18:69

The Long Noncoding RNA Landscape of the Ischemic Human Left Ventricle. Circulation: Cardiovascular Genetics. 2017, 10:e001534.

Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in C. elegans. Nature. 2017, 541:102–106.


Dpy30 is critical for maintaining the identity and function of adult hematopoietic stem cells. The Journal of Experimental Medicine. 2016, 213(11):2349-2364

Classification and characterization of microsatellite instability across 18 cancer types. Nature Medicine. 2016, 22:1342–1350.

Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nature Genetics. 2016, 48:1436–1442.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell. 2016, 167(5):1369-1384.

Mining kidney toxicogenomic data by using gene co-expression modules. BMC Genomics. 2016, 17:790.

Local microRNA delivery targets Palladin and prevents metastatic breast cancer. Nature Communications. 2016, 7:12868

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nature Microbiology. 2016, 1:16140.

Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nature Communications. 2016, 7:12060.

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. Genome Biology. 2016, 17:191.

TP53 regulates miRNA association with AGO2 to remodel the miRNA–mRNA interaction network. Genome Research. 2016, 26:331-341.

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479.


ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383.

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics. 2015, 31(4):608-609.

Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts. Carcinogenesis. 2015, 36(12):1453-1463.

A neural crest origin for cohesinopathy heart defects. Hum. Mol. Genet. 2015, 24(24): 7005-7016.

Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. Hum. Mol. Genet. 2015, 24(24):7121-7131.

Correlation of clinical features and genetic profiles of stromal interaction molecule 1 (STIM1) in colorectal cancers. Oncotarget. 2015, 6(39):42169–42182.


Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation. eLife 2014,3:e02077

Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs. Genome Biol Evol 2014, 6(6): 1353-1365.

Proteomic analysis of putative heme-binding proteins in Streptococcus pyogenes. Metallomics 2014, 6:1451-1459


Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumoniae. Metallomics 2013,5:928-935.

A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism. Proteomics 2013, 13(1):169–178.