*Corresponding or first author
*Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers2018 Genome Research 
Serine metabolism in the brain regulates starvation-induced sleep suppression in Drosophila melanogaster2018 Proceedings of the National Academy of Sciences
Novel cancer gene variants and gene fusions of triple-negative breast cancers (TNBCs) reveal their molecular diversity conserved in the patient-derived xenograft (PDX) model2018 Cancer Letters 
*Selection on the regulation of sympathetic nervous activity in humans and chimpanzees2018 PLOS Genetics
A long-range interactive DNA methylation marker panel for the promoters of HOXA9 and HOXA10 predicts survival in breast cancer patients 2017 Clinical Epigenetics
*Predictive long-range allele-specific mapping of regulatory variants and target transcripts2017 PLOS ONE
*Network perturbation by recurrent regulatory variants in cancer2017 PLOS Computational Biology
The mutational landscape of ocular marginal zone lymphoma identifies frequent alterations in TNFAIP3 followed by mutations in TBL1XR1 and CREBBP2017 Oncotarget
*Predicting the recurrence of noncoding regulatory mutations in cancer2016 BMC Bioinformatics
*Chromatin structure-based prediction of recurrent noncoding mutations in cancer2016 Nature Genetics
Histone variant H3F3A promotes lung cancer cell migration through intronic regulation2016 Nature Communications 
*Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans2016 Genome Biology
*Frequent hypermethylation of orphan CpG islands with enhancer activity in cancer2016 BMC Medical Genomics
PARP1 enhances lung adenocarcinoma metastasis by novel mechanisms independent of DNA repair2016 Oncogene
*Global mapping of the regulatory interactions of histone residues2015 FEBS Letters
*Intersection of genetics and epigenetics in monozygotic twin genomes2015 Methods
*Genetic architecture of transcription and chromatin regulation  2015 Genomics & Informatics
*Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes2015 Nucleic Acids Research
*Understanding epistatic interactions between genes targeted by non-coding regulatory elements in complex diseases2014 Genomics & Informatics
SET7/9 methylation of the pluripotency factor LIN28A is a nucleolar localization mechanism that blocks let-7 biogenesis in human ESCs2014 Cell Stem Cell
*Genetic factors underlying discordance in chromatin accessibility between monozygotic twins2014 Genome Biology
HBx induces hypomethylation of distal intragenic CGIs required for active expression of developmental regulators2014 Proceedings of the National Academy of Sciences
Genome-wide methylation profiling of ADPKD identified epigenetically regulated genes associated with renal cyst development2014 Human Genetics
*Genome-wide reorganization of histone H2AX toward particular fragile sites on cell activation2014 Nucleic Acids Research
*Regulation of the boundaries of accessible chromatin2013 PLOS Genetics
*Genetic landscape of open chromatin in yeast 2013 PLOS Genetics
*ENCODE: A sourcebook of epigenomes and chromatin language2013 Genomics & Informatics
The characteristics of genome-wide DNA methylation in naive CD4+ T cells of patients with psoriasis or atopic dermatitis2012 Biochemical and Biophysical Research Communications
*Genome-wide profiles of H2AX and γ-H2AX differentiate endogenous and exogenous DNA damage hotspots in human cells2012 Nucleic Acids Research
Identification of DNA methylation changes associated with human gastric cancer2011 BMC Medical Genomics
*Genetic and metabolic characterization of insomnia2011 PLOS ONE
*Controlling transcriptional programs for cellular adaptation by chromatin regulation2011 Molecular BioSystems
*Contrasting chromatin organization of CpG islands and exons in the human genome2010 Genome Biology
*Systems biology and epigenetic gene regulation2010 IET Systems Biology
*An international showcase of the rapid expansion of epigenetics2009 Epigenomics
*Nucleosome deposition and DNA methylation at coding region boundaries2009 Genome Biology
*Implications of the nucleosome code in regulatory variation, adaptation and evolution2009 Epigenetics
*Intrinsic variability of gene expression encoded in nucleosome positioning sequences2009 Nature Genetics
Requirement of Split ends for epigenetic regulation of Notch signal-dependent genes during infection-induced hemocyte differentiation2009 Molecular and Cellular Biology
*Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes2008 PLOS ONE
*Epigenetic regulation and the variability of gene expression2008 Nature Genetics
Microarray analysis of the gene expression profiles of SL2 cells stimulated by LPS/PGN and curdlan2008 Molecules and Cells
*Environmental effects on gene expression phenotype have regional biases in the human genome2007 Genetics
*Impact of transcriptional properties on essentiality and evolutionary rate2007 Genetics
*Differential coexpression analysis using microarray data and its application to human cancer2005 Bioinformatics
TO-GO: a Java-based Gene Ontology navigation environment2005 Bioinformatics
*Integrative analysis of multiple gene expression profiles applied to liver cancer study2004 FEBS Letters
*Combining multiple microarray studies and modeling interstudy variation2003 Bioinformatics
Domain and genomic sequence analysis of bdellin-KL, a leech-derived trypsin-plasmin inhibitor2002 Journal of Biochemistry