Dr. Sun specializes in the development of statistical methods and bioinformatics software, and the computational analysis on high-throughput sequencing data, such as Bisulfite-Seq, ChIP-Seq, and RNA-Seq, to extract biological insights especially in transcriptional and epigenetic regulation in development and diseases.
Dr. Sun’s primary research generally lies in bioinformatics, a growing research area where computational, mathematical, and statistical methods are applied to solve biological problems. Biology is digital by nature, demonstrated by the fact that all living organisms store their genetic information in DNA using 4 nucleotides. The detection of 5th and 6th nucleotides, 5-methylcytosine and 5-hydroxymethycytosine as epigenetic modification to nucleotide C, also becomes digital through popular bisulfite sequencing and promising single molecule direct sequencing. In addition to DNA methylation, the other two major epigenetic factors are histone modification and nucleosome positioning. Long Noncoding RNA has also gained attention in the past several years. With the fast growing technology, the question of how Epigenome interacts with Genome and Transcriptome is gradually approached with systematic computation using big data on genome scale.
1. Dnmt3b has distinct roles than Dnmt3a in maintaining balance of hematopoietic stem cells. GA Challen*, D Sun*, A Mayle, M Luo, M Jeong, B Rodriguez, Cates Mallaney, X Zheng, S Cullen, GJ Darlington, W Li, and MA Goodell; Cell Stem Cell, 2014
2. Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal. D Sun*, M Luo*, M Jeong*, B Rodriguez, R Hanna, H Wang, T Le, K Faull, R Chen, H Gu, C Bock, A Meissner, B Gottgens, GJ Darlington, W Li, and MA Goodell; Cell Stem Cell, 2014
3. MOABS: Model based Analysis of Bisulfite Sequencing data. D Sun, Y Xi, B Rodriguez, HJ Park, T Pan, M Meong, MA Goodell, W Li; Genome Biology, 2014
4. Large conserved domains of low DNA methylation maintained by Dnmt3a. M Jeong*, D Sun*, M Luo*, Y Huang, GA Challen, B Rodriguez, X Zhang, L Chavez, H Wang, R Hannah, S Kim, L Yang, M Ko, R Chen, B Gottgens, J Lee, P Gunaratne, LA Godley, GJ Darlington, A Rao, W Li, MA Goodell; Nature Genetics, 2013
5. BSeQC: Quality Control of Bisulfite Sequencing Experiments. X Lin, D Sun, B Rodriguez, Y Zhang, W Li; Bioinformatics, 2013
6. Sexually Dimorphic Genome-Wide Binding of Retinoid X Receptor alpha (RXRα) Determines Male-Female Differences in the Expression of Hepatic Lipid Processing Genes in Mice. A Kosters*, D Sun*, H Wu, F Tian, JC Felix , W Li, SJ Karpen; PLoS ONE 8(8): e71538, (2013).
7. Research Resource: The Estrogen Receptor α Cistrome Defined by DamIP. R Xiao, D Sun, S Ayers, Y Xi, W Li, JD Baxter, DD Moore; Molecular Endocrinology 26, 349 (2012)
8. RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing. Y Xi, C Bock, F Müller, D Sun, A Meissner, W Li; Bioinformatics 28, 430 (2011)
9. Dnmt3a is essential for hematopoietic stem cell differentiation. GA Challen, D Sun*, M Jeong*, M Luo*, J Jelinek, JS Berg, C Bock, A Vasanthakumar, H Gu, Y Xi, S Liang, Y Lu, GJ Darlington, A Meissner, JJ Issa, LA Godley, W Li, MA Goodell; Nature Genetics 44, 23 (2011)