Computational Epigenetics & Bioinformatics

    Selected Bioinformatics Publications.    Citations @ Google Scholar.

     Lab MemberCo-First Author^Senior Author*.

26. Li J, Zhao S, Lee M, Yue Y, Li J, Zhou Y, Ballester L, Esquenazi Y, Dashwood R, Davies P, Parsons D, Li X*, Huang Y*, Sun D*. 2020. Reliable tumor detection by whole-genome methylation sequencing of cell-free DNA in cerebrospinal fluid of pediatric medulloblastoma. Science advances 6 (42), eabb5427. PMID:33067228.


25. Zeng H, He H, Guo L, Li J, Lee M, Han W, Guzman AG, Zang S, Zhou Y, Zhang X, Goodell MA, King KY, Sun D*, Huang Y*. 2019. Antibiotic treatment ameliorates Ten-eleven Translocation 2 (TET2) loss-of-function associated hematological malignancies. Cancer Letters 467:1-8. PMID:31563502.


24. Fang S^, Li J^, Xiao Y, Lee M, Guo L, Han W, Li T, Hill MC, Hong T, Mo W, Xu R, Zhang P, Wang F, Chang J, Zhou Y,Sun D*, Martin JF*, Huang Y*. 2019. Tet inactivation disrupts YY1 binding and long-range chromatin interactions during embryonic heart development. Nature Communication 10(1):4297. PMID:31541101.


23. Rajendran R, Johnson G, Li L, Chen Y, Dashwood M, Nguyen N, Ulusan A, Ertem F, Zhang M, Li J, Sun D, Huang Y, Wang S, Leung H, Lieberman D, Beaver L, Ho E, Bedford M, Chang K, Vilar E, Dashwood R. 2019. Acetylation of CCAR2 establishes a BET/BRD9 acetyl switch in response to combined deacetylase and bromodomain inhibition. Cancer Research 79 (5), 918-927. PMID:30643017.


22. Yang J, Horton J, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal R, Cheng X. 2018. Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Nucleic Acids Research 47 (4), 1774-1785. PMID:30566668.


21. Zhang J, Tan P, Guo L, Gong J, Ma J, Li J, Lee M, Fang S, Jing J, Johnson G, Sun D, Cao W, Dashwood R, Han L, Zhou Y, Dong W, Huang Y. 2018. p53-dependent autophagic degradation of TET2 modulates cancer therapeutic resistance. Oncogene 38 (11), 1905. PMID:30390073.


20. Lee J, Matthias N, Pothiawala A, Ang B, Lee M, Li J, Sun D, Pigeot S, Martin I, Huard J, Huang Y, Nakayama N. 2018. Pre-transplantational Control of the Post-transplantational Fate of Human Pluripotent Stem Cell-Derived Cartilage. Stem cell reports 11 (2), 440-453. PMID:30057264.


19. Gu T, Lin X, Cullen S, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi L, Chen J, Kyba M, Huang Y, Chen T, Li W, Goodell M. 2018. DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells. Genome biology 19 (1), 88. PMID:30001199.


18. Zhang P, Xiao Z, Wang S, Zhang M, Wei Y, Hang Q, Kim J, Yao F, Rodriguez-Aguayo C, Ton B, Lee M, Wang Y, Zhou Z, Zeng L, Hu X, Lawhon S, Siverly A, Su X, Li J, Xie X, Cheng X, Liu L, Chang H, Chiang S, Lopez-Berestein G, Sood A, Chen J, You J, Sun S, Liang H, Huang Y, Yang X, Sun D, Sun Y, Hung M, Ma L. 2018. ZRANB1 is an EZH2 deubiquitinase and a potential therapeutic target in breast cancer. Cell reports 23 (3), 823-837.PMID:29669287.


17. Li J^, Wu X^, Zhou Y^, Lee M, Guo L, Han W, Mo W, Cao W, Sun D*, Xie R*, Huang Y*. Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC. 2018. Nucleic Acids Research.PMID:29394393.


16. Cai Y, Huang G, Ma L, Dong L, Chen S, Shen X, Zhang S, Xue R, Sun D*, Zhang S*. Smurf2, an E3 ubiquitin ligase, interacts with PDE4B and attenuates liver fibrosis through miR-132 mediated CTGF inhibition. 2018. BBA – Molecular Cell Research. 1865 (2), 297-308PMID: 29100790.


15. Zang S^, Li J^, Yang H, Zeng H, Han W, Zhang J, Lee M, Moczygemba M, Isgandarova S, Yang Y, Zhou Y, Rao A, You M, Sun D*, Huang Y*. Mutational cooperativity of TET2 and RHOA disrupts peripheral T-cell homeostasis. 2017. J. Clin. Invest. 127(8):2998–3012. PMID: 28691928 .


14. Lee M^, Li J^, Liang Li, Ma G, Zhang J, He L, Liu Y, Li Q, Li M, Sun D, Zhou Y, Huang Y. 2017. Engineered Split-TET2 Enzyme for Inducible Epigenetic Remodeling. 2017. J Am Chem Soc. 139 (13), 4659-4662. PMID: 28294608.


13. Ertem F. U., Zhang W^, Chang K., Mohaiza Dashwood W., Rajendran P., Sun D, Abudayyeh A., Vilar E., Abdelrahim M. and Dashwood R. H. (2017), Oncogenic targets Mmp7, S100a9, Nppb and Aldh1a3 from transcriptome profiling of FAP and Pirc adenomas are downregulated in response to tumor suppression by Clotam. 2017. Int. J. Cancer, 140: 460–468. PMCID: 27706811


12. Matatall K. A., Jeong M., Chen S., Sun D, Chen F., Mo Q., … King K. Y. (2016). Chronic Infection Depletes Hematopoietic Stem Cells Through Stress-Induced Terminal Differentiation. Cell reports 17.10 (2016): 2584–2595. PMCID:27926863


11. Johnson G, Li J^, Beaver L, Dashwood W, Sun D, Rajendran P,  Williams D, Ho E,  Dashwood R. (2016) A functional pseudogene, NMRAL2P, is regulated by Nrf2 and serves as a coactivator of NQO1 in sulforaphane-treated colon cancer cells. Mol. Nutr. Food Res. 61 (2016), 1600769. PMCID:27860235


10. Luo M^, Jeong M^, Sun D^, Park HJ^, Rodriguez BA, Xia Z, Yang L, Zhang X, Sheng K, Darlington GJ, Li W, Goodell MA. Long Non-Coding RNAs Control Hematopoietic Stem Cell Function. Cell stem cell 16 (2015) 426-438. PMCID: 4388783 pdf


9. Challen GA^, Sun D^, Mayle A, Jeong M, Luo M, Rodrigues B, Mallaney C, Celik H, Yang L, Xia Z, Culleng S, Berg JS, Zheng Y, Darlington GJ, Li W*, Goodell MA*: Dnmt3a and Dnmt3b have Overlapping and Distinct Functions in Hematopoietic Stem Cells. 
Cell Stem Cell 15 (2014) 350-364. PMCID: 4163922 pdf


8. Sun D^, Luo M^, Jeong M^, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Gottgens B, Darlington GJ*, Li W*, Goodell MA*: Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal.
 Cell Stem Cell 14 (2014) 673-688. PMCID: 4070311 pdf


7. Jeong M^, Sun D^, Luo M^, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W*, Goodell MA*: Large Conserved Domains of Low DNA Methylation Maintained by Dnmt3a. Nature Genetics 46 (2014) 17-23. PMCID: 3920905 pdf


6. Sun D, Xi Y, Rodriguez B, Park HJ, Pan T, Meong M, Goodell MA, Li W: MOABS: Model Based Analysis of Bisulfite Sequencing Data.
 Genome Biology 15 (2014) R38. PMCID: 4054608 pdf


5. Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W: BseQC: Quality Control of Bisulfite Sequencing Experiments.
 Bioinformatics 29 (2013) 3227-3229. PMCID: 3842756 pdf


4. Kosters A^, Sun D^, Tian F, Felix J, Wu H, Li W, Karpen S: 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. PLoS ONE 8 (2013) e71538.PMCID: 3747242 pdf


3. Xiao R, Sun D, Ayers S, Xi Y, Li W, Baxter JD, Moore DD: Research resource: The Estrogen Receptor Alpha Cistrome Defined by DamIP.
 Mol Endocrinol 26 (2012) 349-357. PMCID: 3384088 pdf


2. Xi Y, Bock C, Muller F, Sun D, Meissner A, Li W: RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing.
 Bioinformatics 28 (2012) 430-432. PMCID: 3268241 pdf


1. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JJ, Godley LA, Li W*, Goodell MA*: Dnmt3a is Essential for Hematopoietic Stem Cell Differentiation.
 Nature Genetics 44 (2012) 23-31. PMCID: 3637952 pdf


Selected Physics Publications
Lab MemberCo-First Author^Senior Author*Citations @ Google Scholar.


3.Sun DQ^, Abanov A, Pokrovsky VL: Molecular Production at a Broad Feshbach Resonance in a Fermi Gas of Cooled Atoms. Europhysics Letters 83 (2008). Accession Number: WOS:000259020300020 pdf


2. Pokrovsky VL, Sun D*: Fast Quantum Noise in the Landau-Zener Transition. Physical Review B 76 (2007). Accession Number: WOS:000248496200053 pdf


1. Grandchamp L, Lumpkins S, Sun D, van Hees H, Rapp R: Bottomonium Production at Root s(NN)=200 GeV and Root s(NN)=5.5 TeV. Physical Review C 73 (2006). Accession Number: WOS:000238697500034 pdf