We are working on a number of research projects that all are related to applying bioinformatics approaches to the study of gene regulation, with particular but not exclusive attention to the regulation of retinal gene expression. We have performed large-scale computational analysis of transcription factor (TF) interactions both in the yeast S. cerevisiae and human tissues. The identified TF interactions can help in our understanding of gene regulation and tissue specificity in eukaryotic systems. In a recent project, we collaborated with Drs. Heng Zhu and Seth Blackshaw’s labs to work on large-scale identification of human protein-DNA interactions.
We are also interested in studying aspects of post-transcriptional gene regulation. In one project our analysis generated data that suggests that the interaction patterns between TFs and microRNAs can influence the biological functions of microRNAs.
Another area that we are studying concerns epigenetic gene regulation. We took advantage of available genome wide data sets of nucleosome positions to analyze the rules that determine nucleosome positioning, and their effects on biological functions.
Lab Website: Wilmer Bioinformatics
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Xie, Z.; Hu, S.; Blackshaw, S.; Zhu, H.; Qian, J. hPDI: a database of experimental human protein-DNA interactions. Bioinformatics. 2010 Jan 15;26(2):287-289.
Lin, J.; Xie, Z.; Zhu, H.; Qian, J. Understanding protein phosphorylation on a systems level. Brief Funct Genomics. 2010 Jan;9(1):32-42.
Wan, J.; Lin, J.; Zack, D.J.; Qian, J. Relating periodicity of nucleosome organization and gene regulation. Bioinformatics. 2009 Jul 15;25(14):1782-1788.
Lin, Y.Y.; Lu, J.Y.; Zhang, J.; Walter, W.; Dang, W.; Wan, J.; Tao, S.C.; Qian, J.; Zhao, Y.; Boeke, J.D.; Berger, S.L.; Zhu, H. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell. 2009 Mar 20;136(6):1073-1084.
Kung, L.A.; Tao, S.C.; Qian, J.; Smith, M.G.; Snyder, M.; Zhu, H. Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol. 2009;5:308.
Hu, S.; Xie, Z.; Onishi, A.; Yu, X.; Jiang, L.; Lin, J.; Rho, H.S.; Woodard, C.; Wang, H.; Jeong, J.S.; Long, S.; He, X.; Wade, H.; Blackshaw, S.; Qian, J.; Zhu, H. Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell. 2009 Oct 30;139(3):610-622.