Research Summary
The Wilmer bioinformatics lab develops and applies bioinformatics approaches to the study of gene regulation, with particular, but not exclusive, attention to the regulation of retinal gene expression. In particular, the lab is interested in understanding transcriptional networks and protein/DNA interactions.
We integrate large biological datasets and develop computational algorithms to predict regulatory mechanisms controlling coordinated gene expression in specific tissues and cell types in both development and disease.
Recently, we have been interested in analyzing gene expression, epigenetic regulation, and single-cell datasets to construct regulatory networks and cell-cell communication pathways.
Lab
Lab Website: Wilmer Bioinformatics
Selected Publications
View all on PubMed
Hoang T, Wang J, Boyd P, Wang F, Santiago C, Jiang L, Yoo S, Lahne M, Todd LJ, Jia M, Saez C, Keuthan C, Palazzo I, Squires N, Campbell WA, Rajaii F, Parayil T, Trinh V, Kim DW, Wang G, Campbell LJ, Ash J, Fischer AJ, Hyde DR, Qian J, Blackshaw S. “Gene regulatory networks controlling vertebrate retinal regeneration”, Science, 2020, 370: eabb8598.
Gao T, Qian J. “EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species.”, Nucleic Acids Res. 2020 Jan 8;48(D1):D58-D64.
Hu MW, Kim DW, Liu S, Zack DJ, Blackshaw S, Qian J. “PanoView: An iterative clustering method for single-cell RNA sequencing data”, PLoS Comput Biol. 2019 Aug 30;15(8):e1007040.
Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs S, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. “ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration”, Nat Communications, 2018, 9(1):1364.
Zhu H, Wang G, Qian J, “Transcription factors as readers and effectors of DNA methylation.” Nature Reviews Genetics, 2016, 17, 551-65.
