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This is a short list of publications that represents our primary research interests. Members of the Zhang lab are highlighted in bold.
Lake BB*, Ai R*, Kaeser GE*, Salathia NS*, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vjayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fang JB, Wang W, Chun J, Zhang K. (2016) Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science, 352:1586-90
Sos B, Fung HL, Gao DR, Osothprarop TF, Kia A, He MM, Zhang K. (2016) Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biology, 17:20
Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nature Biotechnology, doi:10.1038/nbt.2720 [MIDAS animation]
Diep D*, Plongthongkum N*, Gore A*, Fung HL, Shoemaker R, Zhang K. (2012) Library-free methylation sequencing with bisulfite padlock probes. Nature Methods, 9:270-2 [Supplementary website]
Gore A*, Li Z*, Fung HL, Young JE, Agarwal S, Antosiewica-Gourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JK, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Belmonte JCI, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LSB, Zhang K. (2011) Somatic coding mutations in human induced pluripotent stem cells. Nature 471:63-7
Shoemaker R, Deng J, Wang W, Zhang K. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Research 20:883-9 [Supplementary website]
Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K.(2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology, 27:353-60 [Supplementary website]