Bai D., Zhang X., Xiang H., Guo Z., Zhu C.#, Yi C.#, Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq. Nat. Biotechnol. (2024) SharedIt Link
Read our "Tools of the Trade": Bai D.# and Zhu C.#, SIMPLE-seq to decode DNA methylation dynamics in single cells. Nat. Rev. Genetics (2024)

Xie Y.*, Zhu C.*, Wang Z., Tastemel M., Chang L., Li E.Y., Ren B.#, Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nat. Struct. Mol. Biol.. (2023): https://doi.org/10.1038/s41594-023-01060-1 Free full text
Read our Research Briefing: Zhu C. and Ren B., Single-cell joint analysis of gene expression and histone modifications in droplets. Nat. Struct. Mol. Biol.. (2023)
        

Bai D., Zhu C.#, Single-cell technologies for multimodal omics measurements. Front. Syst. Biol. (2023) 3: https://doi.org/10.3389/fsysb.2023.1155990 Free full text

Zhu C., Wang Z., Ren B.#, Single-cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq.  Methods Mol Biol. (2023) 2611:155-185.

Li Y.E., Preissl S., Miller M., Johnson N.D., Wang Z., Jiao H., Zhu C., Wang Z., Xie Y., Poirion O., Kern C., Pinto-Duarte A., Tian W., Siletti K., Emerson N., Osteen J., Lucero J., Lin L., Yang Q., Zhu Q., Zemke N., Espinoza S., Yanny A.M., Nyhus J., Dee N., Casper T., Shapovalova N., Hirschstein D., Hodge R.D., Linnarsson S., Bakken T., Levi B., Keene C.D., Shang J., Lein E., Wang A., Behrens M.M., Ecker J.R., Ren B.#, A comparative atlas of single-cell chromatin accessibility in the human brain. Science (2023) 382(6667):eadf7044

Lee L.*, Yu M.*, Li X., Zhu C., Zhang Y., Yu H., Chen Z., Mishra S., Ren B., Li Y.#, Hu M.#, SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C data. Brief. Bioinform. (2023) 24(5):bbad315

Lee L.*, Yu H, Jia B., Jusslia A., Zhu C., Chen J., Xie L., Hafner A., Mishra S, Wang D, Strambio-De-Castillia C., Boettiger A., Ren B., Li Y.#, Hu M.#, SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nat. Commun. 2023 14(1):4873

Raviram R., Raman A., Preissl S., Ning J., Wu S., Koga T., Zhang K., Brennan C.W., Zhu C., Luebeck J., Van Deynze K., Han J.Y., Hou X., Ye Z., Mischel A.K., Li Y.E., Fang R., Baback T., Mugford J., Han C.Z., Glass C.K., Barr C.L., Mischel P.S., Bafna V., Escoubet L., Ren B.#, Chen C.C.#, Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proc. Natl. Acad. Sci. USA. (2023) 120(20):e2210991120.

Zhu C., Zhang Y., Li Y.E., Lucero J., Behrens M.M., Ren B.#. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nat. Methods (2021) 18(3): 283-292. (Highlighted in Nat. Methods) Free full text

Liu M.*, Zhang J.*, Zhu C.*, Zhang X., Xiao W., Yan Y., Liu L., Zeng H., Gao Y.#, and Yi C.#. DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes. Nat. Commun. (2021) 12(1): 1-12 Free full text

Zhu C., Preissl S., Ren B.#. Single-cell multimodal omics: the power of many. Nat. Methods (2020) 17(1):11-14. (Comments for Method of the Year 2019) 

Song J.*, Zhuang Y.*, Zhu C.*, Meng H., Lu B., Xie B., Peng J., Li M.#, Yi C.#. Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation. Nat. Chem. Biol. (2020) 16, 160-169. (Cover story, and highlighted in Nat. Chem. Biol.)

Zhu C., Yu M., Huang H., Juric I., Abnousi A., Hu R., Lucero J., Behrens M.M., Hu M., Ren B.#. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat. Struct. Mol. Biol. (2019) 26(11):1063-1070. Free full text

Zhu C., Gao Y., Peng J., Tang F., Yi C.#. Single-Cell 5fC Sequencing. Methods Mol. Biol. (2019) 1979:251-267.

Zhu C.*, Gao Y.*, Guo H.*, Xia B.*, Song J., Wu X., Zeng H., Tang F.#, Yi C.#. Single-cell 5-formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-base Resolution. Cell Stem Cell (2017) 20, 720-731.e5.

Zhu C.*, Lu L.*, Zhang J.*, Yue Z., Song J., Zong S., Liu M., Stovicek O., Gao Y.#, and Yi C.#. Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair. Proc. Natl. Acad. Sci. USA. (2016) 113, 7792-7797. Free full text

Zhu C. and Yi C.#. Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues. Angew. Chem. Int. Ed. (2014) 53, 3659-3662.

Zhang Y.*, Amaral M.*, Zhu C., Grieco S., Hou X., Lin L., Buchanan J., Tong L., Preissl S.#, Ren B.#, Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Cell Res. (2022) 32: 1008-1021 Free full text

Lu B., Dong L., Yi D., Zhang M., Zhu C., Li X., Yi C.#. Transposase assisted tagmentation of RNA/DNA hybrid duplexes. Elife (2020) 9, e54919

Zeng H.*, He B.*, Xia B., Bai D., Lu X., Cai J., Chen L., Zhou A., Zhu C., Meng H., Gao Y., Guo H., He C.#, Dai Q.# and Yi C.#. Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution. J. Am. Chem. Soc. (2018) 140(41):13190-13194. 

Zeng H.*, Mondal M.*, Song R.*, Zhang J., Xia B., Liu M., Zhu C., He B., Gao.Y.# and Yi C.#. Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. (2018) 131, 136-139.

Shu X.*, Liu M.*, Lu Z.*, Zhu C., Meng H., Huang S. and Yi C.#. Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA. Nat. Chem. Biol. (2018) 14(7):680-687.

Zhang Y.*, Liu L.*, Guo S.*, Song J.*, Zhu C., Yue Z., Wei W.# and Yi C.#. Deciphering TAL effectors for 5-methylcytosine and 5-hydroxymethylcytosine recognition. Nat. Commun. (2017) 8(1):901. Free full text

Song J., Zhu C., Zhang X., Wen X., Liu L., Peng J., Guo H.# and Yi C.#. Biochemical and structural insights into the mechanism of DNA recognition by Arabidopsis ETHYLENE INSENSITIVE3. PLoS ONE (2015) 10, e0137439. Free full text

Lu L., Zhu C., Xia B. and Yi C.#. Oxidative demethylation of DNA and RNA mediated by non-heme iron-dependent dioxygenases. Chem. Asian. J. (2014) 9, 2018-2029.