Chenxu Zhu, Ph.D.

Assistant Professor of Physiology and Biophysics

Assistant Professor of Computational Cancer Systems Biology and Genomics in Computational Biomedicine


646-977-7020

1305 York Avenue, Room Y.13.09
New York, New York 10021

Lab website: https://czhulab.github.io/

Techniques

Research Areas

Member of:

Research Summary:

Complex molecular networks control cell type-specific gene expression. Dissecting the underlying principles is critical for understanding the cause of human diseases and for developing treatments. However, such investigation remains highly challenging in cancer due to the stochastic accumulation of genetic and epigenetic alternations in the heterogeneous cellular populations. Technology advancements in single-cell genomics provided excellent opportunities to access the comprehensive profiles from complex tissues. We focused on both development of cutting-edge genomic technologies for multimodal single-cell analysis and applying these technologies to study the combined effects of multiple regulatory layers in cell fate specification and maintenance during development, diseases, and cancer.

Recent Publications:

  1. Bai, D, Zhu, C. SIMPLE-seq to decode DNA methylation dynamics in single cells. Nat Rev Genet. 2024;25 (6):377. doi: 10.1038/s41576-024-00729-7. PubMed PMID:38609549 .
  2. Bai, D, Zhang, X, Xiang, H, Guo, Z, Zhu, C, Yi, C et al.. Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq. Nat Biotechnol. 2024; :. doi: 10.1038/s41587-024-02148-9. PubMed PMID:38336903 .
  3. Lee, L, Yu, H, Jia, BB, Jussila, A, Zhu, C, Chen, J et al.. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nat Commun. 2023;14 (1):4873. doi: 10.1038/s41467-023-40658-3. PubMed PMID:37573342 PubMed Central PMC10423204.
  4. Xie, Y, Zhu, C, Wang, Z, Tastemel, M, Chang, L, Li, YE et al.. Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nat Struct Mol Biol. 2023;30 (10):1428-1433. doi: 10.1038/s41594-023-01060-1. PubMed PMID:37563440 PubMed Central PMC10584685.
  5. Liu, M, Zhang, J, Zhu, C, Zhang, X, Xiao, W, Yan, Y et al.. DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes. Nat Commun. 2021;12 (1):4108. doi: 10.1038/s41467-021-24431-y. PubMed PMID:34226550 PubMed Central PMC8257757.
  6. Zhu, C, Zhang, Y, Li, YE, Lucero, J, Behrens, MM, Ren, B et al.. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nat Methods. 2021;18 (3):283-292. doi: 10.1038/s41592-021-01060-3. PubMed PMID:33589836 PubMed Central PMC7954905.
  7. Lu, B, Dong, L, Yi, D, Zhang, M, Zhu, C, Li, X et al.. Transposase-assisted tagmentation of RNA/DNA hybrid duplexes. Elife. 2020;9 :. doi: 10.7554/eLife.54919. PubMed PMID:32701057 PubMed Central PMC7402673.
  8. Song, J, Zhuang, Y, Zhu, C, Meng, H, Lu, B, Xie, B et al.. Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation. Nat Chem Biol. 2020;16 (2):160-169. doi: 10.1038/s41589-019-0420-5. PubMed PMID:31819270 .
  9. Zhu, C, Yu, M, Huang, H, Juric, I, Abnousi, A, Hu, R et al.. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat Struct Mol Biol. 2019;26 (11):1063-1070. doi: 10.1038/s41594-019-0323-x. PubMed PMID:31695190 PubMed Central PMC7231560.
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