This is one aspect of our contributions to science. If you have difficulties getting the full text, drop me an email.

2024

Qiushi Xu$^§$, Yunlong Zhang$^§$, Wei Xu, Dong Liu, Wenfei Jin, Xi Chen* & Ni Hong* (2024) The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. Nucleic Acids Res. 52:3106-3120. doi: 10.1093/nar/gkae095. Click here to see some behind-the-scene stories that are not in the paper.

2023

A. Sina Booeshaghi*, Xi Chen & Lior Pachter* (2023) A machine-readable specification for genomics assays. bioRxiv. doi: 10.1101/2023.03.17.533215
Hechen Li, Ziqi Zhang, Michael Squires, Xi Chen & Xiuwei Zhang (2023) scMultiSim: simulation of single cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions. ResearchSquare. doi: 10.21203/rs.3.rs-2675530/v1
Danling Zhu$^§$, Yi Wen$^§$, Wanyue Yao, Haiyan Zheng, Sixian Zhou, Qiqi Zhang, Li-Jia Qu, Xi Chen* & Zhe Wu* (2023) Distinct chromatin signatures in the Arabidopsis male gametophyte. Nat Genet 55:706-720. doi: 10.1038/s41588-023-01329-7
Ziqi Zhang, Haoran Sun, Ragunathan Mariappan, Xi Chen, Xinyu Chen, Mika S. Jain, Mirjana Efremova, Sarah A. Teichmann, Vaibhav Rajan & Xiuwei Zhang (2023) scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection. Nat Commun 14:384. doi: 10.1038/s41467-023-36066-2

Xu W$^§$, Yang W$^§$, Zhang Y, Chen Y, Zhang Q, Wang X, Song K, Jin W*, Chen X* (2022) ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells. Nat Methods 19:1243–1249. doi: 10.1038/s41592-022-01601-4. Click here to see some behind-the-scene stories that are not in the paper.

Xu W, Wen Y, Liang Y, Xu Q, Wang X, Jin W, Chen X (2021) A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility. Nat Protoc 16:4084–4107. doi: 10.1038/s41596-021-00583-5. Click here to see some behind-the-scene stories that are not in the paper.
Tan D, Chen R, Mo Y, Gu S, Ma J, Xu W, Lu X, He H, Jiang F, Fan W, Wang Y, Chen X*, Huang W* (2021) Quantitative control of noise in mammalian gene expression by dynamic histone regulation. Elife 10:e65654. doi: 10.7554/elife.65654
Zheng J, Ye Y, Xu Q, Xu W, Zhang W*, Chen X* (2021) A Modified SMART-Seq Method for Single-Cell Transcriptomic Analysis of Embryoid Body Differentiation. Methods Mol Biology Clifton N J 1–27. doi: 10.1007/7651_2021_435. Click here to see some behind-the-scene stories that are not in the paper.

Xu W$^§$, Ye Y$^§$, Sharrocks AD, Zhang W*, Chen X* (2020) Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation. Star Protoc 1:100187. doi: 10.1016/j.xpro.2020.100187