研究组论文

Cheng Li lab
Recent publications (PDF files)

3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Luo X✯, Liu Y✯, Dang D✯, Hu T, Hou Y, Meng X, Zhang F, Li T, Wang C, Li M, Wu H, Shen Q, Hu Y, Zeng X, He X, Yan L, Zhang S*, Li C*, Su B*. Cell. 2021. 184(3):723-740.e21.(中文介绍

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration. Qu M✯, Xiong L✯, Lyu Y✯, Zhang X, Shen J, Guan J, Chai P, Lin Z, Nie B, Li C*, Xu J*, Deng H*. Cell Res. 2021a. 31(3):259-271.(中文介绍) 

Identification of HSC/MPP expansion units in fetal liver by single-cell spatiotemporal transcriptomics. Gao S✯, Shi Q✯, Zhang Y, Liang G, Kang Z, Huang B, Ma D, Wang L, Jiao J, Fang X, Xu CR, Liu L, Xu X, Göttgens B, Li C*, Liu F*. Cell Res. 2021b. doi: 10.1038/s41422-021-00540-7.(中文介绍一作历程

Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples. Li T✯, Li R✯, Dong X✯, Shi L✯, Lin M✯, Peng T✯, Wu P, Liu Y, Li X, He X, Han X, Kang B, Wang Y, Liu Z, Chen Q, Shen Y, Feng M, Wang X, Wu D*, Wang J*, Li C*. Genomics Proteomics Bioinformatics. 2021. S1672-0229(21)00096-6.(中文介绍

Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions. Jia L, Li C*, Li T*. Methods Mol Biol. 2021. 2351:211-227.

Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection. Xie X✯, Shi Q✯, Wu P, Zhang X, Kambara H, Su J, Yu H, Park SY, Guo R, Ren Q, Zhang S, Xu Y, Silberstein LE, Cheng T, Ma F*, Li C*, Luo HR*. Nat Immunol. 2020. 21(9):1119-1133.(中文介绍一作解读

tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis. Zhang C✯, Xu Z✯, Yang S✯, Sun G✯, Jia L, Zheng Z, Gu Q, Tao W*, Cheng T*, Li C*, Cheng H*. Cell Rep. 2020. 32(13):108206.(中文介绍

Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Chang L✯, Li M✯, Shao S✯, Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A, Li C*, Sun Y*. Protein Cell. 2020. doi: 10.1007/s13238-020-00794-8.(中文介绍

Senescence-activated enhancer landscape orchestrates the senescence-associated secretory phenotype in murine fibroblasts. Guan Y✯, Zhang C✯, Lyu G, Huang X, Zhang X, Zhuang T, Jia L, Zhang L, Zhang C*, Li C*, Tao W*. Nucleic Acids Res. 2020. 48(19):10909-10923.(中文介绍

Architectural proteins for the formation and maintenance of the 3D genome. Li M✯, Gan J✯, Sun Y✯, Xu Z✯, Yang J, Sun Y*, Li C*. Sci China Life Sci. 2020. 63(6):795-810. (Review)

Mixed secondary chromatin structure revealed by modeling radiation-induced DNA fragment length distribution. Ma W✯, Gu C✯, Ma L✯, Fan C✯, Zhang C, Sun Y, Li C*, Yang G*. Sci China Life Sci. 2020. 63(6):825-834. 

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution. Hong H✯, Jiang S✯, Li H, Du G, Sun Y, Tao H, Quan C, Zhao C, Li R, Li W, Yin X, Huang Y, Li C*, Chen H*, Bo X*. PLoS Comput Biol. 2020. 16(2):e1007287. (Web server)

An enrichment model using regular health examination data for early detection of colorectal cancer. Shi Q✯, Gao Z✯, Wu P✯, Heng F, Lei F, Wang Y, Gao Q, Zeng Q, Niu P, Li C*, Gu J*. Chin J Cancer Res. 2019. 31(4):686-698.

Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming. Zhao T✯, Fu Y✯, Zhu J✯, Liu Y✯, Zhang Q✯, Yi Z✯, Chen S, Jiao Z, Xu X, Xu J, Duo S, Bai Y, Tang C, Li C*, Deng H*. Cell Stem Cell. 2018. 23(1):31-45.e7.(中文介绍

OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks. Li T✯, Jia L✯, Cao Y, Chen Q, Li C*. Genome Biol. 2018. 19(1):54.(中文介绍

3D genome and its disorganization in diseases. Li R*✯, Liu Y✯, Hou Y✯, Gan J✯, Wu P, Li C*. Cell Biol Toxicol. 2018. 34(5):351-365.(Review, 中文介绍

iSeq: Web-Based RNA-seq Data Analysis and Visualization. Zhang C✯, Fan C✯, Gan J, Zhu P, Kong L, Li C*. Methods Mol Biol. 2018. 1754:167-181.

Cell-Cycle-Targeting MicroRNAs as Therapeutic Tools against Refractory Cancers. Hydbring P, Wang Y, Fassl A, Li X, Matia V, Otto T, Choi YJ, Sweeney KE, Suski JM, Yin H, Bogorad RL, Goel S, Yuzugullu H, Kauffman KJ, Yang J, Jin C, Li Y, Floris D, Swanson R, Ng K, Sicinska E, Anders L, Zhao JJ, Polyak K, Anderson DG, Li C*, Sicinski P*. Cancer Cell. 2017. 31(4):576-590.e8.(中文介绍

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. Wu P✯, Li T✯, Li R✯, Jia L, Zhu P, Liu Y, Chen Q, Tang D, Yu Y, Li C*. Nat Commun. 2017. 8(1):1937.(中文介绍一作解读

Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome. Wang Y, Fan C, Zheng Y, Li C*. Nucleic Acids Res. 2017. 45(10):e85.(中文介绍

3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data. Li R✯, Liu Y✯, Li T, Li C*. Sci Rep. 2016. 6:34651.(中文介绍