Cheng Li lab, Peking University
Recent publications (PDF files)

Cheng Li Lab at Peking University develops new techniques for omics experiments to study the regulation of cell plasticity. Using a combination of high-throughput experimental technologies and computational methods, we study cell fate regulation from the 3D genomics and multi-omics perspective. Our recent findings include:

  • Discovery of new targets to accelerate stem cell reprogramming (Cell Stem Cell 2018) and to treat refractory tumors (Cancer Cell 2017);
  • Development of new experimental methods for 3D genomics (Nature Commun 2023, Cell Reports 2020, Genome Biology 2018);
  • Generation of new insights for the roles of higher-order chromatin structures in the regulation of human brain evolution and cancer (Cell 2021, Nature Commun 2017);
  • Single-cell reference model for studying neutrophil-related disease mechanisms and therapeutic targets (Nat Immunol 2020).

Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived β cells. Hua H✯, Wang Y✯, Wang X✯, Wang S, Zhou Y, Liu Y, Liang Z, Ren H, Lu S, Wu S, Jiang Y, Pu Y, Zheng X, Tang C, Shen Z, Li C*, Du Y*, Deng H*. Cell Stem Cell. 2024.(中文介绍

The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells. Li M✯, Yang J✯, Xiao R, Liu Y, Hu J, Li T, Wu P, Zhang M*, Huang Y*, Sun Y*, Li C*. Cell Prolif. 2024. e13639.(中文介绍论文解析

Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions. Peng T✯, Hou Y✯, Meng H✯, Cao Y, Wang X, Jia L, Chen Q, Zheng Y, Sun Y, Chen H, Li T*, Li C*. Nat Commun. 2023. 14(1):350.(中文介绍

CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors. Liu Y✯, Wan X✯, Li H✯, Chen Y, Hu X, Chen H, Zhu D*, Li C*, Zhang Y*. Cell Rep. 2023c. 42(10):113259. (中文介绍

PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility. Xu Z✯, He L✯, Wu Y✯, Yang L, Li C*, Wu H*. Cell Rep. 2023b. 42(8):112967. (中文介绍

Chemical-induced epigenome resetting for regeneration program activation in human cells. Wang G✯, Wang Y✯, Lyu Y✯, He H✯, Liuyang S✯, Wang J✯, Sun S✯, Cheng L, Fu Y, Zhu J, Zhong X, Yang Z, Chen Q, Li C*, Guan J*, Deng H*. Cell Rep. 2023a. 42(6):112547. 

TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development. Wang L, Zheng Y, Sun Y, Mao S, Li H, Bo X, Li C*, Chen H*. Commun Biol. 2023. 6(1):901. (中文介绍

A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures. Mao S✯, Su J✯, Wang L, Bo X, Li C*, Chen H*. Genome Res. 2023. 33(8):1381-1394. (中文介绍

CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation. Wei C✯, Jia L✯, Huang X✯, Tan J✯, Wang M, Niu J, Hou Y, Sun J, Zeng P, Wang J, Qing L, Ma L, Liu X, Tang X, Li F, Jiang S, Liu J, Li T, Fan L, Sun Y, Gao J, Li C*, Ding J*. Cell Res. 2022c. 32(8):744-760.(中文介绍

Derivation of totipotent-like stem cells with blastocyst-like structure forming potential. Xu Y✯, Zhao J✯, Ren Y✯, Wang X✯, Lyu Y✯, Xie B, Sun Y, Yuan X, Liu H, Yang W, Fu Y, Yu Y, Liu Y, Mu R, Li C*, Xu J*, Deng H*. Cell Res. 2022b. 32(6):513-529.(Highlight, 中文介绍

In vivo G-CSF treatment activates the GR-SOCS1 axis to suppress IFN-γ secretion by natural killer cells. Zhao X✯, Peng T✯, Cao X✯, Hou Y, Li R, Han T, Fan Z, Zhao M, Chang Y, Chen H, Li C*, Huang X*. Cell Rep. 2022. 40(11):111342.(中文介绍

Multiomics Analysis Identifies SOCS1 as Restraining T Cell Activation and Preventing Graft-Versus-Host Disease. Guo H✯, Li R✯, Wang M, Hou Y, Liu S, Peng T, Zhao XY, Lu L, Han Y, Shao Y, Chang YJ*, Li C*, Huang XJ*. Adv Sci. 2022. 9(21):e2200978.(中文介绍

Polyclonal evolution of Fanconi anemia to MDS and AML revealed at single cell resolution. Chang L✯, Cui Z✯, Shi D✯, Chu Y✯, Wang B, Wan Y, Ma Q, Zhang R, Li H, Cheng X, Cheng T, Zhu X*, Li C*, Yuan W*. Exp Hematol Oncol. 2022. 11(1):64.

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

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. 2022a. 32(1):38-53.(Cover figure中文介绍一作历程

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. 2021. 31(3):259-271.(中文介绍) 

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. 19(5):741-753.(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. 2022. 13(4):258-280.(Cover figure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.

Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease. Lyu G✯, Zhang C✯, Ling T✯, Liu R, Zong L, Guan Y, Huang X, Sun L, Zhang L, Li C*, Nie Y*, Tao W*. BMC Genomics. 2018. 19(1):428. 

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.(Preview, 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.(Web server, 中文介绍