{"id":69,"date":"2020-10-22T15:13:01","date_gmt":"2020-10-22T07:13:01","guid":{"rendered":"http:\/\/3d-genome.life\/?page_id=69"},"modified":"2026-01-16T15:28:05","modified_gmt":"2026-01-16T07:28:05","slug":"papers","status":"publish","type":"page","link":"http:\/\/3d-genome.life\/?page_id=69","title":{"rendered":"Papers"},"content":{"rendered":"\n<h4 class=\"has-text-align-center\">Cheng Li lab, Peking University<br><a href=\"https:\/\/share.weiyun.com\/vZ5QL7AU\" target=\"_blank\" rel=\"noreferrer noopener\">Publication PDF files (since 2016)<\/a><\/h4>\n\n\n\n<p>Cheng Li Lab at Peking University develops new genomics technologies and computational methods to study cell plasticity in development and diseases. Our recent findings include: <\/p>\n\n\n\n<ul><li>Developed new experimental technologies for studying the 3D genome (<strong>Neuron <\/strong>2025, <strong>Nature Commun<\/strong> 2023, <strong>Cell Reports<\/strong> 2020, <strong>Genome Biology<\/strong> 2018).<br><\/li><li>Generated new insights on the roles of 3D chromatin structures in the regulation of human brain evolution and cancer (<strong>Cell <\/strong>2021, <strong>Dev Cell <\/strong>2025, <strong>Nature Commun <\/strong>2017).<br><\/li><li>Discovered new targets to optimize stem cell reprogramming and differentiation (<strong>Cell Stem Cell<\/strong> 2018, 2024) and to treat refractory cancers (<strong>Nat Cancer <\/strong>2025, <strong>Cancer Cell<\/strong> 2017).<\/li><\/ul>\n\n\n\n<figure class=\"wp-block-gallery columns-2 is-cropped\"><ul class=\"blocks-gallery-grid\"><li class=\"blocks-gallery-item\"><figure><img loading=\"lazy\" width=\"782\" height=\"1024\" src=\"http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-782x1024.jpg\" alt=\"\" data-id=\"494\" data-link=\"http:\/\/3d-genome.life\/?attachment_id=494\" class=\"wp-image-494\" srcset=\"http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-782x1024.jpg 782w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-229x300.jpg 229w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-768x1006.jpg 768w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-1173x1536.jpg 1173w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-1564x2048.jpg 1564w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1-1200x1571.jpg 1200w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/01\/HSC-PLUS\u5c01\u9762-1.jpg 1655w\" sizes=\"(max-width: 782px) 100vw, 782px\" \/><\/figure><\/li><li class=\"blocks-gallery-item\"><figure><img loading=\"lazy\" width=\"777\" height=\"1024\" src=\"http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/03\/PC\u5c01\u9762-1-777x1024.jpg\" alt=\"\" data-id=\"564\" data-full-url=\"http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/03\/PC\u5c01\u9762-1.jpg\" data-link=\"http:\/\/3d-genome.life\/?attachment_id=564\" class=\"wp-image-564\" srcset=\"http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/03\/PC\u5c01\u9762-1-777x1024.jpg 777w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/03\/PC\u5c01\u9762-1-228x300.jpg 228w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/03\/PC\u5c01\u9762-1-768x1012.jpg 768w, http:\/\/3d-genome.life\/wp-content\/uploads\/2022\/03\/PC\u5c01\u9762-1.jpg 800w\" sizes=\"(max-width: 777px) 100vw, 777px\" \/><\/figure><\/li><\/ul><\/figure>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/41043423\/\" target=\"_blank\">SCOPE-C reveals long-range enhancer networks emerging as key regulators during human cortical neurogenesis.<\/a> Jia L\u272f, Hou Y\u272f, Cui Z\u272f, Luo X\u272f, Duan J\u272f, Guo J, You B, Fang Q, Wang X, Shi M, Chen H, Zhang F, Mo J, Liao Y, Sun Y, Wang J, Li T*, Su B*, Zhu L*,\u00a0<span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Neuron<\/strong>. 2025. 113(23):4020-4036.e8.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/ImT94SXhyfpk1HEw-2VlXw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/41094030\/\" target=\"_blank\">A continuous totipotent-like cell-based embryo model recapitulates mouse embryogenesis from zygotic genome activation to gastrulation.<\/a> Ren Y\u272f, Wang X\u272f, Liu H\u272f, Xu Y\u272f, Cheng R\u272f, Ren S\u272f, Li Z, Huo Y, Li B, Guan J*,\u00a0<span style=\"text-decoration: underline;\">Li C<\/span>*,\u00a0Deng H*, Xu J*. <strong>Nat Cell Biol<\/strong>. 2025. 27(11):1993-2006.\u00a0\uff08<a href=\"https:\/\/mp.weixin.qq.com\/s\/s_UkfuLBDiDogqiEiJoB7A\" target=\"_blank\" rel=\"noreferrer noopener\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39805956\/\" target=\"_blank\">ETV7 limits the antiviral and antitumor efficacy of CD8<sup>+<\/sup>&nbsp;T cells by diverting their fate toward exhaustion.<\/a> Cheng J\u272f, Xiao Y\u272f, Peng T\u272f, Zhang Z\u272f, Qin Y\u272f, Wang Y, Shi J, Yan J, Zhao Z, Zheng L, He Z, Wang J, Zhang Z*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Zhu H*, Jiang P*. <strong>Nat Cancer<\/strong>. 2025. 6(2):338-356.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/erYb9zddl9-BuFpnU_uUIA\" data-type=\"URL\" data-id=\"https:\/\/mp.weixin.qq.com\/s\/erYb9zddl9-BuFpnU_uUIA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40754682\/\" target=\"_blank\">Multi-omics integration analysis identifies INPP4B as a T-cell-specific activation suppressor.<\/a> Peng T\u272f, Fang Q\u272f, Zhao Z\u272f, Chang Y, Zhao X, <span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Clin Transl Med<\/strong>. 2025. 15(8):e70430.&nbsp;<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40506500\/\" target=\"_blank\">Increased matrix stiffness promotes fibrogenesis of hepatic stellate cells through AP-1-induced chromatin priming.<\/a> Zhao W\u272f, Yuan W\u272f, Dong T\u272f, Qi W, Feng Z*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*,&nbsp;Sun Y*. <strong>Commun Biol<\/strong>. 2025. 8(1):920.<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40038385\/\" target=\"_blank\">3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression.<\/a> Xu X\u272f, Gan J\u272f, Gao Z\u272f, Li R\u272f, Huang D\u272f, Lin L, Luo Y, Yang Q, Xu J, Li Y, Fang Q, Peng T, Wang Y, Xu Z, Huang A, Hong H, Lei F, Huang W, Leng J, Li T, Bo X,&nbsp;Chen H*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Gu J*. <strong>Commun Biol<\/strong>. 2025. 8(1):365. \uff08<a href=\"https:\/\/mp.weixin.qq.com\/s\/bHNuxlGHzzSalL3yxk8c0g\" data-type=\"URL\" data-id=\"https:\/\/mp.weixin.qq.com\/s\/bHNuxlGHzzSalL3yxk8c0g\" target=\"_blank\" rel=\"noreferrer noopener\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40474074\/\" target=\"_blank\">Explosive tumor growth in a patient with colon cancer is associated with reduced neoantigen levels and decreased interferon-gamma (IFN-\u03b3) signaling.<\/a><strong> <\/strong>Wang Y\u272f, Lu J\u272f, Huang D\u272f, Chen P\u272f, Shi J\u272f, Cheng J, Gan J, Li R, Xu J, Gao Z, Wang X, Huang W, Yin Y, Chen H*, Huang J*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Gu J*. <strong>BMC Cancer<\/strong>. 2025. 25(1):1005.<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39825205\/\" target=\"_blank\">Transient chemical-mediated epigenetic modulation confers unrestricted lineage potential on human primed pluripotent stem cells.<\/a><strong> <\/strong>Chen S\u272f, He Y\u272f, Lv L, Liu B*, <span style=\"text-decoration: underline;\">Li C<\/span>*, Deng H*, Xu J*. <strong>Science China Life Sciences<\/strong>. 2025. 68(4):1084-1101.\uff08<a href=\"https:\/\/mp.weixin.qq.com\/s\/u3VpP9dqOFSLdASmjTawfw\" target=\"_blank\" rel=\"noreferrer noopener\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40808575\/\" target=\"_blank\">Trophectoderm-like cells from EPS cells enable generating EPS cell-derived post-implantation embryoids that complete gastrulation.<\/a> Wang X\u272f, Cheng R\u272f, Wu C\u272f, Liu H, Li Z, Huo Y, Li B, Zhao D*, <span style=\"text-decoration: underline;\">Li C<\/span>*,&nbsp;Deng H*, Xu J*. <strong>Protein Cell<\/strong>. 2025.\uff08<a href=\"https:\/\/mp.weixin.qq.com\/s\/ddeG8dR736dGJq-vdMfg0A\" target=\"_blank\" rel=\"noreferrer noopener\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39481377\/\" target=\"_blank\">Comparative single-cell multiome identifies evolutionary changes in neural progenitor cells during primate brain development.<\/a> Liu Y\u272f, Luo X\u272f*, Sun Y\u272f, Chen K\u272f, Hu T\u272f, You B, Xu J, Zhang F, Cheng Q, Meng X, Yan T, Li X, Qi X, He X, Guo X,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*,&nbsp;Su B*. <strong>Dev Cell<\/strong>. 2025. 60(3):414-428.e8.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/rQ2IWfrr9p3Bc3os1M4P-Q\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38697109\/\" target=\"_blank\">Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived \u03b2 cells.<\/a> Hua H\u272f, Wang Y\u272f, Wang X\u272f, Wang S, Zhou Y, Liu Y, Liang Z, Ren H, Lu S, Wu S, Jiang Y, Pu Y, Zheng X, Tang C, Shen Z,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Du Y*,&nbsp;Deng H*. <strong>Cell Stem Cell<\/strong>. 2024. 31(6):850-865.e10.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/aPxf-ugxtJrLKVX9HFmr6w\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38553796\/\" target=\"_blank\">The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells.<\/a><strong> <\/strong>Li M\u272f, Yang J\u272f, Xiao R, Liu Y, Hu J, Li T, Wu P, Zhang M*, Huang Y*, Sun Y*, <span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Cell Prolif<\/strong>. 2024. e13639.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/xeYm6Lq4MpIkuwjLYpcsfQ\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff0c<a href=\"https:\/\/mp.weixin.qq.com\/s\/vGltAVArfVtj9wQwjvtNTg\" target=\"_blank\" rel=\"noreferrer noopener\">\u8bba\u6587\u89e3\u6790<\/a>\uff09<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36681699\/\" target=\"_blank\">Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions.<\/a><strong> <\/strong>Peng T\u272f, Hou Y\u272f, Meng H\u272f, Cao Y, Wang X, Jia L, Chen Q, Zheng Y, Sun Y, Chen H, Li T*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*<strong>.<\/strong> <strong>Nat Commun<\/strong>. 2023. 14(1):350.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/DPurr7EdpYQKFogMiMEDIw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37851578\/\" target=\"_blank\">CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.<\/a> Liu Y\u272f, Wan X\u272f, Li H\u272f, Chen Y, Hu X, Chen H, Zhu D*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Zhang Y*. <strong>Cell Rep<\/strong>. 2023c. 42(10):113259.&nbsp;\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/G80VY_-x_G6BMESXJvhxBQ\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37561626\/\" target=\"_blank\">PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility.<\/a> Xu Z\u272f, He L\u272f, Wu Y\u272f, Yang L,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Wu H*. <strong>Cell Rep<\/strong>. 2023b. 42(8):112967.&nbsp;\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/vZFZa9rJQAKJlvOyOiJ2xw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37224020\/\" target=\"_blank\">Chemical-induced epigenome resetting for regeneration program activation in human cells.<\/a> Wang G\u272f, Wang Y\u272f, Lyu Y\u272f, He H\u272f, Liuyang S\u272f, Wang J\u272f, Sun S\u272f, Cheng L, Fu Y, Zhu J, Zhong X, Yang Z, Chen Q, <span style=\"text-decoration: underline;\">Li C<\/span>*, Guan J*,&nbsp;Deng H*. <strong>Cell Rep<\/strong>. 2023a. 42(6):112547.&nbsp;<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37660148\/\" target=\"_blank\">TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development.<\/a> Wang L, Zheng Y, Sun Y, Mao S, Li H, Bo X,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Chen H*. <strong>Commun Biol<\/strong>. 2023. 6(1):901.&nbsp;\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/0L6xx-P_hr7uU_mwoeqiBA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37524436\/\" target=\"_blank\">A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures.<\/a> Mao S\u272f, Su J\u272f, Wang L, Bo X,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*,&nbsp;Chen H*. <strong>Genome Res<\/strong>. 2023. 33(8):1381-1394.&nbsp;\uff08<a href=\"https:\/\/mp.weixin.qq.com\/s\/J6hjcws87_pY4QZLb_DCCw\" target=\"_blank\" rel=\"noreferrer noopener\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35768498\/\" target=\"_blank\">CTCF&nbsp;organizes inter-A compartment interactions through RYBP-dependent phase separation.<\/a> Wei C\u272f, Jia L\u272f, Huang X\u272f, Tan J\u272f, 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, <span style=\"text-decoration: underline;\">Li C<\/span>*, Ding J*. <strong>Cell Res<\/strong>. 2022c. 32(8):744-760.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/URDBLR7mfBLp68cGljLmIA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35508506\/\" target=\"_blank\">Derivation of totipotent-like stem cells with blastocyst-like structure forming potential.<\/a> Xu Y\u272f, Zhao J\u272f, Ren Y\u272f, Wang X\u272f,&nbsp;Lyu Y\u272f, Xie B, Sun Y, Yuan X, Liu H, Yang W, Fu Y, Yu Y, Liu Y, Mu R,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Xu J*, Deng H*. <strong>Cell Res<\/strong>. 2022b. 32(6):513-529.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/s41422-022-00686-y\" target=\"_blank\">Highlight<\/a>, <a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/_lSSawscrQlPOctvv4WkDw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36103837\/\" target=\"_blank\">In&nbsp;vivo G-CSF treatment activates the GR-SOCS1 axis to suppress IFN-\u03b3 secretion by natural killer cells.<\/a> Zhao X\u272f, Peng T\u272f, Cao X\u272f, Hou Y, Li R, Han T, Fan Z, Zhao M, Chang Y, Chen H,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Huang X*. <strong>Cell Rep<\/strong>. 2022. 40(11):111342.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/Q20mPUGfD2wQL_Fqyb14Nw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35585676\/\" target=\"_blank\">Multiomics Analysis Identifies SOCS1 as Restraining T Cell Activation and Preventing Graft-Versus-Host Disease.<\/a> Guo H\u272f, Li R\u272f, Wang M, Hou Y, Liu S,&nbsp;Peng T, Zhao XY, Lu L, Han Y, Shao Y, Chang YJ*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Huang XJ*. <strong>Adv Sci<\/strong>. 2022. 9(21):e2200978.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/NXPEOrfrXhyemhDY3sq-AA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09 <\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36167633\/\" target=\"_blank\">Polyclonal evolution of Fanconi anemia to MDS and AML revealed at single cell resolution.<\/a> Chang L\u272f, Cui Z\u272f, Shi D\u272f, Chu Y\u272f, Wang B, Wan Y, Ma Q, Zhang R, Li H, Cheng X, Cheng T, Zhu X*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Yuan W*. <strong>Exp Hematol Oncol<\/strong>. 2022. 11(1):64.<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33508230\/\" target=\"_blank\">3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis.<\/a> Luo X\u272f, Liu Y\u272f, Dang D\u272f, 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*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Su B*. <strong>Cell<\/strong>. 2021. 184(3):723-740.e21.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/CTZg60C9CiGdCzlY9HPSFQ\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34341490\/\" target=\"_blank\">Identification of HSC\/MPP expansion units in fetal liver by single-cell spatiotemporal transcriptomics.<\/a> Gao S\u272f, Shi Q\u272f, Zhang Y, Liang G, Kang Z, Huang B, Ma D, Wang L, Jiao J, Fang X, Xu CR, Liu L, Xu X, G\u00f6ttgens B,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Liu F*. <strong>Cell Res<\/strong>. 2022a. 32(1):38-53.\uff08<a rel=\"noreferrer noopener\" href=\"http:\/\/www.cell-research.com\/Issue.php?id=254\" target=\"_blank\">Cover figure<\/a>\uff0c<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/H92teq7EM57pCBz_fQEdgw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff0c<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/koyPYmc_W9GcMJmMPoCntQ\" target=\"_blank\">\u4e00\u4f5c\u5386\u7a0b<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33420425\/\" target=\"_blank\">Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration.<\/a> Qu M\u272f, Xiong L\u272f, Lyu Y\u272f, Zhang X, Shen J, Guan J, Chai P, Lin Z, Nie B,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Xu J*, Deng H*. <strong>Cell Res<\/strong>. 2021. 31(3):259-271.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/K3hOXuFqebViF0Aa7xftWw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09&nbsp;<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34116262\/\" target=\"_blank\">Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples.<\/a> Li T\u272f, Li R\u272f, Dong X\u272f, Shi L\u272f, Lin M\u272f, Peng T\u272f, 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*,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Genomics Proteomics Bioinformatics<\/strong>. 2021. 19(5):741-753.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/_Kj7rwxVm_Kc4gb5gRImZw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34382192\/\" target=\"_blank\">Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions.<\/a> Jia L,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Li T*. <strong>Methods Mol Biol<\/strong>. 2021. 2351:211-227.<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32719519\/\" target=\"_blank\">Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection.<\/a> Xie X\u272f, Shi Q\u272f, 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*,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Luo HR*. <strong>Nat Immunol<\/strong>. 2020. 21(9):1119-1133.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/O9Ej_MATpcpC7MNJuUDyaQ\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff0c<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/H93uUuOpOyNJHAnws9_Lvg\" target=\"_blank\">\u4e00\u4f5c\u89e3\u8bfb<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32997998\/\" target=\"_blank\">tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis.<\/a> Zhang C\u272f, Xu Z\u272f, Yang S\u272f, Sun G\u272f, Jia L, Zheng Z, Gu Q, Tao W*, Cheng T*,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Cheng H*. <strong>Cell Rep<\/strong>. 2020. 32(13):108206.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/j0q5VvCWpZIhVNsRH0VLIQ\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33155082\/\" target=\"_blank\">Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells.<\/a> Chang L\u272f, Li M\u272f, Shao S\u272f,&nbsp;Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Sun Y*. <strong>Protein Cell<\/strong>. 2022. 13(4):258-280.\uff08<a rel=\"noreferrer noopener\" href=\"http:\/\/www.protein-cell.org\/en\/article\/2022\/4\" target=\"_blank\">Cover figure<\/a>\uff0c<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/MHEBqbagA-vntoKxNwW1ug\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33045748\/\" target=\"_blank\">Senescence-activated enhancer landscape orchestrates the senescence-associated secretory phenotype in murine fibroblasts.<\/a> Guan Y\u272f, Zhang C\u272f, Lyu G, Huang X, Zhang X, Zhuang T, Jia L, Zhang L, Zhang C*,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Tao W*. <strong>Nucleic Acids Res<\/strong>. 2020. 48(19):10909-10923.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/YrRyaUTDmxgA8baHyxgIAA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32249389\/\" target=\"_blank\">Architectural proteins for the formation and maintenance of the 3D genome.<\/a> Li M\u272f, Gan J\u272f, Sun Y\u272f, Xu Z\u272f, Yang J, Sun Y*,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Sci China Life Sci<\/strong>. 2020. 63(6):795-810.&nbsp;(Review)<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32279284\/\" target=\"_blank\">Mixed secondary chromatin structure revealed by modeling radiation-induced DNA fragment length distribution.<\/a> Ma W\u272f, Gu C\u272f, Ma L\u272f, Fan C\u272f, Zhang C, Sun Y,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Yang G*. <strong>Sci China Life Sci<\/strong>. 2020. 63(6):825-834.&nbsp;<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32084131\/\" target=\"_blank\">DeepHiC: A generative adversarial network for enhancing Hi-C data resolution.<\/a> Hong H\u272f, Jiang S\u272f, Li H, Du G, Sun Y, Tao H, Quan C, Zhao C, Li R, Li W, Yin X, Huang Y,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Chen H*, Bo X*. <strong>PLoS Comput Biol<\/strong>. 2020. 16(2):e1007287. (<a rel=\"noreferrer noopener\" href=\"http:\/\/sysomics.com\/deephic\/\" target=\"_blank\">Web server<\/a>)<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31564811\/\" target=\"_blank\">An enrichment model using regular health examination data for early detection of colorectal cancer.<\/a><strong> <\/strong>Shi Q\u272f, Gao Z\u272f, Wu P\u272f, Heng F, Lei F, Wang Y, Gao Q, Zeng Q, Niu P,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*, Gu J*. <strong>Chin J Cancer Res<\/strong>. 2019. 31(4):686-698.<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29937202\/\" target=\"_blank\">Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming.<\/a> Zhao T\u272f, Fu Y\u272f, Zhu J\u272f, Liu Y\u272f, Zhang Q\u272f, Yi Z\u272f, Chen S, Jiao Z, Xu X, Xu J, Duo S, Bai Y, Tang C,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Deng H*. <strong>Cell Stem Cell<\/strong>. 2018. 23(1):31-45.e7.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/mI5blzG4RDk_pOONYUUZkw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29690904\/\" target=\"_blank\">OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks.<\/a> Li T\u272f, Jia L\u272f, Cao Y, Chen Q,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Genome Biol<\/strong>. 2018. 19(1):54.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/MXqLjARn15u-IHz7w8DhzA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29796744\/\" target=\"_blank\">3D genome and its disorganization in diseases.<\/a> Li R\u272f*, Liu Y\u272f, Hou Y\u272f, Gan J\u272f, Wu P,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*.<em><strong> <\/strong><\/em><strong>Cell Biol Toxicol<\/strong>. 2018. 34(5):351-365.\uff08Review, <a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/TWM7mMked9JsIVa3N4ROwA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29536443\/\" target=\"_blank\">iSeq: Web-Based RNA-seq Data Analysis and Visualization.<\/a> Zhang C\u272f, Fan C\u272f, Gan J, Zhu P, Kong L,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Methods Mol Biol<\/strong>. 2018. 1754:167-181.<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29866040\/\" target=\"_blank\">Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease.<\/a> Lyu G\u272f, Zhang C\u272f, Ling T\u272f, Liu R, Zong L, Guan Y, Huang X, Sun L, Zhang L, <span style=\"text-decoration: underline;\">Li C<\/span><strong>*<\/strong>, Nie Y<strong>*<\/strong>, Tao W<strong>*<\/strong>. <strong>BMC Genomics<\/strong>. 2018. 19(1):428.&nbsp;<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28399412\/\" target=\"_blank\">Cell-Cycle-Targeting MicroRNAs as Therapeutic Tools against Refractory Cancers.<\/a> 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,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*, Sicinski P*. <strong>Cancer Cell<\/strong>. 2017. 31(4):576-590.e8.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28399406\/\" target=\"_blank\">Preview<\/a>, <a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/vcEb5RJGavCRlOKD_P2uMA\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29203764\/\" target=\"_blank\">3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations.<\/a> Wu P\u272f, Li T\u272f, Li R\u272f, Jia L, Zhu P, Liu Y, Chen Q, Tang D, Yu Y,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Nat Commun<\/strong>. 2017. 8(1):1937.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/G30qEp5-KeTkgOQuDbh1fw\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff0c<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/sH04On4anPd7TMklQaq1VQ\" target=\"_blank\">\u4e00\u4f5c\u89e3\u8bfb<\/a>\uff09<\/p>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28180283\/\" target=\"_blank\">Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome.<\/a> Wang Y, Fan C, Zheng Y,<strong>&nbsp;<\/strong><span style=\"text-decoration: underline;\">Li C<\/span>*.<strong> Nucleic Acids Res<\/strong>. 2017. 45(10):e85.\uff08<a rel=\"noreferrer noopener\" href=\"https:\/\/mp.weixin.qq.com\/s\/ULgThtOJo7KNCrYNZz-8ew\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<hr>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27734896\/\" target=\"_blank\">3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data.<\/a> Li R\u272f, Liu Y\u272f, Li T,&nbsp;<span style=\"text-decoration: underline;\">Li C<\/span>*. <strong>Sci Rep<\/strong>. 2016. 6:34651.\uff08<a rel=\"noreferrer noopener\" href=\"http:\/\/sysomics.com\/3Disease\" target=\"_blank\">Web server<\/a>, <a rel=\"noreferrer noopener\" href=\"http:\/\/www.bio.pku.edu.cn\/homes\/Index\/news_cont\/22\/4186.html\" target=\"_blank\">\u4e2d\u6587\u4ecb\u7ecd<\/a>\uff09<\/p>\n\n\n\n<hr>\n\n\n\n<p><strong><a href=\"https:\/\/share.weiyun.com\/7YP5FJ00\" target=\"_blank\" rel=\"noreferrer noopener\">Publication <strong>PDF files (2000 &#8211; 2014)<\/strong><\/a><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Cheng Li lab, Peking UniversityPublication PDF files (s [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"http:\/\/3d-genome.life\/index.php?rest_route=\/wp\/v2\/pages\/69"}],"collection":[{"href":"http:\/\/3d-genome.life\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/3d-genome.life\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/3d-genome.life\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/3d-genome.life\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=69"}],"version-history":[{"count":170,"href":"http:\/\/3d-genome.life\/index.php?rest_route=\/wp\/v2\/pages\/69\/revisions"}],"predecessor-version":[{"id":2899,"href":"http:\/\/3d-genome.life\/index.php?rest_route=\/wp\/v2\/pages\/69\/revisions\/2899"}],"wp:attachment":[{"href":"http:\/\/3d-genome.life\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=69"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}