Works by Chen, Kaifu

Results: 43

Deficits in mitochondrial dynamics and iron balance result in templated insertions.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60546-2

By:

Fox, Jordan;
Yu, Yang;
Thakre, Pilendra;
Fox, Chloe;
Li, Qian;
Wang, Yunxia;
Hughes, Adam;
Wang, Xin;
Chen, Kaifu;
Ira, Grzegorz

Publication type:

Article

Role of Endothelial and Mesenchymal Cell Transitions in Heart Failure and Recovery Thereafter.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.609262

By:

Wang, Guangyu;
Cruz, Ana Sofia;
Youker, Keith;
Marcos-Abdala, Hernan G.;
Thandavarayan, Rajarajan A.;
Cooke, John P.;
Torre-Amione, Guillermo;
Chen, Kaifu;
Bhimaraj, Arvind

Publication type:

Article

Robust differentiation of human pluripotent stem cells into mural progenitor cells via transient activation of NKX3.1.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52678-8

By:

Lee, Umji;
Zhang, Yadong;
Zhu, Yonglin;
Luo, Allen Chilun;
Gong, Liyan;
Tremmel, Daniel M.;
Kim, Yunhye;
Villarreal, Victoria Sofia;
Wang, Xi;
Lin, Ruei-Zeng;
Cui, Miao;
Ma, Minglin;
Yuan, Ke;
Wang, Kai;
Chen, Kaifu;
Melero-Martin, Juan M.

Publication type:

Article

Yeast EndoG prevents genome instability by degrading extranuclear DNA species.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52147-2

By:

Yu, Yang;
Wang, Xin;
Fox, Jordan;
Yu, Ruofan;
Thakre, Pilendra;
McCauley, Brenna;
Nikoloutsos, Nicolas;
Li, Qian;
Hastings, P. J.;
Dang, Weiwei;
Chen, Kaifu;
Ira, Grzegorz

Publication type:

Article

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-01992-7

By:

Wang, Guangyu;
Meng, Qingshu;
Xia, Bo;
Zhang, Shuo;
Lv, Jie;
Zhao, Dongyu;
Li, Yanqiang;
Wang, Xin;
Zhang, Lili;
Cooke, John P.;
Cao, Qi;
Chen, Kaifu

Publication type:

Article

A novel DNA sequence periodicity decodes nucleosome positioning.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 19, p. 6228, doi. 10.1093/nar/gkn626

By:

Chen, Kaifu;
Meng, Qingshu;
Ma, Lina;
Liu, Qingyou;
Tang, Petrus;
Chiu, Chungshung;
Hu, Songnian;
Yu, Jun

Publication type:

Article

Homeobox oncogene activation by pan-cancer DNA hypermethylation.

Published in:

Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1492-3

By:

Su, Jianzhong;
Huang, Yung-Hsin;
Cui, Xiaodong;
Wang, Xinyu;
Zhang, Xiaotian;
Lei, Yong;
Xu, Jianfeng;
Lin, Xueqiu;
Chen, Kaifu;
Lv, Jie;
Goodell, Margaret A.;
Li, Wei

Publication type:

Article

Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1296-x

By:

Xueqiu Lin;
Jianzhong Su;
Kaifu Chen;
Rodriguez, Benjamin;
Wei Li

Publication type:

Article

Discovering Thiamine Transporters as Targets of Chloroquine Using a Novel Functional Genomics Strategy.

Published in:

PLoS Genetics, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.pgen.1003083

By:

Zhiwei Huang;
Srinivasan, Sankaranarayanan;
Jianhuai Zhang;
Kaifu Chen;
Yongxiang Li;
Wei Li;
Quiocho, Florante A.;
Xuewen Pan

Publication type:

Article

Beclin 2 negatively regulates innate immune signaling and tumor development.

Published in:

2020

By:

Zhu, Motao;
Deng, Guangtong;
Tan, Peng;
Xing, Changsheng;
Guan, Cuiping;
Jiang, Chongming;
Zhang, Yinlong;
Ning, Bo;
Li, Chaoran;
Yin, Bingnan;
Chen, Kaifu;
Zhao, Yuliang;
Wang, Helen Y;
Levine, Beth;
Nie, Guangjun;
Wang, Rong-Fu

Publication type:

journal article

A comprehensive analysis of protein phosphatases in rice and Arabidopsis.

Published in:

Plant Systematics & Evolution, 2010, v. 289, n. 3/4, p. 111, doi. 10.1007/s00606-010-0336-8

By:

Meng Yang;
Shuhui Song;
Guiming Liu;
Kaifu Chen;
Xiangjun Tian;
Zhizhuang Joe Zhao;
Songnian Hu;
Jun Yu

Publication type:

Article

LIM Domain Only 2 Regulates Endothelial Proliferation, Angiogenesis, and Tissue Regeneration.

Published in:

Journal of the American Heart Association, 2016, v. 5, n. 10, p. 1, doi. 10.1161/JAHA.116.004117

By:

Meng, Shu;
Matrone, Gianfranco;
Lv, Jie;
Chen, Kaifu;
Wong, Wing Tak;
Cooke, John P.

Publication type:

Article

Embryonic alcohol exposure in zebrafish predisposes adults to cardiomyopathy and diastolic dysfunction.

Published in:

Cardiovascular Research, 2024, v. 120, n. 13, p. 1607, doi. 10.1093/cvr/cvae139

By:

Weeks, Olivia;
Gao, Xinlei;
Basu, Sandeep;
Galdieri, Jennifer;
Chen, Kaifu;
Burns, C Geoffrey;
Burns, Caroline E

Publication type:

Article

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes.

Published in:

Nature Genetics, 2015, v. 47, n. 10, p. 1149, doi. 10.1038/ng.3385

By:

Chen, Kaifu;
Chen, Zhong;
Wu, Dayong;
Lin, Xueqiu;
Su, Jianzhong;
Rodriguez, Benjamin;
Xi, Yuanxin;
Xia, Zheng;
Shi, Xiaobing;
Wang, Qianben;
Li, Wei;
Zhang, Lili;
Chen, Xi

Publication type:

Article

TNIK regulation of interferon signaling and endothelial cell response to virus infection.

Published in:

Frontiers in Cardiovascular Medicine, 2024, p. 1, doi. 10.3389/fcvm.2023.1213428

By:

Chau, Khanh M.;
Dominic, Abishai;
Davis, Eleanor L.;
Kotla, Sivareddy;
Berrios, Estefani Turcios;
Fahim, Arsany;
Arunesh, Ashwin;
Shengyu Li;
Dongyu Zhao;
Kaifu Chen;
Davis, Alan R.;
Nguyen, Minh T. H.;
Yongxing Wang;
Evans, Scott E.;
Guangyu Wang;
Cooke, John P.;
Jun-ichi Abe;
Huston, David P.;
Nhat-Tu Le

Publication type:

Article

Epigenetic landscape reveals MECOM as an endothelial lineage regulator.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38002-w

By:

Lv, Jie;
Meng, Shu;
Gu, Qilin;
Zheng, Rongbin;
Gao, Xinlei;
Kim, Jun-dae;
Chen, Min;
Xia, Bo;
Zuo, Yihan;
Zhu, Sen;
Zhao, Dongyu;
Li, Yanqiang;
Wang, Guangyu;
Wang, Xin;
Meng, Qingshu;
Cao, Qi;
Cooke, John P.;
Fang, Longhou;
Chen, Kaifu;
Zhang, Lili

Publication type:

Article

Publisher Correction: Epigenetic landscape reveals MECOM as an endothelial lineage regulator.

Published in:

2023

By:

Lv, Jie;
Meng, Shu;
Gu, Qilin;
Zheng, Rongbin;
Gao, Xinlei;
Kim, Jun-dae;
Chen, Min;
Xia, Bo;
Zuo, Yihan;
Zhu, Sen;
Zhao, Dongyu;
Li, Yanqiang;
Wang, Guangyu;
Wang, Xin;
Meng, Qingshu;
Cao, Qi;
Cooke, John P.;
Fang, Longhou;
Chen, Kaifu;
Zhang, Lili

Publication type:

Correction Notice

Epigenetic landscape reveals MECOM as an endothelial lineage regulator.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38002-w

By:

Lv, Jie;
Meng, Shu;
Gu, Qilin;
Zheng, Rongbin;
Gao, Xinlei;
Kim, Jun-dae;
Chen, Min;
Xia, Bo;
Zuo, Yihan;
Zhu, Sen;
Zhao, Dongyu;
Li, Yanqiang;
Wang, Guangyu;
Wang, Xin;
Meng, Qingshu;
Cao, Qi;
Cooke, John P.;
Fang, Longhou;
Chen, Kaifu;
Zhang, Lili

Publication type:

Article

Epigenetic landscape reveals MECOM as an endothelial lineage regulator.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38002-w

By:

Lv, Jie;
Meng, Shu;
Gu, Qilin;
Zheng, Rongbin;
Gao, Xinlei;
Kim, Jun-dae;
Chen, Min;
Xia, Bo;
Zuo, Yihan;
Zhu, Sen;
Zhao, Dongyu;
Li, Yanqiang;
Wang, Guangyu;
Wang, Xin;
Meng, Qingshu;
Cao, Qi;
Cooke, John P.;
Fang, Longhou;
Chen, Kaifu;
Zhang, Lili

Publication type:

Article

A matter of access.

Published in:

Transcription (2154-1264), 2014, v. 5, p. 1, doi. 10.4161/trns.29355

By:

Hu, Zheng;
Chen, Kaifu;
Li, Wei;
Tyler, Jessica K.

Publication type:

Article

Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.94001

By:

Zulong Chen;
Xin Wang;
Xinlei Gao;
Arslanovic, Nina;
Kaifu Chen;
Tyler, Jessica K.

Publication type:

Article

mt‐Ty 5'tiRNA regulates skeletal muscle cell proliferation and differentiation.

Published in:

Cell Proliferation, 2023, v. 56, n. 8, p. 1, doi. 10.1111/cpr.13416

By:

Cao, Jun;
Wang, Xin;
Advani, Vivek;
Lu, Yao Wei;
Malizia, Andrea P.;
Singh, Gurinder Bir;
Huang, Zhan‐Peng;
Liu, Jianming;
Wang, Chunbo;
Oliveira, Edilamar M.;
Mably, John D.;
Chen, Kaifu;
Wang, Da‐Zhi

Publication type:

Article

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses.

Published in:

2016

By:

Kaifu Chen;
Zheng Hu;
Zheng Xia;
Dongyu Zhao;
Wei Li;
Tyler, Jessica K.

Publication type:

Opinion

Polycomb group proteins EZH2 and EED directly regulate androgen receptor in advanced prostate cancer.

Published in:

International Journal of Cancer, 2019, v. 145, n. 2, p. 415, doi. 10.1002/ijc.32118

By:

Liu, Qipeng;
Wang, Guangyu;
Li, Qiaqia;
Jiang, Weihua;
Kim, Jung‐Sun;
Wang, Rui;
Zhu, Sen;
Wang, Xiaoju;
Yan, Lin;
Yi, Yang;
Zhang, Lili;
Meng, Qingshu;
Li, Chao;
Zhao, Dongyu;
Qiao, Yuanyuan;
Li, Yong;
Gursel, Demirkan B.;
Chinnaiyan, Arul M.;
Chen, Kaifu;
Cao, Qi

Publication type:

Article

An evolutionary analysis of trypanosomatid GP63 proteases.

Published in:

Parasitology Research, 2011, v. 109, n. 4, p. 1075, doi. 10.1007/s00436-011-2348-x

By:

Ma, Lina;
Chen, Kaifu;
Meng, Qingshu;
Liu, Qingyou;
Tang, Petrus;
Hu, Songnian;
Yu, Jun

Publication type:

Article

SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 10, p. 1, doi. 10.1093/nar/gkaf431

By:

Arulsamy, Kulandaisamy;
Xia, Bo;
Yu, Yang;
Chen, Hong;
Pu, William T;
Zhang, Lili;
Chen, Kaifu

Publication type:

Article

RPA and Rad27 limit templated and inverted insertions at DNA breaks.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 1, p. 1, doi. 10.1093/nar/gkae1159

By:

Yu, Yang;
Wang, Xin;
Fox, Jordan;
Li, Qian;
Hastings, P J;
Chen, Kaifu;
Ira, Grzegorz

Publication type:

Article

Low RNA stability signifies strong expression regulatability of tumor suppressors.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 21, p. 11534, doi. 10.1093/nar/gkad838

By:

Gao, Xinlei;
Yi, Yang;
Lv, Jie;
Li, Yanqiang;
Arulsamy, Kulandaisamy;
Babu, Sahana Suresh;
Bruno, Ivone;
Zhang, Lili;
Cao, Qi;
Chen, Kaifu

Publication type:

Article

Low RNA stability signifies increased post-transcriptional regulation of cell identity genes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 12, p. 6020, doi. 10.1093/nar/gkad300

By:

Li, Yanqiang;
Yi, Yang;
Lv, Jie;
Gao, Xinlei;
Yu, Yang;
Babu, Sahana Suresh;
Bruno, Ivone;
Zhao, Dongyu;
Xia, Bo;
Peng, Weiqun;
Zhu, Jun;
Chen, Hong;
Zhang, Lili;
Cao, Qi;
Chen, Kaifu

Publication type:

Article

CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 21, p. 12186, doi. 10.1093/nar/gkac1090

By:

Zhao, Dongyu;
Zhang, Min;
Huang, Shaodong;
Liu, Qi;
Zhu, Sen;
Li, Yanqiang;
Jiang, Weihua;
Kiss, Daniel L;
Cao, Qi;
Zhang, Lili;
Chen, Kaifu

Publication type:

Article

A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4 and c-Myc to regulate stemness.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 22, p. 10603, doi. 10.1093/nar/gkw788

By:

Sung-Hun Lee;
Tsai-Yu Chen;
Dhar, Shilpa S.;
Bingnan Gu;
Kaifu Chen;
Young Zoon Kim;
Wei Li;
Min Gyu Lee

Publication type:

Article

An essential role for UTX in resolution and activation of bivalent promoters.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 8, p. 3659, doi. 10.1093/nar/gkv1516

By:

Dhar, Shilpa S.;
Sung-Hun Lee;
Kaifu Chen;
Guangjing Zhu;
WonKyung Oh;
Allton, Kendra;
Gafni, Ohad;
Young Zoon Kim;
Tomoiga, Alin S.;
Barton, Michelle Craig;
Hanna, Jacob H.;
Zhibin Wang;
Wei Li;
Min Gyu Lee

Publication type:

Article

MACE: model based analysis of ChIP-exo.

Published in:

Nucleic Acids Research, 2014, v. 42, n. 20, p. e156, doi. 10.1093/nar/gku846

By:

Wang, Liguo;
Chen, Junsheng;
Wang, Chen;
Uusküla-Reimand, Liis;
Chen, Kaifu;
Medina-Rivera, Alejandra;
Young, Edwin J.;
Zimmermann, Michael T.;
Yan, Huihuang;
Sun, Zhifu;
Zhang, Yuji;
Wu, Stephen T.;
Huang, Haojie;
Wilson, Michael D.;
Kocher, Jean-Pierre A.;
Li, Wei

Publication type:

Article

BMI1 regulates androgen receptor in prostate cancer independently of the polycomb repressive complex 1.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-02863-3

By:

Sen Zhu;
Dongyu Zhao;
Lin Yan;
Weihua Jiang;
Jung-Sun Kim;
Bingnan Gu;
Qipeng Liu;
Rui Wang;
Bo Xia;
Zhao, Jonathan C.;
Gang Song;
Wenyi Mi;
Rong-Fu Wang;
Xiaobing Shi;
Hung-Ming Lam;
Xuesen Dong;
Jindan Yu;
Kaifu Chen;
Qi Cao

Publication type:

Article

Fano Resonance-Plasmonic Biosensors Based on Strong Coupling of Hybrid Plasmonic-Photonic Modes.

Published in:

Plasmonics, 2024, v. 19, n. 6, p. 2961, doi. 10.1007/s11468-024-02216-5

By:

Chen, Kaifu;
Li, Xingbing;
Huang, Tianye;
Wang, Yuye;
Zeng, Shuwen

Publication type:

Article

Broad genic repression domains signify enhanced silencing of oncogenes.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-18913-8

By:

Zhao, Dongyu;
Zhang, Lili;
Zhang, Min;
Xia, Bo;
Lv, Jie;
Gao, Xinlei;
Wang, Guangyu;
Meng, Qingshu;
Yi, Yang;
Zhu, Sen;
Tomoiaga, Alin S.;
Lee, Min Gyu;
Cooke, John P.;
Cao, Qi;
Chen, Kaifu

Publication type:

Article

Machine learning uncovers cell identity regulator by histone code.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16539-4

By:

Xia, Bo;
Zhao, Dongyu;
Wang, Guangyu;
Zhang, Min;
Lv, Jie;
Tomoiaga, Alin S.;
Li, Yanqiang;
Wang, Xin;
Meng, Shu;
Cooke, John P.;
Cao, Qi;
Zhang, Lili;
Chen, Kaifu

Publication type:

Article

The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.).

Published in:

PLoS ONE, 2010, v. 5, n. 9, p. 1, doi. 10.1371/journal.pone.0012762

By:

Meng Yang;
Xiaowei Zhang;
Guiming Liu;
Yuxin Yin;
Kaifu Chen;
Quanzheng Yun;
Duojun Zhao;
Al-Mssallem, Ibrahim S.;
Jun Yu

Publication type:

Article

The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends.

Published in:

Nature, 2012, v. 489, n. 7417, p. 576, doi. 10.1038/nature11355

By:

Chen, Xuefeng;
Cui, Dandan;
Papusha, Alma;
Zhang, Xiaotian;
Chu, Chia-Dwo;
Tang, Jiangwu;
Chen, Kaifu;
Pan, Xuewen;
Ira, Grzegorz

Publication type:

Article

SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.

Published in:

Nature, 2012, v. 487, n. 7405, p. 114, doi. 10.1038/nature11043

By:

Barber, Matthew F.;
Michishita-Kioi, Eriko;
Xi, Yuanxin;
Tasselli, Luisa;
Kioi, Mitomu;
Moqtaderi, Zarmik;
Tennen, Ruth I.;
Paredes, Silvana;
Young, Nicolas L.;
Chen, Kaifu;
Struhl, Kevin;
Garcia, Benjamin A.;
Gozani, Or;
Li, Wei;
Chua, Katrin F.

Publication type:

Article

Comprehensive analysis of intercellular communication in the thermogenic adipose niche.

Published in:

Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05140-2

By:

Shamsi, Farnaz;
Zheng, Rongbin;
Ho, Li-Lun;
Chen, Kaifu;
Tseng, Yu-Hua

Publication type:

Article

Discovery of novel determinants of endothelial lineage using chimeric heterokaryons.

Published in:

eLife, 2017, p. 1, doi. 10.7554/eLife.23588

By:

Wing Tak Wong;
Matrone, Gianfranco;
Xiaoyu Tian;
Tomoiaga, Simion Alin;
Kin Fai Au;
Shu Meng;
Yamazoe, Sayumi;
Sieveking, Daniel;
Kaifu Chen;
Burns, David M.;
Chen, James K.;
Blau, Helen M.;
Cooke, John P.

Publication type:

Article

An improved numerical approach in surrounding rock incorporating rockbolt effectiveness and seepage force.

Published in:

Acta Geotechnica, 2018, v. 13, n. 3, p. 707, doi. 10.1007/s11440-018-0635-8

By:

Zou, Jinfeng;
Chen, Kaifu;
Pan, Qiujing

Publication type:

Article