Chen Lab @ Harvard

Publication

*co-First authorship; ^co-corresponding authorship; Bold title indicates selected representative research.

Preprint

Rongbin Zheng, Yang Zhang, Tadataka Tsuji, Lili Zhang, Yu-Hua Tseng, Kaifu Chen. MEBOCOST: Metabolic Cell-Cell Communication Modeling by Single Cell Transcriptome. BioRxiv.

Xin Wang, Dongyu Zhao, Yanqiang Li, Yang Yu, Grzegorz Ira, Lili Zhang, Kaifu Chen. Mutation of mutator genes marks immunotherapy efficacy. Research Square.

Papers

  1. Yanqiang Li, Yang Yi, Xinlei Gao, Xin Wang, Dongyu Zhao, Rui Wang, Li-Sheng Zhang, Boyang Gao, Yadong Zhang, Lili Zhang, Qi Cao^, Kaifu Chen^. 2’-O-Methylation at internal sites on mRNA promotes mRNA stability. Molecular Cell. (06/20/2024)

  2. Umji Lee*, Yadong Zhang*, Yonglin Zhu, Allen Chilun Luo, Liyan Gong, Daniel M. Tremmel, Yunhye Kim, Victoria Sofia Villarreal, Xi Wang, Ruei-Zeng Lin, Miao Cui, Minglin Ma, Ke Yuan, Kai Wang^, Kaifu Chen^, and Juan M. Melero-Martin^. Robust differentiation of human pluripotent stem cells into mural progenitor cells via transient activation of NKX3.1. Nature Communications. (Accepted in principle, 08/20/2024)

  3. Yang Yu*, Xin Wang*, Jordan Fox*, Ruofan Yu, Pilendra Thakre, Brenna McCauley, Nicolas Nikoloutsos, Yang Yu, Qian Li, P J Hastings, Weiwei Dang, Kaifu Chen^, Grzegorz Ira^. Yeast EndoG prevents genome instability by degrading extranuclear DNA species. Nature Communications. (Accepted in principle, 07/30/2024)

  4. Yang Yu*, Xin Wang*, Jordan Fox, Qian Li, Yang Yu, P.J. Hastings, Kaifu Chen^ and Grzegorz Ira^. RPA and Rad27 limit templated and inverted insertions at DNA breaks. Nucleic Acids Research. (Accepted 11/04/2024)

  5. Qingshu Meng, Jiangchuan Shen, Yanan Ren, Qi Liu, Rui Wang, Qiaqia Li, Weihua Jiang, Quan Wang, Yixiang Zhang, Jonathan C Trinidad, Xiaotong Lu, Tingyou Wang, Yanqiang Li, Chaehyun Yum, Yang Yi, Yongyong Yang, Dongyu Zhao, Clair Harris, Sundeep Kalantry, Kaifu Chen, Rendong Yang, Hengyao Niu, Qi Cao. EZH2 directly methylates PARP1 and regulates its activity in cancer. Science Advances (Accepted, 10/14/2024)

  6. Olivia Weeks, Xinlei Gao, Sandeep Basu, Jennifer Galdieri1, Kaifu Chen,Geoffrey Burns, Caroline E. Burns. Embryonic Alcohol Exposure in Zebrafish Predisposes Adults to Cardiomyopathy and Diastolic Dysfunction. Cardiovascular Research. (05/23/2024)

  7. Zulong Chen*, Xin Wang*, Xinlei Gao, Nina Arslanovic, Kaifu Chen^ and Jessica Tyler^. Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression. Elife. (02/07/2024).

  8. Min Zhang, Kaiyuan Wu, Weijie Zhang, Xia Lin, Qi Cao, Lili Zhang, Kaifu Chen. The therapeutic potential of targeting the CHD protein family in cancer. Pharmacology and Therapeutics. (02/15/2024).

  9. Khanh M. Chau, Abishai Dominic, Eleanor L. Davis, Arsany Fahim, Shengyu Li, Dongyu Zhao, Kaifu Chen, Alan R. Davis, Minh T. H. Nguyen, Yongxing Wang, Scott E Evans, Guangyu Wang, John Cooke, Jun-ichi Abe, David P. Huston and Nhat-Tu Le. TNIK regulation of Interferon signaling and endothelial cell response to virus infection. Frontiers in Cardiovascular Medicine. (01/09/2024).

  10. Xinlei Gao*, Yang Yi*, Jie Lv*, Yanqiang Li, Kulandaisamy Arulsamy, Sahana Babu, Ivone Bruno, Lili Zhang, Qi Cao^, Kaifu Chen^. Low RNA stability signifies strong expression regulatability of tumor suppressors. Nucleic Acids Research. (10/13/2023).

  11. Yanqiang Li*, Yang Yi*, Jie Lv, Xinlei Gao, Yang Yu, Sahana Suresh Babu, Ivone Bruno, Dongyu Zhao, Bo Xia, Weiqun Peng, Jun Zhu, Hong Chen, Lili Zhang^, Qi Cao^, Kaifu Chen^. Low RNA stability signifies increased post-transcriptional regulation of cell identity gene. Nucleic Acids Research. (07/07/2023).

  12. Abhijit Chakraborty, Yanming Li, Chen Zhang, Yang Li, Kimberly Rebello, Shengyu Li, Samantha Xu, Hernan Vasquez, Lin Zhang, Wei Luo, Guangyu Wang, Kaifu Chen, Joseph Coselli, Scott LeMaire, and Ying Shen. Epigenetic Induction of Smooth Muscle Cell Phenotypic Alterations in Aortic Aneurysms and Dissections. Circulation. (08/09/2023).

  13. Farnaz Shamsi*, Rongbin Zheng*, Li-Lun Ho, Kaifu Chen^, Yu-Hua Tseng^. Comprehensive analysis of intercellular communication in the thermogenic adipose niche. Communication Biology (07/21/2023).

  14. Jie Lv*, Shu Meng*, Qilin Gu*, Rongbin Zheng, Xinlei Gao, Yihan Zuo, Sen Zhu Jun-dae Kim Bo Xia Dongyu Zhao , Yanqiang Li , Guangyu Wang , Xin Wang , Qingshu Meng, Qi Cao, John P. Cooke^, Longhou Fang^, Kaifu Chen^, Lili Zhang^. Epigenetic Landscape Reveals MECOM As an Endothelial Lineage Regulator. Nature Communications. (04/25/2023).

  15. Pingzhu Zhou*, Nathan J. VanDusen*, Yanchun Zhang*, Yangpo Cao*, Isha Sethi Rong Hu, Shuo Zhang, Guangyu Wang, Lincai Ye, Neil Mazumdar Jian Chen Xiaoran Zhang Yuxuan Guo, Bin Li, Qing Ma Julianna Y. Lee Wei-liang Gu, Guo-Cheng Yuan, Bing Ren, Kaifu Chen^, William T. Pu^. Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation.
    Developmental Cell. (04/17/2023; 05/22/2023).

  16. Kui Cui*, Xinlei Gao*, Beibei Wang*, Hao Wu, Kulandaisamy Arulsamy, Yunzhou Dong, Yuling Xiao, Xingya Jiang, Marina V. Malovichko, Kathryn Li, Qianman Peng, Yao Wei Lu, Bo Zhu, Rongbin Zheng, Scott Wong, Douglas B. Cowan, MacRae Linton, Sanjay Srivastava, Jinjun Shi, Kaifu Chen^ and Hong Chen^. Epsin Nanotherapy Regulates Cholesterol Transport to Fortify Atheroma Regression. Circulation Research. (11/29/2022; 01/06/2023)

  17. Mason E. Sweat, Yangpo Cao, Xiaoran Zhang, Ozanna Burnicka-Turek, Carlos Perez-Cervantes, Kulandai Arulsamy, Fujian Lu, Erin M. Keating, Brynn N. Akerberg, Qing Ma, Hiroko Wakimoto, Joshua M. Gorham, Lauren D. Hill, Mi Kyoung Song, Michael A. Trembley, Peizhe Wang, Matteo Gianeselli, Maksymilian Prondzynski, Raul H. Bortolin, Vassilios J. Bezzerides, Kaifu Chen, Jonathan G. Seidman, Christine E. Seidman, Ivan P. Moskowitz, William T. Pu. Tbx5 maintains atrial identity by regulating an atrial enhancer network. Nature Cardiovascular Research. (10/12/2023)

  18. Jun Cao*, Xin Wang*, Vivek Advani, Yao Wei Lu, Andrea P. Malizia, Gurinder Bir Singh, Zhan-Peng Huang, Jianming Liu, Chunbo Wang, Edilamar M. Oliveira, John D. Mably, Kaifu Chen^, Da-Zhi Wang^. mt-Ty 5 ́tiRNA regulates skeletal muscle cell proliferation and differentiation. Cell Proliferation. (02/08/2023; 08/01/2023).

  19. Keman Xu; Fatma Saaoud; Ying Shao; Yifan Lu; Sheng Wu; Huaqing Zhao; Kaifu Chen; Roberto Vazquez-Padron; Xiaohua Jiang; Hong Wang, Xiaofeng Yang. Early hyperlipidemia triggers metabolomic reprogramming with increased SAH, increased acetyl-CoA-cholesterol synthesis, and decreased glycolysis. Redox Biology. (06/16/2022; 08/01/2023)

  20. Yang Yi, Yanqiang Li, Kaifu Chen and Qi Cao. Unveiling the non-canonical functions of EZH2 in prostate cancer. Oncotarget. (02/11/2023).

  21. Sana Nasim , Jill Wylie-Sears , Xinlei Gao , Qianman Peng , Bo Zhu , Kaifu Chen , Hong Chen, Joyce Bischoff. CD45 is sufficient to initiate EndMT in human endothelial cells. ATVB. (05/01/2023)

  22. Xiaolei Liu, Kui Cui, Hao Wu, Kathryn S. Li, Qianman Peng, Donghai Wang, Douglas B. Cowan, J. Brandon Dixon, R. Sathish Srinivasan, Diane R. Bielenberg, Kaifu Chen, Da-Zhi Wang, Yabing Chen, Hong Chen. Promoting Lymphangiogenesis and Lymphatic Growth and Remodeling to Treat Cardiovascular and Metabolic Diseases. ATVB. (01/01/2023).

  23. Yunzhou Dong, Beibei Wang, Mulong Du, Bo Zhu, Kui Cui, Douglas Cowan, Sudarshan Bhattacharjee, Scott Wong, Da-Zhi Wang, Kaifu Chen, Joyce Bischoff, MacRae Linton, and Hong Chen. Targeting Epsins to Inhibit FGF Signaling while Potentiating TGF-β Signaling Constrains Endothelial-to-Mesenchymal-Transition in Atherosclerosis. Circulation. (01/02/2023)

  24. Dongyu Zhao*, Min Zhang*, Shaodong Liu, Qi Liu, Sen Zhu, Yanqiang Li, Weihua Jiang, Dan Kiss, Qi Cao^, Lili Zhang*^, Kaifu Chen^. CHD6 Promotes Broad Nucleosome Eviction for Transcriptional Activation in Prostate Cancer Cells. Nucleic Acids Research. (11/28/2022).

  25. Krishan Gupta*, Guangyu Wang*, Shuo Zhang*, Xinlei Gao, Rongbin Zheng, Yanchun Zhang, Qingshu Meng, Lili Zhang, Qi Cao, Kaifu Chen. StripeDiff: Model-based Algorithm for Differential Analysis of Chromatin Stripe. Science Advances. (12/07/2022).

  26. Bandana Singh, Kathryn Li, Kui Cui, Qianman Peng, Douglas B Cowan, Da-Zhi Wang, Kaifu Chen, Hong Chen. Defective Efferocytosis of Vascular Cells in Heart Disease. Front Cardiovasc Med. (9/30/2022).

  27. Yang Yi*, Yanqiang Li*, Chao Li*, Longxiang Wu, Dongyu Zhao, Fuxi Li, Ladan Fazli, Rui Wang, Long Wang, Xuesen Dong, Wei Zhao, Kaifu Chen^, Qi Cao^. Methylation-dependent and -independent roles of EZH2 synergize in CDCA8 activation in prostate cancer. Oncogene. (03/01/2022)

  28. Yang Yi*, Yanqiang Li*, Qingshu Meng*, Qiaqia Li, Fuxi Li, Bing Lu, Jiangchuan Shen, Ladan Fazli, Dongyu Zhao, Chao Li, Weihua Jiang, Rui Wang, Qipeng Liu, Aileen Szczepanski, Qianru Li, Wei Qin, Adam B. Weiner, Tamara L. Lotan, Zhe Ji, Sundeep Kalantry, Lu Wang, Edward M. Schaeffer, Hengyao Niu, Xuesen Dong, Wei Zhao, Kaifu Chen^, Qi Cao^. A PRC2-independent function for EZH2 in regulating rRNA 2′-O methylation and IRES-dependent translation. Nature Cell Biology. (2021)

  29. Guangyu Wang*, Bo Xia*, Jie Lv, Dongyu Zhao, Yanqiang Li, Yiwen Bu, Xin Wang, John P. Cooke, Qi Cao, Min Gyu Lee, Lili Zhang, Kaifu Chen^. MACMIC Reveals Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes. Genomics, Proteomics, and Bioinformatics. (2021)

  30. Christopher J Terranova, Ming Tang, Mayinuer Maitituoheti, Ayush T Raman, Archit K Ghosh, Jonathan Schulz, Samir B Amin, Elias Orouji, Katarzyna Tomczak, Sharmistha Sarkar, Junna Oba, Caitlin Creasy, Chang-Jiun Wu, Samia Khan, Rossana Lazcano, Khalida Wani, Anand Singh, Praveen Barrodia, Dongyu Zhao, Kaifu Chen, Lauren E Haydu, Wei-Lien Wang, Alexander J Lazar, Scott E Woodman, Chantale Bernatchez, Kunal Rai. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Report. (2021)

  31. Gianfranco Matrone, Bo Xia, Kaifu Chen, Martin A. Denvir, Andrew H. Baker, and John P. Cooke. Fli1+ cells transcriptional analysis reveals an Lmo2–Prdm16 axis in angiogenesis. PNAS. (2021)

  32. Guangyu Wang*, Ana Sofia Cruz*, Keith Youker, Hernan G. Marcos-Abdala, Rajarajan A. Thandavarayan, John P. Cooke, Guillermo Torre-Amione, Kaifu Chen^, Arvind Bhimaraj^. Role of Endothelial and Mesenchymal Cell Transitions in Heart Failure and Recovery Thereafter. Frontiers in Genetics. (2021).

  33. Shu Meng*^, Jie Lv*, Palas K. Chanda, Iris Owusu, Kaifu Chen^, John P. Cooke^. Reservoir of Fibroblasts Promotes Recovery from Limb Ischemia. Circulation. (2020)

  34. Dongyu Zhao*, Lili Zhang*, Min Zhang, Bo Xia, Jie Lv, Guangyu Wang, Qingshu Meng, Yang Yi, Sen Zhu, Alin S. Tomoiaga, Min Gyu Lee, John P. Cooke, Qi Cao^, Kaifu Chen^. Broad Genic Repression Domains Signify Enhanced Silencing of Oncogenes. Nature Communications. (2020b)

  35. Bo Xia*, Dongyu Zhao*, Guangyu Wang*, Min Zhang, Jie Lv, Alin S. Tomoiaga, Yanqiang Li, Xin Wang, Shu Meng, John P. Cooke, Qi Cao^, Lili Zhang^, Kaifu Chen^. Machine learning reveals cell identity regulator by histone codes. Nature Communications. (2020a)

  36. Guangyu Wang, Qingshu Meng, Bo Xia, Jie Lu, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao^, Kaifu Chen^. TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription. Genome Biology. (2020)

  37. Qiang Wang, Dongyu Zhao, Miao Xian, Zhuo Wang, Enguang Bi, Pan Su, Jianfei Qian, Xingzhe Ma, Maojie Yang, Lintao Liu, Youli Zu, Sai Ravi Pingali, Kaifu Chen, and Zhen Cai, Qing Yi. MIF as a biomarker and therapeutic target for overcoming resistance to proteasome inhibitors in human myeloma. Blood. (2020)

  38. Sen Zhu*, Dongyu Zhao*, Chao Li*, Qiaqia Li, Weihua Jiang, Qipeng Liu, Rui Wang, Ladan Fazli, Yinan Li, Lili Zhang, Yang Yi, Qingshu Meng, Wanyi Wang, Guangyu Wang, Min Zhang, Xiongbing Zu, Wei Zhao, Tuo Deng, Jindan Yu, Xuesen Dong, KaiFu Chen^, Qi Cao^. BMI1 is directly regulated by androgen receptor to promote castration-resistance in prostate cancer. Oncogene. (2020)

  39. Motao Zhu, Guangtong Deng, Peng Tan, Changsheng Xing, Cuiping Guan, Chongming Jiang, Yinlong Zhang, Bo Ning, Chaoran Li, Bingnan Yin, Kaifu Chen, Yuliang Zhao, Helen Y Wang, Beth Levine, Guangjun Nie, Rong-Fu Wang. Beclin 2 negatively regulates innate immune signaling and tumor development. The Journal of clinical investigation. (2020)

  40. Qiaqia Li*, Kilia Y. Liu*, Qipeng Liu*, Guangyu Wang*, Weihua Jiang, Dongyu Zhao,Qingshu Meng, Yang Yi, Yongyong Yang, Rui Wang, Sen Zhu, Chao Li, Lin Yan, Lili Zhang, Jung-Sun Kim, Xiongbing Zu, Anthony Kozielski, Wei Qian, Jenny Chang, Akash Patnaik, Kaifu Chen^ and Qi Cao. Antihistamine Drug Ebastine inhibits cancer growth by targeting Polycomb Group Protein EZH2. Molecular Cancer Therapeutics.

  41. Qilin Gu, Xiaojie Yang, Jie Lv, Jiaxiong Zhang, Bo Xia, Jun-dae Kim, Ruoyu Wang, Feng Xiong, Shu Meng, Thomas P. Clements, Bhavna Tandon, Daniel S. Wagner, Miguel F. Diaz, Pamela L. Wenzel, Yury I. Miller, David Traver, John P. Cooke, Wenbo Li, Leonard I. Zon, Kaifu Chen^, Yongping Bai^, Longhou Fang^. AIBP-mediated Cholesterol Efflux Instructs Hematopoietic Stem and Progenitor Cell Fate. Science. (2019)

  42. Qipeng Liu*, Guangyu Wang*, Qiaqia Li*, Weihua Jiang, Jung‐Sun Kim, Rui Wang, Sen Zhu, Xiaoju Wang, Lin Yan, Yang Yi, Lili Zhang, Qingshu Meng, Chao Li, Dongyu Zhao, Yuanyuan Qiao, Yong Li, Demirkan B. Gursel, Arul M. Chinnaiyan, Kaifu Chen^, Qi Cao^. Polycomb Group Proteins EZH2 and EED Directly Regulate Androgen Receptor in Advanced Prostate Cancer. International Journal of Cancer. (2019)

  43. Palas K. Chanda, Shu Meng, Jieun Lee, Honchiu E. Leung, Kaifu Chen, John P. Cooke. Nuclear S-nitrosylation defines an optimal zone for inducing pluripotency. Circulation. (2019)

  44. Zhi Long, Yinan Li, Yu Gan, Dongyu Zhao, Guangyu Wang, Ning Xie, Jessica M Lovnicki, Ladan Fazli, Qi Cao, Kaifu Chen, Xuesen Dong. Roles of the HOXA10 Gene during Castrate Resistant Prostate Cancer Progression. Endocrine-Related Cancer (2019)

  45. Yang Yu*, Nhung Pham*, Bo Xia*, Alma Papusha, Guangyu Wang, Zhenxin Yan, Guang Peng, Kaifu Chen^, Grzegorz Ira1^. Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks. Nature. (2018)

  46. Sen Zhu*, Dongyu Zhao*, Lin Yan*, Weihua Jiang, Jungsun Kim, Bingnan Gu, Qipeng Liu, Rui Wang, Bo Xia, Jonathan Zhao, Gang Song, Xiaobing Shi, HungMing Lam, Xuesen Dong, Jindan Yu, Kaifu Chen^, Qi Cao^. BMI1 Regulates Androgen Receptor in Prostate Cancer Independently of the Polycomb Repressive Complex I. Nature Communications. (2018) Featured in Editors’ Highlights Webpage

  47. Shilpa S. Dhar*, Dongyu Zhao*, Tao Lin, Bingnan Gu, Khusboo Pal, Hunain Alam, Jie Lv, Vidya Gopalakrishnan, Wei Li, Ali Shilatifard, Roy V. Sillitoe, Kaifu Chen^, Min Gyu Lee^. MLL4 is required to maintain broad H3K4me3 peaks and super-enhancers at tumor suppressor genes. Molecular Cell. (2018)

  48. Zheng Hu*, Bo Xia*, Spike Postnikoff, Troy A Harkness, JaHwan Seol, Alin S Tomoiaga, Wei Li, Kaifu Chen^, and Jessica K. Tyler^. Ssd1 and Gcn2 suppress global translational efficiency in replicatively aged yeast. Elife. (2018)

  49. Hyun Jung Park, Ping Ji, Soyeon Kim, Zheng Xia, Benjamin Rodriguez, Lei Li, Jianzhong Su, Kaifu Chen, Chioniso Masamha, David Baillat, Ms. Camilla Fontes, Ann-Bin Shyu, Joel Neilson, Eric Wagner, Wei Li. 3ʹ-UTR Shortening Represses Tumor Suppressor Genes in trans by Disrupting ceRNA Crosstalk. Nature Genetics. (2018)

  50. Shu Meng*, Qilin Gu*, Xiaojie Yang, Jie Lv, Iris B Owusu, Gianfranco Matrone, Kaifu Chen, John Cooke^, and Longhou Fang^. TBX20 Regulates Angiogenesis through the PROK2-PROKR1 Pathway. Circulation. (2018)

  51. Su J, Huang YH, Cui X, Zhang X, Lei Y, Wang X, Lin X, Chen K, Lv J, Goodell MA, Li W*. Homeobox Oncogene Activation by Pan-Cancer DNA Hypermethylation. Genome Biology (2018)

  52. Hunain Alam, Na Li, Shilpa S. Dhar, Ms. Sarah J. Wu, Jie Lv, Kaifu Chen, Elsa R. Flores, Laura Baseler, Min Gyu Lee. HP1γ promotes lung adenocarcinoma by downregulating the transcription-repressive regulators NCOR2 and ZBTB7A. Cancer Research. (2018)

  53. Xiaolong Zhang, Xiang Xiao, Peixiang Lan, Junhui Li, Yaling Dou, Wenhao Chen, Naoto Ishii, Shuqiu Chen, Bo Xia, Kaifu Chen, Elizabeth Taparowsky, and Xian C. Li. OX40 Costimulation Inhibits Foxp3 Expression and Treg Induction via BATF3-Dependent and Independent Mechanisms. Cell Reports. (2018)

  54. Moon Jong Kim, Bo Xia, Han Na Suh, Sung Ho Lee, Sohee Jun, Esther M. Lien, Jie Zhang, Kaifu Chen, and Jae-Il Park. PAF-Myc-Controlled Cell Stemness Is Required for Intestinal Regeneration and Tumorigenesis. Developmental Cell. (2018)

  55. Shaofeng Liu*, Zhiyun Xu*, He Leng*, Pu Zheng, Jiayi Yang, Kaifu Chen, Jianxun Feng, Qing Li. RPA binds histone H3-H4 and functions in DNA replication–coupled nucleosome assembly. Science. (2017)

  56. Narkhyun Bae*, Monica Viviano*, Xiaonan Su*, Jie LV, Donghang Cheng, Cari Sagum, Sabrina Castellano, Xue Bai, Claire Johnson, Mahmoud Ibrahim Khalil, Kaifu Chen, Haitao Li^, Gianluca Sbardella^ and Mark T. Bedford^. Evolving Spindlin1 Small Molecule Inhibitors Using Protein Microarrays. Nature Chemical Biology. (2017)

  57. Xueqiu Lin, Jianzhong Su, Kaifu Chen, Benjamin Rodrigues, Wei Li^: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure. Genome Biology (2017)

  58. Wing Tak Wong, Gianfranco Matrone, Xiaoyu Tian, Simion Alin Tomoiaga, Kin Fai Au, Shu Meng, Sayumi Yamazoe, Kaifu Chen, Helen M. Blau, John P. Cooke. Discovery of Novel Determinants of Endothelial Lineage using Chimeric Heterokaryons. Elife. (2017)

  59. Gianfranco Matrone, Shu Meng, Qilin Gu, Jie Lv, Longhou Fang, Kaifu Chen, John P. Cooke. Lmo2 (LIM-Domain-Only 2) Modulates Sphk1 (Sphingosine Kinase) and Promotes Endothelial Cell Migration Arteriosclerosis, Thrombosis, and Vascular Biology. (2017)

  60. Rebecca Jean Watters, Ryan Hartmaier, Hatice Ulku Osmanbeyoglu, Ryan Gillihan, James Rae, Lan Liao, Kaifu Chen, Wei Li, Xinghua Lu, steffi oesterreich. Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen. Molecular and Cellular Endocrinology. (2017)

  61. Li N*, Li Y*, Lv J*, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, Wang Z, Shiekhattar R, Shi X, Lan F, Chen K, Li W, Li H, Lee MG. ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes. Molecular Cell (2016)

  62. Jie Lv, Chen K. Broad H3K4me3 as a Novel Epigenetic Signature for Normal Development and Disease. Genomics, proteomics & bioinformatics (2016)

  63. Lee S, Chen T, Dhar S, Gu B, Chen K, Kim Y, Li W, Lee M. A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4, c-Myc to regulate stemness. Nucleic Acids Research. (2016)

  64. Meng S, Matrone G, Lv J, Chen K, Wong W, Cooke J. LMO2 Regulates Endothelial Proliferation, Angiogenesis and Tissue Regeneration. Journal of the American Heart Association. (2016)

  65. Chen K*, Chen Z*, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q, Li W. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes. Nature Genetics. (2015) highlighted by the Cancer Discovery journal

  66. Dhar Shilpa*, Lee Sung-Hun*, Chen Kaifu*, Zhu Guangjing, Oh WonKyung, Allton Kendra, Gafni Ohad, Alin S. Tomoiga, Kim Young Zoon, Barton Michelle, Hanna Jacob H, Wang Zhibin, Li Wei, Lee Min Gyu. An essential role for UTX in resolution and activation of bivalent promoters. Nucleic Acids Research. (2015)

  67. Chen Kaifu*, Zheng Hu*, Zheng Xia, Dongyu Zhao, Wei Li, Jessica K. Tyler. The overlooked fact: fundamental need of spike-in controls for virtually all genome-wide analyses. Molecular and Cellular Biology. (2015)

  68. Chen L*, Chen K*, Baker S A, Shaw C, Li W, Zoghbi H Y. MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome. PNAS. (2015) (Highlighted by the Science journal)

  69. Hu Z*, Chen K*, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W, Tyler J K. Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging. Genes & Development. (2014). (Highlighted by the Science journal), (Recommended by Faculty of 1000)

  70. Wang L, Chen J, Wang C, Zimmermann M T, Yan H, Sun Z, Zhang Y, Chen K, Huang H, Kocher J A, Li W. MACE: Model based Analysis of ChIP-exo. Nucleic Acids Research. (2014).

  71. Hu Z, Chen K, Li W, Tyler J. A matter of access: Nucleosome disassembly from gene promoters is the central goal of transcriptional activators. Transcription. (2014)

  72. Hu Z, Chen K, Li W, Tyler JK. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast. Microbial Cell. (2014)

  73. Chen K*, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S YR, He X, Li W. DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. Genome Research (2013). (Highlighted in headlines by Epigenie).

  74. Chen K*, Wilson M A*, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent S YR. Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. Genome Research. (2013).

  75. Huang Z*, Chen K*, Zhang J*, Li Y*, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Chen R, Sucgang R S, Pan X. A functional variomics tool for discovering resistance genes and targets of small molecule compounds. Cell Reports. (2013).

  76. Al-Mssallem I S, Hu S, Zhang X, Tan J, Lin Q, Liu W, Yu X, … Chen K, Alkhaldi S R, Liu G, Zhang M, Guo H, Yu J. Genome Sequences and Genetic Variations of Date Palm. Nature Communications. (2013).

  77. Li Z, Gadue P, Chen K, Tuteja G, Schug J, Li W, Kaestner K H. Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation. Cell. (2012).

  78. Chen X, Cui D, Papusha A, Zhang X, Chu C, Tang J, Chen K, Pan X, Ira G, The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends. Nature. (2012)

  79. Barber M F, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen R I, Chen K, et al. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature. (2012)

  80. Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho F A, Pan X. Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy. PLOS Genetics. (2012)

  81. Badeaux A I, Yang Y, Cardenas K, Vemulapalli V, Chen K, Kusewitt D, Richie E, et al. Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF. The Journal of biological chemistry. (2012)

  82. Kuo A J*, Cheung P*, Chen K*, Zee B M, Kioi M, Lauring J, Xi Y, et al. NSD2 Links Dimethylation of Histone H3 at Lysine 36 to Oncogenic Programming. Molecular cell. (2011)

  83. Huang Z, Chen K, Xu T, Zhang J, Li Y, Li W, Agarwal A K, et al. Sampangine inhibits heme biosynthesis in both yeast and human. Eukaryotic cell, (2011)

  84. Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. An evolutionary analysis of trypanosomatid GP63 proteases. Parasitology research. (2011)

  85. Meng Q, Chen K, Ma L, Hu S, Yu J. A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases. Journal of genetics and genomics. (2011)

  86. Chen K*, Wang L, Yang M, Liu J, Xin C, Hu S, Yu J. Sequence signatures of nucleosome positioning in Caenorhabditis elegans. Genomics, proteomics & bioinformatics. (2010)

  87. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, et al. The complete chloroplast genome sequence of date palm. PlOS ONE. (2010)

  88. Yang M, Song S, Liu G, Chen K, Tian X, Zhao Z J, et al. A comprehensive analysis of protein phosphatases in rice and Arabidopsis. Plant Systematics and Evolution. (2010)

  89. Chen K*, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, et al. A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic acids research. (2008)

Abstracts

  1. Kaifu Chen, Wei Li. Broad H3k4me3 marks tumor suppressors for increased transcriotion elongation. NIH Epigenome Roadmap Investigators’ Meeting (Bethesda, MD, May 13-15, 2012)
  2. Shu Meng, Qilin Gu, Xiaojie Yang Jie Lv Iris Owusu Gianfranco Matrone, Kaifu Chen, L onghou Fan, and John Cooke. Discovery of a Novel Angiogenic Factor TBX20. Circulation. 2017
  3. Sen Zhu, Dongyu Zhang, Lin Yan, Weihua Jiang, Qipeng Liu, Rui Wang, Bo Xia, Jonathan C Zhao, Rong-Fu Wang, Xiaobing Shi, Hung-ming Lam, Xuesen Dong, Jindan Yu, Kaifu Chen, Qi Cao. A novel role for polycomb group protein BMI1 in prostate cancer. Cancer Research. 2018
  4. Shu Meng , Jie Lv , Palas K Chanda , Iris Owusu , Kaifu Chen , John P Cooke. A Reservoir of Fibroblasts Promotes Recovery From Limb Ischemia. Circulation, 2019.
  5. Raquel A Araujo-Gutierrez, Guangyu Wang, Areeba Ali, Hernan G Marcos-Abdala, Cesar Uribe, Hilda M Gonzalez-Bonilla, Alpana Senapati, Keith A Youker, Guillermo Torre-Amione, Kaifu Chen, Arvind Bhimaraj. Genetic Determinants of Allograft Hypertrophy-A Human Myocardial Biopsy Study. Journal of Cardiac Failure. 2019.
  6. A Mojiri, B Walter, C Jiang, G Matrone, R Holgate, Q Qiu, K Chen, J Cooke. Telomerase Therapy Reverses Vascular Senescence in HGPS. Canadian Journal of Cardiology. 2020.
  7. Shilpa S. Dhar, Dongyu Zhao, Tao Lin, Roy V. Sillitoe, Kaifu Chen, and Min Gyu Lee. Heterozygous knockout of the histone modifier MLL4 promotes Ptch+/−-driven medulloblastoma. Cancer Research. 2020.
  8. Lili Zhang, Jie Lv, Sen Zhu, Kaifu Chen. ITF2 Maintains Endothelial Cell Identity to Oppose Endothelial-Mesenchymal Transition. Circulation Research. 2021.
  9. Shilpa S Dhar, Calena J Brown, Ali S Rizvi, Janak R Abraham, Roy V Sillitoe, Kaifu Chen, Min Gyu Lee. KMT2D loss cooperates with PTCH loss for medulloblastoma genesis. Cancer Research. 2022.
  10. Yang Zhang, Rongbin Zheng, Chih-Hao Wang, Justin Darcy, Kaifu Chen, Yu-Hua Tseng. Histone Variant H2A.Z-Mediated Chromatin Organization Regulates Brown Adipocyte Thermogenic Function. Diabetes. 2022.
  11. Kui Cui, Xinlei Gao, Beibei Wang, Hao Wu, Yunzhou Dong, Yuling Xiao, Xingya Jiang, Siu-Lung Chan, Bo Zhu, Sudarshan Bhattacharjee, Dan Shan, Qianman Peng, Marrina Malovichko, Vikram Norton, Scott Wong, Douglas B Cowan, Sanjay Srivastava, MacRae F Linton, Jinjun Shi, Kaifu Chen and Hong Chen. Targeting Macrophage Epsins Inhibits Lipid Uptake And Facilitates Cholesterol Efflux In Atherosclerosis. ATVB. 2022
  12. Kui Cui, Xinlei Gao, Beibei Wang, Hao Wu, Yunzhou Dong, Douglas B Cowan, Jinjun Shi, Kaifu Chen and Hong Chen. Nano-targeting Epsin In Cholesterol Uptake-efflux Fortifies Atheroma Regression. ATVB. 2023.
  13. Sana Nasim, Jill Wylie-Sears, Xinlei Gao, Kaifu Chen, Bo Zhu, Qianman Peng, Hong Chen and Joyce Bischoff. Endogenous Activation of Cd45 Can Induce Endothelial To Mesenchymal Transition In Human Endothelial Cells. ATVB. 2023.
  14. Hui-Min Yin, Xinlei Gao, Kaifu Chen, Caroline Burns, C Geoffrey Burns. Pontin Is Necessary and Sufficient For Driving Cardiomyocyte Proliferation In Zebrafish And Mice. Circulation Research. 2023
  15. Keman Xu, Fatma Saaoud, Ying Shao, Yifan Lu, Huaqing Zhao, Kaifu Chen, Xiaohua Jiang, Hong Wang and Xiaofeng Yang. Cross-omics Identified That Early Hyperlipidemia Increased S-adenosylhomocysteine-hypomethylation And 24 Proinflammatory Metabolites May Synergize In Trained Immunity. ATVB. 2023
  16. Hakan Coskun, Xinlei Gao, Kaifu Chen, C. Geoffrey Burns and Caroline Burns. Cellular Heterogeneity In The Nkx2.5+ Anterior Lateral Plate Mesoderm Underlies Lineage Diversity Of The Cardiovascular System. Circulation Research. 2024