Center for Bioinformatics and Computational Biology
Department of Cardiovascular Sciences, The Methodist Hospital Research Institute
Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University
(*) First authorship; (^) Senior authorship
- 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.
- 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
- 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)
- 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.
- 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)
- 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.
- 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) Accepted
- 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)
- 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)
- 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)
- 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.
- 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)
- 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)
- 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.
- 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)
- 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)
- 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)
- Jie Lv, Chen K. Broad H3K4me3 as a Novel Epigenetic Signature for Normal Development and Disease.
Genomics, proteomics & bioinformatics (2016)
- 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)
- 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)
- 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 (IF 20.26)
- 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) Accepted.
- 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) accepted.
------------Joined Methodist to start Chen Lab------------
- 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)
- 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)
- 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).
- Hu Z, Chen K, Li W, Tyler J. A matter of access: Nucleosome disassembly from gene promoters is the central goal of transcriptional activators.
- Hu Z, Chen K, Li W, Tyler JK. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast.
Microbial Cell. (2014)
- 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).
- 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).
- 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).
- 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).
- 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.
- 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.
- 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.
- 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)
- 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)
- 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)
- 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)
- Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. An evolutionary analysis of trypanosomatid GP63 proteases.
Parasitology research. (2011)
- 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)
2010 and before
- 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)
- 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)
- 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)
------------Joined the Li lab at BCM------------
- 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)