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Kaifu Chen, PhD

Associate Professor of Cardiovascular Sciences, Institute for Academic Medicine
Associate Member, Research Institute
Director, Center for Bioinformatics and Computational Biology
Houston Methodist
Weill Cornell Medical College


kchen2@houstonmethodist.org
Publications

BMI1 regulates androgen receptor in prostate cancer independently of the polycomb repressive complex 1
Zhu, S, Zhao, D, Yan, L, Jiang, W, Kim, JS, Gu, B, Liu, Q, Wang, R, Xia, B, Zhao, JC, Song, G, Mi, W, Wang, RF, Shi, X, Lam, HM, Dong, X, Yu, J, Chen, K & Cao, Q 2018, Nature Communications, vol. 9, no. 1, 500. DOI: 10.1038/s41467-018-02863-3

Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespan
Hu, Z, Xia, B, Postnikoff, SDL, Shen, ZJ, Tomoiaga, AS, Harkness, TA, Seol, JH, Li, W, Chen, K & Tyler, JK 2018, eLife, vol. 7, e35551. DOI: 10.7554/eLife.35551

Homeobox oncogene activation by pan-cancer DNA hypermethylation
Su, J, Huang, YH, Cui, X, Wang, X, Zhang, X, Lei, Y, Xu, J, Lin, X, Chen, K, Lv, J, Goodell, MA & Li, W 2018, Genome Biology, vol. 19, no. 1, 108. DOI: 10.1186/s13059-018-1492-3

OX40 Costimulation Inhibits Foxp3 Expression and Treg Induction via BATF3-Dependent and Independent Mechanisms
Zhang, X, Xiao, X, Lan, P, Li, J, Dou, Y, Chen, W, Ishii, N, Chen, S, Xia, B, Chen, K, Taparowsky, E & Li, XC 2018, Cell Reports, vol. 24, no. 3, pp. 607-618. DOI: 10.1016/j.celrep.2018.06.052

HP1? promotes lung adenocarcinoma by downregulating the transcription-repressive regulators NCOR2 and ZBTB7A
Alam, H, Li, N, Dhar, SS, Wu, SJ, Lv, J, Chen, K, Flores, ER, Baseler, L & Lee, MG 2018, Cancer Research, vol. 78, no. 14, pp. 3834-3848. DOI: 10.1158/0008-5472.CAN-17-3571

3' UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk
Park, HJ, Ji, P, Kim, S, Xia, Z, Rodriguez, B, Li, L, Su, J, Chen, K, Masamha, CP, Baillat, D, Fontes-Garfias, CR, Shyu, AB, Neilson, JR, Wagner, EJ & Li, W 2018, Nature Genetics, pp. 1-7. DOI: 10.1038/s41588-018-0118-8

PAF-Myc-Controlled Cell Stemness Is Required for Intestinal Regeneration and Tumorigenesis
Kim, MJ, Xia, B, Suh, HN, Lee, SH, Jun, S, Lien, EM, Zhang, J, Chen, K & Park, JI 2018, Developmental Cell, vol. 44, no. 5, pp. 582-596.e4. DOI: 10.1016/j.devcel.2018.02.010

MLL4 Is Required to Maintain Broad H3K4me3 Peaks and Super-Enhancers at Tumor Suppressor Genes
Dhar, SS, Zhao, D, Lin, T, Gu, B, Pal, K, Wu, SJ, Alam, H, Lv, J, Yun, K, Gopalakrishnan, V, Flores, ER, Northcott, PA, Rajaram, V, Li, W, Shilatifard, A, Sillitoe, RV, Chen, K & Lee, MG 2018, Molecular Cell. DOI: 10.1016/j.molcel.2018.04.028

Sparse conserved under-methylated CpGs are associated with high-order chromatin structure
Lin, X, Su, J, Chen, K, Rodriguez, B & Li, W 2017, Genome Biology, vol. 18, no. 1, 163. DOI: 10.1186/s13059-017-1296-x

Lmo2 (LIM-Domain-Only 2) Modulates Sphk1 (Sphingosine Kinase) and Promotes Endothelial Cell Migration
Matrone, G, Meng, S, Gu, Q, Lv, J, Fang, L, Chen, K & Cooke, JP 2017, Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 37, no. 10, pp. 1860-1868. DOI: 10.1161/ATVBAHA.117.309609

Developing Spindlin1 small-molecule inhibitors by using protein microarrays
Bae, N, Viviano, M, Su, X, Lv, J, Cheng, D, Sagum, C, Castellano, S, Bai, X, Johnson, C, Khalil, MI, Shen, J, Chen, K, Li, H, Sbardella, G & Bedford, MT 2017, Nature Chemical Biology, vol. 13, no. 7, pp. 750-756. DOI: 10.1038/nchembio.2377

Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen
Watters, RJ, Hartmaier, RJ, Osmanbeyoglu, HU, Gillihan, RM, Rae, JM, Liao, L, Chen, K, Li, W, Lu, X & Oesterreich, S 2017, Molecular and Cellular Endocrinology, vol. 448, pp. 21-27. DOI: 10.1016/j.mce.2017.03.005

Discovery of novel determinants of endothelial lineage using chimeric heterokaryons
Wong, J, Matrone, G, Tian, X, Tomoiaga, SA, Au, KF, Meng, S, Yamazoe, S, Sieveking, D, Chen, K, Burns, DM, Chen, JK, Blau, HM & Cooke, JP 2017, eLife, vol. 6, e23588. DOI: 10.7554/eLife.23588

RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly
Liu, S, Xu, Z, Leng, H, Zheng, P, Yang, J, Chen, K, Feng, J & Li, Q 2017, Science (New York, N.Y.), vol. 355, no. 6323, pp. 415-420. DOI: 10.1126/science.aah4712

LIM domain only 2 regulates endothelial proliferation, angiogenesis, and tissue regeneration
Meng, S, Matrone, G, Lv, J, Chen, K, Wong, JWT & Cooke, JP 2016, Journal of the American Heart Association, vol. 5, no. 10, e004117. DOI: 10.1161/JAHA.116.004117

Broad H3K4me3 as A Novel Epigenetic Signature for Normal Development and Disease
Lv, J & Chen, K 2016, Genomics, Proteomics and Bioinformatics, vol. 14, no. 5, pp. 262-264. DOI: 10.1016/j.gpb.2016.09.001

A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4 and c-Myc to regulate stemness
Lee, SH, Chen, TY, Dhar, SS, Gu, B, Chen, K, Kim, YZ, Li, W & Lee, MG 2016, Nucleic acids research, vol. 44, no. 22, pp. 10603-10618. DOI: 10.1093/nar/gkw788

An essential role for UTX in resolution and activation of bivalent promoters
Dhar, SS, Lee, SH, Chen, K, Zhu, G, Oh, WK, Allton, K, Gafni, O, Kim, YZ, Tomoiga, AS, Barton, MC, Hanna, JH, Wang, Z, Li, W & Lee, MG 2016, Nucleic Acids Research, vol. 44, no. 8, pp. 3659-3674. DOI: 10.1093/nar/gkv1516

The overlooked fact: Fundamental need for spike-in control for virtually all genome-wide analyses
Chen, K, Hu, Z, Xi, Z, Zhao, D, Li, W & Tyler, JK 2016, Molecular and Cellular Biology, vol. 36, no. 5, pp. 662-667. DOI: 10.1128/MCB.00970-14

ZMYND8 Reads the Dual Histone Mark H3K4me1-H3K14ac to Antagonize the Expression of Metastasis-Linked Genes
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, GM 2016, Molecular Cell. DOI: 10.1016/j.molcel.2016.06.035