Difference between revisions of "Kaifu"

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* first or co-first authorship
* first or co-first authorship

Revision as of 22:05, 24 August 2014

Contact Info

Kaifu Chen
  • Kaifu Chen
  • Dan L. Duncan Cancer Center,Department of Molecular and Cellular Biology, Baylor College of Medicine
  • 1 Baylor Plaza, suite 450A, Houston, Texas,77030.
  • kaifuc at bcm dot edu



Research interest

Based on high throughput DNA sequencing platforms and bioinformatic technologies, we investigate genetic variation, epigenetic regulation of gene expression, and their implications in biological phenotypes, e.g. cancer, stem cell differentiation, aging, and neuron diseases.

  1. Epigenetic: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and DNA repair proteins.
  2. Transcription: gene expression, alternative splicing, LINC RNA.
  3. Genetics: SNP, indel, and structural variation.

Software development

  1. DANPOS: a software for Dyanmic Analysis of Nucleosome and Protein Occupancy by Sequencing.


* first or co-first authorship


1. Hu Z*, Chen K*, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W, Tyler JK. Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging.

Genes Dev. (2014). Recommended by FACULTY of 1000, Highlighted by SCIENCE editor

2. Ibrahim S. Al-Mssallem, Songnian Hu, Xiaowei Zhang, Jun Tan, Qiang Lin, Wanfei Liu, Xiaoguang Yu, … Kaifu Chen, Samiyah R. Alkhaldi, Guiming Liu, Meng Zhang, Haiyan Guo, and Jun Yu. Genome Sequences and Genetic Variations of Date Palm (Phoenix dactylifera L.).

Nature Communications (2013). Visited by Chinese President Hu Jingtao

3. Chen K*,Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.

Genome Research (2012).Highlighted in headlines by Epigenie

4. Chen K*, Wilson MA*, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent S: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.

Genome Res. (2012).

5. Li Z, Gadue P, Chen K, Tuteja G, Schug J, Li W, Kaestner KH: Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation.

Cell (2012).

6. Huang Z*, Chen, K*, Zhang J*, Li Y*, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Chen R, Sucgang RS, Pan X: A functional variomics tool for discovering resistance genes and targets of small molecule compounds.

Cell Reports (2013).

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

Nature. (2012) doi:10.1038/nature11355

8. 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) 44(4), 609–620. Elsevier. doi:10.1016/j.molcel.2011.08.042

9. 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) doi:10.1038/nature11043

10. 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) 36(19), 6228–6236. doi:10.1093/nar/gkn626

11. 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) 8(2), 92–102. doi:10.1016/S1672-0229(10)60010-1


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

Transcription, (2014)

13. Hu Z, Chen K, Li W, Tyler JK. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast.

Microbial Cell, (2014) Vol. 1, No. 4, pp. 133 - 136 .

14. Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho FA, Pan X. Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy.

PLOS Genetics (2012)

15. 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) 287(1), 429–437. doi:10.1074/jbc.M111.271163

16. 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) 10(11), 1536–1544. doi:10.1128/EC.05170-11

17. Ma, L., Chen K., Meng, Q., Liu, Q., Tang, P., Hu, S., & Yu, J. An evolutionary analysis of trypanosomatid GP63 proteases.

Parasitology research. (2011) doi:10.1007/s00436-011-2348-x

18. 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) 38(2), 63–70. doi:10.1016/j.jcg.2011.01.003

19. Yang, M., Zhang, X., Liu, G., Yin, Y., Chen K., Yun, Q., Zhao, D., et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)

PloS one, (2010) 5(9), e12762. doi:10.1371/journal.pone.0012762

20. 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) 289(3-4), 111–126. doi:10.1007/s00606-010-0336-8