Difference between revisions of "Kaifu"

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4. <u>Chen K*</u>,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.  
4. <u>Chen K*</u>,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).[http://epigenie.com/danpos-reveals-dynamic-nucleosomes/ Highlited by Epigenie headlines]
'''Genome Research''' (2012).[http://epigenie.com/danpos-reveals-dynamic-nucleosomes/ Highlighted by Epigenie headlines]

Revision as of 08:40, 7 March 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



  • 2013.07 - Present, Instructor, Baylor College of Medicine, Houston, Texas, USA.
  • 2009.09 - 2013.07, Postdoctorial Associate, Baylor College of Medicine, Houston, Texas, USA.
  • 2008.08 - 2009.08, Research Associate, KACST, Riyadh, Saudi Arabia.
  • 2005.03 - 2008.08, Research Assistant, BGI, Beijing, China.

Research interest

Based on high throughput DNA sequencing platforms and bioinformatic technologies, we investigate genetic/epigenetic mechanisms in gene function variation and expression regulation, and finally their implication in biological phenotypes, e.g. stem cell differentiation, aging, cancer, and heart diseases.

  1. ChIP- or MNase-seq: nucleosome positioning/occupancy, histone modifications, and other chromatin components, e.g. DNA repair proteins.
  2. RNA-seq or Microarray: gene expression, alternative splicing, LINC RNA.
  3. Genome sequencing: SNP, indel, and structural variation.

Software development

  1. DANPOS: a software for dyanmic analysis of nucleosome position and occupancy.
  2. DyChIPS: a software for dyanmic analysis of ChIP-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). 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).

4. 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 by Epigenie headlines

3. 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).

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. 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).

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 (2012). The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends.

Nature. doi:10.1038/nature11355

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

Molecular cell, 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. (2012). SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.

Nature. doi:10.1038/nature11043

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

Nucleic acids research, 36(19), 6228–6236. doi:10.1093/nar/gkn626

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

Genomics, proteomics & bioinformatics, 8(2), 92–102. doi:10.1016/S1672-0229(10)60010-1


12. 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) Accepted

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

The Journal of biological chemistry, 287(1), 429–437. doi:10.1074/jbc.M111.271163

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

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

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

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

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

Journal of genetics and genomics. 38(2), 63–70. doi:10.1016/j.jcg.2011.01.003

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

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

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

Plant Systematics and Evolution, 289(3-4), 111–126. doi:10.1007/s00606-010-0336-8