View source for Kaifu

==Contact Info==
[[Image:kaifu.jpg|thumb|right|Kaifu Chen]]

*Kaifu Chen
*Dan L. Duncan Cancer Center,Department of Molecular and Cellular Biology, [http://www.bcm.edu/ Baylor College of Medicine]
*1 Baylor Plaza, suite 450A, Houston, Texas,77030. 
*kaifuc at bcm dot edu


==Education==
* 2009, PhD of Genomics and bioinformatics, [http://english.big.cas.cn/ Beijing Institute of Genomics], [http://english.cas.cn/ Chinese Academy of Sciences], Beijing, China.
* 2004, BS of Biophysics, Institute of Physics, [http://www.nankai.edu.cn/english/ Nankai University], Tianjin, China.



==Experience==
* 2009 - present, Postdoctorial Associate, [http://www.bcm.edu/ Baylor College of Medicine], Houston, Texas, USA.
* 2008 - 2009, Research Associate, [http://www.kacst.edu.sa/en/Pages/default.aspx KACST], Riyadh, Saudi Arabia.
* 2004 - 2008, [http://www.genomics.cn/en/index.php Beijing Genomics Institute], 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. cancer, aging and heart diseases.
# Genome sequencing: SNP, indel, and structural variation.
# RNA-seq or Microarray: gene expression, alternative splicing, LINC RNA.
# ChIP- or MNase-seq: nucleosome positioning/occupancy, histone modifications, and other chromatin components, e.g. DNA repair proteins.

==Software==
# [http://code.google.com/p/dychips/ DyChIPS]: a software for dyanmic analysis of ChIP-sequencing.
# [http://code.google.com/p/danpos/ DANPOS]: a software for dyanmic analysis of nucleosome position and occupancy. 

==Publication==
'''*''' first or co-first authorship
# <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) Accepted.
# Li Z, Gadue P,  <u>Chen K</u>, Tuteja G, Schug J, Li W, Kaestner KH: Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation. '''Cell''' (2012) Accepted. 
# <u>Chen K*</u>, 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) Accepted. 
# Chen, X., Cui, D., Papusha, A., Zhang, X., Chu, C., Tang, J., <u>Chen, K.</u>, 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
# Barber, M. F., Michishita-Kioi, E., Xi, Y., Tasselli, L., Kioi, M., Moqtaderi, Z., Tennen, R. I.,<u> Chen, K</u>., et al. (2012). SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. '''Nature'''. doi:10.1038/nature11043
# Huang Z, Srinivasan S, Zhang J, <u>Chen K</u>, 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 
# Badeaux, A. I., Yang, Y., Cardenas, K., Vemulapalli, V., <u>Chen, K</u>., 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
# Kuo, A. J.*, Cheung, P.*, <u>Chen, K*</u>., 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
# Huang, Z., <u>Chen, K</u>., 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
# Ma, L., <u>Chen, K</u>., 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
# Meng, Q., <u>Chen, K</u>., 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
# <u>Chen, K*</u>., 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
# Yang, M., Zhang, X., Liu, G., Yin, Y., <u>Chen, K</u>., 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
# <u>Chen, K*</u>., 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








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