Kaifu: Difference between revisions
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==Research interests== | ==Research interests== | ||
Based on high throughput sequencing platforms and bioinformatic technologies, we investigate genetic/epigenetic variations and their implication in biological phenotypes, e.g. cancer, aging and heart diseases. | Based on high throughput sequencing platforms and bioinformatic technologies, we investigate genetic/epigenetic variations and their implication in gene function regulation as well as biological phenotypes, e.g. cancer, aging and heart diseases. | ||
# Genome sequencing: SNP, indel, and structural variation. | # Genome sequencing: SNP, indel, and structural variation. | ||
# RNA-seq or Microarray: gene expression, alternative splicing, LINC RNA. | # RNA-seq or Microarray: gene expression, alternative splicing, LINC RNA. |
Revision as of 14:31, 31 October 2012
Contact Info
- 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
Education
- 2009, PhD of Genomics and bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- 2004, BS of Biophysics, Institute of Physics, Nankai University, Tianjin, China.
Experience
- 2009 - present, Postdoctorial Associate, Baylor College of Medicine, Houston, Texas, USA.
- 2008 - 2009, Research Associate, KACST, Riyadh, Saudi Arabia.
- 2004 - 2008, Beijing Genomics Institute, Beijing, China.
Research interests
Based on high throughput sequencing platforms and bioinformatic technologies, we investigate genetic/epigenetic variations and their implication in gene function regulation as well as 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
- DyChIPS: a software for dyanmic analysis of ChIP-sequencing.
- DANPOS: a software for dyanmic analysis of nucleosome position and occupancy.
Publication
* first or co-first authorship
- 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) Accepted.
- 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) Accepted.
- 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) Accepted.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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