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==Education==
==Educations==
* 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 - 2009, PhD of Genomics, [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.
* 2000 - 2004, BS of Biophysics, [http://physics.nankai.edu.cn Institute of Physics], [http://www.nankai.edu.cn/english/ Nankai University], Tianjin, China.






==Experience==
==Academic Experiences==
* 2009 - present, Postdoctorial Associate, [http://www.bcm.edu/ Baylor College of Medicine], Houston, Texas, USA.
* 2013 - Present, Instructor, [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.
* 2009 - 2013, Postdoctoral Associate, [http://www.bcm.edu/ Baylor College of Medicine], Houston, Texas, USA.
* 2004 - 2008, [http://www.genomics.cn/en/index.php Beijing Genomics Institute], Beijing, China.
* 2008 - 2009, Invited visiting scholar, [http://www.kacst.edu.sa/en/Pages/default.aspx KACST], Riyadh, Saudi Arabia.
* 2005 - 2008, Joint PhD student, [http://www.genomics.cn/en/index BGI], Beijing, China.




==Research interest==
==Research Interests==
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.
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, such as cancer, stem cell differentiation, aging, and neuron diseases, etc.
# Genome sequencing: SNP, indel, and structural variation.
# Epigenetic: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and DNA repair proteins.
# RNA-seq or Microarray: gene expression, alternative splicing, LINC RNA.
# Gene expression: RNA transcription, splicing, translation (Ribo-Seq); LINC RNA, small RNA, RNA editing, etc.
# ChIP- or MNase-seq: nucleosome positioning/occupancy, histone modifications, and other chromatin components, e.g. DNA repair proteins.
# Genetics: SNP, indel, translocation, copy number variation, etc.


==Software development==
==Software development==
# [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 and Protein Occupancy by Sequencing.
# [http://code.google.com/p/danpos/ DANPOS]: a software for dyanmic analysis of nucleosome position and occupancy.  


==Publication==
==Publications==
<u>underlined</u> first or co-first authorship
* first or co-first authorship


Selected:
# <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''', Wilson MA</u>, 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
# <u>Kuo, A. J., Cheung, P., '''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
# 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
# <u>Huang Z, '''Chen, K'''</u>., , 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) Accepted.
# <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
# <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


Other:
2014 published
# 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
 
# 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
1. Hu Z*, Chen K*, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W, Tyler J K. Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging.
# 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
Genes & Development. (2014).           [IF 12.08]
# 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
(Highlighted by the Science journal). 
# 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
(Recommended by Faculty of 1000)
 
2. Wang L, Chen J, Wang C, Zimmermann M T, Yan H, Sun Z, Zhang Y, Chen K, Huang H, Kocher J A, Li W. MACE: Model based Analysis of ChIP-exo. 
Nucleic Acids Research. (2014).            [IF 8.81]
 
3. Hu Z, Chen K, Li W, Tyler J. A matter of access: Nucleosome disassembly from gene promoters is the central goal of transcriptional activators.
Transcription. (2014)            [IF N/A]
 
4. Hu Z, Chen K, Li W, Tyler JK. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast.
Microbial Cell. (2014)           [IF N/A]
 
 
2013 published
 
 
5. Chen K*, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S YR, He X, Li W. DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
Genome Research (2013).           [IF 14.40]
(Highlighted in headlines by Epigenie). 
 
6. Chen K*, Wilson M A*, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent S YR: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.
Genome Research. (2013).            [IF 14.40]
 
7. Huang Z*, Chen K*, Zhang J*, Li Y*, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Chen R, Sucgang R S, Pan X: A functional variomics tool for discovering resistance genes and targets of small molecule compounds.
Cell Reports. (2013).           [IF 7.21]
 
8. Al-Mssallem I S, Hu S, Zhang X, Tan J, Lin Q, Liu W, Yu X, … Chen K, Alkhaldi S R, Liu G, Zhang M, Guo H, Yu J. Genome Sequences and Genetic Variations of Date Palm.
Nature Communications. (2013).           [IF 10.70]
(Praised by Chinese President Hu Jingtao) 
 
 
2012 published
 
 
9. Li Z, Gadue P, Chen K, Tuteja G, Schug J, Li W, Kaestner K H. Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation.
Cell. (2012).           [IF 31.96]
 
10. 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.
Nature. (2012)            [IF 38.60]
 
11. 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)           [IF 38.60]
 
12. Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho F A, Pan X. Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy.  
PLOS Genetics. (2012)           [IF 8.52]
 
13. 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)           [IF 4.65]
 
 
2011 published
 
 
14. 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)            [IF 15.28]
 
15. 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)           [IF 3.59]
 
16. Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. An evolutionary analysis of trypanosomatid GP63 proteases.  
Parasitology research. (2011)            [IF 2.85]
 
17. 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)           [IF 2.08]
 
 
2010 and before
 
 
18. 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)            [IF 8.81]
 
19. 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)           [IF N/A]
 
20. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, et al. The complete chloroplast genome sequence of date palm.  
PlOS ONE, (2010)             [IF 3.53]
 
21. 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)           [IF 2.31]
 




Latest revision as of 20:26, 12 December 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


Educations


Academic Experiences


Research Interests

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, such as cancer, stem cell differentiation, aging, and neuron diseases, etc.

  1. Epigenetic: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and DNA repair proteins.
  2. Gene expression: RNA transcription, splicing, translation (Ribo-Seq); LINC RNA, small RNA, RNA editing, etc.
  3. Genetics: SNP, indel, translocation, copy number variation, etc.

Software development

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

Publications

* first or co-first authorship


2014 published


1. Hu Z*, Chen K*, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W, Tyler J K. Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging. Genes & Development. (2014). [IF 12.08] (Highlighted by the Science journal). (Recommended by Faculty of 1000)

2. Wang L, Chen J, Wang C, Zimmermann M T, Yan H, Sun Z, Zhang Y, Chen K, Huang H, Kocher J A, Li W. MACE: Model based Analysis of ChIP-exo. Nucleic Acids Research. (2014). [IF 8.81]

3. Hu Z, Chen K, Li W, Tyler J. A matter of access: Nucleosome disassembly from gene promoters is the central goal of transcriptional activators. Transcription. (2014) [IF N/A]

4. Hu Z, Chen K, Li W, Tyler JK. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast. Microbial Cell. (2014) [IF N/A]


2013 published


5. Chen K*, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S YR, He X, Li W. DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. Genome Research (2013). [IF 14.40] (Highlighted in headlines by Epigenie).

6. Chen K*, Wilson M A*, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent S YR: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. Genome Research. (2013). [IF 14.40]

7. Huang Z*, Chen K*, Zhang J*, Li Y*, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Chen R, Sucgang R S, Pan X: A functional variomics tool for discovering resistance genes and targets of small molecule compounds. Cell Reports. (2013). [IF 7.21]

8. Al-Mssallem I S, Hu S, Zhang X, Tan J, Lin Q, Liu W, Yu X, … Chen K, Alkhaldi S R, Liu G, Zhang M, Guo H, Yu J. Genome Sequences and Genetic Variations of Date Palm. Nature Communications. (2013). [IF 10.70] (Praised by Chinese President Hu Jingtao)


2012 published


9. Li Z, Gadue P, Chen K, Tuteja G, Schug J, Li W, Kaestner K H. Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation. Cell. (2012). [IF 31.96]

10. 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. Nature. (2012) [IF 38.60]

11. 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) [IF 38.60]

12. Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho F A, Pan X. Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy. PLOS Genetics. (2012) [IF 8.52]

13. 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) [IF 4.65]


2011 published


14. 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) [IF 15.28]

15. 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) [IF 3.59]

16. Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. An evolutionary analysis of trypanosomatid GP63 proteases. Parasitology research. (2011) [IF 2.85]

17. 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) [IF 2.08]


2010 and before


18. 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) [IF 8.81]

19. 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) [IF N/A]

20. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, et al. The complete chloroplast genome sequence of date palm. PlOS ONE, (2010) [IF 3.53]

21. 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) [IF 2.31]  





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