Kaifu

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==Education==
==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.
+
* 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.
+
* 2004, BS of Biophysics, [http://physics.nankai.edu.cn Institute of Physics], [http://www.nankai.edu.cn/english/ Nankai University], Tianjin, China.
==Experience==
==Experience==
-
* 2009 - present, Postdoctorial Associate, [http://www.bcm.edu/ Baylor College of Medicine], Houston, Texas, USA.
+
* 2013.07 - 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.
+
* 2009.09 - 2013.07, 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.
+
* 2008.08 - 2009.08, [http://www.kacst.edu.sa/en/Pages/default.aspx KACST], Riyadh, Saudi Arabia.
 +
* 2005.03 - 2008.08, [http://www.genomics.cn/en/index BGI], Beijing, China.
==Research interest==
==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.
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.
-
# Genome sequencing: SNP, indel, and structural variation.
+
# Epigenetics: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and other chromatin components such as DNA repair proteins.
-
# RNA-seq or Microarray: gene expression, alternative splicing, LINC RNA.
+
# Transcription: gene expression, alternative splicing, LINC RNA.
-
# ChIP- or MNase-seq: nucleosome positioning/occupancy, histone modifications, and other chromatin components, e.g. DNA repair proteins.
+
# Genetics: SNP, indel, and structural variation.
==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 position and occupancy.  
# [http://code.google.com/p/danpos/ DANPOS]: a software for dyanmic analysis of nucleosome position and occupancy.  
 +
# [http://code.google.com/p/dychips/ DyChIPS]: a software for dyanmic analysis of ChIP-sequencing.
==Publication==
==Publication==
-
<u>underlined:</u> first or co-first authorship
+
\* first or co-first authorship
Selected:
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,   '''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.  
+
1. Hu Z*, <u>Chen K*</u>, 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.
-
# <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
+
'''Genes Dev'''. (2014).  [http://f1000.com/prime/718277680?subscriptioncode=0933b40d-0bbd-45c3-ab83-4023573b940c  Recommended by FACULTY of 1000],  [http://www.sciencemag.org/content/343/6175/1058.4.full?sid=6db4babf-0f6f-4cd9-baa1-a8fd9857428d Highlighted by SCIENCE editor]
-
# <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.
+
2. Ibrahim S. Al-Mssallem, Songnian Hu, Xiaowei Zhang, Jun Tan, Qiang Lin, Wanfei Liu, Xiaoguang Yu, … <u>Kaifu Chen</u>, Samiyah R. Alkhaldi, Guiming Liu, Meng Zhang, Haiyan Guo, and Jun Yu. Genome Sequences and Genetic Variations of Date Palm (Phoenix dactylifera L.).
-
# <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
+
'''Nature Communications''' (2013). [http://english.big.cas.cn/ns/es/200908/t20090827_34506.html  Visited by Chinese President Hu Jingtao]
 +
 
 +
 
 +
3. <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/  Highlighted in headlines by Epigenie]
 +
 
 +
 
 +
4. <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).
 +
 
 +
 
 +
5. 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).  
 +
 
 +
 
 +
6. Huang Z*, <u>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).  
 +
 
 +
 
 +
7. 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. The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends.  
 +
 
 +
'''Nature'''. (2012) doi:10.1038/nature11355
 +
 
 +
 
 +
8. Kuo, A. J.*, Cheung, P.*, <u>Chen, K*</u>., 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.,<u>Chen, K.</u>, et al. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.  
 +
 
 +
'''Nature'''. (2012) doi:10.1038/nature11043
 +
 
 +
 
 +
10. <u>Chen, K*</u>., 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. <u>Chen, K*</u>., 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
 +
 
 +
 
Other:
Other:
-
# 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
 
-
# 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
 
-
# 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
 
 +
12. Hu, Z., <u>Chen K</u>, 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, <u>Chen K</u>, 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, <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) 
 +
 +
 +
15. Badeaux, A. I., Yang, Y., Cardenas, K., Vemulapalli, V., <u>Chen K</u>., 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.,  <u>Chen K</u>., 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.,  <u>Chen K</u>., 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.,  <u>Chen K</u>., 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.,  <u>Chen K</u>., 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.,<u>Chen K</u>., 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

Current revision

Contents

Contact Info

Kaifu Chen
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


Education


Experience


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. Epigenetics: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and other chromatin components such as 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 position and occupancy.
  2. DyChIPS: a software for dyanmic analysis of ChIP-sequencing.

Publication

\* first or co-first authorship

Selected:

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


Other:

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




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