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== | ==Educations== | ||
* 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 - 2009, PhD of Genomics, [http://english.big.cas.cn/ Beijing Institute of Genomics], [http://english.cas.cn/ Chinese Academy of Sciences], Beijing, China. | ||
* 2000 - 2004, BS of Biophysics, [http://physics.nankai.edu.cn 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. | ||
| Line 14: | Line 14: | ||
== | ==Academic Experiences== | ||
* 2013 - Present, Instructor, [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. | ||
* 2009 - 2013, Postdoctoral Associate, [http://www.bcm.edu/ Baylor College of Medicine], Houston, Texas, USA. | * 2009 - 2013, Postdoctoral Associate, [http://www.bcm.edu/ Baylor College of Medicine], Houston, Texas, USA. | ||
| Line 21: | Line 21: | ||
==Research | ==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. | 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. | ||
# Epigenetic: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and DNA repair proteins. | # Epigenetic: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and DNA repair proteins. | ||
# | # Gene expression: RNA transcription, splicing, translation (Ribo-Seq); LINC RNA, small RNA, RNA editing, etc. | ||
# Genetics: SNP, indel, translocation, copy number variation, etc. | # Genetics: SNP, indel, translocation, copy number variation, etc. | ||
| Line 30: | Line 30: | ||
# [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 and Protein Occupancy by Sequencing. | ||
== | ==Publications== | ||
* first or co-first authorship | * first or co-first authorship | ||
2014 published | 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. | 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] | Genes & Development. (2014). [IF 12.08] | ||
(Highlighted by the Science journal). | (Highlighted by the Science journal). | ||
(Recommended by Faculty of 1000) | (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. | 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] | 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. | 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] | 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. | 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] | Microbial Cell. (2014) [IF N/A] | ||
2013 published | 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. | 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] | Genome Research (2013). [IF 14.40] | ||
(Highlighted in headlines by Epigenie). | (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. | 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] | 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. | 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] | 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. | 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] | Nature Communications. (2013). [IF 10.70] | ||
(Praised by Chinese President Hu Jingtao) | (Praised by Chinese President Hu Jingtao) | ||
2012 published | 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. | 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] | 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. | 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] | 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. | 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] | 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. | 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] | PLOS Genetics. (2012) [IF 8.52] | ||
13 | |||
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] | The Journal of biological chemistry. (2012) [IF 4.65] | ||
2011 published | 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] | 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] | 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] | 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] | Journal of genetics and genomics. (2011) [IF 2.08] | ||
2010 and before | 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] | 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] | 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] | 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] | Plant Systematics and Evolution, (2010) [IF 2.31] | ||
Latest revision as of 20:26, 12 December 2014
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
Educations
- 2004 - 2009, PhD of Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- 2000 - 2004, BS of Biophysics, Institute of Physics, Nankai University, Tianjin, China.
Academic Experiences
- 2013 - Present, Instructor, Baylor College of Medicine, Houston, Texas, USA.
- 2009 - 2013, Postdoctoral Associate, Baylor College of Medicine, Houston, Texas, USA.
- 2008 - 2009, Invited visiting scholar, KACST, Riyadh, Saudi Arabia.
- 2005 - 2008, Joint PhD student, BGI, Beijing, China.
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.
- Epigenetic: nucleosome and chromatin structure, DNA methylation, histone modifications, transcription factors, and DNA repair proteins.
- Gene expression: RNA transcription, splicing, translation (Ribo-Seq); LINC RNA, small RNA, RNA editing, etc.
- Genetics: SNP, indel, translocation, copy number variation, etc.
Software development
- 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]
