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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


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.


* 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]