Prof. Kun He
Senior Bioinformatics Scientist

Monsanto Company, USA


2000-2006 Ph.D., Bioinformatics, Peking University, China

Publications (Selected)
  1. Lee J*, He K*, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, and Deng XW (2007). Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development. The Plant Cell, 19:731-749.
  2. He K#, Li XY, Zhou JL, Deng XW, Zhao HY, Luo JC#(2009). NTAP: For NimbleGen Tiling Array ChIP-chip Data Analysis. Bioinformatics, 25(14):1838-1840.
  3. Guo AY Chen X, Gao G, Zhang He, Liu XC, Zhu QH, Zhong YF, Gu XC, He K#and Luo JC#(2008), Plant TFDB: a Comprehensive Plant Transcription Factor Database. Nuclear Acids Research,36: 966-969.
  4. Gong W*, He, K*, Covington M, Dinesh-Kumar S.P., Snyder M, Harmer S, Zhu YX, and Deng XW (2007). The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Molecular Plant 1: 27-41.
  5. Chen YH*, Yang XY*, He K*, Liu M, Li JG, Gao ZF, Lin ZQ, Zhang YF, Wang XX, Qiu XM, Shen YP, Zhang L, Deng XH, Luo JC, Deng XW, Chen ZL, Gu HY and Qu L-J (2006) The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family. Plant Molecular Biology, 60:107-123.
  6. Guo A*, He K*, Liu D, Bai S, Gu X, Wei L and Luo J (2005). DATF: a database of Arabidopsis transcription factors. Bioinformatics, 21(10): 2568-2569.
  7. Quanbeck S.M., Brachova L., Campbeli A.A., Guan X, Perera A, He K, Rhee S.Y., Bais P,., Nikolau B.J. (2012), Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”, Front. Plant Sci., 3:15.
  8. Zhang XJ, Zhao XM, He K, Lu L et al. (2011), Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information, Bioinformatics, 28(1), 98-104.
  9. Bais P, Moon S.M., He K, Leitao R, Dreher K, Walk T, .., Rhee S.Y., Dickerson Julie A (2010), Plant Metabolomics. org: a web portal for plant metabolomics experiments. Plant physiology, 152(4):1807-16.
  10. Zhou J, Wang XF, He K, Charron JF, Elling AA, Deng XW, (2010)  Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Molecular Biology 72:585–595.
  11. Sun Y, Fan, X.-Y., Cao, D.-M., He K, He JX, Hou BH, Hao YQ, Ji HK, Somerville S, Wong WH, Rhee S, and Wang ZY (2010), Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis, Developmental Cell, 19, 756-777.
  12. Li XY, Wang XF, He K, Ma YQ, Su N, He H, Stolc V, Tongprasit W, Jin WW, Jiang JM, Terzaghi W, Li SG, and Deng XW (2008). High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression. The Plant Cell, 20:259-276.
  13. Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW (2007). Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Molecular Biology, 63(5):591-608.
  14. Su N*, He K*, Jiao YL*, Chen C, Zhou JL, Li L, Bai SL, Li XY, Deng X.W (2006). Distinct reorganization of genome transcription is associated with organogenesis of somatic embryos, shoots and roots in rice. Plant Molecular Biology, 63(3):337-349.
  15. Li J, Li X, Guo L, Lu F, Feng X, He K, Wei L, Chen Z, Qu LJ and Gu H (2006) A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice.J. Exp. Bot, 57(6):1263-73.
  16. Su H, Qu L-J, He K, Zhang Z, Wang J, Chen Z and Gu H (2003) The Great Wall of China: a physical barrier to gene flow? Heredity, 90: 212-219.
  17. Gao G, Yu P, Liu D, He K, Wu X and Luo JC (2002) BiDMAP - A Biological Data Management and Analysis Platform. Computer Engineering, 28: 145-153.