Kun He

DPB, Carnegie Institution for Sciences

260 Panama ST

Stanford, CA 94305

Telephone: +01-650-325-1521 x 397

E-mail: kun.he at stanford dot edu

EDUCATION

09/2000-06/2006 Peking University, Beijing, China

Ph. D. in Bioinformatics

Advisor: Prof. Jingchu Luo

04/2004-04/2006 Yale University, New Haven, CT, U.S.

Visiting student in Biostatistics

Advisor: Prof. Xing-Wang Deng and Hongyu Zhao

09/1996-07/2000 Peking University, Beijing, China

B.S. in Biotechnology

EXPERIENCE

Work Experience * 06/2006-Present, Postdoctoral Fellow, Center for Bioinformatics, Peking University, China

* 04/2004-04/2006, Research Assistant, Yale University, U.S.

* 09/2000-03/2004, Research Assistant, Center for Bioinformatics, Peking University, China

* 01/2001-12/2003, System Administrator of Linux/Unix servers, Center for Bioinformatics, Peking University, China

Research Experience * 2004-2005, Microarray (cDNA array) data analysis and functional genomics analysis

* 2004-2006, ChIP-chip (NimbleGen tiling array) data analysis in the research of identifying direct binding targets of HY5, a key transcription factor in photomorphogenesis

* 2005-2006, NimbleGen tiling array data analysis in the research of epigenetics including histone modifications and DNA methylation

* 2000-2003, Phylogenetic analysis of the rice and Arabidopsis MYB transcription factor family

* 2000-2003, Participate in the construction of the Arabidopsis transcription factor database

* 1999-2000, Analysis of genetic differentiation between the two subpopulations of plant species on both sides of the Great Wall in China using RAPD markers

* Developing software packages and web applications for biologists to use, construct databases to share data with the community

Teaching Assistant * 2002-2003, Applied Bioinformatics Course

* 2001-2002, C programming

RESEARCH SKILLS

* Strong background in molecular biology, genomics and bioinformatics;

* Fundamental knowledge of statistics: HMM, Bayesian networks, hypothesis tests;

* Microarray data analysis (Affymetrix, NimbleGen, cDNA arrays);

* Extensive knowledge of R and S-Plus statistical programs;

* Phylogenetic analysis;

* Comparative genomics analysis, functional analysis including GO, pathway and network analysis.

COMPUTER SKILLS

* Strong knowledge of various Linux/Unix systems (Debian, RedHat, Gentoo);

* Various servers maintenance skills: Apache, Tomcat, Sendmail, Bind, Squid, Samba and FTP;

* Database utilization and management (MySQL, Oracle);

* Excellent skills in Perl, Java and Unix shell programming;

* Excellent skills in web application development by CGI, PHP and JSP;

* Office software including Photoshop and Illustrator.

PUBLICATIONS (* Equal contribution)

Guo AY Chen X, Gao G, Zhang He, Liu XC, Zhu QH, Zhong YF, Gu XC, He K* and Luo JC* (2007), PlantTFDB: a Comprehensive Plant Transcription Factor Database. Nuclear Acids Research ,in press
He K, Li XY, Zhou JL, Deng XW, Zhao HY, Luo JC (2007). NTAP: NimbleGen Tiling Array Data Analysis and Post-processing Package. Intelligent Systems for Molecular Biology (ISMB) 2007 ,Vienna, Austria.
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.
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, in press.
Su N*, He K*, Jiao YL*, Chen C, Zhou JL, Li L, Bai SL, Li XY, Deng X.W (2007). Distinct reorganization of genome transcription is associated with organogenesis of somatic embryos, shoots and roots in rice. Plant Molecular Biology, 63(3):337-349.
He K, Gao G (2006). Introduction to DNA microarray technology. Computer Education (China), 33:19-23. (in Chinese)
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.
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.
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.
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.
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.
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.

AWARDS

2006, First-class funding granted by the postdoctoral science foundation of China
2004, Monsanto Fellowship of the Peking-Yale Joint Research Center
2001, "WuSi" Excellent Graduate Student Scholarship
1998, Social Activities Award from Peking University

RESEARCH INTERESTS

Metabolomics and pathway network modeling, systems biology research
Transcriptional regulatory network analysis by integrating high-throughput generated data.
Biological applications development and database construction.
Microarray data analysis.
Genetics analysis.

AWARDS

RESEARCH INTERESTS

References will be provided upon request