User:Kun Zhang

Kun Zhang, Ph.D. Assistant Professor Department of Bioengineering University of California, San Diego 9500 Gilman Drive, MC0412 La Jolla, CA 92903

Education

• Post-doc, Department of Genetics, Harvard Medical School
• Ph.D., Human and Molecular Genetics, University of Texas-Houston/MD-Anderson Cancer Center
• M.S., Neuroscience, Fudan University, China
• B.S., Biophysics, Fudan University, China

Research Interests

We are developing genome technologies based on single-molecule sequencing, single-cell manipulation/amplification, and chip-based synthesis and manipulation of complex DNA libraries. We apply these novel technologies to stem cell genomics, personal genome and bioenergy research.

Publications

1. Chen AE, Egli D, Niakan K, Deng J, Akutsu H, Yamaki M, Cowan C, Fitz-Gerald C, Zhang K, Melton DA, and Eggan K. (2009) Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines. Cell Stem Cell 4:103-6
2. Porreca PJ, Zhang K (co-first author), Li JB, Xie B, Austin D, Vassallo SL, Leproust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. (2007) Multiplex amplification of large sets of human exons. Nat. Methods 4:931-6.
3. Kowalchuk GA, Speksnijder AG, Zhang K, Goodman RM, van Veen JA. (2007) Finding the needles in the metagenome haystack. Microb. Ecol. 53:475-85
4. Zhang K, Lott ST, Jin L, Killary AM. (2007) Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12. Biochem. Biophys. Res. Commun. 360:531-538
5. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. (2006) Sequencing genomes from single cells by polymerase cloning. Nat. Biotech. 24:680-686
6. Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. (2006) Polony haplotyping of individual human chromosome molecules. Nat. Genet. 38:382-387.
7. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732.
8. Zhang K, and Jin L. (2003) HaploBlockFinder: haplotype block analyses. Bioinformatics 19:1300-1301
9. Zhang K, Akey JM (co-first author), Wang N, Xiong M, Chakraborty R, Jin L.(2003) Randomly distributed crossovers may generate block-like pattern of linkage disequibrium: An act of genetic drift. Hum. Genet. 113: 51-59.
10. Akey JM, Zhang K, Xiong M, and Jin L. (2003) The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol Biol Evol. 20: 232-242.
11. Akey JM, Zhang G, Zhang K, Jin L and Shriver M. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12: 1805-1814.
12. Wang N, Akey JM, Zhang K, Chakraborty R, Jin L. (2002) Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am. J. Hum. Genet. 71: 1227-1234.
13. Akey DT, Akey JM, Zhang K, Jin L. (2002) Assaying DNA methylation based on high-throughput melting curve approaches. Genomics 80: 376-384.
14. Akey JM, Zhang K (co-first author), Xiong M, Doris P, Jin L. (2001) The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. Am. J. Hum. Genet., 68:1447-1456.