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| |[[Image:Kun_zhang_pic1.jpg|100px]]|| | | |[[Image:Kun_zhang_pic1.jpg|100px]]|| |
| <b>Kun Zhang, Ph.D.</b><br> | | <b>Kun Zhang, Ph.D.</b><br> |
| Assistant Professor<br>
| | Associate Professor<br> |
| Department of Bioengineering<br> | | Department of Bioengineering<br> |
| University of California, San Diego<br> | | University of California, San Diego<br> |
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| [http://zhang.openwetware.org Zhang Lab Website] | | [http://zhang.openwetware.org Zhang Lab Website] |
| |} | | |} |
| ==Education==
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| *Post-doc, Department of Genetics, Harvard Medical School
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| *Ph.D., Human and Molecular Genetics, University of Texas-Houston/MD-Anderson Cancer Center
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| *M.S., Neuroscience, Fudan University, China
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| *B.S., Biophysics, Fudan University, China
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| ==Research Interests== | | ==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 genomes and human common diseases. | | We are developing genome technologies related to single-cell analyses of genome, transcriptome and epigenome, as well as single-cell imaging and lineage tracing. We apply these novel technologies to stem cell fate conversion, human brain mapping and human disease studies. |
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| ==Publications== | | ==Publications== |
| #<b>Zhang K</b>, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, LeProust EM, Eggan K, Church GM (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. <b>Nature Methods</b>, 6:613-8
| | *[https://scholar.google.com/citations?user=CYeurYgAAAAJ&hl=en Google Scholar Page]. |
| #Li JB, Gao Y, Aach J, <b>Zhang K</b>, Kryukov G, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, ElProust E, Sunyaev S, Church GM. (2009) Multiplex padlock capture and sequencing reveal human hypermutable CpG variations. <b>Genome Research</b>, [http://genome.cshlp.org/content/early/2009/06/12/gr.092213.109.abstract Advanced Online Articles]
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| #Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, LeProust E, <b>Zhang K</b>, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing, <b>Science</b> 324:1210-13
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| #Deng J, Shoemaker R, Xie B, Gore A, Leproust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, <b>Zhang K</b>. (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. <b>Nature Biotechnology</b>, 27:353-60 [http://genome-tech.ucsd.edu/public/NBT-RA20324/Deng-NBT-2009.pdf PDF]
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| #Chen AE, Egli D, Niakan K, Deng J, Akutsu H, Yamaki M, Cowan C, Fitz-Gerald C, <b>Zhang K</b>, 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. <b>Cell Stem Cell</b> 4:103-6
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| #Porreca PJ, <b>Zhang K (co-first author)</b>, 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. <b>Nature Methods</b> 4:931-6.
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| #Kowalchuk GA, Speksnijder AG, <b>Zhang K</b>, Goodman RM, van Veen JA. (2007) Finding the needles in the metagenome haystack. <b>Microbial Ecology</b> 53:475-85
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| #<b>Zhang K</b>, Lott ST, Jin L, Killary AM. (2007) Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12. <b>Biochemical and Biophysical Research Communications</b> 360:531-538
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| #<b>Zhang K</b>, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. (2006) Sequencing genomes from single cells by polymerase cloning. <b>Nature Biotechnology</b> 24:680-686
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| #<b>Zhang K</b>, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. (2006) Polony haplotyping of individual human chromosome molecules. <b>Nature Genetics</b> 38:382-387.
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| #Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, <b>Zhang K</b>, Mitra RD, Church GM. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. <b>Science</b> 309:1728-1732.
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| #<b>Zhang K</b>, and Jin L. (2003) HaploBlockFinder: haplotype block analyses. <b>Bioinformatics</b> 19:1300-1301
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| #<b>Zhang K</b>, 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. <b>Human Genetics</b> 113: 51-59.
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| #Akey JM, <b>Zhang K</b>, Xiong M, and Jin L. (2003) The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. <b>Molecular Biology and Evolution</b> 20: 232-242.
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| #Chen Z, <b>Zhang K</b>, Zhang X, Yuan XH, Yuan Z, Jin L, and Xiong M. (2003) Comparison of gene expression between metastatic derivatives and their poorly metastatic parental cells implicates crucial tumor-environment interaction in metastasis of head and neck squamous cell carcinoma. <b>Clinical and Experimental Metastasis</b> 20:335-342.
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| #Akey JM, Zhang G, Z<b>hang K</b>, Jin L and Shriver M. (2002) Interrogating a high-density SNP map for signatures of natural selection. <b>Genome Research</b> 12: 1805-1814.
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| #Wang N, Akey JM, <b>Zhang K</b>, Chakraborty R, Jin L. (2002) Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. <b>American Journal of Human Genetics</b> 71: 1227-1234.
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| #Akey DT, Akey JM, <b>Zhang K</b>, Jin L. (2002) Assaying DNA methylation based on high-throughput melting curve approaches. <b>Genomics</b> 80: 376-384.
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| #Akey JM, <b>Zhang K (co-first author)</b>, Xiong M, Doris P, Jin L. (2001) The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. <b>American Journal of Human Genetics</b>, 68:1447-1456.
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