Zhang:Publications

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===2010===
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#Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C., Gibbs R, <b>Zhang K</b>, Chen R. (2010). Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. <b>Genome Research</b>, doi:10.1101/gr.102921.109.
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<biblio>
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#Shoemaker R, Deng J, Wang W, <b>Zhang K</b>. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. <b>Genome Research</b> Advance Online Article (doi:10.1101/gr.104695.109)
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#Shoemaker-WIRSBM-2010 pmid=20878927
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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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#Shoemaker-GR-2010 pmid=20418490
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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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#Wang-GR-2010 pmid=20472684
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#Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, <b>Zhang K*</b>, Church GM*. (2009) A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. <b>PLoS Genetics, </b>[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000718  5(11):e1000718].
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</biblio>
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#<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
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#Li JB*, Gao Y*, Aach J*, <b>Zhang K*</b>, Kryukov G, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev S, Church GM. (2009) Multiplex padlock capture and sequencing reveal human hypermutable CpG variations. <b>Genome Research</b>, 19:1606-15.
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===2009===
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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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<biblio>
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#Porreca PJ*, <b>Zhang K*</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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#Lee-PLoS-Genet-2009 pmid=19911041
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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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#Zhang-NMeth-2009 pmid=19620972
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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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#LiJB-GenomeRes-2009 pmid=19525355
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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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#LiJB-Science-2009 pmid=19478186
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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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#Deng-NatBiotech-2009 pmid=19330000
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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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#Chen-Egli-CellStemCell-2009 pmid=19200798
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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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</biblio>
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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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===2007===
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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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<biblio>
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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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#Porreca-Zhang-NatMethod-2007 pmid=17934468
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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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#Kowalchuk-MicrobEcol-2007 pmid=17345132
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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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#Zhang-BBRC-2007 pmid=17624313
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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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</biblio>
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===2006===
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<biblio>
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#Zhang-NatBiotech-2006 pmid=16732271
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#Zhang-NatGenet-2006 pmid=16493423
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</biblio>
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===2005===
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<biblio>
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#Shendure-Science-2005 pmid=16081699
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</biblio>
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===2003===
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<biblio>
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#Zhang-Bioinformatics-2003 pmid=12835279
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#Zhang-HumGenet-2003 pmid=12677424
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#Chen-ClinExpMet-2003 pmid=12856721
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#Akey-MBE-2003 pmid=12598690
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</biblio>
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===2002===
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<biblio>
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#Akey-GenomeRes-2002 pmid=12466284
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#Wang-AJHG-2002 pmid=12384857
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#Akey-Genomics-2002 pmid=12376091
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</biblio>
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===2001===
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<biblio>
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#Akey-AJHG-2001 pmid=11359212
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</biblio>
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Revision as of 00:22, 26 November 2010

  1. Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C., Gibbs R, Zhang K, Chen R. (2010). Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Research, doi:10.1101/gr.102921.109.
  2. Shoemaker R, Deng J, Wang W, Zhang K. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Research Advance Online Article (doi:10.1101/gr.104695.109)
  3. 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, Zhang K.(2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology, 27:353-60 PDF
  4. 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
  5. Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K*, Church GM*. (2009) A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. PLoS Genetics, 5(11):e1000718.
  6. Zhang K, 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. Nature Methods, 6:613-8
  7. Li JB*, Gao Y*, Aach J*, Zhang K*, Kryukov G, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev S, Church GM. (2009) Multiplex padlock capture and sequencing reveal human hypermutable CpG variations. Genome Research, 19:1606-15.
  8. Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing, Science 324:1210-13
  9. Porreca PJ*, Zhang K*, 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. Nature Methods 4:931-6.
  10. Kowalchuk GA, Speksnijder AG, Zhang K, Goodman RM, van Veen JA. (2007) Finding the needles in the metagenome haystack. Microbial Ecology 53:475-85
  11. Zhang K, Lott ST, Jin L, Killary AM. (2007) Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12. Biochemical and Biophysical Research Communications 360:531-538
  12. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. (2006) Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 24:680-686
  13. Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. (2006) Polony haplotyping of individual human chromosome molecules. Nature Genetics 38:382-387.
  14. 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.
  15. Zhang K, and Jin L. (2003) HaploBlockFinder: haplotype block analyses. Bioinformatics 19:1300-1301
  16. 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. Human Genetics 113: 51-59.
  17. Akey JM, Zhang K, Xiong M, and Jin L. (2003) The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Molecular Biology and Evolution 20: 232-242.
  18. Chen Z, Zhang K, 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. Clinical and Experimental Metastasis 20:335-342.
  19. Akey JM, Zhang G, Zhang K, Jin L and Shriver M. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research 12: 1805-1814.
  20. 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. American Journal of Human Genetics 71: 1227-1234.
  21. Akey DT, Akey JM, Zhang K, Jin L. (2002) Assaying DNA methylation based on high-throughput melting curve approaches. Genomics 80: 376-384.
  22. 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. American Journal of Human Genetics, 68:1447-1456.
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