Zhang:Publications

2010

1. Shoemaker R, Deng J, Wang W, and Zhang K. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res. 2010 Jul;20(7):883-9. DOI:10.1101/gr.104695.109 |
2. Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, Gibbs R, Zhang K, and Chen R. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010 Jul;20(7):981-8. DOI:10.1101/gr.102921.109 |

2009

3. Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, and Church GM. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 2009 Nov;5(11):e1000718. DOI:10.1371/journal.pgen.1000718 |
4. Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, and Church GM. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods. 2009 Aug;6(8):613-8. DOI:10.1038/nmeth.1357 |
5. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, and Church GM. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res. 2009 Sep;19(9):1606-15. DOI:10.1101/gr.092213.109 |
6. Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, and Church GM. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science. 2009 May 29;324(5931):1210-3. DOI:10.1126/science.1170995 |
7. 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, and Zhang K. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009 Apr;27(4):353-60. DOI:10.1038/nbt.1530 |
8. Chen AE, Egli D, Niakan K, Deng J, Akutsu H, Yamaki M, Cowan C, Fitz-Gerald C, Zhang K, Melton DA, and Eggan K. 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. 2009 Feb 6;4(2):103-6. DOI:10.1016/j.stem.2008.12.001 |

2007

9. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, and Shendure J. Multiplex amplification of large sets of human exons. Nat Methods. 2007 Nov;4(11):931-6. DOI:10.1038/nmeth1110 |
10. Kowalchuk GA, Speksnijder AG, Zhang K, Goodman RM, and van Veen JA. Finding the needles in the metagenome haystack. Microb Ecol. 2007 Apr;53(3):475-85. DOI:10.1007/s00248-006-9201-2 |
11. Zhang K, Lott ST, Jin L, and Killary AM. Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12. Biochem Biophys Res Commun. 2007 Aug 31;360(3):531-8. DOI:10.1016/j.bbrc.2007.06.066 |

2006

12. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, and Church GM. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006 Jun;24(6):680-6. DOI:10.1038/nbt1214 |
13. Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, and Church GM. Long-range polony haplotyping of individual human chromosome molecules. Nat Genet. 2006 Mar;38(3):382-7. DOI:10.1038/ng1741 |

2005

14. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, and Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 2005 Sep 9;309(5741):1728-32. DOI:10.1126/science.1117389 |

2003

15. Zhang K and Jin L. HaploBlockFinder: haplotype block analyses. Bioinformatics. 2003 Jul 1;19(10):1300-1. DOI:10.1093/bioinformatics/btg142 |
16. Zhang K, Akey JM, Wang N, Xiong M, Chakraborty R, and Jin L. Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift. Hum Genet. 2003 Jul;113(1):51-9. DOI:10.1007/s00439-003-0941-5 |
17. Chen Z, Zhang K, Zhang X, Yuan XH, Yuan Z, Jin L, and Xiong M. 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. Clin Exp Metastasis. 2003;20(4):335-42. DOI:10.1023/a:1024039802134 |
18. Akey JM, Zhang K, Xiong M, and Jin L. The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Mol Biol Evol. 2003 Feb;20(2):232-42. DOI:10.1093/molbev/msg032 |

2002

19. Akey JM, Zhang G, Zhang K, Jin L, and Shriver MD. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 2002 Dec;12(12):1805-14. DOI:10.1101/gr.631202 |
20. Wang N, Akey JM, Zhang K, Chakraborty R, and Jin L. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am J Hum Genet. 2002 Nov;71(5):1227-34. DOI:10.1086/344398 |
21. Akey DT, Akey JM, Zhang K, and Jin L. Assaying DNA methylation based on high-throughput melting curve approaches. Genomics. 2002 Oct;80(4):376-84. DOI:10.1006/geno.2002.6851 |

2001

22. Akey JM, Zhang K, Xiong M, Doris P, and Jin L. The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. Am J Hum Genet. 2001 Jun;68(6):1447-56. DOI:10.1086/320607 |