Kun Zhang

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi request reprint Sequencing genomes from single cells by polymerase cloning
    Kun Zhang
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:680-6. 2006
  2. ncbi request reprint Long-range polony haplotyping of individual human chromosome molecules
    Kun Zhang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:382-7. 2006
  3. doi request reprint Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    Jin Billy Li
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Science 324:1210-3. 2009
  4. pmc Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics
    Li Shen
    Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Cell 153:692-706. 2013
  5. pmc Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming
    Shinpei Yamaguchi
    Howard Hughes Medical Institute, WAB 149G, 200 Longwood Av, Boston, MA 02115, USA
    Cell Res 23:329-39. 2013
  6. ncbi request reprint Multiplex amplification of large sets of human exons
    Gregory J Porreca
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 4:931-6. 2007
  7. ncbi request reprint Accurate multiplex polony sequencing of an evolved bacterial genome
    Jay Shendure
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 309:1728-32. 2005
  8. pmc Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    Jin Billy Li
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:1606-15. 2009
  9. pmc A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells
    Je Hyuk Lee
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 5:e1000718. 2009
  10. pmc Tet1 controls meiosis by regulating meiotic gene expression
    Shinpei Yamaguchi
    Howard Hughes Medical Institute, Harvard Medical School, WAB 149G, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 492:443-7. 2012

Collaborators

Detail Information

Publications21

  1. ncbi request reprint Sequencing genomes from single cells by polymerase cloning
    Kun Zhang
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:680-6. 2006
    ..Polymerase cloning should provide a critical tool for systematic characterization of genome diversity in the biosphere...
  2. ncbi request reprint Long-range polony haplotyping of individual human chromosome molecules
    Kun Zhang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:382-7. 2006
    ..This haplotyping method is well suited for candidate gene-based association studies as well as for investigating the pattern of recombination in mammalian cells...
  3. doi request reprint Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    Jin Billy Li
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Science 324:1210-3. 2009
    ..This efficient approach greatly expands the repertoire of RNA editing targets and can be applied to studies involving RNA editing-related human diseases...
  4. pmc Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics
    Li Shen
    Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Cell 153:692-706. 2013
    ..Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome...
  5. pmc Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming
    Shinpei Yamaguchi
    Howard Hughes Medical Institute, WAB 149G, 200 Longwood Av, Boston, MA 02115, USA
    Cell Res 23:329-39. 2013
    ..5. Thus, our study not only reveals the dynamics of 5mC and 5hmC during PGC reprogramming and germ cell development, but also their potential role in epigenetic reprogramming and transcriptional regulation of meiotic and imprinted genes...
  6. ncbi request reprint Multiplex amplification of large sets of human exons
    Gregory J Porreca
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 4:931-6. 2007
    ..We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing...
  7. ncbi request reprint Accurate multiplex polony sequencing of an evolved bacterial genome
    Jay Shendure
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 309:1728-32. 2005
    ..Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents...
  8. pmc Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    Jin Billy Li
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:1606-15. 2009
    ..In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation...
  9. pmc A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells
    Je Hyuk Lee
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 5:e1000718. 2009
    ..We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells...
  10. pmc Tet1 controls meiosis by regulating meiotic gene expression
    Shinpei Yamaguchi
    Howard Hughes Medical Institute, Harvard Medical School, WAB 149G, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 492:443-7. 2012
    ..Our study thus establishes a function for Tet1 in meiosis and meiotic gene activation in female germ cells...
  11. pmc A public resource facilitating clinical use of genomes
    Madeleine P Ball
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 109:11920-7. 2012
    ..We offer our public resource and methods to further personalized medical research...
  12. ncbi request reprint Cloning, expression, and characterization of an acetate kinase from a high rate of biohydrogen bacterial strain Ethanoligenens sp. hit B49
    Nan qi Ren
    School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090 People s Republic of China
    Curr Microbiol 55:167-72. 2007
    ..Ack was heterologously expressed in E.coli BL21 (DE3). Ack specific activities of the refolded ack inclusion body from Ethanoligenens sp. hit B49 is 42.12 U at 25 degrees C, and the renaturation percent is 14.36%...
  13. pmc Finding the needles in the metagenome haystack
    George A Kowalchuk
    Centre for Terrestrial Ecology, Netherlands Institute of Ecology NIOO KNAW, P O Box 40, 6666 ZG, Heteren, The Netherlands
    Microb Ecol 53:475-85. 2007
    ....
  14. ncbi request reprint Cytogenetic analysis of human bone marrow-derived mesenchymal stem cells passaged in vitro
    Zhen Xing Zhang
    Department of Neurosurgery, Weifang People s Affiliated Hospital, Weifang Medical College, Weifang 261041, PR China
    Cell Biol Int 31:645-8. 2007
    ..The results indicate that the in vitro cultured MSCs retained normal cytogenetics before being transplanted back into the patients...
  15. ncbi request reprint Phenylobacterium zucineum sp. nov., a facultative intracellular bacterium isolated from a human erythroleukemia cell line K562
    Kun Zhang
    Cancer Institute, The Second Affiliated Hospital, Zhejiang University Medical School, 88 Jiefang Road, Hangzhou 310009, PR China
    Syst Appl Microbiol 30:207-12. 2007
    ..On the basis of the phylogenetic and phenotypic characterization, strain HLK1(T) is proposed to be classified in the genus Phenylobacterium, as P. zucineum sp. nov. The type strain is HLK1(T) (=CGMCC 1.3786(T), DSM=18354)...
  16. ncbi request reprint Down-regulation of DNA polymerases kappa, eta, iota, and zeta in human lung, stomach, and colorectal cancers
    Qiangrong Pan
    Cancer Institute, The Second Affiliated Hospital, The Medical Collage, Zhejiang University, 88 Jiefang Road, Hangzhou, Zhejiang Province, P R China
    Cancer Lett 217:139-47. 2005
    ....
  17. ncbi request reprint HaploBlockFinder: haplotype block analyses
    Kun Zhang
    Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
    Bioinformatics 19:1300-1. 2003
    ..A greedy algorithm was used to improve the efficiency. Two separate utilities were also provided to assist visual inspection of haplotype block structure and pattern of linkage disequilibrium...
  18. ncbi request reprint Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift
    Kun Zhang
    Center for Genome Information, 130 Kettering, Department of Environmental Health, University of Cincinnati, OH 45215, Cincinnati, USA
    Hum Genet 113:51-9. 2003
    ..Our findings highlight the necessity of characterizing haplotype blocks in world-wide populations...
  19. ncbi request reprint The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium
    Joshua M Akey
    Center for Genome Information, University of Cincinnati, Cincinnati, Ohio, USA
    Mol Biol Evol 20:232-42. 2003
    ..Finally, we validate our theoretical predictions by comparing our results to publicly available data from ten genes sequenced in 24 African American and 23 European American individuals...
  20. pmc Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation
    Ning Wang
    Center for Genome Information, University of Cincinnati, Cincinnati, OH 45267 0056, USA
    Am J Hum Genet 71:1227-34. 2002
    ..Finally, we provide practical guidelines for designing and interpreting studies investigating haplotype block structure...
  21. ncbi request reprint Assaying DNA methylation based on high-throughput melting curve approaches
    Dayna T Akey
    Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio 45267, USA
    Genomics 80:376-84. 2002
    ..We demonstrate that McCOBRA and McMSP provide several advantages over existing methods, as they are simple, accurate, and high-throughput, which makes them widely applicable to large-scale methylation studies...