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    Kun Zhang

    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0412
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Single-nucleus sequencing and in situ mapping of mRNA molecules in human kidney
      NIH/NIDDK UG3DK114933Sep 15, 2017 - Jun 30, 2019
      Role: Principal Investigator
      Next-generation Functional Genetic Screening of Un-screenable Traits
      NIH/NHGRI R01HG009285Aug 25, 2017 - Jul 31, 2021
      Role: Co-Principal Investigator
      Improving cell fate conversion by tracking cells and RNA over time and space
      NIH/NHLBI R01HL123755May 5, 2015 - Apr 30, 2019
      Role: Principal Investigator
      Single-stranded sequencing using microfluidic reactors (SISSOR)
      NIH/NHGRI R01HG007836Aug 1, 2014 - May 31, 2018
      Role: Principal Investigator
      Single-cell sequencing and in situ mapping of RNA transcripts in human brains
      NIH/NIMH U01MH098977Sep 19, 2012 - May 31, 2017
      Role: Principal Investigator
      NIH/NHLBI U01HL107442Jul 15, 2011 - Jun 30, 2017
      Role: Principal Investigator
      Genome-methylome Interactions
      NIH/NIGMS R01GM097253Apr 1, 2011 - Mar 31, 2015
      Role: Principal Investigator
      Xavier's RCMI Cancer Research Program
      NIH G12RR026260Sep 24, 2009 - Jul 31, 2014
      Role: Co-Investigator
      An Integrated lab-on-chip system for genome sequencing of single microbial cells
      NIH/NHGRI R01HG004876Sep 26, 2008 - Jul 31, 2013
      Role: Principal Investigator
      Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing
      NIH/NIDA R01DA025779Sep 15, 2008 - Jul 31, 2013
      Role: Principal Investigator
      Louisiana Biomedical Research Network (LBRN)
      NIH P20RR016456Sep 25, 2001 - Apr 30, 2015
      Role: Co-Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Guo S, Diep D, Plongthongkum N, Fung HL, Zhang K, Zhang K. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat Genet. 2017 Apr; 49(4):635-642. PMID: 28263317.
        View in: PubMed
      2. Zhang K. Stratifying tissue heterogeneity with scalable single-cell assays. Nat Methods. 2017 Feb 28; 14(3):238-239. PMID: 28245217.
        View in: PubMed
      3. Song HW, Bettegowda A, Lake BB, Zhao AH, Skarbrevik D, Babajanian E, Sukhwani M, Shum EY, Phan MH, Plank TD, Richardson ME, Ramaiah M, Sridhar V, de Rooij DG, Orwig KE, Zhang K, Wilkinson MF. The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment. Cell Rep. 2016 Sep 27; 17(1):149-64. PMID: 27681428.
        View in: PubMed
      4. Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 2016 Jun 24; 352(6293):1586-90. PMID: 27339989; PMCID: PMC5038589.
      5. Sos BC, Fung HL, Gao DR, Osothprarop TF, Kia A, He MM, Zhang K. Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biol. 2016 Feb 04; 17:20. PMID: 26846207; PMCID: PMC4743176.
      6. Zhao T, Zhang ZN, Westenskow PD, Todorova D, Hu Z, Lin T, Rong Z, Kim J, He J, Wang M, Clegg DO, Yang YG, Zhang K, Friedlander M, Xu Y. Humanized Mice Reveal Differential Immunogenicity of Cells Derived from Autologous Induced Pluripotent Stem Cells. Cell Stem Cell. 2015 Sep 03; 17(3):353-9. PMID: 26299572.
        View in: PubMed
      7. Plongthongkum N, Diep DH, Zhang K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014 Oct; 15(10):647-61. PMID: 25159599.
        View in: PubMed
      8. Plongthongkum N, van Eijk KR, de Jong S, Wang T, Sul JH, Boks MP, Kahn RS, Fung HL, Ophoff RA, Zhang K. Characterization of genome-methylome interactions in 22 nuclear pedigrees. PLoS One. 2014; 9(7):e99313. PMID: 25019935; PMCID: PMC4096397.
      9. Li Z, Lu H, Yang W, Yong J, Zhang ZN, Zhang K, Deng H, Xu Y. Mouse SCNT ESCs have lower somatic mutation load than syngeneic iPSCs. Stem Cell Reports. 2014 Apr 08; 2(4):399-405. PMID: 24749065; PMCID: PMC3986627.
      10. Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol. 2013 Dec; 31(12):1126-32. PMID: 24213699; PMCID: PMC3875318.
      11. Lee HS, Chu WK, Zhang K, Huang X. Microfluidic devices with permeable polymer barriers for capture and transport of biomolecules and cells. Lab Chip. 2013 Sep 07; 13(17):3389-97. PMID: 23828542; PMCID: PMC3818112.
      12. Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A, Wu W, Corominas R, Peoples A, Koren A, Gore A, Kang S, Lin GN, Estabillo J, Gadomski T, Singh B, Zhang K, Akshoomoff N, Corsello C, McCarroll S, Iakoucheva LM, Li Y, Wang J, Sebat J. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell. 2012 Dec 21; 151(7):1431-42. PMID: 23260136; PMCID: PMC3712641.
      13. Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, Zhang K. Library-free methylation sequencing with bisulfite padlock probes. Nat Methods. 2012 Feb 05; 9(3):270-2. PMID: 22306810; PMCID: PMC3461232.
      14. Chen CH, Cho SH, Chiang HI, Tsai F, Zhang K, Lo YH. Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. Anal Chem. 2011 Oct 01; 83(19):7269-75. PMID: 21809842.
        View in: PubMed
      15. Diep D, Zhang K. Genome-wide mapping of the sixth base. Genome Biol. 2011 Jun 20; 12(6):116. PMID: 21682934; PMCID: PMC3218833.
      16. Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LS, Zhang K. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011 Mar 03; 471(7336):63-7. PMID: 21368825; PMCID: PMC3074107.
      17. Shoemaker R, Wang W, Zhang K. Mediators and dynamics of DNA methylation. Wiley Interdiscip Rev Syst Biol Med. 2011 May-Jun; 3(3):281-98. PMID: 20878927.
        View in: PubMed
      18. Shoemaker R, Deng J, Wang W, 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. PMID: 20418490; PMCID: PMC2892089.
      19. Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods. 2009 Aug; 6(8):613-8. PMID: 19620972; PMCID: PMC2742772.
      20. 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. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009 Apr; 27(4):353-60. PMID: 19330000; PMCID: PMC2715272.