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Kun Zhang

TitleResearcher
InstitutionUniversity of California San Diego
DepartmentBioengineering
Address9500 Gilman Drive #0412
La Jolla CA 92093
Phone858-822-7876
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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
    REGULATORY GENOMIC STUDIES IN A COHORT OF IPS CELL DERIVED CARDIOMYOCYTES
    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.
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    1. Diep D, Zhang K. Efficient and fast identification of differentially methylated regions using whole-genome bisulfite sequencing data. J Genet Genomics. 2018 Aug 09. PMID: 30172582.
      View in: PubMed
    2. Diep D, Zhang K. Reply to 'DNA methylation haplotypes as cancer markers'. Nat Genet. 2018 Aug; 50(8):1063-1066. PMID: 30054596.
      View in: PubMed
    3. Diep D, Plongthongkum N, Zhang K. Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes. Methods Mol Biol. 2018; 1708:365-382. PMID: 29224154.
      View in: PubMed
    4. Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat Biotechnol. 2018 Jan; 36(1):70-80. PMID: 29227469.
      View in: PubMed
    5. Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K. Ultraaccurate genome sequencing and haplotyping of single human cells. Proc Natl Acad Sci U S A. 2017 Nov 21; 114(47):12512-12517. PMID: 29078313.
      View in: PubMed
    6. Lake BB, Codeluppi S, Yung YC, Gao D, Chun J, Kharchenko PV, Linnarsson S, Zhang K. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci Rep. 2017 Jul 20; 7(1):6031. PMID: 28729663.
      View in: PubMed
    7. 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
    8. Zhang K. Stratifying tissue heterogeneity with scalable single-cell assays. Nat Methods. 2017 02 28; 14(3):238-239. PMID: 28245217.
      View in: PubMed
    9. Song HW, Bettegowda A, Lake BB, Zhao AH, Skarbrevik D, Babajanian E, Sukhwani M, Shum EY, Phan MH, Plank TM, 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 09 27; 17(1):149-164. PMID: 27681428.
      View in: PubMed
    10. 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.
      View in: PubMed, PubMed Central
    11. 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.
      View in: PubMed, PubMed Central
    12. 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
    13. 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
    14. 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.
      View in: PubMed, PubMed Central
    15. 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.
      View in: PubMed, PubMed Central
    16. Woodruff G, Young JE, Martinez FJ, Buen F, Gore A, Kinaga J, Li Z, Yuan SH, Zhang K, Goldstein LS. The presenilin-1 ?E9 mutation results in reduced ?-secretase activity, but not total loss of PS1 function, in isogenic human stem cells. Cell Rep. 2013 Nov 27; 5(4):974-85. PMID: 24239350; PMCID: PMC3867011.
      View in: PubMed, PubMed Central
    17. 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.
      View in: PubMed, PubMed Central
    18. 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.
      View in: PubMed, PubMed Central
    19. 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.
      View in: PubMed, PubMed Central
    20. 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.
      View in: PubMed, PubMed Central
    21. 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
    22. Diep D, Zhang K. Genome-wide mapping of the sixth base. Genome Biol. 2011 Jun 20; 12(6):116. PMID: 21682934; PMCID: PMC3218833.
      View in: PubMed, PubMed Central
    23. 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.
      View in: PubMed, PubMed Central
    24. 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
    25. 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.
      View in: PubMed, PubMed Central
    26. 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.
      View in: PubMed, PubMed Central
    27. 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.
      View in: PubMed, PubMed Central
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