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Kun Zhang

Title(s)Professor, Bioengineering
SchoolAcademic Aff
Address9500 Gilman Drive #0412
La Jolla CA 92093
Phone858-822-7876
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    KULMAP: Human Kidney, urinary tract and lung mapping center
    NIH/NHLBI U54HL145608Aug 1, 2019 - Jun 30, 2022
    Role: Principal Investigator
    Toward a human adult brain cell atlas with single-cell technologies
    NIH/NIMH U01MH114828Aug 22, 2018 - May 31, 2023
    Role: Principal Investigator
    Single-nucleus sequencing and in situ mapping of mRNA molecules in human kidney
    NIH/NIDDK UH3DK114933Sep 15, 2017 - Jun 30, 2022
    Role: Principal Investigator
    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 - Sep 29, 2010
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Tools for the analysis of high-dimensional single-cell RNA sequencing data. Nat Rev Nephrol. 2020 Jul; 16(7):408-421. Wu Y, Zhang K. PMID: 32221477.
      View in: PubMed   Mentions:    Fields:    
    2. RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. Genome Res. 2020 Apr; 30(4):602-610. Wei CJ, Zhang K. PMID: 32127417.
      View in: PubMed   Mentions:    Fields:    
    3. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat Biotechnol. 2019 12; 37(12):1452-1457. Chen S, Lake BB, Zhang K. PMID: 31611697.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    4. A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys. Nat Commun. 2019 06 27; 10(1):2832. Lake BB, Chen S, Hoshi M, Plongthongkum N, Salamon D, Knoten A, Vijayan A, Venkatesh R, Kim EH, Gao D, Gaut J, Zhang K, Jain S. PMID: 31249312.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    5. Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. Cell Syst. 2018 12 26; 7(6):656-666.e4. Wu Y, Tamayo P, Zhang K. PMID: 30528274.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    6. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. Cell Syst. 2018 11 28; 7(5):548-555.e8. Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. PMID: 30448000.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. Efficient and fast identification of differentially methylated regions using whole-genome bisulfite sequencing data. J Genet Genomics. 2018 08 20; 45(8):455-457. Diep D, Zhang K. PMID: 30172582.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    8. Reply to 'DNA methylation haplotypes as cancer markers'. Nat Genet. 2018 08; 50(8):1063-1066. Diep D, Zhang K. PMID: 30054596.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    9. Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes. Methods Mol Biol. 2018; 1708:365-382. Diep D, Plongthongkum N, Zhang K. PMID: 29224154.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat Biotechnol. 2018 01; 36(1):70-80. Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K. PMID: 29227469.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    11. Ultraaccurate genome sequencing and haplotyping of single human cells. Proc Natl Acad Sci U S A. 2017 11 21; 114(47):12512-12517. Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K. PMID: 29078313.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    12. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci Rep. 2017 07 20; 7(1):6031. Lake BB, Codeluppi S, Yung YC, Gao D, Chun J, Kharchenko PV, Linnarsson S, Zhang K. PMID: 28729663.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    13. 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. Guo S, Diep D, Plongthongkum N, Fung HL, Zhang K, Zhang K. PMID: 28263317.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    14. Stratifying tissue heterogeneity with scalable single-cell assays. Nat Methods. 2017 02 28; 14(3):238-239. Zhang K. PMID: 28245217.
      View in: PubMed   Mentions:    Fields:    
    15. The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment. Cell Rep. 2016 09 27; 17(1):149-164. 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. PMID: 27681428.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    16. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 2016 Jun 24; 352(6293):1586-90. 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. PMID: 27339989.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansCells
    17. Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biol. 2016 Feb 04; 17:20. Sos BC, Fung HL, Gao DR, Osothprarop TF, Kia A, He MM, Zhang K. PMID: 26846207.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    18. Humanized Mice Reveal Differential Immunogenicity of Cells Derived from Autologous Induced Pluripotent Stem Cells. Cell Stem Cell. 2015 Sep 03; 17(3):353-9. 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. PMID: 26299572.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    19. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014 Oct; 15(10):647-61. Plongthongkum N, Diep DH, Zhang K. PMID: 25159599.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    20. Characterization of genome-methylome interactions in 22 nuclear pedigrees. PLoS One. 2014; 9(7):e99313. Plongthongkum N, van Eijk KR, de Jong S, Wang T, Sul JH, Boks MP, Kahn RS, Fung HL, Ophoff RA, Zhang K. PMID: 25019935.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    21. Mouse SCNT ESCs have lower somatic mutation load than syngeneic iPSCs. Stem Cell Reports. 2014 Apr 08; 2(4):399-405. Li Z, Lu H, Yang W, Yong J, Zhang ZN, Zhang K, Deng H, Xu Y. PMID: 24749065.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    22. 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. Woodruff G, Young JE, Martinez FJ, Buen F, Gore A, Kinaga J, Li Z, Yuan SH, Zhang K, Goldstein LS. PMID: 24239350.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    23. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat Biotechnol. 2013 Dec; 31(12):1126-32. Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K. PMID: 24213699.
      View in: PubMed   Mentions: 66     Fields:    
    24. Microfluidic devices with permeable polymer barriers for capture and transport of biomolecules and cells. Lab Chip. 2013 Sep 07; 13(17):3389-97. Lee HS, Chu WK, Zhang K, Huang X. PMID: 23828542.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    25. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell. 2012 Dec 21; 151(7):1431-42. 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. PMID: 23260136.
      View in: PubMed   Mentions: 184     Fields:    Translation:HumansAnimalsCells
    26. Library-free methylation sequencing with bisulfite padlock probes. Nat Methods. 2012 Feb 05; 9(3):270-2. Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, Zhang K. PMID: 22306810.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    27. 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. Chen CH, Cho SH, Chiang HI, Tsai F, Zhang K, Lo YH. PMID: 21809842.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    28. Genome-wide mapping of the sixth base. Genome Biol. 2011 Jun 20; 12(6):116. Diep D, Zhang K. PMID: 21682934.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    29. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011 Mar 03; 471(7336):63-7. 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. PMID: 21368825.
      View in: PubMed   Mentions: 453     Fields:    Translation:HumansCells
    30. Mediators and dynamics of DNA methylation. Wiley Interdiscip Rev Syst Biol Med. 2011 May-Jun; 3(3):281-98. Shoemaker R, Wang W, Zhang K. PMID: 20878927.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    31. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res. 2010 Jul; 20(7):883-9. Shoemaker R, Deng J, Wang W, Zhang K. PMID: 20418490.
      View in: PubMed   Mentions: 141     Fields:    Translation:HumansCells
    32. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods. 2009 Aug; 6(8):613-8. Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM. PMID: 19620972.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansCells
    33. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol. 2009 Apr; 27(4):353-60. 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. PMID: 19330000.
      View in: PubMed   Mentions: 199     Fields:    Translation:HumansCells
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