Kun Zhang

Title(s)Professor, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0002-7596-522 Additional info
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    Collapse Research 
    Collapse Research Activities and Funding
    KULMAP: Human Kidney, urinary tract and lung mapping center
    NIH U54HL145608Sep 25, 2018 - Jun 30, 2022
    Role: Principal Investigator
    Toward a human adult brain cell atlas with single-cell technologies
    NIH U01MH114828Aug 22, 2018 - May 31, 2023
    Role: Principal Investigator
    Single-nucleus sequencing and in situ mapping of mRNA molecules in human kidney
    NIH UH3DK114933Sep 15, 2017 - Jun 30, 2022
    Role: Principal Investigator
    Single-nucleus sequencing and in situ mapping of mRNA molecules in human kidney
    NIH UG3DK114933Sep 15, 2017 - Jun 30, 2019
    Role: Principal Investigator
    Next-generation Functional Genetic Screening of Un-screenable Traits
    NIH R01HG009285Aug 25, 2017 - Jul 31, 2021
    Role: Co-Principal Investigator
    Improving cell fate conversion by tracking cells and RNA over time and space
    NIH R01HL123755May 5, 2015 - Apr 30, 2020
    Role: Principal Investigator
    Single-stranded sequencing using microfluidic reactors (SISSOR)
    NIH R01HG007836Aug 1, 2014 - May 31, 2019
    Role: Principal Investigator
    Single-cell sequencing and in situ mapping of RNA transcripts in human brains
    NIH U01MH098977Sep 19, 2012 - May 31, 2018
    Role: Principal Investigator
    REGULATORY GENOMIC STUDIES IN A COHORT OF IPS CELL DERIVED CARDIOMYOCYTES
    NIH U01HL107442Jul 15, 2011 - Jun 30, 2017
    Role: Principal Investigator
    Genome-methylome Interactions
    NIH R01GM097253Apr 1, 2011 - Mar 31, 2016
    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 R01HG004876Sep 26, 2008 - Jul 31, 2013
    Role: Principal Investigator
    Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing
    NIH 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. 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. An atlas of healthy and injured cell states and niches in the human kidney. Nature. 2023 Jul; 619(7970):585-594. Lake BB, Menon R, Winfree S, Hu Q, Ferreira RM, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB, KPMP Consortium, Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S. PMID: 37468583; PMCID: PMC10356613.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    2. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep. 2023 05 11; 13(1):7678. Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. PMID: 37169829; PMCID: PMC10175263.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    3. A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. Cell Genom. 2022 Mar 09; 2(3). Duong TE, Wu Y, Sos BC, Dong W, Limaye S, Rivier LH, Myers G, Hagood JS, Zhang K. PMID: 35434692; PMCID: PMC9012447.
      View in: PubMed   Mentions: 4  
    4. Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics. Dev Cell. 2022 02 07; 57(3):398-414.e5. Liang Y, Kaneko K, Xin B, Lee J, Sun X, Zhang K, Feng GS. PMID: 35134346; PMCID: PMC8842999.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    5. Discovery of genomic loci of the human cerebral cortex using genetically informed brain atlases. Science. 2022 02 04; 375(6580):522-528. Makowski C, van der Meer D, Dong W, Wang H, Wu Y, Zou J, Liu C, Rosenthal SB, Hagler DJ, Fan CC, Kremen WS, Andreassen OA, Jernigan TL, Dale AM, Zhang K, Visscher PM, Yang J, Chen CH. PMID: 35113692; PMCID: PMC9469470.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    6. Single-cell transcriptomics reveals opposing roles of Shp2 in Myc-driven liver tumor cells and microenvironment. Cell Rep. 2021 11 09; 37(6):109974. Chen WS, Liang Y, Zong M, Liu JJ, Kaneko K, Hanley KL, Zhang K, Feng GS. PMID: 34758313; PMCID: PMC8656042.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    7. Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). Nat Protoc. 2021 11; 16(11):4992-5029. Plongthongkum N, Diep D, Chen S, Lake BB, Zhang K. PMID: 34650278.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    8. Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas. iScience. 2021 Oct 22; 24(10):103149. Parekh U, McDonald D, Dailamy A, Wu Y, Cordes T, Zhang K, Tipps A, Metallo C, Mali P. PMID: 34646987; PMCID: PMC8496177.
      View in: PubMed   Mentions: 1  
    9. 5-Azacytidine Transiently Restores Dysregulated Erythroid Differentiation Gene Expression in TET2-Deficient Erythroleukemia Cells. Mol Cancer Res. 2021 03; 19(3):451-464. Reilly BM, Luger T, Park S, Lio CJ, González-Avalos E, Wheeler EC, Lee M, Williamson L, Tanaka T, Diep D, Zhang K, Huang Y, Rao A, Bejar R. PMID: 33172974; PMCID: PMC7925369.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    10. Defining the Teratoma as a Model for Multi-lineage Human Development. Cell. 2020 11 25; 183(5):1402-1419.e18. McDonald D, Wu Y, Dailamy A, Tat J, Parekh U, Zhao D, Hu M, Tipps A, Zhang K, Mali P. PMID: 33152263; PMCID: PMC7704916.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    11. The role of the NMD factor UPF3B in olfactory sensory neurons. Elife. 2020 08 10; 9. Tan K, Jones SH, Lake BB, Chousal JN, Shum EY, Zhang L, Chen S, Sohni A, Pandya S, Gallo RL, Zhang K, Cook-Andersen H, Wilkinson MF. PMID: 32773035; PMCID: PMC7452722.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    12. Non-invasive early detection of cancer four years before conventional diagnosis using a blood test. Nat Commun. 2020 07 21; 11(1):3475. Chen X, Gole J, Gore A, He Q, Lu M, Min J, Yuan Z, Yang X, Jiang Y, Zhang T, Suo C, Li X, Cheng L, Zhang Z, Niu H, Li Z, Xie Z, Shi H, Zhang X, Fan M, Wang X, Yang Y, Dang J, McConnell C, Zhang J, Wang J, Yu S, Ye W, Gao Y, Zhang K, Liu R, Jin L. PMID: 32694610; PMCID: PMC7374162.
      View in: PubMed   Mentions: 154     Fields:    Translation:HumansCells
    13. Tools for the analysis of high-dimensional single-cell RNA sequencing data. Nat Rev Nephrol. 2020 07; 16(7):408-421. Wu Y, Zhang K. PMID: 32221477.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    14. RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. Genome Res. 2020 04; 30(4):602-610. Wei CJ, Zhang K. PMID: 32127417; PMCID: PMC7197472.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    15. 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; PMCID: PMC6893138.
      View in: PubMed   Mentions: 220     Fields:    Translation:AnimalsCells
    16. 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; PMCID: PMC6597610.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    17. 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; PMCID: PMC6311449.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    18. 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; PMCID: PMC6311450.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    19. 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
    20. 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
    21. 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
    22. 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; PMCID: PMC5951394.
      View in: PubMed   Mentions: 356     Fields:    Translation:HumansCells
    23. 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; PMCID: PMC5703283.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    24. 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; PMCID: PMC5519641.
      View in: PubMed   Mentions: 105     Fields:    Translation:AnimalsCells
    25. 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; PMCID: PMC5374016.
      View in: PubMed   Mentions: 182     Fields:    Translation:HumansCells
    26. 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: 1     Fields:    
    27. 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; PMCID: PMC5063083.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    28. 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; PMCID: PMC5038589.
      View in: PubMed   Mentions: 417     Fields:    Translation:HumansCells
    29. 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; PMCID: PMC4743176.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    30. 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; PMCID: PMC9721102.
      View in: PubMed   Mentions: 112     Fields:    Translation:HumansAnimalsCells
    31. 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: 96     Fields:    Translation:HumansAnimalsCells
    32. 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; PMCID: PMC4096397.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    33. 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; PMCID: PMC3986627.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    34. The presenilin-1 ΔE9 mutation results in reduced γ-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; PMCID: PMC3867011.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansCells
    35. 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; PMCID: PMC3875318.
      View in: PubMed   Mentions: 101     Fields:    
    36. 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; PMCID: PMC3818112.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    37. 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; PMCID: PMC3712641.
      View in: PubMed   Mentions: 280     Fields:    Translation:HumansAnimalsCells
    38. 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; PMCID: PMC3461232.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    39. 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: 13     Fields:    Translation:Cells
    40. Genome-wide mapping of the sixth base. Genome Biol. 2011 Jun 20; 12(6):116. Diep D, Zhang K. PMID: 21682934; PMCID: PMC3218833.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    41. 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; PMCID: PMC3074107.
      View in: PubMed   Mentions: 586     Fields:    Translation:HumansCells
    42. 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
    43. 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; PMCID: PMC2892089.
      View in: PubMed   Mentions: 191     Fields:    Translation:HumansCells
    44. 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; PMCID: PMC2742772.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansCells
    45. 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; PMCID: PMC2715272.
      View in: PubMed   Mentions: 238     Fields:    Translation:HumansCells
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