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Kun Zhang

Title	Professor
School	University of California, San Diego
Department	Bioengineering
Address	9500 Gilman Drive #0412 CA La Jolla 92093
Phone	858-822-7876
vCard	Download vCard

Research

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

Bibliographic

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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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.

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Zhang K. Stratifying tissue heterogeneity with scalable single-cell assays. Nat Methods. 2017 Feb 28; 14(3):238-239. PMID: 28245217.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Diep D, Zhang K. Genome-wide mapping of the sixth base. Genome Biol. 2011 Jun 20; 12(6):116. PMID: 21682934; PMCID: PMC3218833.

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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.

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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.

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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.

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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.

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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.

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