Kun Zhang * UCSD Profiles

Kun Zhang

Title(s)	Professor, Bioengineering
School	Academic Aff
Phone	858-822-7876
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Research

Research Activities and Funding

KULMAP: Human Kidney, urinary tract and lung mapping center
NIH/NHLBI U54HL145608Sep 25, 2018 - 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 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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Wu Y, Tamayo P, Zhang K. Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. Cell Syst. 2018 Dec 26; 7(6):656-666.e4. PMID: 30528274.

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Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. Cell Syst. 2018 Nov 28; 7(5):548-555.e8. PMID: 30448000.

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Diep D, Zhang K. Efficient and fast identification of differentially methylated regions using whole-genome bisulfite sequencing data. J Genet Genomics. 2018 Aug 20; 45(8):455-457. PMID: 30172582.

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Diep D, Zhang K. Reply to 'DNA methylation haplotypes as cancer markers'. Nat Genet. 2018 Aug; 50(8):1063-1066. PMID: 30054596.

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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.

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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 01; 36(1):70-80. PMID: 29227469.

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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 11 21; 114(47):12512-12517. PMID: 29078313.

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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 07 20; 7(1):6031. PMID: 28729663.

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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 02 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 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.

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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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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.

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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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