Zhang:Publications: Difference between revisions

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#Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, <b>Diep D</b>, Briem E, <b>Zhang K</b>, Irizarry RA, Feinberg AP. <b>(2011)</b> Increased methylation variation in epigenetic domains across cancer types. <b>Nature Genetics</b>. [http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.865.html AOP].
===Key Publications:===
#<b>Diep D, Zhang K. (2011)</b> Genome-wide mapping of the sixth base. <b>Genome Biology</b>, 12:116 [http://genomebiology.com/2011/12/6/116 Journal web link]
<u>This is a short list of publications that represents our primary research interests. Members of the Zhang lab are highlighted in bold.</u>
#Liu GH, Suzuki K, Qu J, Yi F, Li M, Sancho-Martinez I, Yi F, Li M, Kumar S, Nivet E, Kim J, Soligalla RD, Dubova I, Goebl A, <b>Plongthongkum N, Fung HL, Zhang K,</b> Loring JF, Laurent LC, Belmonte JC. <b>(2011)</b> Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. <b>Cell Stem Cell</b> 8:688-94 [http://www.cell.com/cell-stem-cell/abstract/S1934-5909%2811%2900220-7 Journal web link]
#<b>Lake BB*</b>, Ai R*, Kaeser GE*, Salathia NS*, Yung YC, <b>Liu R</b>, Wildberg A, <b>Gao D, Fung HL</b>, Chen S, Vjayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fang JB, Wang W, Chun J, <b>Zhang K</b>. (2016) Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. <b>Science</b>, 352:1586-90
#Xu Y, Wu F, Tan L, Kong L, Xiong L, <b>Deng J</b>, Barbera AJ, Zheng L, Zhang H, Huang S, Min J, Nicholson T, Chen T, Xu G, Shi Y, <b>Zhang K</b>, Shi YG. (2011). Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells. <b>Molecular cell</b>. [http://www.cell.com/molecular-cell/abstract/S1097-2765%2811%2900283-8 AOP]
#<b>Sos B, Fung HL, Gao DR</b>, Osothprarop TF, Kia A, He MM, <b>Zhang K</b>. (2016) Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. <b>Genome Biology</b>, 17:20
#Howden SE, <b>Gore A, Li Z, Fung HL</b>, Nisler BS, Nie J, Chen G, McIntosh BE, Goulbranson DR, Diol NR, Taapken SM, Vereide DT, Montgomery KD, <b>Zhang K</b>, Gamm DM, Thomson JA. (2011) Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy.<b>PNAS</b> [http://www.pnas.org/content/early/2011/03/30/1103388108.abstract 108:6537-42]  
#<b>Gole J, Gore A, Richards A</b>, Chiu YJ, <b>Fung HL</b>, Bushman D, <b>Chiang HI</b>, Chun J, Lo YH, <b>Zhang K</b>. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. <b>Nature Biotechnology</b>, doi:10.1038/nbt.2720 [[http://youtu.be/-oSp8iBXdgk MIDAS animation]]
#Liu GH, Barkho BZ, Ruiz S, <b>Diep D</b>, Qu J, Yang SL, Panopoulos AD, Suzuki K, Kurian L, Walsh C, Thompson J, Boue S, <b>Fung HL</b>, Sancho-Martinez I, <b>Zhang K</b>, Iii JY, Belmonte JC. (2011). Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. <b>Nature</b> 472:221-5
#<b>Diep D*, Plongthongkum N*, Gore A*, Fung HL, Shoemaker R, Zhang K</b>. (2012) Library-free methylation sequencing with bisulfite padlock probes. <b>Nature Methods</b>, 9:270-2 [[http://genome-tech.ucsd.edu/public/Gen2_BSPP/ Supplementary website]]
# <b>Gore A*, Li Z*, Fung HL</b>, Young JE, Agarwal S, Antosiewica-Gourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JK, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Belmonte JCI, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LSB, <b>Zhang K</b>. (2011) Somatic coding mutations in human induced pluripotent stem cells. <b>Nature</b> 471:63-7
# <b>Gore A*, Li Z*, Fung HL</b>, Young JE, Agarwal S, Antosiewica-Gourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JK, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Belmonte JCI, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LSB, <b>Zhang K</b>. (2011) Somatic coding mutations in human induced pluripotent stem cells. <b>Nature</b> 471:63-7
#Shoemaker R, Wang W, <b>Zhang K</b> (2010) Mediators and dynamics of DNA methylation. <b>WIRES Biol Med.</b> [PMID: 20878927]
#<b>Shoemaker R, Deng J</b>, Wang W, <b>Zhang K</b>. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. <b>Genome Research</b> 20:883-9 [[http://genome-tech.ucsd.edu/public/ASM/ Supplementary website]]
#Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C., Gibbs R, <b>Zhang K</b>, Chen R. (2010). Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. <b>Genome Research</b>, 20: 981-988.
#<b>Deng J, Shoemaker R</b>, Xie B, <b>Gore A</b>, 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, <b>Zhang K</b>.(2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. <b>Nature Biotechnology</b>, 27:353-60 [[http://zhang.be.ucsd.edu/Users/kunzhang/www/public/NBT-RA20324 Supplementary website]]
#Shoemaker R, Deng J, Wang W, <b>Zhang K</b>. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. <b>Genome Research</b> 20:883-9
 
#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, <b>Zhang K</b>.(2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. <b>Nature Biotechnology</b>, 27:353-60 [http://genome-tech.ucsd.edu/public/NBT-RA20324/Deng-NBT-2009.pdf PDF]
===[http://zhang.eng.ucsd.edu/about-us All Publications]===
#Chen AE, Egli D, Niakan K, Deng J, Akutsu H, Yamaki M, Cowan C, Fitz-Gerald C, <b>Zhang K</b>, Melton DA, and Eggan K. (2009) Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines. <b>Cell Stem Cell</b> 4:103-6
#Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, <b>Zhang K*</b>, Church GM*. (2009) A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. <b>PLoS Genetics, </b>[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000718  5(11):e1000718].
#<b>Zhang K</b>, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, LeProust EM, Eggan K, Church GM (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. <b>Nature Methods</b>, 6:613-8
#Li JB*, Gao Y*, Aach J*, <b>Zhang K*</b>, Kryukov G*, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev S, Church GM. (2009) Multiplex padlock capture and sequencing reveal human hypermutable CpG variations. <b>Genome Research</b>, 19:1606-15.
#Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, LeProust E, <b>Zhang K</b>, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing, <b>Science</b> 324:1210-13
#Porreca PJ*, <b>Zhang K*</b>, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. (2007) Multiplex amplification of large sets of human exons. <b>Nature Methods</b> 4:931-6.
#Kowalchuk GA, Speksnijder AG, <b>Zhang K</b>, Goodman RM, van Veen JA. (2007) Finding the needles in the metagenome haystack. <b>Microbial Ecology</b> 53:475-85
#<b>Zhang K</b>, Lott ST, Jin L, Killary AM. (2007) Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12. <b>Biochemical and Biophysical Research Communications</b> 360:531-538
#<b>Zhang K</b>, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. (2006) Sequencing genomes from single cells by polymerase cloning. <b>Nature Biotechnology</b> 24:680-686
#<b>Zhang K</b>, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. (2006) Polony haplotyping of individual human chromosome molecules. <b>Nature Genetics</b> 38:382-387.
#Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, <b>Zhang K</b>, Mitra RD, Church GM. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. <b>Science</b> 309:1728-1732.
#<b>Zhang K</b>, and Jin L. (2003) HaploBlockFinder: haplotype block analyses. <b>Bioinformatics</b> 19:1300-1301
#<b>Zhang K*</b>, Akey JM* (co-first author), Wang N, Xiong M, Chakraborty R, Jin L.(2003) Randomly distributed crossovers may generate block-like pattern of linkage disequibrium: An act of genetic drift. <b>Human Genetics</b> 113: 51-59.
#Akey JM, <b>Zhang K</b>, Xiong M, and Jin L. (2003) The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. <b>Molecular Biology and  Evolution</b> 20: 232-242. 
#Chen Z, <b>Zhang K</b>, Zhang X, Yuan XH, Yuan Z, Jin L, and Xiong M. (2003) Comparison of gene expression between metastatic derivatives and their poorly metastatic parental cells implicates crucial tumor-environment interaction in metastasis of head and neck squamous cell carcinoma. <b>Clinical and Experimental Metastasis</b> 20:335-342.
#Akey JM, Zhang G, Z<b>hang K</b>, Jin L and Shriver M. (2002) Interrogating a high-density SNP map for signatures of natural selection. <b>Genome Research</b> 12: 1805-1814.
#Wang N, Akey JM, <b>Zhang K</b>, Chakraborty R, Jin L. (2002)  Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. <b>American Journal of Human Genetics</b> 71: 1227-1234.
#Akey DT, Akey JM, <b>Zhang K</b>, Jin L. (2002) Assaying DNA methylation based on high-throughput melting curve approaches. <b>Genomics</b> 80: 376-384.
#Akey JM*, <b>Zhang K*</b>, Xiong M, Doris P, Jin L. (2001) The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. <b>American Journal of Human Genetics</b>, 68:1447-1456.

Latest revision as of 14:37, 22 September 2016

Key Publications:

This is a short list of publications that represents our primary research interests. Members of the Zhang lab are highlighted in bold.

  1. Lake BB*, Ai R*, Kaeser GE*, Salathia NS*, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vjayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fang JB, Wang W, Chun J, Zhang K. (2016) Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science, 352:1586-90
  2. Sos B, Fung HL, Gao DR, Osothprarop TF, Kia A, He MM, Zhang K. (2016) Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. Genome Biology, 17:20
  3. Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K. (2013) Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nature Biotechnology, doi:10.1038/nbt.2720 [MIDAS animation]
  4. Diep D*, Plongthongkum N*, Gore A*, Fung HL, Shoemaker R, Zhang K. (2012) Library-free methylation sequencing with bisulfite padlock probes. Nature Methods, 9:270-2 [Supplementary website]
  5. Gore A*, Li Z*, Fung HL, Young JE, Agarwal S, Antosiewica-Gourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JK, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Belmonte JCI, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LSB, Zhang K. (2011) Somatic coding mutations in human induced pluripotent stem cells. Nature 471:63-7
  6. Shoemaker R, Deng J, Wang W, Zhang K. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Research 20:883-9 [Supplementary website]
  7. 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.(2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology, 27:353-60 [Supplementary website]

All Publications

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