Zhang:Publications

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. 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]
2. 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]
3. 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
4. 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]
5. 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

1. 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]
2. Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K. (2013) On the design of clone-based haplotyping. Genome Biology, 14:R100
3. Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Belmonte JC. (2013) Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell. in press, PMID:23982742
4. Shen L*, Wu H*, Diep D, Yamaguchi S, D'Alessio AC, Fung HL, Zhang K, Zhang Y. (2013) Genome-wide analysis reveals TET- and TDG-Dependent 5-Methylcytosine oxidation dynamics. Cell, 10.1016/j.cell.2013.04.002
5. Ruiz S*, Gore A*, Li Z, Panopoulos AD, Montserrat N, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Schöler HR, Zhang K, Izpisua Belmonte JC. (2013) Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming. Nature Communications, 4:1382, doi:10.1038/ncomms2381
6. Yamaguchi S, Hong K, Liu R, Inoue A, Shen L, Zhang K, Zhang Y. (2013). Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming. Cell Research doi: 10.1038/cr.2013.22
7. Yamaguchi S*, Hong K*, Liu R*, Shen L, Inoue A, Diep D, Zhang K, Zhang Y. (2012) Tet1 controls meiosis by regulating meiotic gene expression. Nature, 492:443-7
8. 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. (2012) Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 151:1431-42
9. Panopoulos AD, Yanes O, Ruiz S, Kida Y, Diep D, Tautenhahn R, Herrerías A, Batchelder EM, Plongthongkum N, Lutz M, Berggren WT, Zhang K, Evans RM, Siuzdak G, Izpisua Belmonte JC. (2011) The metabolome of induced pluripotent stem cells reveals metabolic changes occuring in somatic cell reprogramming. Cell Research doi: 10.1038/cr.2011.177.
10. Ruiz S*, Diep D*, Gore A, Panopoulosa AD, Montserratd N, Plongthongkum N, Kumara S, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Kan NG, Schöler HR, Mercola M, Zhang K, Belmonte JCI. (2012) Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proc Natl Acad Sci USA. 109:16196-201
11. Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo TB, Rebbeck TR, Zhang K, Akey JM, Tishkoff SA. (2012) Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse african hunter-gatherers. Cell, 150:457-69
12. Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow M, Cano C, Chou MF, Chung WK, Douglas SM, Estep P, Gore A, Hulick P, Labarga A, Lee J, Lunshof J, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters B, Raman AM, Reinhoff HY, Robasky K, Wheeler M, Vandewege W, Vorhaus D, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM (2012) A Public Resource Facilitating Clinical Use of Genomes. Proc Natl Acad Sci USA. 109:11920-7
13. 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
14. Noggle S, Fung HL, Gore A, Martinez H, Crumm C, Prosser R, Oum K, Paull D, Druckenmiller S, Freeby M, Greenberg E, Zhang K, Goland R, Sauer MV, Leibel RL, Egli D. (2011) Human oocytes reprogram somatic cells to a pluripotent state. Nature 478:70-5
15. Lee EJ, Pei L, Srivastava G, Trupit J, Kushwaha G, Choi JH, Robertson K, Wang X, Colbourne J, Zhang L, Schroth G, Xu D, Zhang K, Shi H. (2011) Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Research 10.1093/nar/gkr598.
16. Chen CH, Cho SH, Chiang HI, Tsai F, Zhang K, Lo YH. (2011) Specific sorting of single bacterial cells with micro-FACS and tyramide signal amplification-FISH. Analytical Chemistry 83:7269-75
17. Guo J, Ma D, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H. (2011) Neuronal activity modifies DNA methylation landscape in the adult brain. Nature Neuroscience, 14:1345-51
18. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. (2011) Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 14:1345-51 Journal web link.
19. Diep D, Zhang K. (2011) Genome-wide mapping of the sixth base. Genome Biology, 12:116 Journal web link
20. 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, Plongthongkum N, Fung HL, Zhang K, Loring JF, Laurent LC, Belmonte JC. (2011) Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. Cell Stem Cell 8:688-94 Journal web link
21. Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, Min J, Nicholson T, Chen T, Xu G, Shi Y, Zhang K, Shi YG. (2011). Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells. Molecular cell. 42:451-64 Journal web link
22. Howden SE, Gore A, Li Z, Fung HL, Nisler BS, Nie J, Chen G, McIntosh BE, Goulbranson DR, Diol NR, Taapken SM, Vereide DT, Montgomery KD, Zhang K, Gamm DM, Thomson JA. (2011) Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy.PNAS 108:6537-42
23. Liu GH, Barkho BZ, Ruiz S, Diep D, Qu J, Yang SL, Panopoulos AD, Suzuki K, Kurian L, Walsh C, Thompson J, Boue S, Fung HL, Sancho-Martinez I, Zhang K, Iii JY, Belmonte JC. (2011). Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature 472:221-5
24. 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
25. Shoemaker R, Wang W, Zhang K (2010) Mediators and dynamics of DNA methylation. WIRES Biol Med. [PMID: 20878927]
26. Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C., Gibbs R, Zhang K, Chen R. (2010). Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Research, 20: 981-988.
27. 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
28. 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 PDF
29. Chen AE, Egli D, Niakan K, Deng J, Akutsu H, Yamaki M, Cowan C, Fitz-Gerald C, Zhang K, 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. Cell Stem Cell 4:103-6
30. Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K*, Church GM*. (2009) A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. PLoS Genetics, 5(11):e1000718.
31. Zhang K, 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. Nature Methods, 6:613-8