Publications

Key publications [Google scholar page]

  • 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
  • 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
  • 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 Biotechnology31:1126–32 [Journal web link] [MIDAS animation]
  • 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
  • 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 [Journal web link] [Supplementary website]
  • 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 [Journal web link]
  • 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 [Journal web link] [Supplementary website]
  • 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 [Journal web link] [Supplementary website]

All publications:

  1. Bock C, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, Holcomb T, Hussmann D, Ito M, Kläver R, Kreutz M, Kulis M, Lopez V, Nair SS, Paul DS, Plongthongkum N, Qu W, Queirós AC, Reinicke F, Sauter G, Schlomm T, Statham A, Stirzaker C, Strogantsev R, Urdinguio RG, Walter K, Weichenhan D, Weisenberger DJ, Beck S, Clark SJ, Esteller M, Ferguson-Smith AC, Fraga MF, Guldberg P, Hansen LL, Laird PW, Martín-Subero JI, Nygren AO, Peist R, Plass C, Shames DS, Siebert R, Sun X, Tost J, Walter J, Zhang K. (2016) Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology, doi:10.1038/nbt.3605
  2. 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
  3. 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
  4. Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV. (2016) Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nature Methods, doi: 10.1038/nmeth.3734
  5. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nature Protocols. 10:442-58
  6. 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. (2015) Humanized Mice Reveal Differential Immunogenicity of Cells Derived from Autologous Induced Pluripotent Stem Cells. Cell Stem Cell 17:353-9
  7. Jiang W, Liu Y, Liu R, Zhang K, Zhang Y. (2015) LncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression. Cell Reports. 11:137-48
  8. Johannesson B, Sagi I, Gore A, Paull D, Yamada M, Golan-Lev T, Li Z, LeDuc C, Shen Y, Stern S, Xu N, Ma H, Kang E, Mitalipov S, Sauer MV, Zhang K, Benvenisty N, Egli D.(2014). Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors. Cell Stem Cell. 15(5):634-42
  9. Plongthongkum N, Diep DH, Zhang K. (2014) Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 15, 647–661
  10. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. (2014) Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 15:12-3
  11. Plongthongkum N, van Eijk KR, de Jong S, Wang T, Sul JH, Boks MP, Kahn RS, Fung HL, Ophoff RA, Zhang K. (2014) Characterization of genome-methylome interactions in 22 nuclear pedigrees. PLoS One. 9:e99313
  12. Li Z, Lu H, Yang W, Yong J, Zhang Z, Zhang K, Deng H, Xu Y. (2014) Mouse SCNT ESCs Have Lower Somatic Mutation Load Than Syngeneic iPSCs. Stem Cell Reports 2:399-405
  13. Liu GH, Suzuki K, Li M, Qu J, Montserrat N, Tarantino C, Gu Y, Yi F, Xu X, Zhang W, Ruiz S, Plongthongkum N, Zhang K, Masuda S, Nivet E, Tsunekawa Y, Soligalla RD, Goebl A, Aizawa E, Kim NY, Kim J, Dubova I, Li Y, Ren R, Benner C, Del Sol A, Bueren J, Trujillo JP, Surralles J, Cappelli E, Dufour C, Esteban CR, Izpisua Belmonte JC. (2014) Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. Nature Communications. 5:4330
  14. 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. (2014) Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell. 5:59-68
  15. Nag A, Savova V, Fung HL, Miron A, Yuan GC, Zhang K, Gimelbrant AA. (2013) Chromatin signature of widespread monallelic expression. eLife, 2013;2:e01256
  16. Batmalle CS, Chiang HI, Zhang K, Lomas MW, Martiny AC. (2013) Development and bias assessment of a method for targeted metagenomic sequencing of marine Cyanobacteria. Applied and Environmental Microbiology, doi: 10.1128/AEM.02834-13
  17. Woodruff G, Young JE, Martinez FJ, Buen F, Gore A, Kinaga J, Li Z, Yuan SH, Zhang K, Goldstein LS. (2013) The Presenilin-1 ΔE9 Mutation Results in Reduced γ-Secretase Activity, but Not Total Loss of PS1 Function, in Isogenic Human Stem Cells. Cell Report 5(4):974-85
  18. 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, 31:1126–32
  19. 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
  20. 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, 153:692-706
  21. 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
  22. 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 23:329–339
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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 [Journal web link][Supplementary website]
  29. 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 [Journal web link]
  30. 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.
  31. 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 [Journal web link]
  32. Guo JU, Ma DK, 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 the DNA methylation landscape in the adult brain. Nature Neuroscience 14:1345-51[Journal web link]
  33. 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.
  34. 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. 43:768-775
  35. Diep D, Zhang K. (2011) Genome-wide mapping of the sixth base. Genome Biology, 12:116 [Journal web link]
  36. 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]
  37. 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]
  38. 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 [Journal web link]
  39. 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 [Journal web link]
  40. 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, Yates, J III, Belmonte JC.. (2011). Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature [Journal web link]
  41. Shoemaker R, Wang W, Zhang K (2010) Mediators and dynamics of DNA methylation. WIRES Biol Med. [Journal web link]
  42. 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 [Journal web link]
  43. 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.[Journal web link]
  44. 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 [Journal web link]
  45. 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
  46. 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.
  47. 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
  48. Li JB*, Gao Y*, Aach J*, Zhang K*, 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. Genome Research, 19:1606-15.
  49. Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing, Science 324:1210-13
  50. Porreca PJ*, Zhang K*, 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. Nature Methods 4:931-6.
  51. Kowalchuk GA, Speksnijder AG, Zhang K, Goodman RM, van Veen JA. (2007) Finding the needles in the metagenome haystack. Microbial Ecology 53:475-85
  52. Zhang K, Lott ST, Jin L, Killary AM. (2007) Fine mapping of the NRC-1 tumor suppressor locus within chromosome 3p12. Biochemical and Biophysical Research Communications 360:531-538
  53. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. (2006) Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 24:680-686
  54. Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. (2006) Polony haplotyping of individual human chromosome molecules. Nature Genetics 38:382-387.
  55. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732.
  56. Zhang K, and Jin L. (2003) HaploBlockFinder: haplotype block analyses. Bioinformatics 19:1300-1301
  57. Zhang K, 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. Human Genetics 113: 51-59.
  58. Akey JM, Zhang K, Xiong M, and Jin L. (2003) The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium. Molecular Biology and Evolution 20: 232-242.
  59. Chen Z, Zhang K, 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. Clinical and Experimental Metastasis 20:335-342.
  60. Akey JM, Zhang G, Zhang K, Jin L and Shriver M. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research 12: 1805-1814.
  61. Wang N, Akey JM, Zhang K, Chakraborty R, Jin L. (2002) Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. American Journal of Human Genetics 71: 1227-1234.
  62. Akey DT, Akey JM, Zhang K, Jin L. (2002) Assaying DNA methylation based on high-throughput melting curve approaches. Genomics 80: 376-384.
  63. Akey JM, Zhang K (co-first author), Xiong M, Doris P, Jin L. (2001) The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. American Journal of Human Genetics, 68:1447-1456.