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George M. Church, PhD

Publications

  • Yaung SJ, Esvelt KM, Church GM.CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4.PLoS ONE. 2014;9(6):e98811.
    24886988
  • Bonde MT, Kosuri S, Genee HJ, Sarup-Lytzen K, Church GM, Sommer MO, Wang HH.Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides.ACS Synth Biol. 2014 May 23.
    24856730
  • Ball MP, Bobe JR, Chou MF, Clegg T, Estep PW, Lunshof JE, Vandewege W, Zaranek A, Church GM.Harvard Personal Genome Project: lessons from participatory public research.Genome Med. 2014;6(2):10.
    24713084
  • Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM.High-resolution antibody dynamics of vaccine-induced immune responses.Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4928-33.
    24639495
  • Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R.Realizing the potential of synthetic biology.Nat Rev Mol Cell Biol. 2014 Apr;15(4):289-94.
    24622617
  • Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM.Highly multiplexed subcellular RNA sequencing in situ.Science. 2014 Mar 21;343(6177):1360-3.
    24578530
  • Umbarger MA, Kennedy CJ, Saunders P, Breton B, Chennagiri N, Emhoff J, Greger V, Hallam S, Maganzini D, Micale C, Nizzari MM, Towne CF, Church GM, Porreca GJ.Next-generation carrier screening.Genet Med. 2014 Feb;16(2):132-40.
    23765052
  • Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH.Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences.J Immunol. 2014 Feb 1;192(3):867-74.
    24376267
  • Robasky K, Lewis NE, Church GM.The role of replicates for error mitigation in next-generation sequencing.Nat Rev Genet. 2014 Jan;15(1):56-62.
    24322726
  • O'Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D.pLogo: a probabilistic approach to visualizing sequence motifs.Nat Methods. 2013 Dec;10(12):1211-2.
    24097270
  • Tzur YB, Friedland AE, Nadarajan S, Church GM, Calarco JA, Colaiácovo MP.Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system.Genetics. 2013 Nov;195(3):1181-5.
    23979579
  • Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM.Orthogonal Cas9 proteins for RNA-guided gene regulation and editing.Nat Methods. 2013 Nov;10(11):1116-21.
    24076762
  • Eroshenko N, Church GM.Mutants of Cre recombinase with improved accuracy.Nat Commun. 2013;4:2509.
    24056590
  • Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM.CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering.Nat Biotechnol. 2013 Sep;31(9):833-8.
    23907171
  • Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F.Optical control of mammalian endogenous transcription and epigenetic states.Nature. 2013 Aug 22;500(7463):472-6.
    23877069
  • Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA.Heritable genome editing in C. elegans via a CRISPR-Cas9 system.Nat Methods. 2013 Aug;10(8):741-3.
    23817069
  • Eminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG.Quantification of microRNA expression with next-generation sequencing.Curr Protoc Mol Biol. 2013 Jul;Chapter 4:Unit 4.17.
    23821442
  • Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM.Barcoding cells using cell-surface programmable DNA-binding domains.Nat Methods. 2013 Mar 17.
    23503053
  • Dicarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM.Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.Nucleic Acids Res. 2013 Apr 1;41(7):4336-43.
    23460208
  • Larman HB, Laserson U, Querol L, Verhaeghen K, Solimini NL, Xu GJ, Klarenbeek PL, Church GM, Hafler DA, Plenge RM, Nigrovic PA, De Jager PL, Weets I, Martens GA, O'Connor KC, Elledge SJ.PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis.J Autoimmun. 2013 Mar 13.
    23497938
  • Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM.RNA-guided human genome engineering via Cas9.Science. 2013 Feb 15;339(6121):823-6.
    23287722
  • Rockwell G, Guido NJ, Church GM.Redirector: designing cell factories by reconstructing the metabolic objective.PLoS Comput. Biol. 2013 Jan;9(1):e1002882.
    23341769
  • Plank M, Hu G, Silva AS, Wood SH, Hesketh EE, Janssens G, Macedo A, de Magalhães JP, Church GM.An analysis and validation pipeline for large-scale RNAi-based screens.Sci Rep. 2013;3:1076.
    23326633
  • Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi S, Forster AC, Jewett MC, Church GM.Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multi-enzyme catalysis.ACS Synth Biol. 2012 Feb 16;1(2):43-52.
    22737598
  • Church GM, Gao Y, Kosuri S.Next-generation digital information storage in DNA.Science. 2012 Sep 28;337(6102):1628.
    22903519
  • Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM.Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection.Nucleic Acids Res. 2012 Sep 1;40(17):e132.
    22638574
  • Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM.Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases.PLoS ONE. 2012;7(9):e44638.
    22957093
  • Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM.Genome-scale promoter engineering by coselection MAGE.Nat Methods. 2012 Jun;9(6):591-3.
    22484848
  • Alon S, Mor E, Vigneault F, Church GM, Locatelli F, Galeano F, Gallo A, Shomron N, Eisenberg E.Systematic identification of edited microRNAs in the human brain.Genome Res. 2012 Aug;22(8):1533-40.
    22499667
  • Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF.How accurate can genetic predictions be?.BMC Genomics. 2012 Jul 24;13(1):340.
    22827772
  • Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, 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.A public resource facilitating clinical use of genomes.Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7.
    22797899
  • Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R.Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.Nature. 2012 Jul 12;487(7406):190-5.
    22785314
  • Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P.Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription.Nat Biotechnol. 2011 Feb;29(2):149-53.
    21248753
  • Kosuri S, Eroshenko N, Leproust EM, Super M, Way J, Li JB, Church GM.Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips.Nat Biotechnol. 2010 Dec;28(12):1295-9.
    21113165
  • Matzas M, Stähler PF, Kefer N, Siebelt N, Boisguérin V, Leonard JT, Keller A, Stähler CF, Häberle P, Gharizadeh B, Babrzadeh F, Church GM.High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing.Nat Biotechnol. 2010 Dec;28(12):1291-4.
    21113166
  • Mosberg JA, Lajoie MJ, Church GM.Lambda Red Recombination in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate.Genetics. 2010 Nov;186(3):791-9.
    20813883
  • Schwartz D, Church GM.Collection and motif-based prediction of phosphorylation sites in human viruses.Sci Signal. 2010;3(137):rs2.
    20807955
  • Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ.Reprogramming of T cells from human peripheral blood.Cell Stem Cell. 2010 Jul 2;7(1):15-9.
    20621044
  • Zaranek AW, Levanon EY, Zecharia T, Clegg T, Church GM.A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.PLoS Genet. 2010;6(5):e1000954.
    20531933
  • Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB.Clinical assessment incorporating a personal genome.Lancet. 2010 May 1;375(9725):1525-35.
    20435227
  • Lunshof JE, Bobe J, Aach J, Angrist M, Thakuria JV, Vorhaus DB, Hoehe MR, Church GM.Personal genomes in progress: from the human genome project to the personal genome project.Dialogues Clin Neurosci. 2010;12(1):47-60.
    20373666
  • Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA.Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.Science. 2010 Jan 1;327(5961):78-81.
    19892942
  • Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross JA, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I.Generation of functional human hepatic endoderm from human induced pluripotent stem cells.Hepatology. 2010 Jan;51(1):329-35.
    19877180
  • Carr PA, Church GM.Genome engineering.Nat Biotechnol. 2009 Dec;27(12):1151-62. Review.
    20010598
  • Barak M, Levanon EY, Eisenberg E, Paz N, Rechavi G, Church GM, Mehr R.Evidence for large diversity in the human transcriptome created by Alu RNA editing.Nucleic Acids Res. 2009 Nov;37(20):6905-15.
    19740767
  • Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM.A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.PLoS Genet. 2009 Nov;5(11):e1000718.
    19911041
  • Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV.The challenges of sequencing by synthesis.Nat Biotechnol. 2009 Nov;27(11):1013-23. Review.
    19898456
  • Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM.Multiplex padlock targeted sequencing reveals human hypermutable CpG variations.Genome Res. 2009 Sep;19(9):1606-15.
    19525355
  • Sommer MO, Dantas G, Church GM.Functional characterization of the antibiotic resistance reservoir in the human microflora.Science. 2009 Aug 28;325(5944):1128-31.
    19713526
  • Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM.Rapid prototyping of 3D DNA-origami shapes with caDNAno.Nucleic Acids Res. 2009 Aug;37(15):5001-6.
    19531737
  • Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS.A highly annotated whole-genome sequence of a Korean individual.Nature. 2009 Aug 20;460(7258):1011-5.
    19587683
  • Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM.Large-scale identification of genetic design strategies using local search.Mol Syst Biol. 2009;5:296.
    19690565
  • Khoury MJ, McBride CM, Schully SD, Ioannidis JP, Feero WG, Janssens AC, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, Duross A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SL, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts JS, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J, .The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop.Genet Med. 2009 Aug;11(8):559-67.
    19617843
  • Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM.Programming cells by multiplex genome engineering and accelerated evolution.Nature. 2009 Aug 13;460(7257):894-8.
    19633652
  • 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.
    19620972
  • Li JB,Levanon EY,Yoon JK,Aach J,Xie B,Leproust E,Zhang K,Gao Y,Church GM.Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing.Science. 2009 May 29;324(5931):1210-3.
    19478186
  • Ball MP,Li JB,Gao Y,Lee JH,LeProust EM,Park IH,Xie B,Daley GQ,Church GM.Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.Nat Biotechnol. 2009 Apr;27(4):361-8.
    19329998
  • de Magalhaes JP,Curado J,Church GM.Meta-analysis of age-related gene expression profiles identifies common signatures of aging.Bioinformatics. 2009 Apr 1;25(7):875-81.
    19189975
  • Vigneault F,Sismour AM,Church GM.Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation.Nat Methods. 2008 Sep;5(9):777-9.
    19160512
  • de Magalhaes JP,Budovsky A,Lehmann G,Costa J,Li Y,Fraifeld V,Church GM.The Human Ageing Genomic Resources: online databases and tools for biogerontologists.Aging Cell. 2009 Feb;8(1):65-72. Review.
    18986374
  • Schwartz D,Chou MF,Church GM.Predicting protein post-translational modifications using meta-analysis of proteome scale data sets.Mol Cell Proteomics. 2009 Feb;8(2):365-79.
    18974045
  • Snitkin ES,Dudley AM,Janse DM,Wong K,Church GM,Segre D.Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions.Genome Biol. 2008;9(9):R140.
    18808699
  • Lunshof JE,Chadwick R,Church GM.Hippocrates revisited? Old ideals and new realities.Genomic Med. 2008 Jan;2(1-2):1-3.
    18716915
  • Dantas G, Sommer MO, Oluwasegun RD, Church GM.Bacteria subsisting on antibiotics.Science. 2008 Apr 4;320(5872):100-3.
    18388292
  • Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW.Patterns and implications of gene gain and loss in the evolution of Prochlorococcus.PLoS Genet. 2007 Dec;3(12):e231.
    18159947
  • Bang D, Church GM.Gene synthesis by circular assembly amplification.Nat Methods. 2008 Jan;5(1):37-9.
    18037891
  • Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J.Multiplex amplification of large sets of human exons.Nat Methods. 2007 Nov;4(11):931-6.
    17934468
  • Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW.Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution.Nature. 2007 Sep 6;449(7158):83-6.
    17805294
  • Conrad C, Zhu J, Conrad C, Schoenfeld D, Fang Z, Ingelsson M, Stamm S, Church G, Hyman BT.Single molecule profiling of tau gene expression in Alzheimer's disease.J Neurochem. 2007 Nov;103(3):1228-36.
    17727636
  • de Magalhes JP, Church GM.Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging.Mech Ageing Dev.;128(5-6):355-64.
    17459455
  • de Magalhaes JP, Sedivy JM, Finch CE, Austad SN, Church GM.A proposal to sequence genomes of unique interest for research on aging.J Gerontol A Biol Sci Med Sci. 2007 Jun;62(6):583-4.
    17595413
  • Bakal C, Aach J, Church G, Perrimon N.Quantitative morphological signatures define local signaling networks regulating cell morphology.Science. 2007 Jun 22;316(5832):1753-6.
    17588932
  • Wright MA, Kharchenko P, Church GM, Segre D.Chromosomal periodicity of evolutionarily conserved gene pairs.Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10559-64.
    17563360
  • Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, Church GM, Seidman CE, Seidman JG.Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy.Science. 2007 Jun 8;316(5830):1481-4.
    17556586
  • Bugl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, Endy D.DNA synthesis and biological security.Nat Biotechnol. 2007 Jun;25(6):627-9. Review.
    17557094
  • de Magalhes JP, Costa J, Church GM.An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts.J Gerontol A Biol Sci Med Sci. 2007 Feb;62(2):149-60.
    17339640
  • Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K.Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells.Mol Cell. 2006 Nov 17;24(4):593-602.
    17188034
  • Reppas NB, Wade JT, Church GM, Struhl K.The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.Mol Cell. 2006 Dec 8;24(5):747-57.
    17157257
  • Forster AC, Church GM.Synthetic biology projects in vitro.Genome Res. 2007 Jan;17(1):1-6. Review.
    17151344
  • Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA.PEPPeR: A platform for experimental proteomic pattern recognition.Mol Cell Proteomics. 2006 Oct;5(10):1927-41.
    16857664
  • Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW.Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.Mol Syst Biol. 2006;2:53.
    17016519
  • Derti A, Roth FP, Church GM, Wu CT.Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.Nat Genet. 2006 Oct;38(10):1216-20.
    16998490
  • Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification.Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14062-7.
    16968785
  • Forster AC, Church GM.Towards synthesis of a minimal cell.Mol Syst Biol. 2006;2:45. Review.
    16924266
  • Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK.A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.Nat Biotechnol. 2006 Jul;24(7):832-840.
    16823376
  • Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM.Sequencing genomes from single cells by polymerase cloning.Nat Biotechnol. 2006 Jun;24(6):680-6.
    16732271
  • Kharchenko P, Church GM, Vitkup D.Expression dynamics of a cellular metabolic network.Mol Syst Biol. 2005;1:2005.0016.
    16729051
  • Dudley AM, Janse DM, Tanay A, Shamir R, Church GM.A global view of pleiotropy and phenotypically derived gene function in yeast.Mol Syst Biol. 2005;1:2005.0001.
    16729036
  • Church GM.The personal genome project.Mol Syst Biol. 2005;1:2005.0030.
    16729065
  • Church GM.From systems biology to synthetic biology.Mol Syst Biol. 2005;1:2005.0032.
    16729067
  • Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM.Identifying metabolic enzymes with multiple types of association evidence.BMC Bioinformatics. 2006;7:177.
    16571130
  • Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM.Long-range polony haplotyping of individual human chromosome molecules.Nat Genet. 2006 Mar;38(3):382-7.
    16493423
  • Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM.An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes.PLoS Genet. 2006 Feb;2(2):e16.
    16482229
  • Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM.MapQuant: open-source software for large-scale protein quantification.Proteomics. 2006 Mar;6(6):1770-82.
    16470651
  • Church GM.Genomes for all.Sci Am. 2006 Jan;294(1):46-54.
    16468433
  • de Magalhes JP, Church GM.Cells discover fire: employing reactive oxygen species in development and consequences for aging.Exp Gerontol. 2006 Jan;41(1):1-10.
    16226003
  • Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM.Accurate multiplex polony sequencing of an evolved bacterial genome.Science. 2005 Sep 9;309(5741):1728-32.
    16081699
  • de Magalhes JP, Church GM.Genomes optimize reproduction: aging as a consequence of the developmental program.Physiology (Bethesda). 2005 Aug;20:252-9.
    16024513
  • Ahmad QR, Nguyen DH, Wingerd MA, Church GM, Steffen MA.Molecular weight assessment of proteins in total proteome profiles using 1D-PAGE and LC/MS/MS.Proteome Sci. 2005 Jun 8;3(1):6.
    15941491
  • Zhu Z, Shendure J, Church GM.Discovering functional transcription-factor combinations in the human cell cycle.Genome Res. 2005 Jun;15(6):848-55.
    15930495
  • Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G.Accurate multiplex gene synthesis from programmable DNA microchips.Nature. 2004 Dec 23;432(7020):1050-4.
    15616567
  • Kharchenko P, Vitkup D, Church GM.Filling gaps in a metabolic network using expression information.Bioinformatics. 2004 Aug 4;20 Suppl 1:I178-I185.
    15262797
  • Catic A, Collins C, Church GM, Ploegh HL.Preferred in vivo ubiquitination sites.Bioinformatics. 2004 Dec 12;20(18):3302-7.
    15256413
  • Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS.Digital quantitative measurements of gene expression.Biotechnol Bioeng. 2004 Apr 20;86(2):117-24.
    15052631
  • Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G.Identification of many microRNAs that copurify with polyribosomes in mammalian neurons.Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):360-5.
    14691248
  • Zhu J, Shendure J, Mitra RD, Church GM.Single molecule profiling of alternative pre-mRNA splicing.Science. 2003 Aug 8;301(5634):836-8.
    12907803
  • Mitra RD, Shendure J, Olejnik J, Edyta-Krzymanska-Olejnik , Church GM.Fluorescent in situ sequencing on polymerase colonies.Anal Biochem. 2003 Sep 1;320(1):55-65.
    12895469
  • Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M.Identification of foreign gene sequences by transcript filtering against the human genome.Nat Genet. 2002 Feb;30(2):141-2.
    11788827
  • Badarinarayana V, Estep PW, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM.Selection analyses of insertional mutants using subgenic-resolution arrays.Nat Biotechnol. 2001 Nov;19(11):1060-5.
    11689852
  • Pilpel Y, Sudarsanam P, Church GM.Identifying regulatory networks by combinatorial analysis of promoter elements.Nat Genet. 2001 Oct;29(2):153-9.
    11547334
  • Bulyk ML, Huang X, Choo Y, Church GM.Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7158-63.
    11404456
  • Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J.Computational comparison of two draft sequences of the human genome.Nature. 2001 Feb 15;409(6822):856-9.
    11237010
  • Mitra RD, Church GM.In situ localized amplification and contact replication of many individual DNA molecules.Nucleic Acids Res. 1999 Dec 15;27(24):e34.
    10572186
  • Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM.Systematic determination of genetic network architecture.Nat Genet. 1999 Jul;22(3):281-5.
    10391217
  • Bulyk ML, Gentalen E, Lockhart DJ, Church GM.Quantifying DNA-protein interactions by double-stranded DNA arrays.Nat Biotechnol. 1999 Jun;17(6):573-7.
    10385322
  • Chen T, He HL, Church GM.Modeling gene expression with differential equations.Pac Symp Biocomput. 1999:29-40.
    10380183
  • McGuire AM, De Wulf P, Church GM, Lin EC.A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli.Mol Microbiol. 1999 Apr;32(1):219-21.
    10216875
  • Johnson JM, Church GM.Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps.J Mol Biol. 1999 Apr 2;287(3):695-715.
    10092468
  • Robison K, McGuire AM, Church GM.A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.J Mol Biol. 1998 Nov 27;284(2):241-54.
    9813115
  • Roth FP, Hughes JD, Estep PW, Church GM.Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.Nat Biotechnol. 1998 Oct;16(10):939-45.
    9788350
  • Tavazoie S, Church GM.Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli.Nat Biotechnol. 1998 Jun;16(6):566-71.
    9624689
  • Link AJ, Phillips D, Church GM.Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization.J Bacteriol. 1997 Oct;179(20):6228-37.
    9335267
  • Link AJ, Robison K, Church GM.Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.Electrophoresis. 1997 Aug;18(8):1259-313.
    9298646