Photo of George M. Church,  PhD

George M. Church, PhD

Harvard Medical School

Harvard Medical School
Phone: (617) 432-7562
Fax: (617) 432-7266

George M. Church, PhD

Harvard Medical School

EDUCATIONAL TITLES

  • Robert Winthrop Professor of Genetics, Genetics, Harvard Medical School

DF/HCC PROGRAM AFFILIATION

Research Abstract

We use genomic systems biology to model

regulatory and enzymatic networks in mammalian and microbial cells. We develop technologies based on DNA-arrays, mass-spectrometry, automated microfluidics, polonies, and homologous recombination genome engineering. We have used these to discover genes affectng cell proliferation, alternative RNA splicing, and new regulatory sites involved in cell-cycle control and stress responses. We have developed integrated gene expression and functional genomics databases. For additional information see arep.med.harvard.edu.

Publications

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  • Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods 2015. PubMed
  • Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM. Highly efficient Cas9-mediated transcriptional programming. Nat Methods 2015; 12:326-8. PubMed
  • Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc 2015; 10:442-58. PubMed
  • Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res 2015; 43:e21. PubMed
  • Drmanac R, Peters BA, Church GM, Reid CA, Xu X. Accurate whole genome sequencing as the ultimate genetic test. Clin Chem 2014; 61:305-6. PubMed
  • Güell M, Yang L, Church GM. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 2014; 30:2968-70. PubMed
  • Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM. Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature 2014. PubMed
  • Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM, de Magalhães JP. The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics 2014. PubMed
  • Esvelt KM, Smidler AL, Catteruccia F, Church GM. Concerning RNA-guided gene drives for the alteration of wild populations. Elife 2014. PubMed
  • 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. PubMed
  • Kosuri S, Church GM. Large-scale de novo DNA synthesis: technologies and applications. Nat Methods 2014; 11:499-507. PubMed
  • 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; 111:4928-33. PubMed
  • Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 2014; 15:289-94. PubMed
  • 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; 343:1360-3. PubMed
  • 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; 16:132-40. PubMed
  • 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; 192:867-74. PubMed
  • Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol 2014; 10:760. PubMed
  • Robasky K, Lewis NE, Church GM. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet 2013; 15:56-62. PubMed
  • 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; 6:10. PubMed
  • Li J, Gu L, Aach J, Church GM. Improved cell-free RNA and protein synthesis system. PLoS ONE 2014; 9:e106232. PubMed
  • Yang L, Yang JL, Byrne S, Pan J, Church GM. CRISPR/Cas9-Directed Genome Editing of Cultured Cells. Curr Protoc Mol Biol 2014; 107:31.1.1-31.1.17. PubMed
  • Hoehe MR, Church GM, Lehrach H, Kroslak T, Palczewski S, Nowick K, Schulz S, Suk EK, Huebsch T. Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat Commun 2014; 5:5569. PubMed
  • 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:e98811. PubMed
  • O'Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D. pLogo: a probabilistic approach to visualizing sequence motifs. Nat Methods 2013; 10:1211-2. PubMed
  • 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; 195:1181-5. PubMed
  • 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; 10:1116-21. PubMed
  • 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; 31:833-8. PubMed
  • 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; 500:472-6. PubMed
  • 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; 10:741-3. PubMed
  • Eminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG. Quantification of microRNA expression with next-generation sequencing. Curr Protoc Mol Biol 2013; Chapter 4:Unit 4.17. PubMed
  • 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; 41:4336-43. PubMed
  • Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. Barcoding cells using cell-surface programmable DNA-binding domains. Nat Methods 2013. PubMed
  • 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. PubMed
  • 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; 339:823-6. PubMed
  • Rockwell G, Guido NJ, Church GM. Redirector: designing cell factories by reconstructing the metabolic objective. PLoS Comput. Biol. 2013; 9:e1002882. PubMed
  • Eroshenko N, Church GM. Mutants of Cre recombinase with improved accuracy. Nat Commun 2013; 4:2509. PubMed
  • 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. PubMed
  • Church GM, Gao Y, Kosuri S. Next-generation digital information storage in DNA. Science 2012; 337:1628. PubMed
  • 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; 40:e132. PubMed
  • 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; 22:1533-40. PubMed
  • 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; 109:11920-7. PubMed
  • Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? BMC Genomics 2012; 13:340. PubMed
  • 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; 487:190-5. PubMed
  • Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nat Methods 2012; 9:591-3. PubMed
  • 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; 1:43-52. PubMed
  • 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:e44638. PubMed
  • 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; 29:149-53. PubMed
  • 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; 28:1295-9. PubMed
  • 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; 28:1291-4. PubMed
  • Mosberg JA, Lajoie MJ, Church GM. Lambda Red Recombination in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate. Genetics 2010; 186:791-9. PubMed
  • 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; 7:15-9. PubMed
  • 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; 375:1525-35. PubMed
  • 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:e1000954. PubMed
  • 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 2009; 51:329-35. PubMed
  • Schwartz D, Church GM. Collection and motif-based prediction of phosphorylation sites in human viruses. Sci Signal 2010; 3:rs2. PubMed
  • 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; 327:78-81. PubMed
  • 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; 12:47-60. PubMed
  • Carr PA, Church GM. Genome engineering. Nat Biotechnol 2009; 27:1151-62. PubMed
  • 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; 37:6905-15. PubMed
  • 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; 27:1013-23. PubMed
  • 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; 5:e1000718. PubMed
  • 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; 19:1606-15. PubMed
  • Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 2009; 325:1128-31. PubMed
  • 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; 460:1011-5. PubMed
  • 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; 460:894-8. PubMed
  • 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; 11:559-67. PubMed
  • 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; 37:5001-6. PubMed
  • 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; 6:613-8. PubMed
  • 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; 324:1210-3. PubMed
  • 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; 27:361-8. PubMed
  • de Magalhaes JP,Curado J,Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 2009; 25:875-81. PubMed
  • 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 2008; 8:65-72. PubMed
  • Schwartz D,Chou MF,Church GM. Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics 2008; 8:365-79. PubMed
  • 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. PubMed
  • Vigneault F,Sismour AM,Church GM. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods 2009; 5:777-9. PubMed
  • Dantas G, Sommer MO, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science 2008; 320:100-3. PubMed
  • Lunshof JE,Chadwick R,Church GM. Hippocrates revisited? Old ideals and new realities. Genomic Med 2008; 2:1-3. PubMed
  • 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:R140. PubMed
  • Bang D, Church GM. Gene synthesis by circular assembly amplification. Nat Methods 2007; 5:37-9. PubMed
  • 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; 3:e231. PubMed
  • 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; 103:1228-36. PubMed
  • 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; 4:931-6. PubMed
  • 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; 449:83-6. PubMed
  • Bakal C, Aach J, Church G, Perrimon N. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 2007; 316:1753-6. PubMed
  • Wright MA, Kharchenko P, Church GM, Segre D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A 2007; 104:10559-64. PubMed
  • 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; 316:1481-4. PubMed
  • 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; 25:627-9. PubMed
  • 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; 62:583-4. PubMed
  • de Magalh. An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci 2007; 62:149-60. PubMed
  • Forster AC, Church GM. Synthetic biology projects in vitro. Genome Res 2006; 17:1-6. PubMed
  • 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; 24:747-57. PubMed
  • 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; 24:593-602. PubMed
  • Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. PEPPeR: A platform for experimental proteomic pattern recognition. Mol Cell Proteomics 2006; 5:1927-41. PubMed
  • Derti A, Roth FP, Church GM, Wu CT. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat Genet 2006; 38:1216-20. PubMed
  • 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; 103:14062-7. PubMed
  • 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; 24:832-840. PubMed
  • 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; 24:680-6. PubMed
  • Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM. MapQuant: open-source software for large-scale protein quantification. Proteomics 2006; 6:1770-82. PubMed
  • 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; 38:382-7. PubMed
  • 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; 2:e16. PubMed
  • Church GM. Genomes for all. Sci Am 2006; 294:46-54. PubMed
  • de Magalh. Cells discover fire: employing reactive oxygen species in development and consequences for aging. Exp Gerontol 2005; 41:1-10. PubMed
  • Forster AC, Church GM. Towards synthesis of a minimal cell. Mol Syst Biol 2006; 2:45. PubMed
  • Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 2006; 7:177. PubMed
  • 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. PubMed
  • 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; 309:1728-32. PubMed
  • de Magalh. Genomes optimize reproduction: aging as a consequence of the developmental program. Physiology (Bethesda) 2005; 20:252-9. PubMed
  • 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; 3:6. PubMed
  • Zhu Z, Shendure J, Church GM. Discovering functional transcription-factor combinations in the human cell cycle. Genome Res 2005; 15:848-55. PubMed
  • Church GM. From systems biology to synthetic biology. Mol Syst Biol 2006; 1:2005.0032. PubMed
  • 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 2006; 1:2005.0001. PubMed
  • Church GM. The personal genome project. Mol Syst Biol 2006; 1:2005.0030. PubMed
  • Kharchenko P, Church GM, Vitkup D. Expression dynamics of a cellular metabolic network. Mol Syst Biol 2006; 1:2005.0016. PubMed
  • Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 2004; 432:1050-4. PubMed
  • Catic A, Collins C, Church GM, Ploegh HL. Preferred in vivo ubiquitination sites. Bioinformatics 2004; 20:3302-7. PubMed
  • Kharchenko P, Vitkup D, Church GM. Filling gaps in a metabolic network using expression information. Bioinformatics 2004; 20 Suppl 1:I178-I185. PubMed
  • Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS. Digital quantitative measurements of gene expression. Biotechnol Bioeng 2004; 86:117-24. PubMed
  • 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 2003; 101:360-5. PubMed
  • Mitra RD, Shendure J, Olejnik J, Edyta-Krzymanska-Olejnik , Church GM. Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 2003; 320:55-65. PubMed
  • Zhu J, Shendure J, Mitra RD, Church GM. Single molecule profiling of alternative pre-mRNA splicing. Science 2003; 301:836-8. PubMed
  • 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; 30:141-2. PubMed
  • 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; 19:1060-5. PubMed
  • Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 2001; 29:153-9. PubMed
  • 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; 98:7158-63. PubMed
  • Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J. Computational comparison of two draft sequences of the human genome. Nature 2001; 409:856-9. PubMed
  • de Magalh. Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. Mech Ageing Dev 2007; 128:355-64. PubMed
  • Mitra RD, Church GM. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 1999; 27:e34. PubMed
  • Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet 1999; 22:281-5. PubMed
  • Bulyk ML, Gentalen E, Lockhart DJ, Church GM. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 1999; 17:573-7. PubMed
  • 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; 287:695-715. PubMed
  • 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; 32:219-21. PubMed
  • Chen T, He HL, Church GM. Modeling gene expression with differential equations. Pac Symp Biocomput 1999. PubMed
  • 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; 284:241-54. PubMed
  • 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; 16:939-45. PubMed
  • Tavazoie S, Church GM. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Nat Biotechnol 1998; 16:566-71. PubMed
  • 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; 179:6228-37. PubMed
  • 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; 18:1259-313. PubMed
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