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Last Name
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George McDonald Church, Ph.D.

TitleRobert Winthrop Professor of Genetics
InstitutionHarvard Medical School
DepartmentGenetics
AddressHarvard Medical School
Genetics NRB Room 238
77 Avenue Louis Pasteur
Boston MA 02115
Phone617/432-7562
Fax617/432-6513
Other Positions
TitleMember of the Affiliated Faculty of the Harvard-MIT Division of Health Sciences and Technology
InstitutionMassachusetts Institute of Technology
DepartmentHealth Sciences and Technology


 Mentoring 
 completed student projects
A Computational Genomics Approach to Defining probes for Alternative Splice Variants
Summer, 06/26/00 - 08/18/00

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
List All   |   Timeline
  1. Lunshof JE, Church GM, Prainsack B. Information access. Raw personal data: providing access. Science. 2014 Jan 24; 343(6169):373-4.
    View in: PubMed
  2. 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.
    View in: PubMed
  3. 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.
    View in: PubMed
  4. Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P. The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies. PLoS Pathog. 2013 Nov; 9(11):e1003754.
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  5. Li JB, Church GM. Deciphering the functions and regulation of brain-enriched A-to-I RNA editing. Nat Neurosci. 2013 Nov; 16(11):1518-22.
    View in: PubMed
  6. Marblestone AH, Zamft BM, Maguire YG, Shapiro MG, Cybulski TR, Glaser JI, Amodei D, Stranges PB, Kalhor R, Dalrymple DA, Seo D, Alon E, Maharbiz MM, Carmena JM, Rabaey JM, Boyden ES, Church GM, Kording KP. Physical principles for scalable neural recording. Front Comput Neurosci. 2013; 7:137.
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  7. Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ. Genomically recoded organisms expand biological functions. Science. 2013 Oct 18; 342(6156):357-60.
    View in: PubMed
  8. Lajoie MJ, Kosuri S, Mosberg JA, Gregg CJ, Zhang D, Church GM. Probing the limits of genetic recoding in essential genes. Science. 2013 Oct 18; 342(6156):361-3.
    View in: PubMed
  9. Church G. Improving genome understanding. Nature. 2013 Oct 10; 502(7470):143.
    View in: PubMed
  10. 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.
    View in: PubMed
  11. 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.
    View in: PubMed
  12. Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods. 2013 Sep 27; 10(10):957-63.
    View in: PubMed
  13. Goodman DB, Church GM, Kosuri S. Causes and effects of N-terminal codon bias in bacterial genes. Science. 2013 Oct 25; 342(6157):475-9.
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  14. Eroshenko N, Church GM. Mutants of Cre recombinase with improved accuracy. Nat Commun. 2013 Sep 23; 4:2509.
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  15. Ling J, Daoud R, Lajoie MJ, Church GM, Söll D, Lang BF. Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Res. 2014 Jan 7; 42(1):499-508.
    View in: PubMed
  16. Church GM. BRAIN: innovative neurotechnologies for imaging and therapeutics. Dialogues Clin Neurosci. 2013 Sep; 15(3):241-3.
    View in: PubMed
  17. Church G. Please reanimate. Sci Am. 2013 Sep; 309(3):12.
    View in: PubMed
  18. 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.
    View in: PubMed
  19. 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.
    View in: PubMed
  20. Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol. 2013 Aug 8; 31(8):688-91.
    View in: PubMed
  21. Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, Endy D, Church GM. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A. 2013 Aug 20; 110(34):14024-9.
    View in: PubMed
  22. 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.
    View in: PubMed
  23. Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 2013 Oct 1; 41(19):9049-61.
    View in: PubMed
  24. Payne AC, Andregg M, Kemmish K, Hamalainen M, Bowell C, Bleloch A, Klejwa N, Lehrach W, Schatz K, Stark H, Marblestone A, Church G, Own CS, Andregg W. Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface. PLoS One. 2013; 8(7):e69058.
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  25. Glaser JI, Zamft BM, Marblestone AH, Moffitt JR, Tyo K, Boyden ES, Church G, Kording KP. Statistical analysis of molecular signal recording. PLoS Comput Biol. 2013 Jul; 9(7):e1003145.
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  26. 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:Unit4.17.
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  27. 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.
    View in: PubMed
  28. Jewett MC, Fritz BR, Timmerman LE, Church GM. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol Syst Biol. 2013; 9:678.
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  29. Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X. Nanotools for neuroscience and brain activity mapping. ACS Nano. 2013 Mar 26; 7(3):1850-66.
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  30. Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. Barcoding cells using cell-surface programmable DNA-binding domains. Nat Methods. 2013 May; 10(5):403-6.
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  31. Zhu J, Larman HB, Gao G, Somwar R, Zhang Z, Laserson U, Ciccia A, Pavlova N, Church G, Zhang W, Kesari S, Elledge SJ. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Nat Biotechnol. 2013 Apr; 31(4):331-4.
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  32. 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 Jun; 43:1-9.
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  33. Alivisatos AP, Chun M, Church GM, Deisseroth K, Donoghue JP, Greenspan RJ, McEuen PL, Roukes ML, Sejnowski TJ, Weiss PS, Yuste R. Neuroscience. The brain activity map. Science. 2013 Mar 15; 339(6125):1284-5.
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  34. 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.
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  35. Church GM. Reading and writing omes. Mol Syst Biol. 2013 Jan 22; 9:642.
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  36. Rockwell G, Guido NJ, Church GM. Redirector: designing cell factories by reconstructing the metabolic objective. PLoS Comput Biol. 2013 Jan; 9(1):e1002882.
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  37. 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.
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  38. 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.
    View in: PubMed
  39. Chou MF, Prisic S, Lubner JM, Church GM, Husson RN, Schwartz D. Using bacteria to determine protein kinase specificity and predict target substrates. PLoS One. 2012; 7(12):e52747.
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  40. Lin C, Jungmann R, Leifer AM, Li C, Levner D, Church GM, Shih WM, Yin P. Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem. 2012 Oct; 4(10):832-9.
    View in: PubMed
  41. 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.
    View in: PubMed
  42. Juhas M, Eberl L, Church GM. Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol. 2012 Nov; 30(11):601-7.
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  43. Zamft BM, Marblestone AH, Kording K, Schmidt D, Martin-Alarcon D, Tyo K, Boyden ES, Church G. Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. PLoS One. 2012; 7(8):e43876.
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  44. Lajoie MJ, Gregg CJ, Mosberg JA, Washington GC, Church GM. Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering. Nucleic Acids Res. 2012 Dec 1; 40(22):e170.
    View in: PubMed
  45. Church GM, Gao Y, Kosuri S. Next-generation digital information storage in DNA. Science. 2012 Sep 28; 337(6102):1628.
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  46. Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? BMC Genomics. 2012; 13:340.
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  47. 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.
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  48. 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.
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  49. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. 2012 Aug; 40(15):e117.
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  50. Alivisatos AP, Chun M, Church GM, Greenspan RJ, Roukes ML, Yuste R. The brain activity map project and the challenge of functional connectomics. Neuron. 2012 Jun 21; 74(6):970-4.
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  51. Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, Silver PA. A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 2012; 6(1):8.
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  52. 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.
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  53. Rios X, Briggs AW, Christodoulou D, Gorham JM, Seidman JG, Church GM. Stable gene targeting in human cells using single-strand oligonucleotides with modified bases. PLoS One. 2012; 7(5):e36697.
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  54. Thakuria JV, Zaranek AW, Church GM, Berry GT. Back to the future: from genome to metabolome. Hum Mutat. 2012 May; 33(5):809-12.
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  55. 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.
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  56. 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.
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  57. Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA. Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PLoS Genet. 2012; 8(3):e1002558.
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  58. Ji J, Ng SH, Sharma V, Neculai D, Hussein S, Sam M, Trinh Q, Church GM, McPherson JD, Nagy A, Batada NN. Elevated coding mutation rate during the reprogramming of human somatic cells into induced pluripotent stem cells. Stem Cells. 2012 Mar; 30(3):435-40.
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  59. Douglas SM, Bachelet I, Church GM. A logic-gated nanorobot for targeted transport of molecular payloads. Science. 2012 Feb 17; 335(6070):831-4.
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  60. Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth Biol. 2012 Feb 17; 1(2):43-52.
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  61. Yu C, Li Y, Holmes A, Szafranski K, Faulkes CG, Coen CW, Buffenstein R, Platzer M, de Magalhães JP, Church GM. RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice. PLoS One. 2011; 6(11):e26729.
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  62. Carmi S, Church GM, Levanon EY. Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat Commun. 2011; 2:519.
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  63. Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell. 2011 Oct 21; 44(2):252-64.
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  64. Church GM. New technologies for integrating genomic, environmental and trait data. J Clin Sleep Med. 2011 Oct 15; 7(5 Suppl):S43-4.
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  65. Quan SF, Shaw PJ, Naidoo N, Haeggström E, Krueger JM, Church GM. Panel discussion: can there be a biomarker for sleepiness? J Clin Sleep Med. 2011 Oct 15; 7(5 Suppl):S45-8.
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  66. Shendure JA, Porreca GJ, Church GM, Gardner AF, Hendrickson CL, Kieleczawa J, Slatko BE. Overview of DNA sequencing strategies. Curr Protoc Mol Biol. 2011 Oct; Chapter 7:Unit7.1.
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  67. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011 Sep; 7(9):e1002280.
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  68. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science. 2011 Jul 15; 333(6040):348-53.
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  69. Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 2011 Sep; 21(9):1506-11.
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  70. Wang HH, Xu G, Vonner AJ, Church G. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res. 2011 Sep 1; 39(16):7336-47.
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  71. Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, Gakidis MA, Church GM, Kesari S, Leproust EM, Solimini NL, Elledge SJ. Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol. 2011 Jun; 29(6):535-41.
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  72. Robertson DE, Jacobson SA, Morgan F, Berry D, Church GM, Afeyan NB. A new dawn for industrial photosynthesis. Photosynth Res. 2011 Mar; 107(3):269-77.
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  73. 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.
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  74. Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP, Church GM. Proteome-wide systems analysis of a cellulosic biofuel-producing microbe. Mol Syst Biol. 2011 Jan 18; 7:461.
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  75. Wang HH, Church GM. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol. 2011; 498:409-26.
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  76. Vigneault F, Woods M, Buzon MJ, Li C, Pereyra F, Crosby SD, Rychert J, Church G, Martinez-Picado J, Rosenberg ES, Telenti A, Yu XG, Lichterfeld M. Transcriptional profiling of CD4 T cells identifies distinct subgroups of HIV-1 elite controllers. J Virol. 2011 Mar; 85(6):3015-9.
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  77. Shee K, Strong M, Guido NJ, Lue RA, Church GM, Viel A. Research, collaboration, and open science using web 2.0. J Microbiol Biol Educ. 2010; 11(2):130-4.
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  78. Fabsitz RR, McGuire A, Sharp RR, Puggal M, Beskow LM, Biesecker LG, Bookman E, Burke W, Burchard EG, Church G, Clayton EW, Eckfeldt JH, Fernandez CV, Fisher R, Fullerton SM, Gabriel S, Gachupin F, James C, Jarvik GP, Kittles R, Leib JR, O'Donnell C, O'Rourke PP, Rodriguez LL, Schully SD, Shuldiner AR, Sze RK, Thakuria JV, Wolf SM, Burke GL. Ethical and practical guidelines for reporting genetic research results to study participants: updated guidelines from a National Heart, Lung, and Blood Institute working group. Circ Cardiovasc Genet. 2010 Dec; 3(6):574-80.
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  79. 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.
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  80. 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.
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  81. Mosberg JA, Lajoie MJ, Church GM. Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics. 2010 Nov; 186(3):791-9.
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  82. Schwartz D, Church GM. Collection and motif-based prediction of phosphorylation sites in human viruses. Sci Signal. 2010; 3(137):rs2.
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  83. 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.
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  84. Sommer MO, Church GM, Dantas G. The human microbiome harbors a diverse reservoir of antibiotic resistance genes. Virulence. 2010 Jul-Aug; 1(4):299-303.
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  85. Bedau M, Church G, Rasmussen S, Caplan A, Benner S, Fussenegger M, Collins J, Deamer D. Life after the synthetic cell. Nature. 2010 May 27; 465(7297):422-4.
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  86. 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 May; 6(5):e1000954.
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  87. 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.
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  88. Sommer MO, Church GM, Dantas G. A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol Syst Biol. 2010 Apr 13; 6:360.
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  89. Prisic S, Dankwa S, Schwartz D, Chou MF, Locasale JW, Kang CM, Bemis G, Church GM, Steen H, Husson RN. Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci U S A. 2010 Apr 20; 107(16):7521-6.
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  90. 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.
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  91. 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.
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  92. Carr PA, Church GM. Genome engineering. Nat Biotechnol. 2009 Dec; 27(12):1151-62.
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  93. 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.
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  94. 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.
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  95. 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.
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  96. Church G, Heeney C, Hawkins N, de Vries J, Boddington P, Kaye J, Bobrow M, Weir B. Public access to genome-wide data: five views on balancing research with privacy and protection. PLoS Genet. 2009 Oct; 5(10):e1000665.
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  97. Tolonen AC, Chilaka AC, Church GM. Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol. 2009 Dec; 74(6):1300-13.
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  98. 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.
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  99. 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.
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  100. 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.
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  101. 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.
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  102. 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.
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  103. 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.
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  104. 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.
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  105. 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.
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  106. 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.
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  107. 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.
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  108. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Synthetic gene networks that count. Science. 2009 May 29; 324(5931):1199-202.
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  109. 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.
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  110. Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB. Tuberculosis drug resistance mutation database. PLoS Med. 2009 Feb 10; 6(2):e2.
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  111. de Magalhães 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.
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  112. de Magalhães 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.
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  113. 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.
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  114. Isenbarger TA, Carr CE, Johnson SS, Finney M, Church GM, Gilbert W, Zuber MT, Ruvkun G. The most conserved genome segments for life detection on Earth and other planets. Orig Life Evol Biosph. 2008 Dec; 38(6):517-33.
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  115. Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segrè 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.
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  116. Vigneault F, Sismour AM, Church GM. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods. 2008 Sep; 5(9):777-9.
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  117. Lunshof JE, Chadwick R, Church GM. Hippocrates revisited? Old ideals and new realities. Genomic Med. 2008 Jan; 2(1-2):1-3.
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  118. Lunshof JE, Chadwick R, Vorhaus DB, Church GM. From genetic privacy to open consent. Nat Rev Genet. 2008 May; 9(5):406-11.
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  119. Dantas G, Sommer MO, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science. 2008 Apr 4; 320(5872):100-3.
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  120. Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Curr Protoc Mol Biol. 2008 Jan; Chapter 7:Unit 7.1.
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  121. 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.
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  122. Bang D, Church GM. Gene synthesis by circular assembly amplification. Nat Methods. 2008 Jan; 5(1):37-9.
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  123. 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.
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  124. 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.
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  125. 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.
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  126. Nardi V, Raz T, Cao X, Wu CJ, Stone RM, Cortes J, Deininger MW, Church G, Zhu J, Daley GQ. Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors. Oncogene. 2008 Jan 31; 27(6):775-82.
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  127. 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.
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  128. Wright MA, Kharchenko P, Church GM, Segrè D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A. 2007 Jun 19; 104(25):10559-64.
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  129. 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.
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  130. de Magalhães 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.
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  131. Bügl 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.
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  132. Strong M, Church G. Gem of an idea for a unique machine. Nature. 2007 May 3; 447(7140):112.
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  133. de Magalhães JP, Church GM. Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. Mech Ageing Dev. 2007 May-Jun; 128(5-6):355-64.
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  134. de Magalhães 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.
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  135. 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.
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  136. Forster AC, Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan; 17(1):1-6.
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  137. 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.
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  138. Porreca GJ, Shendure J, Church GM. Polony DNA sequencing. Curr Protoc Mol Biol. 2006 Nov; Chapter 7:Unit 7.8.
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  139. 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.
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  140. 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.
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  141. 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.
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  142. Forster AC, Church GM. Towards synthesis of a minimal cell. Mol Syst Biol. 2006; 2:45.
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  143. 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.
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  144. 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, 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):832-40.
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  145. Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C, Hurles ME. Assaying chromosomal inversions by single-molecule haplotyping. Nat Methods. 2006 Jun; 3(6):439-45.
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  146. Engineering life: building a fab for biology. Sci Am. 2006 Jun; 294(6):44-51.
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  147. 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.
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  148. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics. 2006; 7:177.
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  149. 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.
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  150. 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.
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  151. 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.
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  152. Church G, Shendure J, Porreca G. Sequencing thoroughbreds. Nat Biotechnol. 2006 Feb; 24(2):139.
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  153. Church GM. Genomes for all. Sci Am. 2006 Jan; 294(1):46-54.
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  154. Church GM. The personal genome project. Mol Syst Biol. 2005; 1:2005.0030.
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  155. Church G. Let us go forth and safely multiply. Nature. 2005 Nov 24; 438(7067):423.
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  156. Wade JT, Reppas NB, Church GM, Struhl K. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 2005 Nov 1; 19(21):2619-30.
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  157. Gao Y, Church G. Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics. 2005 Nov 1; 21(21):3970-5.
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  158. Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 2005 Nov 3; 438(7064):86-9.
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  159. de Magalhães JP, Church GM. Cells discover fire: employing reactive oxygen species in development and consequences for aging. Exp Gerontol. 2006 Jan; 41(1):1-10.
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  160. Petti AA, Church GM. A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae. Genome Res. 2005 Sep; 15(9):1298-306.
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  161. 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.
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  162. Kharchenko P, Church GM, Vitkup D. Expression dynamics of a cellular metabolic network. Mol Syst Biol. 2005; 1:2005.0016.
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  163. de Magalhães JP, Church GM. Genomes optimize reproduction: aging as a consequence of the developmental program. Physiology (Bethesda). 2005 Aug; 20:252-9.
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  164. 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.
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  165. Aach J, Church GM. Accommodation or prediction? Science. 2005 Jun 3; 308(5727):1409-12; author reply 1409-12.
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  166. Zhu Z, Shendure J, Church GM. Discovering functional transcription-factor combinations in the human cell cycle. Genome Res. 2005 Jun; 15(6):848-55.
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  167. Church GM. From systems biology to synthetic biology. Mol Syst Biol. 2005; 1:2005.0032.
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  168. 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.
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  169. Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. 2005; 6(2):R16.
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  170. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 Jan; 23(1):137-44.
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  171. 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.
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  172. Segrè D, Deluna A, Church GM, Kishony R. Modular epistasis in yeast metabolism. Nat Genet. 2005 Jan; 37(1):77-83.
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  173. Grainger DC, Overton TW, Reppas N, Wade JT, Tamai E, Hobman JL, Constantinidou C, Struhl K, Church G, Busby SJ. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol. 2004 Oct; 186(20):6938-43.
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  174. Kharchenko P, Vitkup D, Church GM. Filling gaps in a metabolic network using expression information. Bioinformatics. 2004 Aug 4; 20 Suppl 1:i178-85.
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  175. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM. The complete genome and proteome of Mycoplasma mobile. Genome Res. 2004 Aug; 14(8):1447-61.
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  176. Catic A, Collins C, Church GM, Ploegh HL. Preferred in vivo ubiquitination sites. Bioinformatics. 2004 Dec 12; 20(18):3302-7.
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  177. Grad YH, Roth FP, Halfon MS, Church GM. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics. 2004 Nov 1; 20(16):2738-50.
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  178. Aach J, Church GM. Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J Theor Biol. 2004 May 7; 228(1):31-46.
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  179. Shendure J, Mitra RD, Varma C, Church GM. Advanced sequencing technologies: methods and goals. Nat Rev Genet. 2004 May; 5(5):335-44.
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  180. 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.
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  181. Janse DM, Crosas B, Finley D, Church GM. Localization to the proteasome is sufficient for degradation. J Biol Chem. 2004 May 14; 279(20):21415-20.
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  182. Bulyk ML, McGuire AM, Masuda N, Church GM. A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res. 2004 Feb; 14(2):201-8.
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  183. Lelandais G, Le Crom S, Devaux F, Vialette S, Church GM, Jacq C, Marc P. yMGV: a cross-species expression data mining tool. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D323-5.
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  184. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan; 4(1):59-77.
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  185. D'haeseleer P, Church GM. Estimating and improving protein interaction error rates. Proc IEEE Comput Syst Bioinform Conf. 2004; 216-23.
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  186. 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.
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  187. Vitkup D, Sander C, Church GM. The amino-acid mutational spectrum of human genetic disease. Genome Biol. 2003; 4(11):R72.
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  188. Mitra RD, Shendure J, Olejnik J. Fluorescent in situ sequencing on polymerase colonies. Anal Biochem. 2003 Sep 1; 320(1):55-65.
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  189. Zhu J, Shendure J, Mitra RD, Church GM. Single molecule profiling of alternative pre-mRNA splicing. Science. 2003 Aug 8; 301(5634):836-8.
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  190. Merritt J, DiTonno JR, Mitra RD, Church GM, Edwards JS. Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. Nucleic Acids Res. 2003 Aug 1; 31(15):e84.
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  191. Selinger DW, Wright MA, Church GM. On the complete determination of biological systems. Trends Biotechnol. 2003 Jun; 21(6):251-4.
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  192. Mitra RD, Butty VL, Shendure J, Williams BR, Housman DE, Church GM. Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci U S A. 2003 May 13; 100(10):5926-31.
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  193. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J. Computational and experimental identification of C. elegans microRNAs. Mol Cell. 2003 May; 11(5):1253-63.
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  194. Masuda N, Church GM. Regulatory network of acid resistance genes in Escherichia coli. Mol Microbiol. 2003 May; 48(3):699-712.
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  195. Cheung KJ, Badarinarayana V, Selinger DW, Janse D, Church GM. A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res. 2003 Feb; 13(2):206-15.
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  196. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 2003 Feb; 13(2):216-23.
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  197. Anderson LM, Choe SE, Yukhananov RY, Hopfner RL, Church GM, Pratt RE, Dzau VJ. Identification of a novel set of genes regulated by a unique liver X receptor-alpha -mediated transcription mechanism. J Biol Chem. 2003 Apr 25; 278(17):15252-60.
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  198. Yao MW, Lim H, Schust DJ, Choe SE, Farago A, Ding Y, Michaud S, Church GM, Maas RL. Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the preimplantation uterus. Mol Endocrinol. 2003 Apr; 17(4):610-27.
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  199. Segrè D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA, Church GM. From annotated genomes to metabolic flux models and kinetic parameter fitting. OMICS. 2003; 7(3):301-16.
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  200. King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP. Predicting phenotype from patterns of annotation. Bioinformatics. 2003; 19 Suppl 1:i183-9.
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  201. Lee ML, Bulyk ML, Whitmore GA, Church GM. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics. 2002 Dec; 58(4):981-8.
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  202. Wright MA, Church GM. An open-source oligomicroarray standard for human and mouse. Nat Biotechnol. 2002 Nov; 20(11):1082-3.
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  203. Steffen M, Petti A, Aach J, D'haeseleer P, Church G. Automated modelling of signal transduction networks. BMC Bioinformatics. 2002 Nov 1; 3:34.
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  204. Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):15112-7.
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  205. Sudarsanam P, Pilpel Y, Church GM. Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 2002 Nov; 12(11):1723-31.
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  206. Masuda N, Church GM. Escherichia coli gene expression responsive to levels of the response regulator EvgA. J Bacteriol. 2002 Nov; 184(22):6225-34.
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  207. Shendure J, Church GM. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 2002 Aug 22; 3(9):RESEARCH0044.
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  208. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol. 2002 Aug; 184(16):4582-93.
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  209. Halfon MS, Grad Y, Church GM, Michelson AM. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 2002 Jul; 12(7):1019-28.
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  210. Dudley AM, Aach J, Steffen MA, Church GM. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A. 2002 May 28; 99(11):7554-9.
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  211. Cohen BA, Pilpel Y, Mitra RD, Church GM. Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks. Mol Biol Cell. 2002 May; 13(5):1608-14.
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  212. Zhu Z, Pilpel Y, Church GM. Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol. 2002 Apr 19; 318(1):71-81.
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  213. Bulyk ML, Johnson PL, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 2002 Mar 1; 30(5):1255-61.
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  214. 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.
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  215. Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001 Dec; 29(4):482-6.
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  216. 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.
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  217. Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001 Oct; 29(2):153-9.
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  218. 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.
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  219. Aach J, Church GM. Aligning gene expression time series with time warping algorithms. Bioinformatics. 2001 Jun; 17(6):495-508.
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  220. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 2001 Mar; 17(3):286-7.
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  221. 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.
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  222. Chen T, Kao MY, Tepel M, Rush J, Church GM. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J Comput Biol. 2001; 8(3):325-37.
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  223. Chen T, Jaffe JD, Church GM. Algorithms for identifying protein cross-links via tandem mass spectrometry. J Comput Biol. 2001; 8(6):571-83.
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  224. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol. 2000 Dec; 18(12):1262-8.
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  225. Hoehe MR, Köpke K, Wendel B, Rohde K, Flachmeier C, Kidd KK, Berrettini WH, Church GM. Sequence variability and candidate gene analysis in complex disease: association of mu opioid receptor gene variation with substance dependence. Hum Mol Genet. 2000 Nov 22; 9(19):2895-908.
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  226. Manson McGuire A, Church GM. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res. 2000 Nov 15; 28(22):4523-30.
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  227. Jelinsky SA, Estep P, Church GM, Samson LD. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol. 2000 Nov; 20(21):8157-67.
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  228. Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell. 2000 Oct 27; 103(3):423-33.
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  229. Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet. 2000 Oct; 26(2):183-6.
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  230. McGuire AM, Hughes JD, Church GM. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 2000 Jun; 10(6):744-57.
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  231. Johnson JM, Church GM. Predicting ligand-binding function in families of bacterial receptors. Proc Natl Acad Sci U S A. 2000 Apr 11; 97(8):3965-70.
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  232. Aach J, Rindone W, Church GM. Systematic management and analysis of yeast gene expression data. Genome Res. 2000 Apr; 10(4):431-45.
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  233. Livesey FJ, Furukawa T, Steffen MA, Church GM, Cepko CL. Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol. 2000 Mar 23; 10(6):301-10.
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  234. Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol. 2000 Mar 10; 296(5):1205-14.
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  235. Teichmann SA, Chothia C, Church GM, Park J. Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics. 2000 Feb; 16(2):117-24.
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  236. Cheng Y, Church GM. Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol. 2000; 8:93-103.
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  237. 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.
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  238. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet. 1999 Jul; 22(3):281-5.
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  239. 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.
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  240. 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.
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  241. 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.
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  242. Chen T, He HL, Church GM. Modeling gene expression with differential equations. Pac Symp Biocomput. 1999; 29-40.
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  243. 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.
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  244. 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.
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  245. 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.
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  246. 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.
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  247. Xu L, Bian N, Wang Z, Abdel-Baky S, Pillai S, Magiera D, Murugaiah V, Giese RW, Wang P, O'Keeffe T, Abushamaa H, Kutney L, Church G, Carson S, Smith D, Park M, Wronka J, Laukien F. Electrophore mass tag dideoxy DNA sequencing. Anal Chem. 1997 Sep 1; 69(17):3595-602.
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  248. Smith DR, Richterich P, Rubenfield M, Rice PW, Butler C, Lee HM, Kirst S, Gundersen K, Abendschan K, Xu Q, Chung M, Deloughery C, Aldredge T, Maher J, Lundstrom R, Tulig C, Falls K, Imrich J, Torrey D, Engelstein M, Breton G, Madan D, Nietupski R, Seitz B, Connelly S, McDougall S, Safer H, Gibson R, Doucette-Stamm L, Eiglmeier K, Bergh S, Cole ST, Robison K, Richterich L, Johnson J, Church GM, Mao JI. Multiplex sequencing of 1.5 Mb of the Mycobacterium leprae genome. Genome Res. 1997 Aug; 7(8):802-19.
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  249. 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.
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  250. Bian N, Wang P, Wang Z, Xu L, Church G, Giese RW. Detection via laser desorption and mass spectrometry of multiplex electrophore-labeled albumin. Rapid Commun Mass Spectrom. 1997; 11(16):1781-4.
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  251. Church GM. Databases for gene expression. Nat Biotechnol. 1996 Jul; 14(7):828.
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  252. Robison K, Gilbert W, Church GM. More haemophilus and Mycoplasma genes. Science. 1996 Mar 1; 271(5253):1302b-3b.
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  253. Robison K, Gilbert W, Church GM. More Haemophilus and Mycoplasma genes. Science. 1996 Mar 1; 271(5253):1302-3; author reply 1303-4.
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  254. Richterich P, Lakey ND, Lee HM, Mao JI, Smith D, Church GM. Cytosine specific DNA sequencing with hydrogen peroxide. Nucleic Acids Res. 1995 Dec 11; 23(23):4922-3.
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  255. Chae HZ, Robison K, Poole LB, Church G, Storz G, Rhee SG. Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes. Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15):7017-21.
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  256. Robison K, Gilbert W, Church GM. Large scale bacterial gene discovery by similarity search. Nat Genet. 1994 Jun; 7(2):205-14.
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  257. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J Bacteriol. 1993 Jun; 175(11):3303-16.
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  258. Richterich P, Church GM. DNA sequencing with direct transfer electrophoresis and nonradioactive detection. Methods Enzymol. 1993; 218:187-222.
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  259. Wang MX, Church GM. A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature. 1992 Dec 10; 360(6404):606-10.
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  260. Sikorav JL, Church GM. Complementary recognition in condensed DNA: accelerated DNA renaturation. J Mol Biol. 1991 Dec 20; 222(4):1085-108.
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  261. Church GM, Kieffer-Higgins S. Multiplex DNA sequencing. Science. 1988 Apr 8; 240(4849):185-8.
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  262. Church GM, Ephrussi A, Gilbert W, Tonegawa S. Cell-type-specific contacts to immunoglobulin enhancers in nuclei. Nature. 1985 Feb 28-Mar 6; 313(6005):798-801.
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  263. Ephrussi A, Church GM, Tonegawa S, Gilbert W. B lineage--specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science. 1985 Jan 11; 227(4683):134-40.
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  264. Church GM, Gilbert W. The genomic sequencing technique. Prog Clin Biol Res. 1985; 177:17-21.
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  265. Church GM, Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr; 81(7):1991-5.
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  266. Church GM, Slonimski PP, Gilbert W. Pleiotropic mutations within two yeast mitochondrial cytochrome genes block mRNA processing. Cell. 1979 Dec; 18(4):1209-15.
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  267. Sussman JL, Holbrook SR, Warrant RW, Church GM, Kim SH. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol. 1978 Aug 25; 123(4):607-30.
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  268. Sutcliffe JG, Church GM. The cleavage site of the restriction endonuclease Ava II. Nucleic Acids Res. 1978 Jul; 5(7):2313-9.
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  269. Holbrook SR, Sussman JL, Warrant RW, Church GM, Kim SH. RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe. Nucleic Acids Res. 1977 Aug; 4(8):2811-20.
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  270. Church GM, Sussman JL, Kim SH. Secondary structural complementarity between DNA and proteins. Proc Natl Acad Sci U S A. 1977 Apr; 74(4):1458-62.
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