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Shapiro JA. All living cells are cognitive. Biochem Biophys Res Commun. 2020 Sep 21. PMID: 32972747.
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Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci. 2019 07; 1447(1):21-52. PMID: 30900279.
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. Biology (Basel). 2017 Dec 06; 6(4). PMID: 29211049.
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Shapiro JA. Biological action in Read-Write genome evolution. Interface Focus. 2017 Oct 06; 7(5):20160115. PMID: 28839913.
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Shapiro JA. Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol. 2017 Feb; 52(1):1-17. PMID: 27599542.
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. Biology (Basel). 2016 Jun 08; 5(2). PMID: 27338490.
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Shapiro JA. The basic concept of the read-write genome: Mini-review on cell-mediated DNA modification. Biosystems. 2016 Feb; 140:35-7. PMID: 26571358.
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Shapiro JA. Physiology of the read-write genome. J Physiol. 2014 Jun 01; 592(11):2319-41. PMID: 24882816.
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet. 2014; 5:87. PMID: 24795749.
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Shapiro JA. Constraint and opportunity in genome innovation. RNA Biol. 2014; 11(3):186-96. PMID: 24572460.
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Shapiro JA. Implications of the Read-Write Genome view. Phys Life Rev. 2013 Sep; 10(3):347-50. PMID: 23988879.
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Shapiro JA. How life changes itself: the Read-Write (RW) genome. Phys Life Rev. 2013 Sep; 10(3):287-323. PMID: 23876611.
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Shapiro JA. Rethinking the (im)possible in evolution. Prog Biophys Mol Biol. 2013 Apr; 111(2-3):92-6. PMID: 22986107.
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Shapiro JA. Mobile DNA and evolution in the 21st century. Mob DNA. 2010 Jan 25; 1(1):4. PMID: 20226073.
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Shapiro JA. Letting Escherichia coli teach me about genome engineering. Genetics. 2009 Dec; 183(4):1205-14. PMID: 19996374.
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Shapiro JA. Revisiting the central dogma in the 21st century. Ann N Y Acad Sci. 2009 Oct; 1178:6-28. PMID: 19845625.
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Shapiro JA. Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology. Stud Hist Philos Biol Biomed Sci. 2007 Dec; 38(4):807-19. PMID: 18053935.
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Shapiro JA, von Sternberg R. Why repetitive DNA is essential to genome function. Biol Rev Camb Philos Soc. 2005 May; 80(2):227-50. PMID: 15921050.
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Shapiro JA. Retrotransposons and regulatory suites. Bioessays. 2005 Feb; 27(2):122-5. PMID: 15666350.
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Shapiro JA. A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering. Gene. 2005 Jan 17; 345(1):91-100. PMID: 15716117.
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von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res. 2005; 110(1-4):108-16. PMID: 16093662.
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Shapiro JA. A 21(st) Century View of Evolution. J Biol Phys. 2002 Dec; 28(4):745-64. PMID: 23345811.
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Shapiro JA. Genome organization and reorganization in evolution: formatting for computation and function. Ann N Y Acad Sci. 2002 Dec; 981:111-34. PMID: 12547677.
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Shapiro JA. Repetitive DNA, genome system architecture and genome reorganization. Res Microbiol. 2002 Sep; 153(7):447-53. PMID: 12405352.
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Newman DL, Shapiro JA. Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development. Mol Microbiol. 1999 Jul; 33(1):18-32. PMID: 10411720.
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Shapiro JA. Genome system architecture and natural genetic engineering in evolution. Ann N Y Acad Sci. 1999 May 18; 870:23-35. PMID: 10415470.
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Lamrani S, Ranquet C, Gama MJ, Nakai H, Shapiro JA, Toussaint A, Maenhaut-Michel G. Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol Microbiol. 1999 Apr; 32(2):327-43. PMID: 10231489.
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Shapiro JA. Transposable elements as the key to a 21st century view of evolution. Genetica. 1999; 107(1-3):171-9. PMID: 10952210.
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Shapiro JA. Thinking about bacterial populations as multicellular organisms. Annu Rev Microbiol. 1998; 52:81-104. PMID: 9891794.
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Shapiro JA. Genome organization, natural genetic engineering and adaptive mutation. Trends Genet. 1997 Mar; 13(3):98-104. PMID: 9066268.
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Maenhaut-Michel G, Blake CE, Leach DR, Shapiro JA. Different structures of selected and unselected araB-lacZ fusions. Mol Microbiol. 1997 Mar; 23(6):1133-45. PMID: 9106205.
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Rauprich O, Matsushita M, Weijer CJ, Siegert F, Esipov SE, Shapiro JA. Periodic phenomena in Proteus mirabilis swarm colony development. J Bacteriol. 1996 Nov; 178(22):6525-38. PMID: 8932309.
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Shapiro JA. Response. Science. 1995 Jul 21; 269(5222):286-8. PMID: 17841226.
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Shapiro JA. The significances of bacterial colony patterns. Bioessays. 1995 Jul; 17(7):597-607. PMID: 7646482.
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Shapiro JA. Adaptive mutation: who's really in the garden? Science. 1995 Apr 21; 268(5209):373-4. PMID: 7716540.
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Maenhaut-Michel G, Shapiro JA. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J. 1994 Nov 01; 13(21):5229-39. PMID: 7957088.
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Shapiro JA. Adaptive mutation. Science. 1994 Sep 30; 265(5181):1994-5; author reply 1995-6. PMID: 7993484.
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Shapiro JA. Plasmid transfer. Science. 1994 Feb 11; 263(5148):839-41. PMID: 17770840.
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Shapiro JA. Natural genetic engineering of the bacterial genome. Curr Opin Genet Dev. 1993 Dec; 3(6):845-8. PMID: 8118208.
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Shapiro JA. A role for the Clp protease in activating Mu-mediated DNA rearrangements. J Bacteriol. 1993 May; 175(9):2625-31. PMID: 8386721.
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Shapiro JA. Differential action and differential expression of DNA polymerase I during Escherichia coli colony development. J Bacteriol. 1992 Nov; 174(22):7262-72. PMID: 1331025.
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Shapiro JA. Barbara McClintock, 1902-1992. Bioessays. 1992 Nov; 14(11):791-2. PMID: 1365894.
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Shapiro JA. Natural genetic engineering in evolution. Genetica. 1992; 86(1-3):99-111. PMID: 1334920.
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Shapiro JA. Pattern and control in bacterial colony development. Sci Prog. 1992; 76(301-302 Pt 3-4):399-424. PMID: 1364579.
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Shapiro JA. Genomes as smart systems. Genetica. 1991; 84(1):3-4. PMID: 1874439.
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Shapiro JA, Leach D. Action of a transposable element in coding sequence fusions. Genetics. 1990 Oct; 126(2):293-9. PMID: 2174011.
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Shapiro JA, Higgins NP. Differential activity of a transposable element in Escherichia coli colonies. J Bacteriol. 1989 Nov; 171(11):5975-86. PMID: 2553666.
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Shapiro JA, Hsu C. Escherichia coli K-12 cell-cell interactions seen by time-lapse video. J Bacteriol. 1989 Nov; 171(11):5963-74. PMID: 2681147.
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Shapiro JA, Higgins NP. Variation of beta-galactosidase expression from Mudlac elements during the development of Escherichia coli colonies. Ann Inst Pasteur Microbiol. 1988 Jan-Feb; 139(1):79-103. PMID: 2838063.
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Shapiro JA. Organization of developing Escherichia coli colonies viewed by scanning electron microscopy. J Bacteriol. 1987 Jan; 169(1):142-56. PMID: 3539913.
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Shapiro JA. Bacterial phylogeny: evolution of prokaryotes. Science. 1985 Dec 06; 230(4730):1155-6. PMID: 17739122.
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Shapiro JA. Scanning electron microscope study of Pseudomonas putida colonies. J Bacteriol. 1985 Dec; 164(3):1171-81. PMID: 4066611.
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Shapiro JA. Mechanisms of DNA reorganization in bacteria. Int Rev Cytol. 1985; 93:25-56. PMID: 2989204.
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Shapiro JA. The use of Mudlac transposons as tools for vital staining to visualize clonal and non-clonal patterns of organization in bacterial growth on agar surfaces. J Gen Microbiol. 1984 May; 130(5):1169-81. PMID: 6206197.
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McBeth DL, Shapiro JA. Reversal by DNA amplifications of an unusual mutation blocking alkane and alcohol utilization in Pseudomonas putida. Mol Gen Genet. 1984; 197(3):384-91. PMID: 6597334.
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Owen DJ, Eggink G, Hauer B, Kok M, McBeth DL, Yang YL, Shapiro JA. Physical structure, genetic content and expression of the alkBAC operon. Mol Gen Genet. 1984; 197(3):373-83. PMID: 6396491.
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Hauer B, Shapiro JA. Control of Tn7 transposition. Mol Gen Genet. 1984; 194(1-2):149-58. PMID: 6328211.
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Shapiro JA, Owen DJ, Kok M, Eggink G. Pseudomonas hydrocarbon oxidation. Basic Life Sci. 1984; 28:229-38. PMID: 6322742.
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Shapiro JA, Brinkley PM. Programming of DNA rearrangements involving mu prophages. Cold Spring Harb Symp Quant Biol. 1984; 49:313-20. PMID: 6241553.
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Burck C, Shapiro JA, Hauer B. The p lambda CM system: phage immunity-specific incompatibility with IncP-1 plasmids. Mol Gen Genet. 1984; 194(1-2):340-2. PMID: 6233471.
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Shapiro JA. Observations on the formation of clones containing araB-lacZ cistron fusions. Mol Gen Genet. 1984; 194(1-2):79-90. PMID: 6233472.
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Muster CJ, Shapiro JA, MacHattie LA. Recombination involving transposable elements: role of target molecule replication in Tn1 delta Ap-mediated replicon fusion. Proc Natl Acad Sci U S A. 1983 Apr; 80(8):2314-7. PMID: 6300910.
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Muster CJ, MacHattie LA, Shapiro JA. p lambda CM system: observations on the roles of transposable elements in formation and breakdown of plasmids derived from bacteriophage lambda replicons. J Bacteriol. 1983 Feb; 153(2):976-90. PMID: 6296061.
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Rehmat S, Shapiro JA. Insertion and replication of the Pseudomonas aeruginosa mutator phage D3112. Mol Gen Genet. 1983; 192(3):416-23. PMID: 6318038.
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Meyer R, Laux R, Boch G, Hinds M, Bayly R, Shapiro JA. Broad-host-range IncP-4 plasmid R1162: effects of deletions and insertions on plasmid maintenance and host range. J Bacteriol. 1982 Oct; 152(1):140-50. PMID: 6288654.
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Shapiro JA. Changes in gene order and gene expression. Natl Cancer Inst Monogr. 1982; 60:87-110. PMID: 6289110.
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Caruso M, Shapiro JA. Interactions of Tn7 and temperate phage F116L of Pseudomonas aeruginosa. Mol Gen Genet. 1982; 188(2):292-8. PMID: 6296632.
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Muster CJ, Shapiro JA. Recombination involving transposable elements: on replicon fusion. Cold Spring Harb Symp Quant Biol. 1981; 45 Pt 1:239-42. PMID: 6271471.
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Shapiro JA, Charbit A, Benson S, Caruso M, Laux R, Meyer R, Banuett F. Perspectives for genetic engineering of hydrocarbon oxidizing bacteria. Basic Life Sci. 1981; 18:243-72. PMID: 6944066.
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Meyer RJ, Shapiro JA. Genetic organization of the broad-host-range IncP-1 plasmid R751. J Bacteriol. 1980 Sep; 143(3):1362-73. PMID: 6251029.
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Cohen SN, Shapiro JA. Transposable genetic elements. Sci Am. 1980 Feb; 242(2):40-9. PMID: 6246575.
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Fennewald MA, Shapiro JA. Transposition of Tn7 in Pseudomonas aeruginosa and isolation of alk::Tn7 mutations. J Bacteriol. 1979 Jul; 139(1):264-9. PMID: 110782.
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Shapiro JA. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc Natl Acad Sci U S A. 1979 Apr; 76(4):1933-7. PMID: 287033.
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Shapiro JA, MacHattie LA. Integration and excision of prophage lambda mediated by the IS 1 element. Cold Spring Harb Symp Quant Biol. 1979; 43 Pt 2:1135-42. PMID: 158467.
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MacHattie LA, Shapiro JA. Chromosomal integration of phage lambda by means of a DNA insertion element. Proc Natl Acad Sci U S A. 1978 Mar; 75(3):1490-4. PMID: 274736.
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Shapiro JA, Sporn P. Tn402: a new transposable element determining trimethoprim resistance that inserts in bacteriophage lambda. J Bacteriol. 1977 Mar; 129(3):1632-5. PMID: 321437.
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Shapiro JA. Observations on lysogeny in glutamic acid bacteria. Appl Environ Microbiol. 1976 Jul; 32(1):179-82. PMID: 823863.
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Shapiro JA, Dean DH, Halvorson HO. Low-frequency specialized transduction with Bacillus subtilis bacteriophage phi 105. Virology. 1974 Dec; 62(2):393-403. PMID: 4215215.
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Ippen, K., J.A. Shapiro and J.R. Beckwith. . , . Transposition of the lac region to the gal region of the Escherichia coli chromosome: Isolation of llac transducing bacteriophages. J. Bacteriol. 1971; 108:5-8.
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Adhya, S. and J.A. Shapiro. The galactose operon of E. coli K-12. I. Structural and pleiotropic mutants of the operon. Genetics. 1969; 62:231-248.
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Shapiro, J.A. and S. Adhya. The galactose operon of E. coli K-12. II. A deletion analysis of operon structure and polarity. Genetics. 1969; 62:249-264.
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Shapiro, J.A. Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J. Molecular Biology. 1969; 40:93-105.
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Shapiro, J., L. MacHattie, L. Eron, G. Ihler, K. Ippen, J. Beckwith. The isolation of pure lac operon DNA. Nature. 1969; 224:768-774.
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Shapiro JA. Chromosomal location of the gene determining uridine diphoglucose formation in Escherichia coli K-12. J Bacteriol. 1966 Aug; 92(2):518-20. PMID: 5330381.