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    Douglas Berg

    TitleAdjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0711
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      NOVEL TRANSPOSONS AND PLASTICITY ZONES OF HELICOBACTER PYLORI
      NIH/NIAID R21AI088337Mar 5, 2010 - Feb 28, 2013
      Role: Principal Investigator
      HELICOBACTER PYLORI GENOME SEQUENCE EVOLUTION
      NIH/NIAID R21AI078237Sep 26, 2009 - Aug 31, 2011
      Role: Principal Investigator
      GENETICS OF POLYPHOSPHATE METABOLISM IN H. PYLORI
      NIH/NIAID R03AI057826Dec 15, 2003 - Nov 30, 2005
      Role: Principal Investigator
      H.PYLORI POPULATION GENETICS AND GENOME EVOLUTION
      NIH/NIDDK R01DK063041Jun 1, 2003 - May 31, 2009
      Role: Principal Investigator
      Molecular Genetics of H. Pylori In India
      NIH/NIAID R03AI049161Sep 1, 2000 - Jan 31, 2003
      Role: Principal Investigator
      H. PYLORI INFECTION AND GI DISEASE IN ALASKA NATIVES
      NIH/NIDDK R01DK053727Sep 30, 1999 - Sep 29, 2004
      Role: Principal Investigator
      H PYLORI INFECTION AND DRUG RESISTANCE IN PERU
      NIH/FIC R03TW000611May 1, 1996 - Apr 30, 1999
      Role: Principal Investigator
      TRANSPOSON-BASED MAPPING AND SEQUENCING OF UREAPLASMA
      NIH/NHGRI R01HG000820Sep 1, 1995 - Aug 31, 1999
      Role: Principal Investigator
      DRUG RESISTANCE AND GENE TRANSFER IN H PYLORI
      NIH/NIAID R01AI038166Jan 1, 1995 - Jul 31, 2004
      Role: Principal Investigator
      VIRULENCE ASSOCIATED HELICOBACTER PYLORI GENES
      NIH/NIDDK R01DK048029Apr 14, 1994 - Mar 31, 1999
      Role: Principal Investigator
      GENOME ANALYSIS WITH STRONG BINDING OLIGONUCLEOTIDES
      NIH/FIC R03TW000039Feb 20, 1992 - Feb 19, 1996
      Role: Principal Investigator
      ANALYSIS OF THE ESSENTIAL GENES OF E COLI
      NIH/NHGRI R01HG000563Apr 1, 1991 - Mar 31, 1994
      Role: Principal Investigator
      TRANSPOSABLE ELEMENTS IN BACTERIA
      NIH/NIGMS R01GM037138Dec 1, 1985 - Nov 30, 1991
      Role: Principal Investigator
      TRANSPOSABLE ELEMENTS IN BACTERIA
      NIH/NIAID R01AI014267Aug 1, 1977 - Mar 31, 1986
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg D, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis. 2016 Feb; 10(2):e0004403. PMID: 26890609; PMCID: PMC4758666.
      2. Secka O, Moodley Y, Antonio M, Berg D, Tapgun M, Walton R, Worwui A, Thomas V, Corrah T, Thomas JE, Adegbola RA. Population genetic analyses of Helicobacter pylori isolates from Gambian adults and children. PLoS One. 2014; 9(10):e109466. PMID: 25310300; PMCID: PMC4195673.
      3. Lind J, Backert S, Pfleiderer K, Berg D, Yamaoka Y, Sticht H, Tegtmeyer N. Systematic analysis of phosphotyrosine antibodies recognizing single phosphorylated EPIYA-motifs in CagA of Western-type Helicobacter pylori strains. PLoS One. 2014; 9(5):e96488. PMID: 24800748; PMCID: PMC4011759.
      4. Kersulyte D, Rossi M, Berg D. Sequence divergence and conservation in genomes of Helicobacter cetorum strains from a dolphin and a whale. PLoS One. 2013; 8(12):e83177. PMID: 24358262; PMCID: PMC3866246.
      5. Miyamoto Y, Kalisiak J, Korthals K, Lauwaet T, Cheung DY, Lozano R, Cobo ER, Upcroft P, Upcroft JA, Berg D, Gillin FD, Fokin VV, Sharpless KB, Eckmann L. Expanded therapeutic potential in activity space of next-generation 5-nitroimidazole antimicrobials with broad structural diversity. Proc Natl Acad Sci U S A. 2013 Oct 22; 110(43):17564-9. PMID: 24101497; PMCID: PMC3808650.
      6. Duncan SS, Bertoli MT, Kersulyte D, Valk PL, Tamma S, Segal I, McClain MS, Cover TL, Berg D. Genome Sequences of Three hpAfrica2 Strains of Helicobacter pylori. Genome Announc. 2013 Sep 26; 1(5). PMID: 24072860; PMCID: PMC3784780.
      7. Tegtmeyer N, Rivas Traverso F, Rohde M, Oyarzabal OA, Lehn N, Schneider-Brachert W, Ferrero RL, Fox JG, Berg D, Backert S. Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger. PLoS One. 2013; 8(8):e71220. PMID: 23940723; PMCID: PMC3733902.
      8. Putty K, Marcus SA, Mittl PR, Bogadi LE, Hunter AM, Arur S, Berg D, Sethu P, Kalia A. Robustness of Helicobacter pylori infection conferred by context-variable redundancy among cysteine-rich paralogs. PLoS One. 2013; 8(3):e59560. PMID: 23555707; PMCID: PMC3608669.
      9. Secka O, Berg D, Antonio M, Corrah T, Tapgun M, Walton R, Thomas V, Galano JJ, Sancho J, Adegbola RA, Thomas JE. Antimicrobial susceptibility and resistance patterns among Helicobacter pylori strains from The Gambia, West Africa. Antimicrob Agents Chemother. 2013 Mar; 57(3):1231-7. PMID: 23263004; PMCID: PMC3591906.
      10. Kupcinskas L, Rasmussen L, Jonaitis L, Kiudelis G, Jørgensen M, Urbonaviciene N, Tamosiunas V, Kupcinskas J, Miciuleviciene J, Kadusevicius E, Berg D, Andersen LP. Evolution of Helicobacter pylori susceptibility to antibiotics during a 10-year period in Lithuania. APMIS. 2013 May; 121(5):431-6. PMID: 23078193.
        View in: PubMed
      11. Pereira L, Zamudio R, Soares-Souza G, Herrera P, Cabrera L, Hooper CC, Cok J, Combe JM, Vargas G, Prado WA, Schneider S, Kehdy F, Rodrigues MR, Chanock SJ, Berg D, Gilman RH, Tarazona-Santos E. Socioeconomic and nutritional factors account for the association of gastric cancer with Amerindian ancestry in a Latin American admixed population. PLoS One. 2012; 7(8):e41200. PMID: 22870209; PMCID: PMC3411699.
      12. Chattopadhyay S, Patra R, Chatterjee R, De R, Alam J, Ramamurthy T, Chowdhury A, Nair GB, Berg D, Mukhopadhyay AK. Distinct repeat motifs at the C-terminal region of CagA of Helicobacter pylori strains isolated from diseased patients and asymptomatic individuals in West Bengal, India. Gut Pathog. 2012 May 25; 4(1):4. PMID: 22631862; PMCID: PMC3405419.
      13. Debowski AW, Carnoy C, Verbrugghe P, Nilsson HO, Gauntlett JC, Fulurija A, Camilleri T, Berg D, Marshall BJ, Benghezal M. Xer recombinase and genome integrity in Helicobacter pylori, a pathogen without topoisomerase IV. PLoS One. 2012; 7(4):e33310. PMID: 22511919; PMCID: PMC3325230.
      14. Secka O, Antonio M, Berg D, Tapgun M, Bottomley C, Thomas V, Walton R, Corrah T, Thomas JE, Adegbola RA. Mixed infection with cagA positive and cagA negative strains of Helicobacter pylori lowers disease burden in The Gambia. PLoS One. 2011; 6(11):e27954. PMID: 22140492; PMCID: PMC3226634.
      15. Camorlinga-Ponce M, Perez-Perez G, Gonzalez-Valencia G, Mendoza I, Peñaloza-Espinosa R, Ramos I, Kersulyte D, Reyes-Leon A, Romo C, Granados J, Muñoz L, Berg D, Torres J. Helicobacter pylori genotyping from American indigenous groups shows novel Amerindian vacA and cagA alleles and Asian, African and European admixture. PLoS One. 2011; 6(11):e27212. PMID: 22073291; PMCID: PMC3207844.
      16. Suzuki M, Kiga K, Kersulyte D, Cok J, Hooper CC, Mimuro H, Sanada T, Suzuki S, Oyama M, Kozuka-Hata H, Kamiya S, Zou QM, Gilman RH, Berg D, Sasakawa C. Attenuated CagA oncoprotein in Helicobacter pylori from Amerindians in Peruvian Amazon. J Biol Chem. 2011 Aug 26; 286(34):29964-72. PMID: 21757722; PMCID: PMC3191037.
      17. Hardwick RJ, Machado LR, Zuccherato LW, Antolinos S, Xue Y, Shawa N, Gilman RH, Cabrera L, Berg D, Tyler-Smith C, Kelly P, Tarazona-Santos E, Hollox EJ. A worldwide analysis of beta-defensin copy number variation suggests recent selection of a high-expressing DEFB103 gene copy in East Asia. Hum Mutat. 2011 Jul; 32(7):743-50. PMID: 21387465; PMCID: PMC3263423.
      18. Secka O, Antonio M, Tapgun M, Berg D, Bottomley C, Thomas V, Walton R, Corrah T, Adegbola RA, Thomas JE. PCR-based genotyping of Helicobacter pylori of Gambian children and adults directly from biopsy specimens and bacterial cultures. Gut Pathog. 2011 Apr 20; 3(1):5. PMID: 21507253; PMCID: PMC3107793.
      19. Choi SS, Chivers PT, Berg D. Point mutations in Helicobacter pylori's fur regulatory gene that alter resistance to metronidazole, a prodrug activated by chemical reduction. PLoS One. 2011 Mar 25; 6(3):e18236. PMID: 21464913; PMCID: PMC3064673.
      20. Patra R, Chattopadhyay S, De R, Datta S, Chowdhury A, Ramamurthy T, Nair GB, Berg D, Mukhopadhyay AK. Intact cag pathogenicity island of Helicobacter pylori without disease association in Kolkata, India. Int J Med Microbiol. 2011 Apr; 301(4):293-302. PMID: 21195664; PMCID: PMC3062673.
      21. Kersulyte D, Kalia A, Gilman RH, Mendez M, Herrera P, Cabrera L, Velapatiño B, Balqui J, Paredes Puente de la Vega F, Rodriguez Ulloa CA, Cok J, Hooper CC, Dailide G, Tamma S, Berg D. Helicobacter pylori from Peruvian amerindians: traces of human migrations in strains from remote Amazon, and genome sequence of an Amerind strain. PLoS One. 2010 Nov 29; 5(11):e15076. PMID: 21124785; PMCID: PMC2993954.
      22. Schoep TD, Fulurija A, Good F, Lu W, Himbeck RP, Schwan C, Choi SS, Berg D, Mittl PR, Benghezal M, Marshall BJ. Surface properties of Helicobacter pylori urease complex are essential for persistence. PLoS One. 2010 Nov 29; 5(11):e15042. PMID: 21124783; PMCID: PMC2993952.
      23. Styer CM, Hansen LM, Cooke CL, Gundersen AM, Choi SS, Berg D, Benghezal M, Marshall BJ, Peek RM, Borén T, Solnick JV. Expression of the BabA adhesin during experimental infection with Helicobacter pylori. Infect Immun. 2010 Apr; 78(4):1593-600. PMID: 20123715; PMCID: PMC2849406.
      24. Gehmert S, Velapatiño B, Herrera P, Balqui J, Santivañez L, Cok J, Vargas G, Combe J, Passaro DJ, Wen S, Meyer F, Berg D, Gilman RH. Interleukin-1 beta single-nucleotide polymorphism's C allele is associated with elevated risk of gastric cancer in Helicobacter pylori-infected Peruvians. Am J Trop Med Hyg. 2009 Nov; 81(5):804-10. PMID: 19861615; PMCID: PMC2833398.
      25. Sidransky E, Nalls MA, Aasly JO, Aharon-Peretz J, Annesi G, Barbosa ER, Bar-Shira A, Berg D, Bras J, Brice A, Chen CM, Clark LN, Condroyer C, De Marco EV, Dürr A, Eblan MJ, Fahn S, Farrer MJ, Fung HC, Gan-Or Z, Gasser T, Gershoni-Baruch R, Giladi N, Griffith A, Gurevich T, Januario C, Kropp P, Lang AE, Lee-Chen GJ, Lesage S, Marder K, Mata IF, Mirelman A, Mitsui J, Mizuta I, Nicoletti G, Oliveira C, Ottman R, Orr-Urtreger A, Pereira LV, Quattrone A, Rogaeva E, Rolfs A, Rosenbaum H, Rozenberg R, Samii A, Samaddar T, Schulte C, Sharma M, Singleton A, Spitz M, Tan EK, Tayebi N, Toda T, Troiano AR, Tsuji S, Wittstock M, Wolfsberg TG, Wu YR, Zabetian CP, Zhao Y, Ziegler SG. Multicenter analysis of glucocerebrosidase mutations in Parkinson's disease. N Engl J Med. 2009 Oct 22; 361(17):1651-61. PMID: 19846850; PMCID: PMC2856322.
      26. Kersulyte D, Lee W, Subramaniam D, Anant S, Herrera P, Cabrera L, Balqui J, Barabas O, Kalia A, Gilman RH, Berg D. Helicobacter Pylori's plasticity zones are novel transposable elements. PLoS One. 2009 Sep 03; 4(9):e6859. PMID: 19727398; PMCID: PMC2731543.
      27. Dumrese C, Slomianka L, Ziegler U, Choi SS, Kalia A, Fulurija A, Lu W, Berg D, Benghezal M, Marshall B, Mittl PR. The secreted Helicobacter cysteine-rich protein A causes adherence of human monocytes and differentiation into a macrophage-like phenotype. FEBS Lett. 2009 May 19; 583(10):1637-43. PMID: 19393649; PMCID: PMC2764743.
      28. Suzuki M, Mimuro H, Kiga K, Fukumatsu M, Ishijima N, Morikawa H, Nagai S, Koyasu S, Gilman RH, Kersulyte D, Berg D, Sasakawa C. Helicobacter pylori CagA phosphorylation-independent function in epithelial proliferation and inflammation. Cell Host Microbe. 2009 Jan 22; 5(1):23-34. PMID: 19154985.
        View in: PubMed
      29. Herrera PM, Mendez M, Velapatiño B, Velapatiõ B, Santivañez L, Santivaez L, Balqui J, Finger SA, Sherman J, Zimic M, Cabrera L, Watanabe J, Rodríguez C, Gilman RH, Berg D. DNA-level diversity and relatedness of Helicobacter pylori strains in shantytown families in Peru and transmission in a developing-country setting. J Clin Microbiol. 2008 Dec; 46(12):3912-8. PMID: 18842944; PMCID: PMC2593267.
      30. Khan R, Nahar S, Mukhopadhyay AK, Berg D, Ahmad MM, Okamoto K, Nair GB, Rahman M. Isolation of tetracycline-resistant clinical Helicobacter pylori without mutations in 16S rRNA gene in Bangladesh. Microbiol Immunol. 2008 Oct; 52(10):508-11. PMID: 18822085.
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      31. Roberts AP, Chandler M, Courvalin P, Guédon G, Mullany P, Pembroke T, Rood JI, Smith CJ, Summers AO, Tsuda M, Berg D. Revised nomenclature for transposable genetic elements. Plasmid. 2008 Nov; 60(3):167-73. PMID: 18778731; PMCID: PMC3836210.
      32. Mimuro H, Berg D, Sasakawa C. Control of epithelial cell structure and developmental fate: lessons from Helicobacter pylori. Bioessays. 2008 Jun; 30(6):515-20. PMID: 18478526.
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      33. Subramaniam D, Ramalingam S, May R, Dieckgraefe BK, Berg D, Pothoulakis C, Houchen CW, Wang TC, Anant S. Gastrin-mediated interleukin-8 and cyclooxygenase-2 gene expression: differential transcriptional and posttranscriptional mechanisms. Gastroenterology. 2008 Apr; 134(4):1070-82. PMID: 18395088.
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      34. Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG, Berg D, Schukken Y, Scherl E, Simpson KW. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J. 2007 Sep; 1(5):403-18. PMID: 18043660.
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      35. Ogura M, Perez JC, Mittl PR, Lee HK, Dailide G, Tan S, Ito Y, Secka O, Dailidiene D, Putty K, Berg D, Kalia A. Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes. PLoS Comput Biol. 2007 Aug; 3(8):e151. PMID: 17696605; PMCID: PMC1941758.
      36. Dailidiene D, Tan S, Ogura K, Zhang M, Lee AH, Severinov K, Berg D. Urea sensitization caused by separation of Helicobacter pylori RNA polymerase beta and beta' subunits. Helicobacter. 2007 Apr; 12(2):103-11. PMID: 17309746.
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      37. Bruce MG, Bruden DL, McMahon BJ, Hennessy TW, Reasonover A, Morris J, Hurlburt DA, Peters H, Sacco F, Martinez P, Swenson M, Berg D, Parks D, Parkinson AJ. Alaska sentinel surveillance for antimicrobial resistance in Helicobacter pylori isolates from Alaska native persons, 1999-2003. Helicobacter. 2006 Dec; 11(6):581-8. PMID: 17083381.
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      38. Kundu P, Mukhopadhyay AK, Patra R, Banerjee A, Berg D, Swarnakar S. Cag pathogenicity island-independent up-regulation of matrix metalloproteinases-9 and -2 secretion and expression in mice by Helicobacter pylori infection. J Biol Chem. 2006 Nov 10; 281(45):34651-62. PMID: 16966323.
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      39. Dailidiene D, Dailide G, Kersulyte D, Berg D. Contraselectable streptomycin susceptibility determinant for genetic manipulation and analysis of Helicobacter pylori. Appl Environ Microbiol. 2006 Sep; 72(9):5908-14. PMID: 16957210; PMCID: PMC1563642.
      40. Lee WK, Ogura K, Loh JT, Cover TL, Berg D. Quantitative effect of luxS gene inactivation on the fitness of Helicobacter pylori. Appl Environ Microbiol. 2006 Oct; 72(10):6615-22. PMID: 16936059; PMCID: PMC1610275.
      41. Simpson KW, Dogan B, Rishniw M, Goldstein RE, Klaessig S, McDonough PL, German AJ, Yates RM, Russell DG, Johnson SE, Berg D, Harel J, Bruant G, McDonough SP, Schukken YH. Adherent and invasive Escherichia coli is associated with granulomatous colitis in boxer dogs. Infect Immun. 2006 Aug; 74(8):4778-92. PMID: 16861666; PMCID: PMC1539603.
      42. Finger SA, Velapatiño B, Kosek M, Santivañez L, Dailidiene D, Quino W, Balqui J, Herrera P, Berg D, Gilman RH. Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation. Appl Environ Microbiol. 2006 Jul; 72(7):4713-6. PMID: 16820463; PMCID: PMC1489368.
      43. Wirth HP, Yang M, Sanabria-Valentín E, Berg D, Dubois A, Blaser MJ. Host Lewis phenotype-dependent Helicobacter pylori Lewis antigen expression in rhesus monkeys. FASEB J. 2006 Jul; 20(9):1534-6. PMID: 16720729; PMCID: PMC2579782.
      44. McMahon BJ, Bruce MG, Hennessy TW, Bruden DL, Sacco F, Peters H, Hurlburt DA, Morris JM, Reasonover AL, Dailide G, Berg D, Parkinson AJ. Reinfection after successful eradication of Helicobacter pylori: a 2-year prospective study in Alaska Natives. Aliment Pharmacol Ther. 2006 Apr 15; 23(8):1215-23. PMID: 16611283.
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      45. Velapatiño B, Balqui J, Gilman RH, Bussalleu A, Quino W, Finger SA, Santivañez L, Herrera P, Piscoya A, Valdivia J, Cok J, Berg D. Validation of string test for diagnosis of Helicobacter pylori infections. J Clin Microbiol. 2006 Mar; 44(3):976-80. PMID: 16517886; PMCID: PMC1393125.
      46. Li GQ, Xia HH, Chen MH, Gu Q, Wang JD, Peng JZ, Chan AO, Cho CH, So HL, Lam SK, Hu PJ, Liang YJ, Lin HL, Berg D, Feng ZH, Langenbach R, Wong BC. Effects of cyclooxygenase-1 and -2 gene disruption on Helicobacter pylori-induced gastric inflammation. J Infect Dis. 2006 Apr 01; 193(7):1037-46. PMID: 16518767.
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      47. Aspholm M, Kalia A, Ruhl S, Schedin S, Arnqvist A, Lindén S, Sjöström R, Gerhard M, Semino-Mora C, Dubois A, Unemo M, Danielsson D, Teneberg S, Lee WK, Berg D, Borén T. Helicobacter pylori adhesion to carbohydrates. Methods Enzymol. 2006; 417:293-339. PMID: 17132512; PMCID: PMC2576508.
      48. Albert TJ, Dailidiene D, Dailide G, Norton JE, Kalia A, Richmond TA, Molla M, Singh J, Green RD, Berg D. Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori. Nat Methods. 2005 Dec; 2(12):951-3. PMID: 16299480.
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      49. Tan S, Fraley CD, Zhang M, Dailidiene D, Kornberg A, Berg D. Diverse phenotypes resulting from polyphosphate kinase gene (ppk1) inactivation in different strains of Helicobacter pylori. J Bacteriol. 2005 Nov; 187(22):7687-95. PMID: 16267293; PMCID: PMC1280296.
      50. Datta S, Chattopadhyay S, Chowdhury A, Santra A, Saha DR, Ramamurthy T, Bhattacharya SK, Berg D, Nair GB, Mukhopadhyay AK. Diagnosis and genotyping of Helicobacter pylori by polymerase chain reaction of bacterial DNA from gastric juice. J Gastroenterol Hepatol. 2005 Aug; 20(8):1253-9. PMID: 16048575.
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      51. Datta S, Chattopadhyay S, Patra R, De R, Ramamurthy T, Hembram J, Chowdhury A, Bhattacharya SK, Berg D, Nair GB, Mukhopadhyay AK. Most Helicobacter pylori strains of Kolkata in India are resistant to metronidazole but susceptible to other drugs commonly used for eradication and ulcer therapy. Aliment Pharmacol Ther. 2005 Jul 01; 22(1):51-7. PMID: 15963080.
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      52. Morris JM, Reasonover AL, Bruce MG, Bruden DL, McMahon BJ, Sacco FD, Berg D, Parkinson AJ. Evaluation of seaFAST, a rapid fluorescent in situ hybridization test, for detection of Helicobacter pylori and resistance to clarithromycin in paraffin-embedded biopsy sections. J Clin Microbiol. 2005 Jul; 43(7):3494-6. PMID: 16000488; PMCID: PMC1169084.
      53. Xia HH, Lam SK, Chan AO, Lin MC, Kung HF, Ogura K, Berg D, Wong BC. Macrophage migration inhibitory factor stimulated by Helicobacter pylori increases proliferation of gastric epithelial cells. World J Gastroenterol. 2005 Apr 07; 11(13):1946-50. PMID: 15800984; PMCID: PMC4305715.
      54. Suto H, Zhang M, Berg D. Age-dependent changes in susceptibility of suckling mice to individual strains of Helicobacter pylori. Infect Immun. 2005 Feb; 73(2):1232-4. PMID: 15664971; PMCID: PMC547055.
      55. McNulty SL, Mole BM, Dailidiene D, Segal I, Ally R, Mistry R, Secka O, Adegbola RA, Thomas JE, Lenarcic EM, Peek RM, Berg D, Forsyth MH. Novel 180- and 480-base-pair insertions in African and African-American strains of Helicobacter pylori. J Clin Microbiol. 2004 Dec; 42(12):5658-63. PMID: 15583296; PMCID: PMC535299.
      56. Bäckström A, Lundberg C, Kersulyte D, Berg D, Borén T, Arnqvist A. Metastability of Helicobacter pylori bab adhesin genes and dynamics in Lewis b antigen binding. Proc Natl Acad Sci U S A. 2004 Nov 30; 101(48):16923-8. PMID: 15557006; PMCID: PMC534723.
      57. Kalia A, Mukhopadhyay AK, Dailide G, Ito Y, Azuma T, Wong BC, Berg D. Evolutionary dynamics of insertion sequences in Helicobacter pylori. J Bacteriol. 2004 Nov; 186(22):7508-20. PMID: 15516562; PMCID: PMC524885.
      58. Kersulyte D, Kalia A, Zhang M, Lee HK, Subramaniam D, Kiuduliene L, Chalkauskas H, Berg D. Sequence organization and insertion specificity of the novel chimeric ISHp609 transposable element of Helicobacter pylori. J Bacteriol. 2004 Nov; 186(22):7521-8. PMID: 15516563; PMCID: PMC524915.
      59. Nahar S, Mukhopadhyay AK, Khan R, Ahmad MM, Datta S, Chattopadhyay S, Dhar SC, Sarker SA, Engstrand L, Berg D, Nair GB, Rahman M. Antimicrobial susceptibility of Helicobacter pylori strains isolated in Bangladesh. J Clin Microbiol. 2004 Oct; 42(10):4856-8. PMID: 15472362; PMCID: PMC522322.
      60. Aspholm-Hurtig M, Dailide G, Lahmann M, Kalia A, Ilver D, Roche N, Vikström S, Sjöström R, Lindén S, Bäckström A, Lundberg C, Arnqvist A, Mahdavi J, Nilsson UJ, Velapatiño B, Gilman RH, Gerhard M, Alarcon T, López-Brea M, Nakazawa T, Fox JG, Correa P, Dominguez-Bello MG, Perez-Perez GI, Blaser MJ, Normark S, Carlstedt I, Oscarson S, Teneberg S, Berg D, Borén T. Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin. Science. 2004 Jul 23; 305(5683):519-22. PMID: 15273394.
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      61. Chattopadhyay S, Patra R, Ramamurthy T, Chowdhury A, Santra A, Dhali GK, Bhattacharya SK, Berg D, Nair GB, Mukhopadhyay AK. Multiplex PCR assay for rapid detection and genotyping of Helicobacter pylori directly from biopsy specimens. J Clin Microbiol. 2004 Jun; 42(6):2821-4. PMID: 15184482; PMCID: PMC427847.
      62. Tan S, Berg D. Motility of urease-deficient derivatives of Helicobacter pylori. J Bacteriol. 2004 Feb; 186(3):885-8. PMID: 14729719; PMCID: PMC321484.
      63. Dailidiene D, Dailide G, Ogura K, Zhang M, Mukhopadhyay AK, Eaton KA, Cattoli G, Kusters JG, Berg D. Helicobacter acinonychis: genetic and rodent infection studies of a Helicobacter pylori-like gastric pathogen of cheetahs and other big cats. J Bacteriol. 2004 Jan; 186(2):356-65. PMID: 14702304; PMCID: PMC305740.
      64. Soto G, Bautista CT, Roth DE, Gilman RH, Velapatiño B, Ogura M, Dailide G, Razuri M, Meza R, Katz U, Monath TP, Berg D, Taylor DN. Helicobacter pylori reinfection is common in Peruvian adults after antibiotic eradication therapy. J Infect Dis. 2003 Nov 01; 188(9):1263-75. PMID: 14593583.
        View in: PubMed
      65. Bury-Moné S, Skouloubris S, Dauga C, Thiberge JM, Dailidiene D, Berg D, Labigne A, De Reuse H. Presence of active aliphatic amidases in Helicobacter species able to colonize the stomach. Infect Immun. 2003 Oct; 71(10):5613-22. PMID: 14500481; PMCID: PMC201111.
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      149. Kersulyte D, Struelens MJ, Deplano A, Berg D. Comparison of arbitrarily primed PCR and macrorestriction (pulsed-field gel electrophoresis) typing of Pseudomonas aeruginosa strains from cystic fibrosis patients. J Clin Microbiol. 1995 Aug; 33(8):2216-9. PMID: 7559985; PMCID: PMC228372.
      150. Madico G, Akopyants NS, Berg D. Arbitrarily primed PCR DNA fingerprinting of Escherichia coli O157:H7 strains by using templates from boiled cultures. J Clin Microbiol. 1995 Jun; 33(6):1534-6. PMID: 7650181; PMCID: PMC228210.
      151. Taylor NS, Fox JG, Akopyants NS, Berg D, Thompson N, Shames B, Yan L, Fontham E, Janney F, Hunter FM. Long-term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting. J Clin Microbiol. 1995 Apr; 33(4):918-23. PMID: 7790461; PMCID: PMC228068.
      152. Krishnan BR, Jamry I, Berg D, Berg CM, Chaplin DD. Construction of a genomic DNA 'feature map' by sequencing from nested deletions: application to the HLA class I region. Nucleic Acids Res. 1995 Jan 11; 23(1):117-22. PMID: 7870576; PMCID: PMC306638.
      153. Akopyants NS, Eaton KA, Berg D. Adaptive mutation and cocolonization during Helicobacter pylori infection of gnotobiotic piglets. Infect Immun. 1995 Jan; 63(1):116-21. PMID: 7806346; PMCID: PMC172966.
      154. Bukanov N, Ravi VN, Miller D, Srivastava K, Berg D. Pseudomonas aeruginosa corneal ulcer isolates distinguished using the arbitrarily primed PCR DNA fingerprinting method. Curr Eye Res. 1994 Nov; 13(11):783-90. PMID: 7851113.
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      155. Geary SJ, Forsyth MH, Aboul Saoud S, Wang G, Berg D, Berg CM. Mycoplasma gallisepticum strain differentiation by arbitrary primer PCR (RAPD) fingerprinting. Mol Cell Probes. 1994 Aug; 8(4):311-6. PMID: 7870072.
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      156. Woods JP, Kersulyte D, Tolan RW, Berg CM, Berg D. Use of arbitrarily primed polymerase chain reaction analysis to type disease and carrier strains of Neisseria meningitidis isolated during a university outbreak. J Infect Dis. 1994 Jun; 169(6):1384-9. PMID: 8195623.
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      157. Lebedev IuB, Shevchenko Iu, Potapov VK, Miasnikov VA, Veselovskaia SV, Brikun I, Berg D, Sverdlov ED. [Comparison of genomes by polymerase chain reaction using random priming with oligonucleotides analogs, forming strong duplexes]. Dokl Akad Nauk. 1994 Apr; 335(6):799-801. PMID: 8025552.
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      158. Wang G, Xu X, Chen JM, Berg D, Berg CM. Inversions and deletions generated by a mini-gamma delta (Tn1000) transposon. J Bacteriol. 1994 Mar; 176(5):1332-8. PMID: 8113172; PMCID: PMC205197.
      159. Brikun I, Suziedelis K, Berg D. DNA sequence divergence among derivatives of Escherichia coli K-12 detected by arbitrary primer PCR (random amplified polymorphic DNA) fingerprinting. J Bacteriol. 1994 Mar; 176(6):1673-82. PMID: 8132463; PMCID: PMC205254.
      160. Bukanov NO, Berg D. Ordered cosmid library and high-resolution physical-genetic map of Helicobacter pylori strain NCTC11638. Mol Microbiol. 1994 Feb; 11(3):509-23. PMID: 8152375.
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      161. Wang G, Whittam TS, Berg CM, Berg D. RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains. Nucleic Acids Res. 1993 Dec 25; 21(25):5930-3. PMID: 8290354; PMCID: PMC310476.
      162. Wang G, Blakesley RW, Berg D, Berg CM. pDUAL: a transposon-based cosmid cloning vector for generating nested deletions and DNA sequencing templates in vivo. Proc Natl Acad Sci U S A. 1993 Aug 15; 90(16):7874-8. PMID: 8395057; PMCID: PMC47245.
      163. Neuwald AF, Krishnan BR, Ahrweiler PM, Frieden C, Berg D. Conditional dihydrofolate reductase deficiency due to transposon Tn5tac1 insertion downstream from the folA gene in Escherichia coli. Gene. 1993 Mar 15; 125(1):69-73. PMID: 8383626.
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      164. Krishnan BR, Berg D. Viability of folA-null derivatives of wild-type (thyA+) Escherichia coli K-12. J Bacteriol. 1993 Feb; 175(3):909-11. PMID: 8423162; PMCID: PMC196245.
      165. Woods JP, Kersulyte D, Goldman WE, Berg D. Fast DNA isolation from Histoplasma capsulatum: methodology for arbitrary primer polymerase chain reaction-based epidemiological and clinical studies. J Clin Microbiol. 1993 Feb; 31(2):463-4. PMID: 8432840; PMCID: PMC262791.
      166. Bryan CS, Smith CW, Berg D, Karp RB. Curvularia lunata endocarditis treated with terbinafine: case report. Clin Infect Dis. 1993 Jan; 16(1):30-2. PMID: 8448316.
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      167. Berg CM, Wang G, Strausbaugh LD, Berg D. Transposon-facilitated sequencing of DNAs cloned in plasmids. Methods Enzymol. 1993; 218:279-306. PMID: 8389964.
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      168. Krishnan BR, Kersulyte D, Brikun I, Huang HV, Berg CM, Berg D. Transposon-based and polymerase chain reaction-based sequencing of DNAs cloned in lambda phage. Methods Enzymol. 1993; 218:258-79. PMID: 8389963.
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      169. Kasai H, Isono S, Kitakawa M, Mineno J, Akiyama H, Kurnit DM, Berg D, Isono K. Efficient large-scale sequencing of the Escherichia coli genome: implementation of a transposon- and PCR-based strategy for the analysis of ordered lambda phage clones. Nucleic Acids Res. 1992 Dec 25; 20(24):6509-15. PMID: 1336178; PMCID: PMC334565.
      170. Akopyanz N, Bukanov NO, Westblom TU, Berg D. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res. 1992 Dec 11; 20(23):6221-5. PMID: 1361982; PMCID: PMC334508.
      171. Kersulyte D, Woods JP, Keath EJ, Goldman WE, Berg D. Diversity among clinical isolates of Histoplasma capsulatum detected by polymerase chain reaction with arbitrary primers. J Bacteriol. 1992 Nov; 174(22):7075-9. PMID: 1429430; PMCID: PMC207395.
      172. Neuwald AF, Berg D, Stauffer GV. Mutational analysis of the Escherichia coli serB promoter region reveals transcriptional linkage to a downstream gene. Gene. 1992 Oct 12; 120(1):1-9. PMID: 1327967.
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      173. Akopyanz N, Bukanov NO, Westblom TU, Kresovich S, Berg D. DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 1992 Oct 11; 20(19):5137-42. PMID: 1408828; PMCID: PMC334296.
      174. Persson BC, Gustafsson C, Berg D, Björk GR. The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli. Proc Natl Acad Sci U S A. 1992 May 01; 89(9):3995-8. PMID: 1373891; PMCID: PMC525618.
      175. Kersulyte D, Krishnan BR, Berg D. Nonrandom orientation of transposon Tn5supF insertions in phage lambda. Gene. 1992 May 01; 114(1):91-6. PMID: 1316868.
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      176. Wikström PM, Lind LK, Berg D, Björk GR. Importance of mRNA folding and start codon accessibility in the expression of genes in a ribosomal protein operon of Escherichia coli. J Mol Biol. 1992 Apr 20; 224(4):949-66. PMID: 1569581.
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      177. Berg CM, Vartak NB, Wang G, Xu X, Liu L, MacNeil DJ, Gewain KM, Wiater LA, Berg D. The m gamma delta-1 element, a small gamma delta (Tn1000) derivative useful for plasmid mutagenesis, allele replacement and DNA sequencing. Gene. 1992 Apr 01; 113(1):9-16. PMID: 1314210.
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      178. Neuwald AF, Krishnan BR, Brikun I, Kulakauskas S, Suziedelis K, Tomcsanyi T, Leyh TS, Berg D. cysQ, a gene needed for cysteine synthesis in Escherichia coli K-12 only during aerobic growth. J Bacteriol. 1992 Jan; 174(2):415-25. PMID: 1729235; PMCID: PMC205732.
      179. Krishnan BR, Kersulyte D, Brikun I, Berg CM, Berg D. Direct and crossover PCR amplification to facilitate Tn5supF-based sequencing of lambda phage clones. Nucleic Acids Res. 1991 Nov 25; 19(22):6177-82. PMID: 1659687; PMCID: PMC329118.
      180. Lodge JK, Weston-Hafer K, Berg D. Tn5 insertion specificity is not influenced by IS50 end sequences in target DNA. Mol Gen Genet. 1991 Aug; 228(1-2):312-5. PMID: 1653404.
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      181. Weston-Hafer K, Berg D. Deletions in plasmid pBR322: replication slippage involving leading and lagging strands. Genetics. 1991 Apr; 127(4):649-55. PMID: 2029966; PMCID: PMC1204393.
      182. Kulakauskas S, Wikström PM, Berg D. Efficient introduction of cloned mutant alleles into the Escherichia coli chromosome. J Bacteriol. 1991 Apr; 173(8):2633-8. PMID: 1826503; PMCID: PMC207830.
      183. Krishnan BR, Blakesley RW, Berg D. Linear amplification DNA sequencing directly from single phage plaques and bacterial colonies. Nucleic Acids Res. 1991 Mar 11; 19(5):1153. PMID: 2020551; PMCID: PMC333799.
      184. Dodson KW, Berg D. A sequence at the inside end of IS50 down regulates transposition. Plasmid. 1991 Mar; 25(2):145-8. PMID: 1650007.
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      185. Weston-Hafer K, Berg D. Limits to the role of palindromy in deletion formation. J Bacteriol. 1991 Jan; 173(1):315-8. PMID: 1846137; PMCID: PMC207189.
      186. Phadnis SH, Kulakauskas S, Krishnan BR, Hiemstra J, Berg D. Transposon Tn5supF-based reverse genetic method for mutational analysis of Escherichia coli with DNAs cloned in lambda phage. J Bacteriol. 1991 Jan; 173(2):896-9. PMID: 1846153; PMCID: PMC207086.
      187. Tomcsanyi T, Berg CM, Phadnis SH, Berg D. Intramolecular transposition by a synthetic IS50 (Tn5) derivative. J Bacteriol. 1990 Nov; 172(11):6348-54. PMID: 2172212; PMCID: PMC526819.
      188. Lodge JK, Berg D. Mutations that affect Tn5 insertion into pBR322: importance of local DNA supercoiling. J Bacteriol. 1990 Oct; 172(10):5956-60. PMID: 2170333; PMCID: PMC526917.
      189. Kazic T, Berg D. Context effects in the formation of deletions in Escherichia coli. Genetics. 1990 Sep; 126(1):17-24. PMID: 2227379; PMCID: PMC1204121.
      190. Cookson BT, Berg D, Goldman WE. Mutagenesis of Bordetella pertussis with transposon Tn5tac1: conditional expression of virulence-associated genes. J Bacteriol. 1990 Apr; 172(4):1681-7. PMID: 2156797; PMCID: PMC208656.
      191. Dodson KW, Berg D. Saturation mutagenesis of the inside end of insertion sequence IS50. Gene. 1989 Dec 21; 85(1):75-81. PMID: 2559878.
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      192. Tomcsanyi T, Berg D. Transposition effect of adenine (Dam) methylation on activity of O end mutants of IS50. J Mol Biol. 1989 Sep 20; 209(2):191-3. PMID: 2555517.
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      193. Phadnis SH, Huang HV, Berg D. Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage lambda. Proc Natl Acad Sci U S A. 1989 Aug; 86(15):5908-12. PMID: 2548192; PMCID: PMC297740.
      194. Weston-Hafer K, Berg D. Specificity of deletion events in pBR322. Plasmid. 1989 May; 21(3):251-3. PMID: 2780896.
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      195. Lodge JK, Kazic T, Berg D. Formation of supercoiling domains in plasmid pBR322. J Bacteriol. 1989 Apr; 171(4):2181-7. PMID: 2649489; PMCID: PMC209875.
      196. Weston-Hafer K, Berg D. Palindromy and the location of deletion endpoints in Escherichia coli. Genetics. 1989 Apr; 121(4):651-8. PMID: 2656400; PMCID: PMC1203650.
      197. Berg CM, Liu L, Coon M, Strausbaugh LD, Gray P, Vartak NB, Brown M, Talbot D, Berg D. pBR322-derived multicopy plasmids harboring large inserts are often dimers in Escherichia coli K-12. Plasmid. 1989 Mar; 21(2):138-41. PMID: 2544913.
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      198. Dodson KW, Berg D. Factors affecting transposition activity of IS50 and Tn5 ends. Gene. 1989; 76(2):207-13. PMID: 2546858.
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      199. Lodge JK, Weston-Hafer K, Berg D. Transposon Tn5 target specificity: preference for insertion at G/C pairs. Genetics. 1988 Nov; 120(3):645-50. PMID: 2852135; PMCID: PMC1203542.
      200. Chow WY, Berg D. Tn5tac1, a derivative of transposon Tn5 that generates conditional mutations. Proc Natl Acad Sci U S A. 1988 Sep; 85(17):6468-72. PMID: 2842773; PMCID: PMC281994.
      201. Nag DK, Huang HV, Berg D. Bidirectional chain-termination nucleotide sequencing: transposon Tn5seq1 as a mobile source of primer sites. Gene. 1988 Apr 15; 64(1):135-45. PMID: 2840345.
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      202. Phadnis SH, Berg D. Identification of base pairs in the outside end of insertion sequence IS50 that are needed for IS50 and Tn5 transposition. Proc Natl Acad Sci U S A. 1987 Dec; 84(24):9118-22. PMID: 2827168; PMCID: PMC299703.
      203. Phadnis SH, Sasakawa C, Berg D. Localization of action of the IS50-encoded transposase protein. Genetics. 1986 Mar; 112(3):421-7. PMID: 3007274; PMCID: PMC1202754.
      204. Sasakawa C, Phadnis SH, Carle GF, Berg D. Sequences essential for IS50 transposition. The first base-pair. J Mol Biol. 1985 Apr 20; 182(4):487-93. PMID: 2989531.
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      205. Phadnis SH, Berg D. recA-independent recombination between repeated IS50 elements is not caused by an IS50-encoded function. J Bacteriol. 1985 Mar; 161(3):928-32. PMID: 2982795; PMCID: PMC214986.
      206. Nag DK, DasGupta U, Adelt G, Berg D. IS50-mediated inverse transposition: specificity and precision. Gene. 1985; 34(1):17-26. PMID: 2989101.
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      207. Berg D, Berg CM, Sasakawa C. Bacterial transposon Tn5: evolutionary inferences. Mol Biol Evol. 1984 Sep; 1(5):411-22. PMID: 6100989.
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      208. Berg D, Lodge J, Sasakawa C, Nag DK, Phadnis SH, Weston-Hafer K, Carle GF. Transposon Tn5: specific sequence recognition and conservative transposition. Cold Spring Harb Symp Quant Biol. 1984; 49:215-26. PMID: 6099236.
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      209. Sasakawa C, Carle GF, Berg D. Sequences essential for transposition at the termini of IS50. Proc Natl Acad Sci U S A. 1983 Dec; 80(23):7293-7. PMID: 6316355; PMCID: PMC390041.
      210. Berg D, Schmandt MA, Lowe JB. Specificity of transposon Tn5 insertion. Genetics. 1983 Dec; 105(4):813-28. PMID: 6315531; PMCID: PMC1202227.
      211. Berg D, Egner C, Lowe JB. Mechanism of F factor-enhanced excision of transposon Tn5. Gene. 1983 Apr; 22(1):1-7. PMID: 6305767.
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      212. Sasakawa C, Lowe JB, McDivitt L, Berg D. Control of transposon Tn5 transposition in Escherichia coli. Proc Natl Acad Sci U S A. 1982 Dec; 79(23):7450-4. PMID: 6296834; PMCID: PMC347357.
      213. Hirschel BJ, Galas DJ, Berg D, Chandler M. Structure and stability of transposon 5-mediated cointegrates. J Mol Biol. 1982 Aug 25; 159(4):557-80. PMID: 6292435.
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      214. Sasakawa C, Berg D. IS50-mediated inverse transposition. Discrimination between the two ends of an IS element. J Mol Biol. 1982 Aug 05; 159(2):257-71. PMID: 6292434.
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      215. Campbell A, Starlinger P, Berg D, Botstein D, Lederberg EM, Novick RP, Szybalski W. Nomenclature of transposable elements in prokaryotes. Plasmid. 1979 Jul; 2(3):466-73. PMID: 384423.
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      216. Campbell A, Berg D, Botstein D, Lederberg EM, Novick RP, Starlinger P, Szybalski W. Nomenclature of transposable elements in prokaryotes. Gene. 1979 Mar; 5(3):197-206. PMID: 467979.
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      217. Berg D, Drummond M. Absence of DNA sequences homologous to transposable element Tn5 (Kan) in the chromosome of Escherichia coli K-12. J Bacteriol. 1978 Oct; 136(1):419-22. PMID: 361699; PMCID: PMC218674.
      218. Davies J, Courvalin P, Berg D. Thoughts on the origins of resistance plasmids. J Antimicrob Chemother. 1977 Nov; 3 Suppl C:7-17. PMID: 599132.
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