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原核生物、病毒、噬菌体测序

我们提供未知基因组信息的对原核生物、病毒、噬菌体的基因组测序。主要基于Roche 454测序平台, 已经成功完成多个细菌的精细图和噬菌体的完成图。 基于我们自主开发的BIOREFER SAP4B微生物自动注释平台能快速完成基因预测、功能注释、功能分类、通路分析、tRNA和rRNA预测等分析。


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 参考文献:

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Draft Genome Sequence of Halomonas smyrnensis AAD6T.  Sogutcu E, Emrence Z, Arikan M, Cakiris A, Abaci N, Oner ET, Ustek D, Arga KY.  (2012) J Bacteriology 194(20): 5690-1.
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Nontypeable Haemophilus influenzae Genetic Islands Associated with Chronic Pulmonary Infection.  Zhang L, Xie J, Patel M, Bakhtyar A, Ehrlich GD, Ahmed A, Earl J, Marrs CF, Clemans D, Murphy TF, Gilsdorf JR.  (2012) PLoS One 7(9): e44730.
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Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance.  Huang H, Yang ZL, Wu XM, Wang Y, Liu YJ, Luo H, Lv X, Gan YR, Song SD, Gao F.  (2012) J Antimicrob Chemother ePub:
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Pyrosequencing-based analysis reveals a novel capsular gene cluster in a KPC-producing Klebsiella pneumoniae clinical isolate identified in Brazil.  Ramos PI, Picão RC, Vespero EC, Pelisson M, Zuleta LF, Almeida LG, Gerber AL, Vasconcelos AT, Gales AC, Nicolás MF.  (2012) BMC Microbiol 12(1): 173.
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Genome-wide detection of spontaneous chromosomal rearrangements in bacteria.  Sun S, Ke R, Hughes D, Nilsson M, Andersson DI. (2012) PLoS One 7(8): e42639.
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Draft genome sequence of the human pathogen Streptomyces somaliensis, a significant cause of actinomycetoma.  Kirby R, Sangal V, Tucker NP, Zakrzewska-Czerwinska J, Wierzbicka K, Herron PR, Chu CJ, Chandra G, Fahal AH, Goodfellow M, Hoskisson PA.  (2012) J Bacteriology 194(13): 3544-5.
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Draft genome sequence of Streptomyces coelicoflavus ZG0656 reveals the putative biosynthetic gene cluster of acarviostatin family á-amylase inhibitors.  Guo X, Geng P, Bai F, Bai G, Sun T, Li X, Shi L, Zhong Q.  (2012) Lett Appl Microbiol ePub:
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Draft genome of a Brazilian avian-pathogenic Escherichia coli strain and in silico characterization of virulence-related genes.  Rojas TC, Parizzi LP, Tiba MR, Chen L, Pereira GA, Sangal V, Yang J, Yu J, Dias da Silveira W.  (2012) J Bacteriology 194(11): 3023.
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Whole Genome Sequencing to Investigate the Emergence of Clonal Complex 23 Neisseria meningitidis Serogroup Y Disease in the United States.  Krauland MG, Dunning Hotopp JC, Riley DR, Daugherty SC, Marsh JW, Messonnier NE, Mayer LW, Tettelin H, Harrison LH.  (2012) PLoS One 7(4): e35699.
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Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates.  Morrison SS, Williams T, Cain A, Froelich B, Taylor C, Baker-Austin C, Verner-Jeffreys D, Hartnell R, Oliver JD, Gibas CJ.  (2012) PLoS One 7(5): e37553.
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Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus.  McAdam PR, Templeton KE, Edwards GF, Holden MT, Feil EJ, Aanensen DM, Bargawi HJ, Spratt BG, Bentley SD, Parkhill J, Enright MC, Holmes A, Girvan EK, Godfrey PA, Feldgarden M, Kearns AM, Rambaut A, Robinson DA, Fitzgerald JR.  (2012) PNAS ePub:
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Determining the Repertoire of Immunodominant Proteins via Whole-Genome Amplification of Intracellular Pathogens.  Dark MJ, Lundgren AM, Barbet AF.  (2012) PLoS One 7(4): e36456.
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Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.  Schroder J, Maus I, Meyer K, Wordemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A.  (2012) BMC Genomics 13(1): 141.
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Genome Sequence of Lactobacillus fructivorans KCTC 3543.  Nam SH, Choi SH, Kang A, Lee KS, Kim DW, Kim RN, Kim DS, Park HS.  (2012) J Bacteriology 194(8): 2111-2.
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Draft Genome Sequence of Marinobacterium stanieri S30, a Strain Isolated from a Coastal Lagoon in Chuuk State in Micronesia.  Choi YU, Kwon YK, Ye BR, Hyun JH, Heo SJ, Affan A, Yoon KT, Park HS, Oh C, Kang DH.  (2012) J Bacteriology 194(5): 1260.
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Comparative Genomics of 2009 Seasonal Plague (Yersinia pestis) in New Mexico.  Gibbons HS, Krepps MD, Ouellette G, Karavis M, Onischuk L, Leonard P, Broomall S, Sickler T, Betters JL, McGregor P, Donarum G, Liem A, Fochler E, McNew L, Rosenzweig CN, Skowronski E.  (2012) PLoS One 7(2): e31604.
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Complete Sequence of a Novel 178 kb Plasmid Carrying blaNDM-1 in a Providencia stuartii Strain Isolated in Afghanistan.  Mc Gann P, Hang J, Clifford RJ, Yang Y, Kwak YI, Kuschner RA, Lesho EP, Waterman PE.  (2012) Antimicrob Agents Chemother ePub:
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High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach.  Allard MW, Luo Y, Strain E, Li C, Keys CE, Son I, Stones R, Musser SM, Brown EW. (2012) BMC Genomics 13(1): 32.
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Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections.  Clark G, Paszkiewicz K, Hale J, Weston V, Constantinidou C, Penn C, Achtman M, McNally A.  (2012) J Antimicrob Chemother ePub:
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Bacterial identification and subtyping using DNA microarray and DNA sequencing.  Al-Khaldi SF, Mossoba MM, Allard MM, Lienau EK, Brown ED.  (2012) Metholds Mol Biol 881:: 73-95.
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Plasmid Localization and Organization of Melamine Degradation Genes in Rhodococcus sp. strain Mel.  Dodge AG, Wackett LP, Sadowsky MJ. (2011) Appl Environ Microbiol ePub:
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6-10× pyrosequencing is a practical approach for whole prokaryote genome studies.  Li J, Jiang J, Leung FC. (2011) Gene ePub:
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Identification, characterisation and recombinant expression of epidermicin NI01, a novel unmodified bacteriocin produced by Staphylococcus epidermidis displaying potent activity against staphylococci.  Sandiford S, Upton M. (2011) Antimicrob Agents Chemother ePub:
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Ethanol-Tolerant Gene Identification in Clostridium thermocellum Using Pyro-Resequencing for Metabolic Engineering.  Yang S, Klingeman DM, Brown SD. (2011) Metholds Mol Biol 834: 111-36.
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Genome sequence of Haemophilus parasuis strain 29755.  Mullins MA, Register KB, Bayles DO, Dyer DW, Kuehn JS, Phillips GJ.  (2011) Stand Genomic Sci 5(1): 61-8.
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Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation.  Schröder J, Maus I, Trost E, Tauch A. (2011) BMC Genomics 12: 545.
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The complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527(T) and comparative analysis of growth in milk with B. animalis subspecies lactis DSM 10140(T).  Loquasto JR, Barrangou R, Dudley EG, Roberts RF.  (2011) J Dairy Sci 94(12): 5864-70.
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Genome Sequence of Leuconostoc carnosum KCTC 3525.  Nam SH, Kim A, Choi SH, Kang A, Kim DW, Kim RN, Kim DS, Park HS. (2011) J Bacteriology 193(21): 6100-1.
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Complete genome sequence and characterization of the N-acylhomoserine lactone-degrading gene of the potato leaf-associated Solibacillus silvestris.  Morohoshi T, Tominaga Y, Someya N, Ikeda T. (2011) J Biosci Bioeng ePub:
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Single Nucleotide Polymorphisms that Differentiate Two Subpopulations of Salmonella Enteritidis Within Phage Type.  Guard J, Morales CA, Fedorka-Cray P, Gast RK. (2011) BMC Res Notes 4(1): 369.
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A partial genome assembly from a candidate division OP11 single cell from an anoxic spring (Zodletone spring, OK, USA).  Youssef NH, Blainey PC, Quake SR, Elshahed MS. (2011) Appl Environ Microbiol ePub:
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Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential.  Procópio L, Alvarez VM, Jurelevicius DA, Hansen L, Sørensen SJ, Cardoso JS, Pádula M, Leitão AC, Seldin L, van Elsas JD. (2011) Antonie Van Leeuwenhoek :
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Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1 causing citrus bacterial spot and related strains provides insights into virulence and host-specificity.  Jalan N, Aritua V, Kumar D, Yu F, Jones JB, Graham JH, Setubal JC, Wang N. (2011) J Bacteriology ePub:
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Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs.  Vogel RF, Pavlovic M, Ehrmann MA, Wiezer A, Liesegang H, Offschanka S, Voget S, Angelov A, Böcker G, Liebl W. (2011) Microb Cell Fact 10 Suppl 1: 6S.
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Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii.  Snitkin ES, Zelazny AM, Montero CI, Stock F, Mijares L; NISC Comparative Sequence Program, Murray PR, Segre JA. (2011) PNAS ePub:
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Whole genome sequencing and phenotypic analysis of mutations found in Bacillus subtilis following evolution under relaxed selection for sporulation.  Brown CT, Fishwick LK, Chokshi BM, Cuff MA, Jackson JM 4th, Oglesby T, Rioux AT, Rodriguez E, Stupp GS, Trupp AH, Woollcombe-Clarke JS, Wright TN, Zaragoza WJ, Drew JC, Triplett EW, Nicholson WL. (2011) Appl Environ Microbiol ePub:
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Genomic Structure of the Cyanobacterium Synechocystis sp. PCC 6803 Strain GT-S.  Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki NV, Kurokawa K, Ohta H, Kanesaki Y, Yoshikawa H, Tabata S, Ikeuchi M, Sato N. (2011) DNA Research ePub:
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Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC).  Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R. (2011) Arch Microbiol ePub:
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Comparative Genomics of Klebsiella pneumoniae strains with Different Antibiotic Resistance Profiles.  Kumar V, Sun P, Vamathevan J, Li Y, Ingraham K, Palmer L, Huang J, Brown JR. (2011) Antimicrob Agents Chemother ePub:
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Yersinia enterocolitica palearctica serobiotype O:3/4--a successful group of emerging zoonotic pathogens.  Batzilla J, Antonenka U, Höper D, Heesemann J, Rakin A.  (2011) BMC Genomics 12: 348.
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Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605.  Clarke DJ, Chaudhuri RR, Martin HM, Campbell BJ, Rhodes JM, Constantinidou C, Pallen MJ, Loman NJ, Cunningham AF, Browning DF, Henderson IR. (2011) J Bacteriology ePub:
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De novo sequencing and assembly of the whole genome of Novosphingobium sp. PP1Y.  D'Argenio V, Petrillo M, Cantiello P, Naso B, Cozzuto L, Notomista E, Paolella G, Di Donato A, Salvatore F. (2011) J Bacteriology ePub:
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Cholesterol degradation by Gordonia cholesterolivorans.  Drzyzga O, Fernández de Las Heras L, Morales V, Navarro Llorens JM, Perera J. (2011) Appl Environ Microbiol ePub:
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Multistrain genome analysis identifies candidate vaccine antigens of Anaplasma marginale.  Dark MJ, Al-Khedery B, Barbet AF. (2011) Vaccines ePub:
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Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy.  Hornsey M, Loman N, Wareham DW, Ellington MJ, Pallen MJ, Turton JF, Underwood A, Gaulton T, Thomas CP, Doumith M, Livermore DM, Woodford N. (2011) J Antimicrob Chemother ePub:
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Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates.  Bailly X, Giuntini E, Sexton MC, Lower RP, Harrison PW, Kumar N, Young JP. (2011) ISME J ePub:
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Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.  Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yates JR 3rd, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L.  (2011) PNAS 108(21): 8815-20.
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Detection and characterisation of SCCmec remnants in multiresistant methicillin-susceptible Staphylococcus aureus causing a clonal outbreak in a Swedish county.  Lindqvist M, Isaksson B, Grub C, Jonassen TO, Hällgren A. (2011) Eur J Clin Microbiol Infect Dis. 31(2): 141-7.
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Genome sequence of Neisseria meningitidis serogroup B strain H44/76.  Piet JR, Huis in 't Veld RA, van Schaik BD, van Kampen AH, Baas F, van de Beek D, Pannekoek Y, van der Ende A. (2011) J Bacteriology 193(9): 2371-2,
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Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses  Pedrosa F et al. (2011) PLoS One 7(5): e1002064.
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An Enterotoxin-Bearing Pathogenicity Island in Staphylococcus epidermidis.  Madhusoodanan J, Seo KS, Remortel B, Park JY, Hwang SY, Fox LK, Park YH, Deobald CF, Wang D, Liu S, Daugherty SC, Gill AL, Bohach GA, Gill SR. (2011) J Bacteriology 193(8): 1854-62.
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Complete genome sequence of Yersinia enterocolitica subsp. palearctica serogroup O:3.  Batzilla J, Höper D, Antonenka U, Heesemann J, Rakin A.  (2011) J Bacteriology 193(8): 2067.
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Comparative whole genome sequence analysis of the carcinogenic bacterial model pathogen Helicobacter felis.  Arnold IC, Zigova Z, Holden M, Lawley T, Rad R, Dougan G, Falkow S, Bentley SD, Müller A.  (2011) Genome Biol Evol 3: 302-8.
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Genome sequence of Acinetobacter baumannii MDR-TJ.  Gao F, Wang Y, Liu YJ, Wu XM, Lv X, Gan YR, Song SD, Huang H. (2011) J Bacteriology 193(9): 2365-6.
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Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing  Lienau EK, Strain E, Wang C, Zheng J, Ottesen AR, Keys CE, Hammack TS, Musser SM, Brown EW, Allard MW, Cao G, Meng J, Stones R.  (2011) New England Journal of Medicine 364(10):: 981-2.
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Helicobacter pylori genome evolution during human infection.  Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B, Droege M, Reinhardt R, Correa P, Meyer TF, Josenhans C, Falush D, Suerbaum S. (2011) PNAS ePub:
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Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110.  Han JI, Choi HK, Lee SW, Orwin PM, Kim J, Laroe SL, Kim TG, O'Neil J, Leadbetter JR, Lee SY, Hur CG, Spain JC, Ovchinnikova G, Goodwin L, Han C. (2011) J Bacteriology 193(5): 1183-90.
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Using Genomic Sequencing for Classical Genetics in E. coli K12.  Lyons E, Freeling M, Kustu S, Inwood W. (2011) PLoS One 6(2): e16717.
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Complete Genome Sequencing of Agrobacterium sp H13-3, the former Rhizobium lupini H13-3, Reveals a Tripartite Genome Consisting of a Circular and a Linear Chromosome and an Accessory Plasmid but Lacking a Tumor-Inducing Ti-Plasmid.  Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Pühler A, Schlüter A. (2011) J Biotechnology 155(1): 50-62.
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Microbes and Health Sackler Colloquium: Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.  Hansen EE, Lozupone CA, Rey FE, Wu M, Guruge JL, Narra A, Goodfellow J, Zaneveld JR, McDonald DT, Goodrich JA, Heath AC, Knight R, Gordon JI.  (2011) PNAS 108 Suppl 1: 4599-606.
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Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018.  Hu S, Zheng H, Gu Y, Zhao J, Zhang W, Yang Y, Wang S, Zhao G, Yang S, Jiang W. (2011) BMC Genomics 12(1): 93.
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Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants.  Powney R, Smits TH, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B. (2011) J Bacteriology 193(3): 785-6.
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Reconstitution of the FK228 Biosynthetic Pathway Reveals Cross Talk between Modular Polyketide Synthases and Fatty Acid Synthase.  Wesener SR, Potharla VY, Cheng YQ. (2011) Appl Environ Microbiol 77(4): 1501-7.
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Genome Sequence and Characterization of the Tsukamurella Bacteriophage TPA2.  Petrovski S, Seviour RJ, Tillett D. (2011) Appl Environ Microbiol 77(4): 1389-98.
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Genome Sequence of the Zoonotic Pathogen Chlamydophila psittaci.  Seth-Smith HM, Harris SR, Rance R, West AP, Severin JA, Ossewaarde JM, Cutcliffe LT, Skilton RJ, Marsh P, Parkhill J, Clarke IN, Thomson NR. (2011) J Bacteriology 193(5): 1282-3.
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Genome Sequence Analyses of Pseudomonas savastanoi pv. glycinea and Subtractive Hybridization-Based Comparative Genomics with Nine Pseudomonads.  Qi M, Wang D, Bradley CA, Zhao Y. (2011) PLoS One 6(1): e16451
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Genome Sequence of Lactobacillus farciminis KCTC 3681.  Nam SH, Choi SH, Kang A, Kim DW, Kim RN, Kim A, Kim DS, Park HS. (2011) J Bacteriology ePub:
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Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution.  Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ. (2011) Genome Biol Evol 3: 168-85.
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The discovery of salinosporamide K from the Marine Bacterium "Salinispora pacifica" by genome mining gives insight into pathway evolution.  Eustáquio AS, Nam SJ, Penn K, Lechner A, Wilson MC, Fenical W, Jensen PR, Moore BS. (2011) Chembiochem 12(1): 61-4.
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Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates.  Stephan R, Lehner A, Tischler P, Rattei T. (2011) J Bacteriol 193(1): 309-10.
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Recent transfer of an iron-regulated gene from the plastid to the nuclear genome in an oceanic diatom adapted to chronic iron limitation.  Lommer M, Roy AS, Schilhabel M, Schreiber S, Rosenstiel P, Laroche J. (2010) BMC Genomics 11(10: 718.
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Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.  Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L, Leshkowitz D, Galatenko V, Nikolaev V, Mugasimangalam RC, Bransburg-Zabary S, Gutnick DL, Lancet D, Ben-Jacob E.  (2010) BMC Genomics 11(1): 710.
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The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.  Trost E et al.  (2010) BMC Genomics 11(1): 728.
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Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.  Morelli G et al. (2010) Nature Genetics ePub:
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Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, Producer of Diverse Secondary Metabolites.  Song JY, Jeong H, Yu DS, Fischbach MA, Park HS, Kim JJ, Seo JS, Jensen SE, Oh TK, Lee KJ, Kim JF. (2010) Journal of Bacteriology 192(23): 6317-8.
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Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection.  Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, Earl J, Janto B, Boissy RJ, Hogg J, Barbadora K, Sampath R, Lonergan S, Post JC, Hu FZ, Ehrlich GD. (2010) PLoS Pathogens 6(9): e1001108.
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Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing.  Chen PE, Willner KM, Butani A, Dorsey S, George M, Stewart A, Lentz SM, Cook CE, Akmal A, Price LB, Keim PS, Mateczun A, Brahmbhatt TN, Bishop-Lilly KA, Zwick ME, Read TD, Sozhamannan S. (2010) PLoS One 5(8): e12397.
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Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics.  Zhang W, Ostash B, Walsh CT. (2010) PNAS 107(39): 16828-33.
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Genomic characterization of Campylobacter jejuni strain M1.  Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW. (2010) PLoS One 5(8): :e12253.
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Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.  Yeoman CJ, Yildirim S, Thomas SM, Durkin AS, Torralba M, Sutton G, Buhay CJ, Ding Y, Dugan-Rocha SP, Muzny DM, Qin X, Gibbs RA, Leigh SR, Stumpf R, White BA, Highlander SK, Nelson KE, Wilson BA. (2010) PLoS One 5(8): e12411.
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Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913.  Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ. (2010) ISME Journal ePub:
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Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation.  Guinane CM, Ben Zakour NL, Tormo-Mas MA, Weinert LA, Lowder BV, Cartwright RA, Smyth DS, Smyth CJ, Lindsay JA, Gould KA, Witney A, Hinds J, Bollback JP, Rambaut A, Penadés JR, Fitzgerald JR. (2010) Genome Biol Evol 2: 454-66.
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Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.  Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. (2010) ISME Journal ePub:
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Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer.  McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. (2010) PLoS One 5(6): e11029.
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De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.  Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL. (2010) PLoS One 5(6): e10922.
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Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses.  Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Mégraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J. (2010) Journal of Bacteriology 192(12): 3078-92.
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The waddlia genome: a window into chlamydial biology.  Bertelli C, Collyn F, Croxatto A, Rückert C, Polkinghorne A, Kebbi-Beghdadi C, Goesmann A, Vaughan L, Greub G. (2010) PLoS One 5(5): e10890.
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Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae.  Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TY, Martin SL, Guo HB, Smith JC, Brown SD. (2010) PNAS 107(23): 10395-400.
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Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche.  Guimaraes AM, Santos AP, Sanmiguel P, Walter T, Timenetsky J, Messick JB. (2010) PLoS One 6(5): e19574.
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The cylindrospermopsin gene cluster of Aphanizomenon sp. strain 10E6: organisation and recombination.  Stüken A, Jakobsen KS. (2010) Microbiology 156(Pt 8): 2438-51.
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One bacterial cell, one complete genome.  Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF. (2010) PLoS One 5(4): e10314.
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Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island.  van Schaik W, Top J, Riley DR, Boekhorst J, Vrijenhoek JE, Schapendonk CM, Hendrickx AP, Nijman IJ, Bonten MJ, Tettelin H, Willems RJ. (2010) BMC Genomics 11(1): 239.
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Genome sequence of a naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1.  Chen C, Kittichotirat W, Chen W, Downey JS, Si Y, Bumgarner R. (2010) Journal of Bacteriology 192(10): 2643-4.
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Complete genome sequence of the probiotic Lactobacillus casei strain BL23.  Mazé A. et al. (2010) Journal of Bacteriology 192(10): 2647-8.
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Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.  Siezen RJ, Bayjanov J, Renckens B, Wels M, van Hijum SA, Molenaar D, van Hylckama Vlieg JE. (2010) Journal of Bacteriology 192(10): 2649-50.
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Genome sequence of hybrid V. cholerae O1 MJ-1236, B-33 and CIRS101 and comparative genomics with V. cholerae.  Grim CJ, Hasan NA, Taviani E, Haley B, Chun J, Brettin TS, Bruce DC, Detter JC, Han CS, Chertkov O, Challacombe J, Huq A, Nair GB, Colwell RR. (2010) Journal of Bacteriology 192(13): 3524-33.
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Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium.  Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, Niazi F, Affourtit JP, Zehr JP. (2010) Nature 464(7285): 90-4.
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High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak.  Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C. (2010) BMC Genomics 11(1): 120.
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Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity.  Smits TH, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B. (2010) BMC Genomics 11(1): 2.
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Genomic characterization of the Yersinia genus.  Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M, Thomason B, Kiley MP, Lentz S, Nolan N, Sozhamannan S, Sulakvelidze A, Mateczun A, Du L, Zwick ME, Read TD. (2010) Genome Biology 11(1): R1.
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Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.  Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G, Wren BW. (2009) Genome Biology 10(9): R102.
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The novel polysaccharide deacetylase homolog Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae.  Milani CJ, Aziz RK, Locke JB, Dahesh S, Nizet V, Buchanan JT. (2009) Microbiology 156(Pt 2): 543-54.
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Genomic Diversity and Evolution of Mycobacterium ulcerans Revealed by Next-Generation Sequencing.  Weihong Qi, Michael Käser, Katharina Röltgen, Dorothy Yeboah-Manu, Gerd Pluschke (2009) PLoS Pathogens 5(9): e10000580.
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Whole genome amplification and de novo assembly of single bacterial cells.  Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. (2009) PLoS One 4(9): e6864.
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A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain.  Rounge TB, Rohrlack T, Nederbragt AJ, Kristensen T, Jakobsen KS. (2009) BMC Genomics 10(1): 396.
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Brucella microti: the genome sequence of an emerging pathogen.  Audic S, Lescot M, Claverie JM, Scholz HC. (2009) BMC Genomics 10(1): 352.
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The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).  Yang et al. (2009) PLoS One 4(7): e6085.
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The Mycoplasma conjunctivae genome sequencing, annotation and analysis.  Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA, Falquet L. (2009) BMC Bioinformatics Suppl 6: S7.
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Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725.  Kataeva IA, Yang SJ, Dam P, Poole FL 2nd, Yin Y, Zhou F, Chou WC, Xu Y, Goodwin L, Sims DR, Detter JC, Hauser LJ, Westpheling J, Adams MW. (2009) Journal of Bacteriology 191(11): 3760-1.
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Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms.  Clawson ML, Keen JE, Smith TP, Durso LM, McDaneld TG, Mandrell RE, Davis MA, Bono JL. (2009) Genome Biology 10(5): R56.
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Complete genome sequence of Lactobacillus plantarum JDM1.  Zhang Z, Liu C, Zhu Y, Zhong Y, Zhu Y, Zheng H, Zhao GP, Wang SY, Guo X. (2009) Journal of Bacteriology 191(15): 5020-1.
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Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.  Di Bonaventura MP, Desalle R, Pop M, Nagarajan N, Figurski D, Fine DH, Kaplan J, Planet P. (2009) Journal of Bacteriology 191(14): 4693-4.
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Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance.  Feng J, Lupien A, Gingras H, Wasserscheid J, Dewar K, Légaré D, Ouellette M. (2009) Genome Research 19(7): 1214-23.
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Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.  Champion MD, Zeng Q, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, Young S, Koehrsen M, Engels R, Pearson M, Howarth C, Larson L, White J, Alvarado L, Forsman M, Bearden SW, Sjöstedt A, Titball R, Michell SL, Birren B, Galagan J. (2009) PLoS Pathogens 5(5): e1000459.
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Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1).  Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, Lapidus A, Hugenholtz P, Brune A. (2009) Applied Environmental Microbiology 75(9): 2841-9.
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Assembling the marine metagenome, one cell at a time.  Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. (2009) PLoS ONE 4(4): e5299.
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Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.  Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, Coûté-Monvoisin AC, Leyer G, Rendulic S, Steele JL, Broadbent JR, Oberg T, Dudley EG, Schuster S, Romero DA, Roberts RF. (2009) Journal of Bacteriology 191(13): 4144-51.
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Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.  Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI. (2009) PNAS 106(14): 5859-64.
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Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.  Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG. (2009) Journal of Bacteriology 191(7): 2371-9
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Whole-genome-based phylogeny and divergence of the genus Brucella.  Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom-Sternberg JS, Chain PS, Roberto FF, Hnath J, Brettin T, Keim P. (2009) Journal of Bacteriology 191(8): 2864-70.
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Evidence that the intra-amoebal Legionella drancourtii acquired a sterol reductase gene from eukaryotes.  Moliner C, Raoult D, Fournier PE. (2009) BMC Research Notes 2: 51.
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Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.  Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P, Albertyn Z, Shaban B, Motro Y, Dunn DS, Schibeci D, Hunter A, Barrero R, Phillips ND, Hampson DJ. (2009) PLoS ONE 4(3): e4641
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Identification of bacillus anthracis spore component antigens conserved across diverse bacillus cereus sensu lato strains.  Mukhopadhyay S, Akmal A, Stewart AC, Hsia RC, Read TD. (2009) Molecular & Cellular Proteomics 8(6): 1174-91.
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De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.  Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL. (2009) Genome Research 19(2): 294-305
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Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage.  Rolain JM, François P, Hernandez D, Bittar F, Richet H, Fournous G, Mattenberger Y, Bosdure E, Stremler N, Dubus JC, Sarles J, Reynaud-Gaubert M, Boniface S, Schrenzel J, Raoult D. (2009) Biology Direct 4: 1
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Conservation in the face of diversity: multistrain analysis of an intracellular bacterium.  Dark MJ, Herndon DR, Kappmeyer LS, Gonzales MP, Nordeen E, Palmer GH, Knowles DP Jr, Brayton KA. (2009) BMC Genomics 10: 16
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Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer.  McClain MS, Shaffer CL, Israel DA, Peek RM Jr, Cover TL. (2009) BMC Genomics 10: 3
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The Complete Genome Sequence of Helicobacter pylori strain G27.  Baltrus DA, Amieva MR, Covacci A, Lowe TM, Merrell DS, Ottemann KM, Stein M, Salama NR, Guillemin K. (2009) Journal of Bacteriology 191(1): 447-8
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A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.  Almeida NF, Yan S, Lindeberg M, Studholme DJ, Schneider DJ, Condon B, Liu H, Viana CJ, Warren A, Evans C, Kemen E, Maclean D, Angot A, Martin GB, Jones JD, Collmer A, Setubal JC, Vinatzer BA. (2009) Mol Plant Microbe Interact 22(1): 52-62.
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High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.  Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P. (2008) BMC Genomics 9: 603
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Aggressive Assembly of Pyrosequencing Reads with Mates.  Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. (2008) Bioinformatics 24(24): 2818-24
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Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter.  Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. (2008) ISME Journal 2(12): 1194-212
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Niche-specificity and the variable fraction of the pectobacterium pan-genome.  Glasner JD, Marquez-Villavicencio M, Kim HS, Jahn CE, Ma B, Biehl BS, Rissman AI, Mole B, Yi X, Yang CH, Dangl JL, Grant SR, Perna NT, Charkowski AO. (2008) Mol Plant Microbe Interactions 21: 1549-60
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Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies.  Poly F, Read TD, Chen YH, Monteiro MA, Serichantalergs O, Pootong P, Bodhidatta L, Mason CJ, Rockabrand D, Baqar S, Porter CK, Tribble D, Darsley M, Guerry P. (2008) Infection and Immunity 76(12): 5655-67.
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Whole-genome mutational biases in bacteria.  Lind PA, Andersson DI. (2008) PNAS 105: 17878-83
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Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis Within Protist Cells in Termite Gut.  Hongoh Y, Sharma VK, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M. (2008) Science 322: 1108
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Globally Distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II.  Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, Shi T, Tripp HJ, Affourtit JP (2008) Science 322: 1110
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Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.  Orsi RH, Borowsky ML, Lauer P, Young SK, Nusbaum C, Galagan JE, Birren BW, Ivy RA, Sun Q, Graves LM, Swaminathan B, Wiedmann M. (2008) BMC Genomics 9(1): 539
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The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism.  Lee HS, Kang SG, Bae SS, Lim JK, Cho Y, Kim YJ, Jeon JH, Cha SS, Kwon KK, Kim HT, Park CJ, Lee HW, Kim SI, Chun J, Colwell RR, Kim SJ, Lee JH. (2008) Journal of Bacteriology 190: 7491-9
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Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak.  Kotewicz ML, Mammel MK, LeClerc JE, Cebula TA. (2008) Microbiology 154: 3518-28
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The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.  Welsh EA, Liberton M, Stöckel J, Loh T, Elvitigala T, Wang C, Wollam A, Fulton RS, Clifton SW, Jacobs JM, Aurora R, Ghosh BK, Sherman LA, Smith RD, Wilson RK, Pakrasi HB. (2008) PNAS 105: 15094-9
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Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment.  Thomas T, Evans FF, Schleheck D, Mai-Prochnow A, Burke C, Penesyan A, Dalisay DS, Stelzer-Braid S, Saunders N, Johnson J, Ferriera S, Kjelleberg S, Egan S. (2008) PLoS ONE 3(9): e3252
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Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T.  Paul D, Bridges S, Burgess SC, Dandass Y, Lawrence ML. (2008) Journal of Bacteriology 190: 5531–5532
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High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.  Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G. (2008) Nature Genetics 40: 987-993
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A Bacillus thuringiensis strain producing a polyglutamate capsule resembling that of Bacillus anthracis.  Cachat E, Barker M, Read TD, Priest FG. (2008) FEMS Microbiology Letters 285(2): 220-6.
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Genomic content of Bordetella pertussis clinical isolates circulating in areas of intensive children vaccination  Bouchez V, Caro V, Levillain E, Guigon G, Guiso N. (2008) PLoS One 3(6): e2737
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The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression  Jung D. Oh, Helene Kling-Backhed, Marios Giannakis, Jian Xu, Robert S. Fulton, Lucinda A. Fulton, Holland S. Cordum, Chunyan Wang, Glendoria Elliott, Jennifer Edwards, Elaine R. Mardis, Lars G. Engstrand, and Jeffrey I. Gordon (2008) PNAS 103: 9999–10004
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Scaffolding and validation of bacterial genome assemblies using optical restriction maps.  Nagarajan N, Read TD, Pop M. (2008) Bioinformatics 24(10): 1229-35.
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Genome Sequence of Brucella abortus Vaccine Strain S19 Compared to Virulent Strains Yields Candidate Virulence Genes  Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, Martino-Catt S, Bricker B, Yu G, Du L, Sobral BW (2008) PLoS ONE 3:
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Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11  Stiens M, Becker A, Bekel T, Gödde V, Goesmann A, Niehaus K, Schneiker-Bekel S, Selbitschka W, Weidner S, Schlüter A, Pühler A (2008) J. Biotechnol :
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The chemical structure and genetic locus of Campylobacter jejuni CG8486 (serotype HS:4) capsular polysaccharide: the identification of 6-deoxy-d-ido-heptopyranose  Yu-Han Chen, Frédéric Poly, Zbigniew Pakulski, Patricia Guerry, Mario A. Monteiro (2008) Carbohydrate Research 343: 1034-1040
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Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm  Bernard La Scola, Khalid Elkarkouri, Wenjun Li, Tara Wahab, Ghislain Fournous, Jean-Marc Rolain, Silpak Biswas, Michel Drancourt, Catherine Robert, Stéphane Audic, Sven Löfdahl and Didier Raoult (2008) Genome Research 18: 742-750
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Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome  Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI (2008) Cell Host & Microbe 3: 213-223
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The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment  Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E, Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, Caballero J, Siefert J, Eguiarte L, Vielle JP, Martínez O, Souza V, Herrera-Estrella A, Herrera-Estrella L (2008) PNAS 105: 5803-5808
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Whole genome pyrosequencing of an epidemic multidrug resistant Acinetobacter baumannii of the European clone II  Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, Bonnal RJ, Sicheritz-Ponten T, De Bellis G, Visca P, Cassone A, Carattoli A (2008) Antimicrob Agents Chemother :
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Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell  Yuichi Hongoh, Vineet K. Sharma, Tulika Prakash, Satoko Noda, Todd D. Taylor, Toshiaki Kudo, Yoshiyuki Sakaki, Atsushi Toyoda, Masahira Hattori, and Moriya Ohkuma (2008) PNAS 105: 5555-5560
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Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Ciénegas Valley in Coahuila, Mexico  Cerritos R, Vinuesa P, Eguiarte LE, Herrera-Estrella L, Alcaraz-Peraza LD, Arvizu-Gómez JL, Olmedo G, Ramirez E, Siefert JL, Souza V (2008) Int J Syst Evol Microbiol 58: 919-923
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Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids   Andreas Tauch, Jessica Schneider, Rafael Szczepanowski, Alexandra Tilker, Prisca Viehoever, Karl-Heinz Gartemann, Walter Arnold, Jochen Blom, Karina Brinkrolf, Iris Brune, Susanne Götker, Bernd Weisshaar, Alexander Goesmann, Marcus Dröge and Alfred Pühler  (2008) Journal of Biotechnology :
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Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species  Paustian ML, Zhu X, Sreevatsan S, Robbe-Austerman S, Kapur V, Bannantine JP (2008) BMC Genomics 9:
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Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells  Giannakis M, Chen SL, Karam SM, Engstrand L, Gordon JI (2008) PNAS 105: 4358-4363
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The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing   Andreas Tauch, Eva Trost, Alexandra Tilker, Ulrike Ludewig, Susanne Schneiker, Alexander Goesmann, Walter Arnold, Thomas Bekel, Karina Brinkrolf, Iris Brune, Susanne Götker, Jörn Kalinowski, Paul-Bertram Kamp, Francisco Pereira Lobo, Prisca Viehoever, Bernd Weisshaar, Francisco Soriano, Marcus Dröge and Alfred Pühler (2008) Journal of Biotechnology :
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Altered utilization of N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak  Mukherjee A, Mammel MK, LeClerc JE, Cebula TA (2008) Journal of Bacteriology 190: 1710-1717
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Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina  Wesley D. Swingley, Min Chen, Patricia C. Cheung, Amber L. Conrad, Liza C. Dejesa, Jicheng Hao, Barbara M. Honchak, Lauren E. Karbach, Ahmet Kurdoglu, Surobhi Lahiri, Stephen D. Mastrian, Hideaki Miyashita, Lawrence Page, Pushpa Ramakrishna, Soichirou Satoh, W. Matthew Sattley, Yuichiro Shimada, Heather L. Taylor, Tatsuya Tomo, Tohru Tsuchiya, Zi T. Wang, Jason Raymond, Mamoru Mimuro, Robert E. Blankenship, and Jeffrey W. Touchman (2008) PNAS 105:
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Mutation in the Transcriptional Regulator PhoP Contributes to Avirulence of Mycobacterium tuberculosis H37Ra Strain  Jong Seok Lee, Roland Krause, Jorg Schreiber, Hans-Joachim Mollenkopf, Jane Kowall, Robert Stein, Bo-Young Jeon, Jeong-Yeon Kwak, Min-Kyong Song, Juan Pablo Patron, Sabine Jorg, Kyoungmin Roh, Sang-Nae Cho, and Stefan H.E. Kaufmann (2008) Cell Host & Microbe 3: 97-103
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Parallel genomic evolution and metabolic interdependence in an ancient symbiosis  John P. McCutcheon and Nancy A. Moran (2007) PNAS 104: 19392–19397
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Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays  Peano C, Bicciato S, Corti G, Ferrari F, Rizzi E, Bonnal RJ, Bordoni R, Albertini A, Rossi Bernardi L, Donadio S, De Bellis G (2007) Microbrial Cell Factories 6:
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Chlamydia trachomatis: Genome sequence analysis of lymphogranuloma venereum isolates  Thomson NR, Holden MT, Carder C, Lennard N, Lockey SJ, Marsh P, Skipp P, O'Connor CD, Goodhead I, Norbertzcak H, Harris B, Ormond D, Rance R, Quail MA, Parkhill J, Stephens RS, Clarke IN (2007) Genome Research :
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Methanotrophy below pH 1 by a new Verrucomicrobia species  Arjan Pol, Klaas Heijmans, Harry R. Harhangi, Dario Tedesco, Mike S. M. Jetten & Huub J. M. Op den Camp (2007) Nature :
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Vibrio furnissii M1: Genomic and Biochemical Studies Demonstrating the Absence of an Alkane-Producing Phenotype  Lawrence P. Wackett, Janice A. Frias, Jennifer L. Seffernick, David J. Sukovich, and Stephan Cameron (2007) Applied Environmental Microbiology :
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Nanoliter Reactors Improve Multiple Displacement Amplification of Genomes from Single Cells  Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR (2007) PLoS Genetics 3:
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The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828  Pearson BM, Gaskin DJ, Segers RP, Wells JM, Nuijten PJ, van Vliet AH (2007) Journal of Bacteriology :
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Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments  Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJ, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD (2007) PLoS Biology 5:
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Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032  Jason Gioia, Shailaja Yerrapragada, Xiang Qin, Huaiyang Jiang, Okezie C. Igboeli, Donna Muzny, Shannon Dugan-Rocha, Yan Ding, Alicia Hawes, Wen Liu, Lesette Perez, Christie Kovar, Huyen Dinh, Sandra Lee, Lynne Nazareth, Peter Blyth, Michael Holder, Christian Buhay, Madhan R. Tirumalai, Yamei Liu, Indrani Dasgupta, Lina Bokhetache, Masaya Fujita, Fathi Karouia, Prahathees Eswara Moorthy, Johnathan Siefert, Akif Uzman, Prince Buzumbo, Avani Verma, Hiba Zwiya, Brian D. McWilliams, Adeola Olowu, Kenneth D. Clinkenbeard, David Newcombe, Lisa Golebiewski, Joseph F. Petrosino, Wayne L. Nicholson, George E. Fox, Kasthuri Venkateswaran, Sarah K. Highlander, George M. Weinstock (2007) PLoS ONE 9:
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Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome  Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley SD, Post JC, Ehrlich GD, Hu FZ (2007) Journal of Bacteriology :
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An ice-binding protein from an Antarctic sea ice bacterium  Raymond JA, Fritsen C, Shen K (2007) FEMS Microbiology Ecology 61: 214-221
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Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305varphi8-36  Thomas JA, Hardies SC, Rolando M, Hayes SJ, Lieman K, Carroll CA, Weintraub ST, Serwer P (2007) Virology :
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Variable-Number Tandem Repeats as Molecular Markers for Biotypes of Pasteuria ramosa in Daphnia spp  Laurence Mouton, Guang Nong, James F. Preston, and Dieter Ebert (2007) Applied Environmental Microbiology 73: 3715–3718
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A Novel Linear Plasmid Mediates Flagellar Variation in Salmonella Typhi  Stephen Baker, Jonathan Hardy, Kenneth E. Sanderson, Michael Quail, Ian Goodhead, Robert A. Kingsley, Julian Parkhill, Bruce Stocker, Gordon Dougan (2007) PLoS Pathogens 3:
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Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand  Frédéric Poly, Timothy Read, David R. Tribble, Shahida Baqar, Maria Lorenzo, and Patricia Guerry (2007) Infection and Immunity 75: 3425-3433
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Mechanism of chimera formation during the Multiple Displacement Amplification reaction  Roger S Lasken and Timothy B Stockwell (2007) BMC Biotechnology 7:
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New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis  Michael G. Smith, Tara A. Gianoulis, Stefan Pukatzki, John J. Mekalanos, L. Nicholas Ornston, Mark Gerstein, and Michael Snyder (2007) Genes & Development 21: 601–614
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The Genome of a Non-01 Vibrio cholerae NRT36S Demonstrates the Presence of Pathogenic Mechanisms that are Distinct from 01 Vibrio cholerae  Yuansha Chen, Judith A. Johnson, Gordon D. Pusch, J. Glenn Morris, Jr., and O. Colin Stine (2007) Infection and Immunity 10: 01317-13106
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The capsule polysaccharide structure and biogenesis for non-O1 Vibrio cholerae NRT36S: genes are embedded in the LPS region  Yuansha Chen, Peter Bystricky, Jacob Adeyeye, Pinaki Panigrahi, Afsar Ali, Judith A Johnson, CA Bush, JG Morris Jr and OC Stine (2007) BMC Microbiology 7:
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Characterization and modeling of the Haemophilus influenzae core- and supra-genomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains   J. S. Hogg, *Fen Z. Hu, Benjamin Janto, Robert Boissy, Jay Hayes, Randy Keefe, J. Christopher Post, and *Garth D. Ehrlich (2007) Genome Biology 8:
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Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus  Highlander SK, Hulten KG, Qin X, Jiang H, Yerrapragada S, Mason EO, Shang Y, Williams TM, Fortunov RM, Liu Y, Igboeli O, Petrosino J, Tirumalai M, Uzman A, Fox GE, Cardenas AM, Muzny DM, Hemphill L, Ding Y, Dugan S, Blyth PR, Buhay CJ, Dinh HH, Hawes AC, Holder M, Kovar CL, Lee SL, Liu W, Nazareth LV, Wang Q, Zhou J, Kaplan SL, Weinstock GM (2007) BMC Microbiology 7:
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Genomic plasticity in prokaryotes: the case of the square haloarchaeon  Sara Cuadros-Orellana, Ana-Belen Martin-Cuadrado, Boris Legault, Giuseppe D’Auria, Olga Zhaxybayeva, R Thane Papke and Francisco Rodriguez-Valera (2007) The ISME Journal 1: 235-245
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Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing  Robert Pinard, Alex de Winter, Gary J Sarkis, Mark B Gerstein, Karrie R Tartaro, Ramona N Plant, Michael Egholm, Jonathan M Rothberg, and John H Leamon (2006) BMC Genomics 7:
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Unique Features of a Highly Pathogenic Campylobacter jejuni Strain  Dirk Hofreuter, Jennifer Tsai, Robert O. Watson, Veronica Novik, Bill Altman, Michelle Benitez, Christina Clark, Clotilde Perbost, Thomas Jarvie, Lei Du, and Jorge E. Galán (2006) Infection and Immunity 74: 4694-4707
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A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes  Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers YH, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC (2006) PNAS 103: 11240-11245
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Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor  Gregory J. Velicer, Gunter Raddatz, Heike Keller, Silvia Deiss, Christa Lanz, Iris Dinkelacker, and Stephan C. Schuster (2006) PNAS  103: 8107–8112
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A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis  Andries, K. et. al.  (2005) Science 307: 223-227
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