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Volumn 8, Issue , 2007, Pages

Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL SPECIES; CAMPYLOBACTER JEJUNI; CLOSTRIDIUM DIFFICILE; DIAGNOSTIC PROCEDURE; DISCRIMINATORY POWER; MICROBIAL SPECIES; SINGLE NUCLEOTIDE POLYMORPHISMS; YERSINIA ENTEROCOLITICA;

EID: 34548503865     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-278     Document Type: Article
Times cited : (21)

References (50)
  • 1
    • 0035351051 scopus 로고    scopus 로고
    • PulseNet: The molecular subtyping network for foodborne bacterial disease surveillance, United States
    • CDC PulseNet Task Force 11384513
    • Swaminathan B Barrett TJ Hunter SB Tauxe RV CDC PulseNet Task Force PulseNet: The molecular subtyping network for foodborne bacterial disease surveillance, United States Emerg Infect Dis 2001 7 382-389 11384513
    • (2001) Emerg Infect Dis , vol.7 , pp. 382-389
    • Swaminathan, B.1    Barrett, T.J.2    Hunter, S.B.3    Tauxe, R.V.4
  • 3
    • 0035182670 scopus 로고    scopus 로고
    • Database-driven multi locus sequence typing (MLST) of bacterial pathogens
    • 10.1093/bioinformatics/17.11.1077 11724739
    • Chan M-S Maiden MC Spratt BG Database-driven multi locus sequence typing (MLST) of bacterial pathogens Bioinformatics 2001 17 1077-1083 10.1093/ bioinformatics/17.11.1077 11724739
    • (2001) Bioinformatics , vol.17 , pp. 1077-1083
    • Chan, M.-S.1    Maiden, M.C.2    Spratt, B.G.3
  • 4
    • 33646596541 scopus 로고    scopus 로고
    • Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity
    • 1482848 16672618 10.1128/JB.188.10.3645-3653.2006
    • Howard SL Gaunt MW Hinds J Witney AA Stabler R Wren BW Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity J Bacteriol 2006 188 3645-3653 1482848 16672618 10.1128/ JB.188.10.3645-3653.2006
    • (2006) J Bacteriol , vol.188 , pp. 3645-3653
    • Howard, S.L.1    Gaunt, M.W.2    Hinds, J.3    Witney, A.A.4    Stabler, R.5    Wren, B.W.6
  • 5
    • 27644572105 scopus 로고    scopus 로고
    • Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source
    • 1276044 16230626 10.1073/pnas.0503252102
    • Champion OL Gaunt MW Gundogdu O Elmi A Witney AA Hinds J Dorrell N Wren BW Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source Proc Natl Acad Sci USA 2005 102 16043-16048 1276044 16230626 10.1073/ pnas.0503252102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 16043-16048
    • Champion, O.L.1    Gaunt, M.W.2    Gundogdu, O.3    Elmi, A.4    Witney, A.A.5    Hinds, J.6    Dorrell, N.7    Wren, B.W.8
  • 6
    • 33749628473 scopus 로고    scopus 로고
    • Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains
    • 1636221 17015669 10.1128/JB.00664-06
    • Stabler RA Gerding DN Songer JG Drudy D Brazier JS Trinh HT Witney AA Hinds J Wren BW Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains J Bacteriol 2006 188 7297-7305 1636221 17015669 10.1128/JB.00664-06
    • (2006) J Bacteriol , vol.188 , pp. 7297-7305
    • Stabler, R.A.1    Gerding, D.N.2    Songer, J.G.3    Drudy, D.4    Brazier, J.S.5    Trinh, H.T.6    Witney, A.A.7    Hinds, J.8    Wren, B.W.9
  • 8
    • 0037622956 scopus 로고    scopus 로고
    • HIV sequence databases
    • Accessed 17 Jan 2007 12875108
    • Kuiken C Korber B Shafer RW HIV sequence databases AIDS Rev 2003 5 52-61 http://hiv-web.lanl.gov/components/hiv-db/combined_search_s_tree/ search.html Accessed 17 Jan 2007 12875108
    • (2003) AIDS Rev , vol.5 , pp. 52-61
    • Kuiken, C.1    Korber, B.2    Shafer, R.W.3
  • 9
    • 0346494850 scopus 로고    scopus 로고
    • coliBASE: Anonline database for Escherichia coli, Shigella and Salmonella comparative genomics
    • 308765 14681417 10.1093/nar/gkh031
    • Chaudhuri RR Khan AM Pallen MJ coliBASE: Anonline database for Escherichia coli, Shigella and Salmonella comparative genomics Nucleic Acids Res 2004 32 D296-D299 308765 14681417 10.1093/nar/gkh031
    • (2004) Nucleic Acids Res , vol.32
    • Chaudhuri, R.R.1    Khan, A.M.2    Pallen, M.J.3
  • 10
    • 13844253602 scopus 로고    scopus 로고
    • The Los Alamos hepatitis C sequence database
    • Accessed 17 Jan 2007 10.1093/bioinformatics/bth485 15377502
    • Kuiken C Yusim K Boykin L Richardson R The Los Alamos hepatitis C sequence database Bioinformatics 2005 21 379-384 http://hcv.lanl.gov/ components/hcv-db/combined_search/searchi.html Accessed 17 Jan 2007 10.1093/bioinformatics/bth485 15377502
    • (2005) Bioinformatics , vol.21 , pp. 379-384
    • Kuiken, C.1    Yusim, K.2    Boykin, L.3    Richardson, R.4
  • 11
    • 33644876482 scopus 로고    scopus 로고
    • xBASE, a collection of online databases for bacterial comparative genomics
    • 1347502 16381881 10.1093/nar/gkj140
    • Chaudhuri RR Pallen MJ xBASE, a collection of online databases for bacterial comparative genomics Nucleic Acids Res 2006 34 D335-D337 1347502 16381881 10.1093/nar/gkj140
    • (2006) Nucleic Acids Res , vol.34
    • Chaudhuri, R.R.1    Pallen, M.J.2
  • 12
    • 33846033843 scopus 로고    scopus 로고
    • Genome Information Broker for Viruses (GIB-V): Database for comparative analysis of virus genomes
    • 1781101 17158166 10.1093/nar/gkl1004
    • Hirahata M Abe T Tanaka N Kuwana Y Shigemoto Y Miyazaki S Suzuki Y Sugawara H Genome Information Broker for Viruses (GIB-V): Database for comparative analysis of virus genomes Nucleic Acids Res 2007 35 D339-D342 1781101 17158166 10.1093/nar/gkl1004
    • (2007) Nucleic Acids Res , vol.35
    • Hirahata, M.1    Abe, T.2    Tanaka, N.3    Kuwana, Y.4    Shigemoto, Y.5    Miyazaki, S.6    Suzuki, Y.7    Sugawara, H.8
  • 13
    • 0346373654 scopus 로고    scopus 로고
    • Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium
    • 1181897 14681826 10.1086/381000
    • Carlson CS Eberle MA Rieder MJ Yi Q Kruglyak L Nickerson DA Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium Am J Hum Genet 2004 74 106-120 1181897 14681826 10.1086/381000
    • (2004) Am J Hum Genet , vol.74 , pp. 106-120
    • Carlson, C.S.1    Eberle, M.A.2    Rieder, M.J.3    Yi, Q.4    Kruglyak, L.5    Nickerson, D.A.6
  • 14
    • 25844500813 scopus 로고    scopus 로고
    • Real-time single-nucleotide polymorphism profiling using TaqMan technology for rapid recognition of Campylobacter jejuni clonal complexes
    • 16157544 16157544 10.1099/jmm.0.45971-0
    • Best EL Fox AJ Frost JA Bolton FJ Real-time single-nucleotide polymorphism profiling using TaqMan technology for rapid recognition of Campylobacter jejuni clonal complexes J Med Microbiol 2005 54 919-925 16157544 16157544 10.1099/jmm.0.45971-0
    • (2005) J Med Microbiol , vol.54 , pp. 919-925
    • Best, E.L.1    Fox, A.J.2    Frost, J.A.3    Bolton, F.J.4
  • 16
    • 0035134454 scopus 로고    scopus 로고
    • Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies
    • 11159763
    • Shi MM Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies Clin Chem 2001 47 164-172 11159763
    • (2001) Clin Chem , vol.47 , pp. 164-172
    • Shi, M.M.1
  • 17
    • 33845996153 scopus 로고    scopus 로고
    • Genotyping with microfluidic devices
    • 10.1002/elps.200600568 17117382
    • Szántai E Guttman A Genotyping with microfluidic devices Electrophoresis 2006 27 4896-4903 10.1002/elps.200600568 17117382
    • (2006) Electrophoresis , vol.27 , pp. 4896-4903
    • Szántai, E.1    Guttman, A.2
  • 18
    • 33846004162 scopus 로고    scopus 로고
    • Towards a portable microchip system with integrated thermal control and polymer waveguides for real-time PCR
    • 10.1002/elps.200600355 17124710
    • Wang Z Sekulovic A Kutter JP Bang DD Wolff A Towards a portable microchip system with integrated thermal control and polymer waveguides for real-time PCR Electrophoresis 2006 27 5051-5058 10.1002/ elps.200600355 17124710
    • (2006) Electrophoresis , vol.27 , pp. 5051-5058
    • Wang, Z.1    Sekulovic, A.2    Kutter, J.P.3    Bang, D.D.4    Wolff, A.5
  • 19
    • 1542426071 scopus 로고    scopus 로고
    • Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases
    • 10.1099/jmm.0.05365-0 14663103
    • Robertson GA Thiruvenkataswamy V Shilling H Price EP Huygens F Henskens FA Giffard PM Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases J Med Microbiol 2004 53 35-45 10.1099/ jmm.0.05365-0 14663103
    • (2004) J Med Microbiol , vol.53 , pp. 35-45
    • Robertson, G.A.1    Thiruvenkataswamy, V.2    Shilling, H.3    Price, E.P.4    Huygens, F.5    Henskens, F.A.6    Giffard, P.M.7
  • 20
    • 0023738045 scopus 로고
    • Numerical index of the discriminatory ability of typing systems: An application of Simpson's index of diversity
    • 266921 3069867
    • Hunter PR Gaston MA Numerical index of the discriminatory ability of typing systems: An application of Simpson's index of diversity J Clin Microbiol 1988 26 2465-2466 266921 3069867
    • (1988) J Clin Microbiol , vol.26 , pp. 2465-2466
    • Hunter, P.R.1    Gaston, M.A.2
  • 23
    • 33747051228 scopus 로고    scopus 로고
    • Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA Short Variable Region Sequencing
    • 10.1099/jmm.0.46460-0 16849726
    • Price EP Thiruvenkataswamy V Mickan L Unicomb L Rios RE Huygens F Giffard PM Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA Short Variable Region Sequencing J Med Microbiol 2006 55 1061-1070 10.1099/ jmm.0.46460-0 16849726
    • (2006) J Med Microbiol , vol.55 , pp. 1061-1070
    • Price, E.P.1    Thiruvenkataswamy, V.2    Mickan, L.3    Unicomb, L.4    Rios, R.E.5    Huygens, F.6    Giffard, P.M.7
  • 24
    • 33845513534 scopus 로고    scopus 로고
    • Fingerprinting of Campylobacter jejuni using resolution-optimized binary gene targets derived from Comparative Genome Hybridization studies
    • 1694235 16997982 10.1128/AEM.01338-06
    • Price EP Huygens F Giffard PM Fingerprinting of Campylobacter jejuni using resolution-optimized binary gene targets derived from Comparative Genome Hybridization studies Appl Environ Microbiol 2006 72 7793-7803 1694235 16997982 10.1128/AEM.01338-06
    • (2006) Appl Environ Microbiol , vol.72 , pp. 7793-7803
    • Price, E.P.1    Huygens, F.2    Giffard, P.M.3
  • 28
    • 13244267001 scopus 로고    scopus 로고
    • mlstdbNet - Distributed multi-locus sequence typing (MLST) databases
    • Accessed 18 January 2007 459211 15222901 10.1186/1471-2105-5-86
    • Jolley KA Chan M-S Maiden MC mlstdbNet - distributed multi-locus sequence typing (MLST) databases BMC Bioinformatics 2004 5 85 http://www.mlst.net/ Accessed 18 January 2007 459211 15222901 10.1186/1471-2105-5-86
    • (2004) BMC Bioinformatics , vol.5 , pp. 85
    • Jolley, K.A.1    Chan, M.-S.2    Maiden, M.C.3
  • 29
    • 0037236212 scopus 로고    scopus 로고
    • Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: Strain diversity, host range, and recombination
    • 149617 12517820 10.1128/JCM.41.1.15-26.2003
    • Schouls LM Reulen S Duim B Wagenaar JA Willems RJ Dingle KE Colles FM Van Embden JD Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: Strain diversity, host range, and recombination J Clin Microbiol 2003 41 15-26 149617 12517820 10.1128/ JCM.41.1.15-26.2003
    • (2003) J Clin Microbiol , vol.41 , pp. 15-26
    • Schouls, L.M.1    Reulen, S.2    Duim, B.3    Wagenaar, J.A.4    Willems, R.J.5    Dingle, K.E.6    Colles, F.M.7    Van Embden, J.D.8
  • 30
    • 0010956475 scopus 로고
    • Interactive analysis of phylogeny and character evolution using the computer program MacClade
    • 2606395
    • Maddison WP Maddison DR Interactive analysis of phylogeny and character evolution using the computer program MacClade Folia Primatol 1989 53 190-202 2606395
    • (1989) Folia Primatol , vol.53 , pp. 190-202
    • Maddison, W.P.1    Maddison, D.R.2
  • 34
    • 11844306009 scopus 로고    scopus 로고
    • Evaluation of the COBAS TaqMan HCV test with automated sample processing using the MagNA pure LC instrument
    • 540141 15634985 10.1128/JCM.43.1.293-298.2005
    • Germer JJ Harmsen WS Mandrekar JN Mitchell PS Yao JD Evaluation of the COBAS TaqMan HCV test with automated sample processing using the MagNA pure LC instrument J Clin Microbiol 2005 43 293-298 540141 15634985 10.1128/JCM.43.1.293-298.2005
    • (2005) J Clin Microbiol , vol.43 , pp. 293-298
    • Germer, J.J.1    Harmsen, W.S.2    Mandrekar, J.N.3    Mitchell, P.S.4    Yao, J.D.5
  • 35
    • 33750951689 scopus 로고    scopus 로고
    • Multiplex real-time reverse transcription-PCR assay for determination of hepatitis C genotypes
    • 1698294 16988019 10.1128/JCM.01230-06
    • Cook L Sullivan K Krantz EM Bagabag A Jerome KR Multiplex real-time reverse transcription-PCR assay for determination of hepatitis C genotypes J Clin Microbiol 2006 44 4149-4156 1698294 16988019 10.1128/ JCM.01230-06
    • (2006) J Clin Microbiol , vol.44 , pp. 4149-4156
    • Cook, L.1    Sullivan, K.2    Krantz, E.M.3    Bagabag, A.4    Jerome, K.R.5
  • 37
    • 26944472802 scopus 로고    scopus 로고
    • Rapid genotyping of hepatitis C virus by primer-specific extension analysis
    • 1248436 16207978 10.1128/JCM.43.10.5158-5163.2005
    • Antonishyn NA Ast VM McDonald RR Chaudhary RK Lin L Andonov AP Horsman GB Rapid genotyping of hepatitis C virus by primer-specific extension analysis J Clin Microbiol 2005 43 5158-5163 1248436 16207978 10.1128/ JCM.43.10.5158-5163.2005
    • (2005) J Clin Microbiol , vol.43 , pp. 5158-5163
    • Antonishyn, N.A.1    Ast, V.M.2    McDonald, R.R.3    Chaudhary, R.K.4    Lin, L.5    Andonov, A.P.6    Horsman, G.B.7
  • 38
    • 0034120427 scopus 로고    scopus 로고
    • Clinical significance of hepatitis C virus genotypes
    • 100152 10755999 10.1128/CMR.13.2.223-235.2000
    • Zein NN Clinical significance of hepatitis C virus genotypes Clin Microbiol Rev 2000 13 223-235 100152 10755999 10.1128/ CMR.13.2.223-235.2000
    • (2000) Clin Microbiol Rev , vol.13 , pp. 223-235
    • Zein, N.N.1
  • 41
    • 0033046861 scopus 로고    scopus 로고
    • Single-tube genotyping without oligonucleotide probes
    • 310703 9927486
    • Germer S Higuchi R Single-tube genotyping without oligonucleotide probes Genome Res 1999 9 72-78 310703 9927486
    • (1999) Genome Res , vol.9 , pp. 72-78
    • Germer, S.1    Higuchi, R.2
  • 42
    • 33846641709 scopus 로고    scopus 로고
    • High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer
    • 1769510 17184525 10.1186/1471-2407-6-295
    • Krypuy M Newnham GM Thomas DM Conron M Dobrovic A High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer BMC Cancer 2006 6 295 1769510 17184525 10.1186/1471-2407-6-295
    • (2006) BMC Cancer , vol.6 , pp. 295
    • Krypuy, M.1    Newnham, G.M.2    Thomas, D.M.3    Conron, M.4    Dobrovic, A.5
  • 43
    • 4444308959 scopus 로고    scopus 로고
    • Anthrax molecular epidemiology and forensics: Using the appropriate marker for different evolutionary scales
    • 10.1016/j.meegid.2004.02.005 15450200
    • Keim P Van Ert MN Pearson T Vogler AJ Huynh LY Wagner DM Anthrax molecular epidemiology and forensics: Using the appropriate marker for different evolutionary scales Infect Genet Evol 2004 205-213 10.1016/ j.meegid.2004.02.005 15450200
    • (2004) Infect Genet Evol , pp. 205-213
    • Keim, P.1    Van Ert, M.N.2    Pearson, T.3    Vogler, A.J.4    Huynh, L.Y.5    Wagner, D.M.6
  • 44
    • 84874650567 scopus 로고    scopus 로고
    • A multilocus sequence typing database system for pathogenic E coli
    • EcMLST
    • EcMLST A multilocus sequence typing database system for pathogenic E coli http://www.shigatox.net/cgi-bin/mlst7/index
  • 47
    • 1342304133 scopus 로고    scopus 로고
    • eBURST: Inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data
    • Accessed 21 December 2006 344416 14973027 10.1128/JB.186.5.1518-1530.2004
    • Feil EJ Li BC Aanensen DM Hanage WP Spratt BG eBURST: Inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data J Bacteriol 2004 186 1518-1530 http://eBURST.mlst.net/ Accessed 21 December 2006 344416 14973027 10.1128/JB.186.5.1518-1530.2004
    • (2004) J Bacteriol , vol.186 , pp. 1518-1530
    • Feil, E.J.1    Li, B.C.2    Aanensen, D.M.3    Hanage, W.P.4    Spratt, B.G.5
  • 48
    • 84886763057 scopus 로고    scopus 로고
    • Bμgσ
    • Bμgσ http://bugs.sgul.ac.uk/
  • 49
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • 147148 9396791 10.1093/nar/25.24.4876
    • Thompson JD Gibson TJ Plewniak F Jeanmougin F Higgins DG The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 1997 4876-4882 147148 9396791 10.1093/nar/25.24.4876
    • (1997) Nucleic Acids Res , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 50
    • 0030203863 scopus 로고    scopus 로고
    • TreeView: An application to display phylogenetic trees on personal computers
    • 8902363
    • Page RD TreeView: An application to display phylogenetic trees on personal computers Comput Appl Biosci 1996 12 357-358 8902363
    • (1996) Comput Appl Biosci , vol.12 , pp. 357-358
    • Page, R.D.1


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