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Volumn 13, Issue 1, 2012, Pages

PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL POPULATION; COMBINED ANALYSIS; DNA SEQUENCING; EVOLUTIONARY RELATIONSHIPS; GLOBAL SCALE; GOLD STANDARDS; INTEGRATED ANALYSIS; JAVA SOFTWARE; MINIMUM SPANNING TREES; MULTIPLE DATA SOURCES; ONLINE DATABASE; PHYLOGENETIC INFERENCE; PLATFORM INDEPENDENT; POPULATION STUDIES; QUERY RESULTS; USER-FRIENDLY TOOL; WHOLE GENOME SEQUENCES;

EID: 84865286374     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-87     Document Type: Article
Times cited : (449)

References (31)
  • 1
    • 13144252236 scopus 로고    scopus 로고
    • Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
    • 10.1073/pnas.95.6.3140, 19708, 9501229
    • Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, et al. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Nat Acad Sci 1998, 95(6):3140. 10.1073/pnas.95.6.3140, 19708, 9501229.
    • (1998) Proc Nat Acad Sci , vol.95 , Issue.6 , pp. 3140
    • Maiden, M.C.J.1    Bygraves, J.A.2    Feil, E.3    Morelli, G.4    Russell, J.E.5    Urwin, R.6    Zhang, Q.7    Zhou, J.8    Zurth, K.9    Caugant, D.A.10
  • 2
    • 22244459534 scopus 로고    scopus 로고
    • Multiplelocus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria
    • 10.1002/elps.200500096, 15937984
    • Lindstedt BA. Multiplelocus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005, 26(13):2567. 10.1002/elps.200500096, 15937984.
    • (2005) Electrophoresis , vol.26 , Issue.13 , pp. 2567
    • Lindstedt, B.A.1
  • 3
    • 0034943577 scopus 로고    scopus 로고
    • Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology
    • 10.1128/CMR.14.3.547-560.2001, 88989, 11432813
    • van Belkum A, Struelens M, de Visser A, Verbrugh H, Tibayrenc M. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin Microbiol Rev 2001, 14(3):547. 10.1128/CMR.14.3.547-560.2001, 88989, 11432813.
    • (2001) Clin Microbiol Rev , vol.14 , Issue.3 , pp. 547
    • van Belkum, A.1    Struelens, M.2    de Visser, A.3    Verbrugh, H.4    Tibayrenc, M.5
  • 4
    • 84872596367 scopus 로고    scopus 로고
    • Multi Locus Sequence Typing.
    • Imperial College of London, MLST
    • MLST Multi Locus Sequence Typing. Imperial College of London, [http://www.mlst.net], MLST.
  • 5
    • 84874628597 scopus 로고    scopus 로고
    • PubMLST.
    • University of Oxford (UK)
    • PubMLST. University of Oxford (UK), [http://pubmlst.org/].
  • 6
    • 84859354261 scopus 로고    scopus 로고
    • Institut Pasteur MLST Databases.
    • Pasteur Institute.
    • Institut Pasteur MLST Databases. Pasteur Institute. [http://www.pasteur.fr/mlst/]..
  • 7
    • 84874593973 scopus 로고    scopus 로고
    • EcMLST.
    • Michigan State University.
    • EcMLST. Michigan State University. [http://www.shigatox.net/cgi-bin/mlst7/index]..
  • 8
    • 84874640028 scopus 로고    scopus 로고
    • MLST Databases at ERI.
    • University College Cork.
    • MLST Databases at ERI. University College Cork. [http://mlst.ucc.ie/]..
  • 12
    • 79251544864 scopus 로고    scopus 로고
    • Rapid pneumococcal evolution in response to clinical interventions
    • 10.1126/science.1198545, 21273480
    • Croucher N, Harris S, Fraser C, Quail M. Rapid pneumococcal evolution in response to clinical interventions. Science 2011, 331:430. 10.1126/science.1198545, 21273480.
    • (2011) Science , vol.331 , pp. 430
    • Croucher, N.1    Harris, S.2    Fraser, C.3    Quail, M.4
  • 13
    • 0036137328 scopus 로고    scopus 로고
    • Sequence type analysis and recombinational tests (START)
    • 10.1093/bioinformatics/17.12.1230, 11751234
    • Jolley KA, Feil EJ, Chan MS, Maiden MCJ. Sequence type analysis and recombinational tests (START). Bioinformatics 2001, 17(12):1230. 10.1093/bioinformatics/17.12.1230, 11751234.
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1230
    • Jolley, K.A.1    Feil, E.J.2    Chan, M.S.3    Maiden, M.C.J.4
  • 14
    • 1342304133 scopus 로고    scopus 로고
    • EBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data
    • 10.1128/JB.186.5.1518-1530.2004, 344416, 14973027
    • 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(5):1518. 10.1128/JB.186.5.1518-1530.2004, 344416, 14973027.
    • (2004) J Bacteriol , vol.186 , Issue.5 , pp. 1518
    • Feil, E.J.1    Li, B.C.2    Aanensen, D.M.3    Hanage, W.P.4    Spratt, B.G.5
  • 15
    • 67650093575 scopus 로고    scopus 로고
    • Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach
    • Francisco AP, Bugalho MF, Ramirez M, Carriço JA. Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinf 2009, 10(152).
    • (2009) BMC Bioinf , vol.10 , Issue.152
    • Francisco, A.P.1    Bugalho, M.F.2    Ramirez, M.3    Carriço, J.A.4
  • 17
    • 13444295058 scopus 로고    scopus 로고
    • Tulip-a huge graph visualization framework
    • Springer Springer,
    • Auber D. Tulip-a huge graph visualization framework. Graph Drawing Software 2003, 105-126. Springer Springer, .
    • (2003) Graph Drawing Software , pp. 105-126
    • Auber, D.1
  • 18
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Res , vol.13 , Issue.11 , pp. 2498
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.4    Wang, J.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 19
    • 35748962289 scopus 로고    scopus 로고
    • Tools for visually exploring biological networks
    • 10.1093/bioinformatics/btm401, 17720984
    • Suderman M, Hallett M. Tools for visually exploring biological networks. Bioinformatics 2007, 23(20):2651. 10.1093/bioinformatics/btm401, 17720984.
    • (2007) Bioinformatics , vol.23 , Issue.20 , pp. 2651
    • Suderman, M.1    Hallett, M.2
  • 20
    • 0029725135 scopus 로고    scopus 로고
    • The Eyes Have It: A Task by Data Type Taxonomy for Information Visualizations
    • Shneiderman B. The Eyes Have It: A Task by Data Type Taxonomy for Information Visualizations. IEEE Symposium on Visual Languages 1996, 336-343. , .
    • (1996) IEEE Symposium on Visual Languages , pp. 336-343
    • Shneiderman, B.1
  • 23
    • 70350674995 scopus 로고
    • On the shortest spanning subtree of a graph and the traveling salesman problem
    • Kruskal JB. On the shortest spanning subtree of a graph and the traveling salesman problem. Proc Am Math Soc 1956, 7:48.
    • (1956) Proc Am Math Soc , vol.7 , pp. 48
    • Kruskal, J.B.1
  • 24
    • 84911584312 scopus 로고
    • Shortest connection networks and some generalizations
    • Prim RC. Shortest connection networks and some generalizations. Bell Syst Tech J 1957, 36:1389.
    • (1957) Bell Syst Tech J , vol.36 , pp. 1389
    • Prim, R.C.1
  • 25
    • 0024107868 scopus 로고
    • Relaxed Heaps: An Alternative to Fibonacci Heaps with Applications to Parallel Computation
    • Driscoll JR, Gabow HN, Shrairman R, Tarjan RE. Relaxed Heaps: An Alternative to Fibonacci Heaps with Applications to Parallel Computation. Commun ACM 1988, 31(11):1343.
    • (1988) Commun ACM , vol.31 , Issue.11 , pp. 1343
    • Driscoll, J.R.1    Gabow, H.N.2    Shrairman, R.3    Tarjan, R.E.4
  • 26
    • 0034111151 scopus 로고    scopus 로고
    • The direction of microsatellite mutations is dependent upon allele length
    • 10.1038/74238, 10742105
    • Xu X, Peng M, Fang Z. The direction of microsatellite mutations is dependent upon allele length. Nat Genet 2000, 24:396. 10.1038/74238, 10742105.
    • (2000) Nat Genet , vol.24 , pp. 396
    • Xu, X.1    Peng, M.2    Fang, Z.3
  • 28
    • 77952247101 scopus 로고    scopus 로고
    • Effects of Environmental Stress on Stability of Tandem Repeats in Escherichia coli O157:H7
    • 10.1128/AEM.02373-09, 2869130, 20348301
    • Cooley MB, Carychao D, Nguyen K, Whitehand L, Mandrell R. Effects of Environmental Stress on Stability of Tandem Repeats in Escherichia coli O157:H7. Appl Environ Microbiol 2010, 76(10):3398. 10.1128/AEM.02373-09, 2869130, 20348301.
    • (2010) Appl Environ Microbiol , vol.76 , Issue.10 , pp. 3398
    • Cooley, M.B.1    Carychao, D.2    Nguyen, K.3    Whitehand, L.4    Mandrell, R.5
  • 30
    • 27144465866 scopus 로고    scopus 로고
    • Mechanisms for penicillin resistance in Streptococcus pneumoniae: penicillin binding proteins, gene transfer, and cell wall metabolism
    • ASM Press, Washington, DC, Tuomanen EI, Mitchell TJ, Morrison DA, Spratt BG
    • Bergmann C, Chi F, Rachid S, Hakenbeck R. Mechanisms for penicillin resistance in Streptococcus pneumoniae: penicillin binding proteins, gene transfer, and cell wall metabolism. The pneumococcus 2004, 339-349. ASM Press, Washington, DC, Tuomanen EI, Mitchell TJ, Morrison DA, Spratt BG.
    • (2004) The pneumococcus , pp. 339-349
    • Bergmann, C.1    Chi, F.2    Rachid, S.3    Hakenbeck, R.4
  • 31
    • 0032729840 scopus 로고    scopus 로고
    • Extensive variation in the ddl gene of penicillin-resistant Streptococcus pneumoniae results from a hitchhiking effect driven by the penicillin-binding protein 2b gene
    • 10.1093/oxfordjournals.molbev.a026082, 10605111
    • Enright MC, Spratt BG. Extensive variation in the ddl gene of penicillin-resistant Streptococcus pneumoniae results from a hitchhiking effect driven by the penicillin-binding protein 2b gene. Mol Biol Evol 1999, 16(12):1687. 10.1093/oxfordjournals.molbev.a026082, 10605111.
    • (1999) Mol Biol Evol , vol.16 , Issue.12 , pp. 1687
    • Enright, M.C.1    Spratt, B.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.