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Volumn 11, Issue SUPPL. 2, 2010, Pages

Classification of genomic islands using decision trees and their ensemble algorithms

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CLASSIFICATION ALGORITHM; CLASSIFIER; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DECISION TREE; GENE CLUSTER; GENETIC ANALYSIS; GENOMIC ISLAND; INTERMETHOD COMPARISON; MACHINE LEARNING; RANDOM FOREST; SALMONELLA; STAPHYLOCOCCUS; STREPTOCOCCUS; ALGORITHM; ARTIFICIAL INTELLIGENCE; ARTIFICIAL NEURAL NETWORK; BAYES THEOREM; COMPARATIVE STUDY; STATISTICAL MODEL;

EID: 78149350199     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S2-S1     Document Type: Article
Times cited : (21)

References (33)
  • 1
    • 0025005169 scopus 로고
    • Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates
    • Hacker J, Bender L, Ott M, Wingender J, Lund B, Marre R, Goebel W. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb Pathog 1990, 8(3):213-25.
    • (1990) Microb Pathog , vol.8 , Issue.3 , pp. 213-225
    • Hacker, J.1    Bender, L.2    Ott, M.3    Wingender, J.4    Lund, B.5    Marre, R.6    Goebel, W.7
  • 2
    • 0033758756 scopus 로고    scopus 로고
    • Pathogenicity islands and the evolution of microbes
    • Hacker J, Kaper JB. Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 2000, 54:641-79.
    • (2000) Annu Rev Microbiol , vol.54 , pp. 641-679
    • Hacker, J.1    Kaper, J.B.2
  • 3
    • 0034978233 scopus 로고    scopus 로고
    • Pathogenicity islands: the tip of the iceberg
    • Hentschel U, Hacker J. Pathogenicity islands: the tip of the iceberg. Microbes Infect 2001, 3(7):545-8.
    • (2001) Microbes Infect , vol.3 , Issue.7 , pp. 545-548
    • Hentschel, U.1    Hacker, J.2
  • 5
    • 25444520987 scopus 로고    scopus 로고
    • Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops
    • 1187871, 16011797
    • Chiapello H, Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, Petit MA, El Karoui M. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics 2005, 6:171. 1187871, 16011797., http://www.biomedcentral.com/1471-2105/6/171
    • (2005) BMC Bioinformatics , vol.6 , pp. 171
    • Chiapello, H.1    Bourgait, I.2    Sourivong, F.3    Heuclin, G.4    Gendrault-Jacquemard, A.5    Petit, M.A.6    El Karoui, M.7
  • 6
    • 50149094265 scopus 로고    scopus 로고
    • Evaluation of genomic island predictors using a comparative genomics approach
    • 2518932, 18680607
    • Langille MG, Hsiao WW, Brinkman FS. Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008, 9:329. 2518932, 18680607.
    • (2008) BMC Bioinformatics , vol.9 , pp. 329
    • Langille, M.G.1    Hsiao, W.W.2    Brinkman, F.S.3
  • 7
    • 0028877016 scopus 로고
    • A role for bacteriophages in the evolution and transfer of bacterial virulence determinants
    • Cheetham BF, Katz ME. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol Microbiol 1995, 18(2):201-8.
    • (1995) Mol Microbiol , vol.18 , Issue.2 , pp. 201-208
    • Cheetham, B.F.1    Katz, M.E.2
  • 8
    • 42149162976 scopus 로고    scopus 로고
    • Genome-Based Identification and Molecular Analyses of Pathogenicity Islands and Genomic Islands in Salmonella enterica
    • Hensel. Genome-Based Identification and Molecular Analyses of Pathogenicity Islands and Genomic Islands in Salmonella enterica. Methods in Molecular Biology 2007, 394:77-88.
    • (2007) Methods in Molecular Biology , vol.394 , pp. 77-88
    • Hensel1
  • 9
    • 33749565756 scopus 로고    scopus 로고
    • Pathogenicity islands: a molecular toolbox for bacterial virulence
    • Gal-Mor O, Finlay BB. Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell Microbiol 2006, 8(11):1707-19.
    • (2006) Cell Microbiol , vol.8 , Issue.11 , pp. 1707-1719
    • Gal-Mor, O.1    Finlay, B.B.2
  • 10
    • 0030901705 scopus 로고    scopus 로고
    • Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution
    • Hacker J, Blum-Oehler G, Muhldorfer I, Tschape H. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 1997, 23(6):1089-97.
    • (1997) Mol Microbiol , vol.23 , Issue.6 , pp. 1089-1097
    • Hacker, J.1    Blum-Oehler, G.2    Muhldorfer, I.3    Tschape, H.4
  • 11
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: rates of change and exchange
    • Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44(4):383-97.
    • (1997) J Mol Evol , vol.44 , Issue.4 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 12
    • 0031720281 scopus 로고    scopus 로고
    • Codon usages in different gene classes of the Escherichia coli genome
    • Karlin S, Mrazek J, Campbell AM. Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol 1998, 29(6):1341-55.
    • (1998) Mol Microbiol , vol.29 , Issue.6 , pp. 1341-1355
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 13
    • 0035399931 scopus 로고    scopus 로고
    • Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    • Karlin S. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 2001, 9(7):335-43.
    • (2001) Trends Microbiol , vol.9 , Issue.7 , pp. 335-343
    • Karlin, S.1
  • 14
    • 13944251386 scopus 로고    scopus 로고
    • A new computational method for the detection of horizontal gene transfer events
    • 549390, 15716310
    • Tsirigos A, Rigoutsos I. A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res 2005, 33(3):922-33. 549390, 15716310.
    • (2005) Nucleic Acids Res , vol.33 , Issue.3 , pp. 922-933
    • Tsirigos, A.1    Rigoutsos, I.2
  • 15
    • 33748689309 scopus 로고    scopus 로고
    • Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
    • Vernikos GS, Parkhill J. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22(18):2196-203.
    • (2006) Bioinformatics , vol.22 , Issue.18 , pp. 2196-2203
    • Vernikos, G.S.1    Parkhill, J.2
  • 16
    • 0345237922 scopus 로고    scopus 로고
    • IslandPath: aiding detection of genomic islands in prokaryotes
    • Hsiao W, Wan I, Jones SJ, Brinkman FS. IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19(3):418-20.
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 418-420
    • Hsiao, W.1    Wan, I.2    Jones, S.J.3    Brinkman, F.S.4
  • 17
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • 310969, 11076857
    • Garcia-Vallve S, Romeu A, Palau J. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 2000, 10(11):1719-25. 310969, 11076857.
    • (2000) Genome Res , vol.10 , Issue.11 , pp. 1719-1725
    • Garcia-Vallve, S.1    Romeu, A.2    Palau, J.3
  • 18
    • 39049169705 scopus 로고    scopus 로고
    • Resolving the structural features of genomic islands: a machine learning approach
    • 2203631, 18071028
    • Vernikos GS, Parkhill J. Resolving the structural features of genomic islands: a machine learning approach. Genome Res 2008, 18(2):331-42. 2203631, 18071028.
    • (2008) Genome Res , vol.18 , Issue.2 , pp. 331-342
    • Vernikos, G.S.1    Parkhill, J.2
  • 19
    • 0029365976 scopus 로고
    • Locating protein coding regions in human DNA using a decision tree algorithm
    • Salzberg S. Locating protein coding regions in human DNA using a decision tree algorithm. J Comput Biol 1995, 2(3):473-85.
    • (1995) J Comput Biol , vol.2 , Issue.3 , pp. 473-485
    • Salzberg, S.1
  • 20
    • 0033492988 scopus 로고    scopus 로고
    • Decision tree-based formation of consensus protein secondary structure prediction
    • Selbig J, Mevissen T, Lengauer T. Decision tree-based formation of consensus protein secondary structure prediction. Bioinformatics 1999, 15(12):1039-46.
    • (1999) Bioinformatics , vol.15 , Issue.12 , pp. 1039-1046
    • Selbig, J.1    Mevissen, T.2    Lengauer, T.3
  • 23
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • 21352, 9689094
    • Lawrence JG, Ochman H. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 1998, 95(16):9413-7. 21352, 9689094.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , Issue.16 , pp. 9413-9417
    • Lawrence, J.G.1    Ochman, H.2
  • 24
    • 39049132182 scopus 로고    scopus 로고
    • Genetic flux over time in the Salmonella lineage
    • 2394748, 17547764
    • Vernikos GS, Thomson NR, Parkhill J. Genetic flux over time in the Salmonella lineage. Genome Biol 2007, 8(6):R100. 2394748, 17547764.
    • (2007) Genome Biol , vol.8 , Issue.6
    • Vernikos, G.S.1    Thomson, N.R.2    Parkhill, J.3
  • 27
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • 146525, 9023104
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-64. 146525, 9023104.
    • (1997) Nucleic Acids Res , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 29
    • 0030211964 scopus 로고    scopus 로고
    • Bagging Predictors
    • Brieman L. Bagging Predictors. Machine Learning 1996, 24:123-140.
    • (1996) Machine Learning , vol.24 , pp. 123-140
    • Brieman, L.1
  • 31
    • 0034247206 scopus 로고    scopus 로고
    • MultiBoosting: a technique for combining boosting and wagging
    • Webb G. MultiBoosting: a technique for combining boosting and wagging. Machine Learning 2000, 40:159-196.
    • (2000) Machine Learning , vol.40 , pp. 159-196
    • Webb, G.1
  • 32
    • 0003660631 scopus 로고    scopus 로고
    • Additive logistic regression: a statistical view of boosting
    • Department of Statistics, Stanford University
    • Friedman J, Hastie T, R T. Additive logistic regression: a statistical view of boosting. Tech. rep. 1998, Department of Statistics, Stanford University.
    • (1998) Tech. rep.
    • Friedman, J.1    Hastie, T.2    R, T.3
  • 33


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.