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Volumn 10, Issue , 2009, Pages 293-

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOASSAY; COST EFFECTIVENESS; GENES; GENETIC ENGINEERING; OLIGONUCLEOTIDES;

EID: 70449432929     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-293     Document Type: Article
Times cited : (21)

References (43)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 10.1126/science.270.5235.467, 7569999
    • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467-470. 10.1126/science.270.5235.467, 7569999.
    • (1995) Science , vol.270 , Issue.5235 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 2
    • 17344371740 scopus 로고    scopus 로고
    • High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
    • 10.1038/2524, 9771718
    • Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20(2):207-211. 10.1038/2524, 9771718.
    • (1998) Nat Genet , vol.20 , Issue.2 , pp. 207-211
    • Pinkel, D.1    Segraves, R.2    Sudar, D.3    Clark, S.4    Poole, I.5    Kowbel, D.6    Collins, C.7    Kuo, W.L.8    Chen, C.9    Zhai, Y.10
  • 3
    • 0032524383 scopus 로고    scopus 로고
    • Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome
    • 10.1126/science.280.5366.1077, 9582121
    • Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998, 280(5366):1077-1082. 10.1126/science.280.5366.1077, 9582121.
    • (1998) Science , vol.280 , Issue.5366 , pp. 1077-1082
    • Wang, D.G.1    Fan, J.B.2    Siao, C.J.3    Berno, A.4    Young, P.5    Sapolsky, R.6    Ghandour, G.7    Perkins, N.8    Winchester, E.9    Spencer, J.10
  • 6
    • 0036899178 scopus 로고    scopus 로고
    • Identification of Listeria species by microarray-based assay
    • 10.1128/JCM.40.12.4720-4728.2002, 154633, 12454178
    • Volokhov D, Rasooly A, Chumakov K, Chizhikov V. Identification of Listeria species by microarray-based assay. J Clin Microbiol 2002, 40(12):4720-4728. 10.1128/JCM.40.12.4720-4728.2002, 154633, 12454178.
    • (2002) J Clin Microbiol , vol.40 , Issue.12 , pp. 4720-4728
    • Volokhov, D.1    Rasooly, A.2    Chumakov, K.3    Chizhikov, V.4
  • 7
    • 10744221486 scopus 로고    scopus 로고
    • New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays
    • 10.1128/IAI.72.2.1072-1083.2004, 321639, 14742555
    • Doumith M, Cazalet C, Simoes N, Frangeul L, Jacquet C, Kunst F, Martin P, Cossart P, Glaser P, Buchrieser C. New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect Immun 2004, 72(2):1072-1083. 10.1128/IAI.72.2.1072-1083.2004, 321639, 14742555.
    • (2004) Infect Immun , vol.72 , Issue.2 , pp. 1072-1083
    • Doumith, M.1    Cazalet, C.2    Simoes, N.3    Frangeul, L.4    Jacquet, C.5    Kunst, F.6    Martin, P.7    Cossart, P.8    Glaser, P.9    Buchrieser, C.10
  • 8
    • 0037316625 scopus 로고    scopus 로고
    • Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes
    • 10.1128/JCM.41.2.632-639.2003, 149708, 12574259
    • Call DR, Borucki MK, Besser TE. Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes. J Clin Microbiol 2003, 41(2):632-639. 10.1128/JCM.41.2.632-639.2003, 149708, 12574259.
    • (2003) J Clin Microbiol , vol.41 , Issue.2 , pp. 632-639
    • Call, D.R.1    Borucki, M.K.2    Besser, T.E.3
  • 9
    • 8644289234 scopus 로고    scopus 로고
    • Selective discrimination of Listeria monocytogenes epidemic strains by a mixed-genome DNA microarray compared to discrimination by pulsed-field gel electrophoresis, ribotyping, and multilocus sequence typing
    • 10.1128/JCM.42.11.5270-5276.2004, 525159, 15528725
    • Borucki MK, Kim SH, Call DR, Smole SC, Pagotto F. Selective discrimination of Listeria monocytogenes epidemic strains by a mixed-genome DNA microarray compared to discrimination by pulsed-field gel electrophoresis, ribotyping, and multilocus sequence typing. J Clin Microbiol 2004, 42(11):5270-5276. 10.1128/JCM.42.11.5270-5276.2004, 525159, 15528725.
    • (2004) J Clin Microbiol , vol.42 , Issue.11 , pp. 5270-5276
    • Borucki, M.K.1    Kim, S.H.2    Call, D.R.3    Smole, S.C.4    Pagotto, F.5
  • 10
    • 0041335360 scopus 로고    scopus 로고
    • Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations
    • 10.1128/JB.185.18.5573-5584.2003, 193770, 12949110
    • Zhang C, Zhang M, Ju J, Nietfeldt J, Wise J, Terry PM, Olson M, Kachman SD, Wiedmann M, Samadpour M. Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations. J Bacteriol 2003, 185(18):5573-5584. 10.1128/JB.185.18.5573-5584.2003, 193770, 12949110.
    • (2003) J Bacteriol , vol.185 , Issue.18 , pp. 5573-5584
    • Zhang, C.1    Zhang, M.2    Ju, J.3    Nietfeldt, J.4    Wise, J.5    Terry, P.M.6    Olson, M.7    Kachman, S.D.8    Wiedmann, M.9    Samadpour, M.10
  • 11
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • 10.1016/j.ygeno.2004.10.005, 15607417
    • Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005, 85(1):1-15. 10.1016/j.ygeno.2004.10.005, 15607417.
    • (2005) Genomics , vol.85 , Issue.1 , pp. 1-15
    • Mockler, T.C.1    Chan, S.2    Sundaresan, A.3    Chen, H.4    Jacobsen, S.E.5    Ecker, J.R.6
  • 13
    • 34547840248 scopus 로고    scopus 로고
    • Optimized design and assessment of whole genome tiling arrays
    • 10.1093/bioinformatics/btm200, 17646297
    • Graf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. Optimized design and assessment of whole genome tiling arrays. Bioinformatics 2007, 23(13):i195-204. 10.1093/bioinformatics/btm200, 17646297.
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Graf, S.1    Nielsen, F.G.2    Kurtz, S.3    Huynen, M.A.4    Birney, E.5    Stunnenberg, H.6    Flicek, P.7
  • 15
    • 25444524604 scopus 로고    scopus 로고
    • Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"
    • 10.1073/pnas.0506758102, 1216834,1216834, 16172379
    • Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci USA 2005, 102(39):13950-13955. 10.1073/pnas.0506758102, 1216834,1216834, 16172379.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.39 , pp. 13950-13955
    • Tettelin, H.1    Masignani, V.2    Cieslewicz, M.J.3    Donati, C.4    Medini, D.5    Ward, N.L.6    Angiuoli, S.V.7    Crabtree, J.8    Jones, A.L.9    Durkin, A.S.10
  • 16
    • 40449093894 scopus 로고    scopus 로고
    • Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
    • 10.1186/gb-2007-8-12-r267, 2246269, 18088402
    • Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 2007, 8(12):R267. 10.1186/gb-2007-8-12-r267, 2246269, 18088402.
    • (2007) Genome Biol , vol.8 , Issue.12
    • Willenbrock, H.1    Hallin, P.F.2    Wassenaar, T.M.3    Ussery, D.W.4
  • 17
    • 34447332244 scopus 로고    scopus 로고
    • A fast and flexible approach to oligonucleotide probe design for genomes and gene families
    • 10.1093/bioinformatics/btm114, 17392329
    • Feng S, Tillier ER. A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics 2007, 23(10):1195-1202. 10.1093/bioinformatics/btm114, 17392329.
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1195-1202
    • Feng, S.1    Tillier, E.R.2
  • 18
    • 27944465771 scopus 로고    scopus 로고
    • Design of long oligonucleotide probes for functional gene detection in a microbial community
    • 10.1093/bioinformatics/bti673, 16159916
    • Chung WH, Rhee SK, Wan XF, Bae JW, Quan ZX, Park YH. Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics 2005, 21(22):4092-4100. 10.1093/bioinformatics/bti673, 16159916.
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4092-4100
    • Chung, W.H.1    Rhee, S.K.2    Wan, X.F.3    Bae, J.W.4    Quan, Z.X.5    Park, Y.H.6
  • 19
    • 0025951915 scopus 로고
    • Listeria monocytogenes, a food-borne pathogen
    • 372831, 1943998
    • Farber JM, Peterkin PI. Listeria monocytogenes, a food-borne pathogen. Microbiol Rev 1991, 55(3):476-511. 372831, 1943998.
    • (1991) Microbiol Rev , vol.55 , Issue.3 , pp. 476-511
    • Farber, J.M.1    Peterkin, P.I.2
  • 20
    • 0030968986 scopus 로고    scopus 로고
    • Ribotypes and virulence gene polymorphisms suggest three distinct Listeria monocytogenes lineages with differences in pathogenic potential
    • 175382, 9199440
    • Wiedmann M, Bruce JL, Keating C, Johnson AE, McDonough PL, Batt CA. Ribotypes and virulence gene polymorphisms suggest three distinct Listeria monocytogenes lineages with differences in pathogenic potential. Infect Immun 1997, 65(7):2707-2716. 175382, 9199440.
    • (1997) Infect Immun , vol.65 , Issue.7 , pp. 2707-2716
    • Wiedmann, M.1    Bruce, J.L.2    Keating, C.3    Johnson, A.E.4    McDonough, P.L.5    Batt, C.A.6
  • 21
    • 33846119130 scopus 로고    scopus 로고
    • The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
    • 10.1093/nar/gkl947, 1751540, 17145713
    • McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res 2007, (35 Database):D347-353. 10.1093/nar/gkl947, 1751540, 17145713.
    • (2007) Nucleic Acids Res , vol.Database , Issue.35
    • McNeil, L.K.1    Reich, C.2    Aziz, R.K.3    Bartels, D.4    Cohoon, M.5    Disz, T.6    Edwards, R.A.7    Gerdes, S.8    Hwang, K.9    Kubal, M.10
  • 23
    • 0003603813 scopus 로고
    • Computers and Intractability: A Guide to the Theory of NP-Completeness
    • New York, NY, USA: W. H. Freeman & Co
    • Garey MR, Johnson DS. Computers and Intractability: A Guide to the Theory of NP-Completeness. 1979, New York, NY, USA: W. H. Freeman & Co.
    • (1979)
    • Garey, M.R.1    Johnson, D.S.2
  • 24
    • 0003895164 scopus 로고    scopus 로고
    • Complexity and Approximation: Combinatorial Optimization Problems and Their Approximability Properties
    • Secaucus, NJ, USA: Springer-Verlag New York, Inc
    • Ausiello G, Protasi M, Marchetti-Spaccamela A, Gambosi G, Crescenzi P, Kann V. Complexity and Approximation: Combinatorial Optimization Problems and Their Approximability Properties. 1999, Secaucus, NJ, USA: Springer-Verlag New York, Inc.
    • (1999)
    • Ausiello, G.1    Protasi, M.2    Marchetti-Spaccamela, A.3    Gambosi, G.4    Crescenzi, P.5    Kann, V.6
  • 26
    • 0032108328 scopus 로고    scopus 로고
    • A threshold of ln n for approximating set cover
    • Feige U. A threshold of ln n for approximating set cover. Journal of the ACM (JACM) 1998, 45(4):634-652.
    • (1998) Journal of the ACM (JACM) , vol.45 , Issue.4 , pp. 634-652
    • Feige, U.1
  • 28
    • 25444516430 scopus 로고    scopus 로고
    • The Vmatch large scale sequence analysis software
    • The Vmatch large scale sequence analysis software. , http://www.vmatch.de
  • 29
    • 84888295985 scopus 로고    scopus 로고
    • Ergatis
    • Ergatis. , http://ergatis.sourceforge.net
  • 30
    • 79951780811 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R: A Language and Environment for Statistical Computing. , http://www.R-project.org
  • 31
    • 55049125445 scopus 로고    scopus 로고
    • Comparative genomics: the bacterial pan-genome
    • 10.1016/j.mib.2008.09.006, 19086349
    • Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 2008, 11(5):472-477. 10.1016/j.mib.2008.09.006, 19086349.
    • (2008) Curr Opin Microbiol , vol.11 , Issue.5 , pp. 472-477
    • Tettelin, H.1    Riley, D.2    Cattuto, C.3    Medini, D.4
  • 34
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • 10.1093/biostatistics/kxh008, 15475419
    • Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5(4):557-572. 10.1093/biostatistics/kxh008, 15475419.
    • (2004) Biostatistics , vol.5 , Issue.4 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 35
    • 27944455289 scopus 로고    scopus 로고
    • A comparison study: applying segmentation to array CGH data for downstream analyses
    • 10.1093/bioinformatics/bti677, 16159913
    • Willenbrock H, Fridlyand J. A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 2005, 21(22):4084-4091. 10.1093/bioinformatics/bti677, 16159913.
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4084-4091
    • Willenbrock, H.1    Fridlyand, J.2
  • 36
    • 44649164484 scopus 로고    scopus 로고
    • Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays
    • 10.1186/1471-2164-9-230, 2410139, 18489741
    • Pinto FR, Aguiar SI, Melo-Cristino J, Ramirez M. Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays. BMC Genomics 2008, 9:230. 10.1186/1471-2164-9-230, 2410139, 18489741.
    • (2008) BMC Genomics , vol.9 , pp. 230
    • Pinto, F.R.1    Aguiar, S.I.2    Melo-Cristino, J.3    Ramirez, M.4
  • 37
    • 65549170302 scopus 로고    scopus 로고
    • Improved analysis of bacterial CGH data beyond the log-ratio paradigm
    • 10.1186/1471-2105-10-91, 2679023, 19298668
    • Snipen L, Nyquist OL, Solheim M, Aakra A, Nes IF. Improved analysis of bacterial CGH data beyond the log-ratio paradigm. BMC Bioinformatics 2009, 10(1):91. 10.1186/1471-2105-10-91, 2679023, 19298668.
    • (2009) BMC Bioinformatics , vol.10 , Issue.1 , pp. 91
    • Snipen, L.1    Nyquist, O.L.2    Solheim, M.3    Aakra, A.4    Nes, I.F.5
  • 38
    • 33748623795 scopus 로고    scopus 로고
    • Detection of divergent genes in microbial aCGH experiments
    • 10.1186/1471-2105-7-181, 1563484, 16573812
    • Snipen L, Repsilber D, Nyquist L, Ziegler A, Aakra A, Aastveit A. Detection of divergent genes in microbial aCGH experiments. BMC Bioinformatics 2006, 7:181. 10.1186/1471-2105-7-181, 1563484, 16573812.
    • (2006) BMC Bioinformatics , vol.7 , pp. 181
    • Snipen, L.1    Repsilber, D.2    Nyquist, L.3    Ziegler, A.4    Aakra, A.5    Aastveit, A.6
  • 40
    • 33845912401 scopus 로고    scopus 로고
    • Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays
    • 10.1093/bioinformatics/btl549, 17068088
    • Tembe W, Zavaljevski N, Bode E, Chase C, Geyer J, Wasieloski L, Benson G, Reifman J. Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics 2007, 23(1):5-13. 10.1093/bioinformatics/btl549, 17068088.
    • (2007) Bioinformatics , vol.23 , Issue.1 , pp. 5-13
    • Tembe, W.1    Zavaljevski, N.2    Bode, E.3    Chase, C.4    Geyer, J.5    Wasieloski, L.6    Benson, G.7    Reifman, J.8
  • 42
    • 35748959649 scopus 로고    scopus 로고
    • Microarray-based genomic selection for high-throughput resequencing
    • 10.1038/nmeth1109, 17934469
    • Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat Methods 2007, 4(11):907-909. 10.1038/nmeth1109, 17934469.
    • (2007) Nat Methods , vol.4 , Issue.11 , pp. 907-909
    • Okou, D.T.1    Steinberg, K.M.2    Middle, C.3    Cutler, D.J.4    Albert, T.J.5    Zwick, M.E.6


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