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Volumn 94, Issue 3, 2014, Pages 346-354

PolyTB: A genomic variation map for Mycobacterium tuberculosis

(16)  Coll, Francesc a   Preston, Mark a   Guerra Assunção, José Afonso a   Hill Cawthorn, Grant b,c   Harris, David d   Perdigão, João e   Viveiros, Miguel f   Portugal, Isabel e   Drobniewski, Francis g   Gagneux, Sebastien h   Glynn, Judith R a   Pain, Arnab b   Parkhill, Julian d   McNerney, Ruth a   Martin, Nigel i   Clark, Taane G a  


Author keywords

Database; Genomics; Molecular epidemiology; Mycobacterium tuberculosis; Software; Whole genome sequencing

Indexed keywords

RIFAMPICIN;

EID: 84900826220     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2014.02.005     Document Type: Article
Times cited : (76)

References (52)
  • 2
    • 84859905115 scopus 로고    scopus 로고
    • Alignment of multiple complete genomes suggests that gene rearrangements may contribute towards the speciation of Mycobacteria
    • J.C. Garcia-Betancur, M.C. Menendez, P. Del Portillo, and M.J. Garcia Alignment of multiple complete genomes suggests that gene rearrangements may contribute towards the speciation of Mycobacteria Infect Genet Evol 12 2011 819 826
    • (2011) Infect Genet Evol , vol.12 , pp. 819-826
    • Garcia-Betancur, J.C.1    Menendez, M.C.2    Del Portillo, P.3    Garcia, M.J.4
  • 6
    • 0032508046 scopus 로고    scopus 로고
    • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    • S. Cole, R. Brosch, J. Parkhill, and T. Garnier Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence Nature 393 1998 357 444
    • (1998) Nature , vol.393 , pp. 357-444
    • Cole, S.1    Brosch, R.2    Parkhill, J.3    Garnier, T.4
  • 9
    • 33846195782 scopus 로고    scopus 로고
    • Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis
    • D. Alland, D.W. Lacher, M.H. Hazbón, A.S. Motiwala, W. Qi, R.D. Fleischmann, and T.S. Whittam Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis J Clin Microbiol 45 2007 39 46
    • (2007) J Clin Microbiol , vol.45 , pp. 39-46
    • Alland, D.1    Lacher, D.W.2    Hazbón, M.H.3    Motiwala, A.S.4    Qi, W.5    Fleischmann, R.D.6    Whittam, T.S.7
  • 10
    • 84859545563 scopus 로고    scopus 로고
    • Microevolution of extensively drug-resistant tuberculosis in Russia
    • N. Casali, and V. Nikolayevskyy Microevolution of extensively drug-resistant tuberculosis in Russia Genome Res 22 2012 735 745
    • (2012) Genome Res , vol.22 , pp. 735-745
    • Casali, N.1    Nikolayevskyy, V.2
  • 11
    • 0028839739 scopus 로고
    • IS6110 based amplityping assay and RFLP fingerprinting of clinical isolates of Mycobacterium tuberculosis
    • K.Y. Yuen, C.M. Chan, K.S. Chan, W.C. Yam, P.L. Ho, and P.Y. Chau IS6110 based amplityping assay and RFLP fingerprinting of clinical isolates of Mycobacterium tuberculosis J Clin Pathol 48 1995 924 928
    • (1995) J Clin Pathol , vol.48 , pp. 924-928
    • Yuen, K.Y.1    Chan, C.M.2    Chan, K.S.3    Yam, W.C.4    Ho, P.L.5    Chau, P.Y.6
  • 13
    • 0034796701 scopus 로고    scopus 로고
    • Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units
    • P. Supply, S. Lesjean, E. Savine, K. Kremer, D. Van Soolingen, and C. Locht Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units J Clin Microbiol 39 2001 3563 3571
    • (2001) J Clin Microbiol , vol.39 , pp. 3563-3571
    • Supply, P.1    Lesjean, S.2    Savine, E.3    Kremer, K.4    Van Soolingen, D.5    Locht, C.6
  • 14
    • 84859885052 scopus 로고    scopus 로고
    • DNA fingerprinting of Mycobacterium tuberculosis: From phage typing to whole-genome sequencing
    • A.C. Schürch, and D. van Soolingen DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing Infect Genet Evol 12 2012 602 609
    • (2012) Infect Genet Evol , vol.12 , pp. 602-609
    • Schürch, A.C.1    Van Soolingen, D.2
  • 15
    • 84859926842 scopus 로고    scopus 로고
    • SITVITWEB - A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology
    • C. Demay, B. Liens, T. Burguière, V. Hill, D. Couvin, J. Millet, I. Mokrousov, C. Sola, T. Zozio, and N. Rastogi SITVITWEB - a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology Infect Genet Evol 12 2012 755 766
    • (2012) Infect Genet Evol , vol.12 , pp. 755-766
    • Demay, C.1    Liens, B.2    Burguière, T.3    Hill, V.4    Couvin, D.5    Millet, J.6    Mokrousov, I.7    Sola, C.8    Zozio, T.9    Rastogi, N.10
  • 20
    • 70649084195 scopus 로고    scopus 로고
    • Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies
    • I. Comas, S. Homolka, S. Niemann, and S. Gagneux Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies PLoS One 4 2009 e7815
    • (2009) PLoS One , vol.4 , pp. 7815
    • Comas, I.1    Homolka, S.2    Niemann, S.3    Gagneux, S.4
  • 24
    • 84863619196 scopus 로고    scopus 로고
    • High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms
    • S. Homolka, M. Projahn, S. Feuerriegel, T. Ubben, R. Diel, and U.N.S. Nübel High resolution discrimination of clinical Mycobacterium tuberculosis complex strains based on single nucleotide polymorphisms PloS One 7 2012 e39855
    • (2012) PloS One , vol.7 , pp. 39855
    • Homolka, S.1    Projahn, M.2    Feuerriegel, S.3    Ubben, T.4    Diel, R.5    Nübel, U.N.S.6
  • 27
    • 84874531408 scopus 로고    scopus 로고
    • Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database
    • D. Stucki, and S. Gagneux Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database Tuberc (Edinb) 30 2012 30 39
    • (2012) Tuberc (Edinb) , vol.30 , pp. 30-39
    • Stucki, D.1    Gagneux, S.2
  • 29
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • C. Alkan, B.P. Coe, and E.E. Eichler Genome structural variation discovery and genotyping Nat Rev Genet 12 2011 363 376
    • (2011) Nat Rev Genet , vol.12 , pp. 363-376
    • Alkan, C.1    Coe, B.P.2    Eichler, E.E.3
  • 30
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol 10 2009 R25.3
    • (2009) Genome Biol , vol.10 , pp. 253
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 34
    • 79961007031 scopus 로고    scopus 로고
    • CREST maps somatic structural variation in cancer genomes with base-pair resolution
    • J. Wang, C. Mullighan, J. Easton, and S. Roberts CREST maps somatic structural variation in cancer genomes with base-pair resolution Nat Methods 8 2011 652 656
    • (2011) Nat Methods , vol.8 , pp. 652-656
    • Wang, J.1    Mullighan, C.2    Easton, J.3    Roberts, S.4
  • 35
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • K. Ye, M.H. Schulz, Q. Long, R. Apweiler, and Z. Ning Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads Bioinformatics 25 2009 2865 2871
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 37
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • A. Abyzov, A.E. Urban, M. Snyder, and M. Gerstein CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing Genome Res 21 2011 974 984
    • (2011) Genome Res , vol.21 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4
  • 38
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • D.R. Zerbino, and E. Birney Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res 18 2008 821 829
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 39
    • 79951961326 scopus 로고    scopus 로고
    • AGE: Defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
    • A. Abyzov, and M. Gerstein AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision Bioinformatics 27 2011 595 603
    • (2011) Bioinformatics , vol.27 , pp. 595-603
    • Abyzov, A.1    Gerstein, M.2
  • 41
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • H. Li, and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 26 2010 589 595
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 43
    • 84869471315 scopus 로고    scopus 로고
    • SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
    • F. Coll, K. Mallard, M.D. Preston, S. Bentley, J. Parkhill, R. McNerney, N. Martin, and T.G. Clark SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences Bioinformatics 28 2012 2991 2993
    • (2012) Bioinformatics , vol.28 , pp. 2991-2993
    • Coll, F.1    Mallard, K.2    Preston, M.D.3    Bentley, S.4    Parkhill, J.5    McNerney, R.6    Martin, N.7    Clark, T.G.8
  • 44
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML Web servers
    • A. Stamatakis, P. Hoover, and J. Rougemont A rapid bootstrap algorithm for the RAxML Web servers Syst Biol 57 2008 758 771
    • (2008) Syst Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 45
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny inference package
    • (Version 3.2)
    • J. Felsenstein PHYLIP - phylogeny inference package (Version 3.2) Cladistics 5 1989 164 166
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 46
    • 77957931761 scopus 로고    scopus 로고
    • JsPhyloSVG: A javascript library for visualizing interactive and vector-based phylogenetic trees on the web
    • S a. Smits, and C.C. Ouverney jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web PloS One 5 2010 e12267
    • (2010) PloS One , vol.5 , pp. 12267
    • Ouverney, C.C.1


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