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Volumn , Issue , 2011, Pages 130-136

QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads

Author keywords

constraint programming; graph coloring; HIV; quasispecies; virology

Indexed keywords

CONSTRAINT PROGRAMMING; GRAPH COLORINGS; HIV; QUASISPECIES; VIROLOGY;

EID: 84856002192     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBMW.2011.6112365     Document Type: Conference Paper
Times cited : (11)

References (56)
  • 3
    • 70349388189 scopus 로고    scopus 로고
    • Transmitted drug resistance in nonsubtype b HIV-1 infection
    • [Online]. Available
    • P. A. Chan and R. Kantor, "Transmitted drug resistance in nonsubtype b HIV-1 infection," HIV Therapy, vol. 3, no. 5, pp. 447-465, 2009. [Online]. Available: http://www.futuremedicine.com/doi/abs/10.2217/hiv.09.30
    • (2009) HIV Therapy , vol.3 , Issue.5 , pp. 447-465
    • Chan, P.A.1    Kantor, R.2
  • 4
  • 6
    • 77950445796 scopus 로고    scopus 로고
    • Public database for HIV drug resistance in southern africa
    • T. de Oliveira, R. W. Shafer, and C. Seebregts, "Public database for HIV drug resistance in southern africa," Nature, vol. 464, no. 7289, pp. 673-673, 2010.
    • (2010) Nature , vol.464 , Issue.7289 , pp. 673-673
    • De Oliveira, T.1    Shafer, R.W.2    Seebregts, C.3
  • 8
    • 84856010124 scopus 로고    scopus 로고
    • Stratification by HIV-1 subtype does not eliminate systematic geographical variation
    • A. Huang, J. Hogan, S. Istrail, and R. Kantor, "Stratification by HIV-1 subtype does not eliminate systematic geographical variation," Antiviral Therapy, vol. 15 Supppl, no. 2, p. A161, 2010.
    • (2010) Antiviral Therapy , vol.15 , Issue.2 SUPPL.
    • Huang, A.1    Hogan, J.2    Istrail, S.3    Kantor, R.4
  • 10
    • 0028874048 scopus 로고
    • Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection
    • D. D. Ho, A. U. Neumann, A. S. Perelson, W. Chen, J. M. Leonard, and M. Markowitz, "Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection," Nature, vol. 373, no. 6510, pp. 123-126, 1995.
    • (1995) Nature , vol.373 , Issue.6510 , pp. 123-126
    • Ho, D.D.1    Neumann, A.U.2    Perelson, A.S.3    Chen, W.4    Leonard, J.M.5    Markowitz, M.6
  • 11
    • 0030060447 scopus 로고    scopus 로고
    • Forward mutation rate of human immunodeficiency virus type 1 in a t lymphoid cell line*
    • L. M. Mansky, "Forward mutation rate of human immunodeficiency virus type 1 in a t lymphoid cell line*," AIDS research and human retroviruses, vol. 12, no. 4, pp. 307-314, 1996.
    • (1996) AIDS Research and Human Retroviruses , vol.12 , Issue.4 , pp. 307-314
    • Mansky, L.M.1
  • 13
    • 0028952146 scopus 로고
    • HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy
    • J. M. Coffin, "HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy," Science, vol. 267, no. 5197, p. 483, 1995.
    • (1995) Science , vol.267 , Issue.5197 , pp. 483
    • Coffin, J.M.1
  • 14
    • 67651100815 scopus 로고    scopus 로고
    • Evolutionary analysis of the dynamics of viral infectious disease
    • O. G. Pybus and A. Rambaut, "Evolutionary analysis of the dynamics of viral infectious disease," Nature Reviews Genetics, vol. 10, no. 8, pp. 540-550, 2009.
    • (2009) Nature Reviews Genetics , vol.10 , Issue.8 , pp. 540-550
    • Pybus, O.G.1    Rambaut, A.2
  • 16
    • 33751099319 scopus 로고    scopus 로고
    • Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo
    • DOI 10.1016/j.gene.2006.07.037, PII S0378111906004720
    • C. Briones, A. de Vicente, C. Molina-Pars, and E. Domingo, "Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo," Gene, vol. 384, pp. 129-138, 2006. (Pubitemid 44767961)
    • (2006) Gene , vol.384 , Issue.1-2 , pp. 129-138
    • Briones, C.1    De Vicente, A.2    Molina-Paris, C.3    Domingo, E.4
  • 17
    • 48449092074 scopus 로고    scopus 로고
    • Minority report: Hidden memory genomes in HIV-1 quasispecies and possible clinical implications
    • C. Briones and E. Domingo, "Minority report: hidden memory genomes in HIV-1 quasispecies and possible clinical implications," AIDS Rev, vol. 10, p. 93109, 2008.
    • (2008) AIDS Rev , vol.10 , pp. 93109
    • Briones, C.1    Domingo, E.2
  • 18
    • 66249094578 scopus 로고    scopus 로고
    • Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo
    • A. M. N. Tsibris, B. Korber, R. Arnaout, C. Russ, C. C. Lo, T. Leitner, B. Gaschen, J. Theiler, R. Paredes, and Z. Su, "Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo," PloS one, vol. 4, no. 5, 2009.
    • (2009) PloS One , vol.4 , Issue.5
    • Tsibris, A.M.N.1    Korber, B.2    Arnaout, R.3    Russ, C.4    Lo, C.C.5    Leitner, T.6    Gaschen, B.7    Theiler, J.8    Paredes, R.9    Su, Z.10
  • 20
    • 20244383737 scopus 로고    scopus 로고
    • Clonal analyses of HIV quasispecies in patients harbouring plasma genotype with K65R mutation associated with thymidine analogue mutations or L74V substitution
    • M. Wirden, I. Malet, A. Derache, A. G. Marcelin, B. Roquebert, A. Simon, M. Kirstetter, L. M. Joubert, C. Katlama, and V. Calvez, "Clonal analyses of HIV quasispecies in patients harbouring plasma genotype with K65R mutation associated with thymidine analogue mutations or L74V substitution," AIDS, vol. 19, no. 6, p. 630, 2005.
    • (2005) AIDS , vol.19 , Issue.6 , pp. 630
    • Wirden, M.1    Malet, I.2    Derache, A.3    Marcelin, A.G.4    Roquebert, B.5    Simon, A.6    Kirstetter, M.7    Joubert, L.M.8    Katlama, C.9    Calvez, V.10
  • 22
    • 34848865282 scopus 로고    scopus 로고
    • Drug resistance in plasma and breast milk after single-dose nevirapine in subtype C HIV type 1: Population and clonal sequence analysis
    • DOI 10.1089/aid.2007.0045
    • S. Kassaye, E. Lee, R. Kantor, E. Johnston, M. Winters, L. Zijenah, P. Mateta, and D. Katzenstein, "Drug resistance in plasma and breast milk after single-dose nevirapine in subtype c HIV type 1: population and clonal sequence analysis," AIDS research and human retroviruses, vol. 23, no. 8, pp. 1055-1061, 2007. (Pubitemid 47492348)
    • (2007) AIDS Research and Human Retroviruses , vol.23 , Issue.8 , pp. 1055-1061
    • Kassaye, S.1    Lee, E.2    Kantor, R.3    Johnston, E.4    Winters, M.5    Zijenah, L.6    Mateta, P.7    Katzenstein, D.8
  • 23
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
    • C. Wang, Y. Mitsuya, B. Gharizadeh, M. Ronaghi, and R. W. Shafer, "Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance," Genome research, vol. 17, no. 8, p. 1195, 2007.
    • (2007) Genome Research , vol.17 , Issue.8 , pp. 1195
    • Wang, C.1    Mitsuya, Y.2    Gharizadeh, B.3    Ronaghi, M.4    Shafer, R.W.5
  • 25
    • 81755185962 scopus 로고    scopus 로고
    • Ultra-deep sequencing for the analysis of viral populations
    • vol. In Press, Corrected Proof. [Online]. Available
    • N. Beerenwinkel and O. Zagordi, "Ultra-deep sequencing for the analysis of viral populations," Current Opinion in Virology, vol. In Press, Corrected Proof. [Online]. Available: http://www.sciencedirect.com/science/ article/pii/S1879625711000629
    • Current Opinion in Virology
    • Beerenwinkel, N.1    Zagordi, O.2
  • 26
    • 77955199812 scopus 로고    scopus 로고
    • Prevalence and clinical significance of HIV drug resistance mutations by Ultra-Deep sequencing in Antiretroviral-Nave subjects in the CASTLE study
    • M. Lataillade, J. Chiarella, R. Yang, S. Schnittman, V. Wirtz, J. Uy, D. Seekins, M. Krystal, M. Mancini, and D. McGrath, "Prevalence and clinical significance of HIV drug resistance mutations by Ultra-Deep sequencing in Antiretroviral-Nave subjects in the CASTLE study," PloS one, vol. 5, no. 6, p. e10952, 2010.
    • (2010) PloS One , vol.5 , Issue.6
    • Lataillade, M.1    Chiarella, J.2    Yang, R.3    Schnittman, S.4    Wirtz, V.5    Uy, J.6    Seekins, D.7    Krystal, M.8    Mancini, M.9    McGrath, D.10
  • 32
    • 79955125679 scopus 로고    scopus 로고
    • ShoRAH: Estimating the genetic diversity of a mixed sample from next-generation sequencing data
    • O. Zagordi, A. Bhattacharya, N. Eriksson, and N. Beerenwinkel, "ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data," BMC bioinformatics, vol. 12, no. 1, p. 119, 2011.
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 119
    • Zagordi, O.1    Bhattacharya, A.2    Eriksson, N.3    Beerenwinkel, N.4
  • 33
    • 0036644865 scopus 로고    scopus 로고
    • Genome sequence assembly: Algorithms and issues
    • M. Pop, S. L. Salzberg, and M. Shumway, "Genome sequence assembly: Algorithms and issues," Computer, pp. 47-54, 2002.
    • (2002) Computer , pp. 47-54
    • Pop, M.1    Salzberg, S.L.2    Shumway, M.3
  • 35
    • 0029312687 scopus 로고
    • A new algorithm for DNA sequence assembly
    • R. M. Idury and M. S. Waterman, "A new algorithm for DNA sequence assembly," Journal of Computational Biology, vol. 2, no. 2, p. 291306, 1995.
    • (1995) Journal of Computational Biology , vol.2 , Issue.2 , pp. 291306
    • Idury, R.M.1    Waterman, M.S.2
  • 36
    • 56149112104 scopus 로고    scopus 로고
    • Whole-genome sequencing and assembly with high-throughput, short-read technologies
    • A. Sundquist, M. Ronaghi, H. Tang, P. Pevzner, and S. Batzoglou, "Whole-genome sequencing and assembly with high-throughput, short-read technologies," PLoS One, vol. 2, no. 5, p. e484, 2007.
    • (2007) PLoS One , vol.2 , Issue.5
    • Sundquist, A.1    Ronaghi, M.2    Tang, H.3    Pevzner, P.4    Batzoglou, S.5
  • 37
    • 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 research, vol. 18, no. 5, p. 821, 2008.
    • (2008) Genome Research , vol.18 , Issue.5 , pp. 821
    • Zerbino, D.R.1    Birney, E.2
  • 39
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • M. J. Chaisson and P. A. Pevzner, "Short read fragment assembly of bacterial genomes," Genome Research, vol. 18, no. 2, p. 324, 2008.
    • (2008) Genome Research , vol.18 , Issue.2 , pp. 324
    • Chaisson, M.J.1    Pevzner, P.A.2
  • 41
    • 0036514657 scopus 로고    scopus 로고
    • Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem
    • R. Lippert, R. Schwartz, G. Lancia, and S. Istrail, "Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem,"Briefings in bioinformatics, vol. 3, no. 1, p. 23, 2002.
    • (2002) Briefings in Bioinformatics , vol.3 , Issue.1 , pp. 23
    • Lippert, R.1    Schwartz, R.2    Lancia, G.3    Istrail, S.4
  • 43
    • 78149456704 scopus 로고    scopus 로고
    • Development of a low bias method for characterizing viral populations using next generation sequencing technology
    • S. M. Willerth, H. A. M. Pedro, L. Pachter, L. M. Humeau, A. P. Arkin, D. V. Schaffer, and J. P. Vartanian, "Development of a low bias method for characterizing viral populations using next generation sequencing technology," PloS one, vol. 5, no. 10, pp. 255-264, 2010.
    • (2010) PloS One , vol.5 , Issue.10 , pp. 255-264
    • Willerth, S.M.1    Pedro, H.A.M.2    Pachter, L.3    Humeau, L.M.4    Arkin, A.P.5    Schaffer, D.V.6    Vartanian, J.P.7
  • 44
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies
    • O. Zagordi, R. Klein, M. Daumer, and N. Beerenwinkel, "Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies," Nucleic Acids Research, 2010.
    • (2010) Nucleic Acids Research
    • Zagordi, O.1    Klein, R.2    Daumer, M.3    Beerenwinkel, N.4
  • 47
    • 77952855601 scopus 로고    scopus 로고
    • Structural variation analysis with strobe reads
    • A. Ritz, A. Bashir, and B. J. Raphael, "Structural variation analysis with strobe reads," Bioinformatics, vol. 26, no. 10, p. 1291, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.10 , pp. 1291
    • Ritz, A.1    Bashir, A.2    Raphael, B.J.3
  • 48
    • 84856008929 scopus 로고    scopus 로고
    • Software download and online material at the website
    • C. Schulte, M. Lagerkvist, and G. Tack, "Gecode," Software download and online material at the website: http://www. gecode. org.
    • Schulte, C.1    Lagerkvist, M.2    Tack, G.3
  • 52
    • 84976668743 scopus 로고
    • Algorithm 457: Finding all cliques of an undirected graph
    • C. Bron and J. Kerbosch, "Algorithm 457: finding all cliques of an undirected graph," Communications of the ACM, vol. 16, no. 9, pp. 575-577, 1973.
    • (1973) Communications of the ACM , vol.16 , Issue.9 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 56
    • 77950840976 scopus 로고    scopus 로고
    • Deep sequencing of a genetically heterogeneous sample: Local haplotype reconstruction and read error correction
    • O. Zagordi, L. Geyrhofer, V. Roth, and N. Beerenwinkel, "Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction," Journal of Computational Biology, vol. 17, no. 3, pp. 417-428, 2010.
    • (2010) Journal of Computational Biology , vol.17 , Issue.3 , pp. 417-428
    • Zagordi, O.1    Geyrhofer, L.2    Roth, V.3    Beerenwinkel, N.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.