메뉴 건너뛰기




Volumn 3, Issue , 2013, Pages

Empirical validation of viral quasispecies assembly algorithms: State-of-the-art and challenges

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOMICS; HEPATITIS B VIRUS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; PHYLOGENY; PROCEDURES; VIRUS ASSEMBLY; VIRUS GENOME;

EID: 84885116145     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep02837     Document Type: Article
Times cited : (39)

References (41)
  • 1
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-The next generation
    • Metzker, ML. Sequencing technologies-The next generation. Nat Rev Genet 11, 31-46 (2010).
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 2
    • 80053628299 scopus 로고    scopus 로고
    • Sequencing technologies and genome sequencing
    • Pareek, C. S., Smoczynski, R. & Tretyn, A. Sequencing technologies and genome sequencing. J Appl Genet 52, 413-435 (2011).
    • (2011) J Appl Genet , vol.52 , pp. 413-435
    • Pareek, C.S.1    Smoczynski, R.2    Tretyn, A.3
  • 3
    • 78651228163 scopus 로고    scopus 로고
    • The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-An ultra-Deep approach
    • Archer, J. et al. The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-An ultra-Deep approach. PLoS Comput Biol 6, e1001022 (2010).
    • (2010) PLoS Comput Biol , vol.6 , pp. 1001022
    • Archer, J.1
  • 4
    • 77956522256 scopus 로고    scopus 로고
    • Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-Generation DNA sequencer
    • Kuroda, M. et al. Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by De novo sequencing using a next-Generation DNA sequencer. PLoS One 5, e10256 (2010).
    • (2010) PLoS One , vol.5 , pp. 10256
    • Kuroda, M.1
  • 5
    • 77952299935 scopus 로고    scopus 로고
    • Phylogenetic analysis of population-Based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1
    • Poon, A. F. et al. Phylogenetic analysis of population-Based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol 27, 819-832 (2010).
    • (2010) Mol Biol Evol , vol.27 , pp. 819-832
    • Poon, A.F.1
  • 6
    • 63549147504 scopus 로고    scopus 로고
    • Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-Populations
    • Rozera, G. et al.Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-Populations. Retrovirology 6, 15 (2009).
    • (2009) Retrovirology , vol.6 , pp. 15
    • Rozera, G.1
  • 7
    • 67651055421 scopus 로고    scopus 로고
    • Detection of low-Frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-Using HIV-1 with ultra-Deep pyrosequencing
    • Archer, J. et al. Detection of low-Frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-Using HIV-1 with ultra-Deep pyrosequencing. AIDS 23, 1209-1218 (2009).
    • (2009) AIDS , vol.23 , pp. 1209-1218
    • Archer, J.1
  • 8
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-Deep pyrosequencing: Application to HIV-1 drug resistance
    • Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M. & Shafer, R. W. Characterization of mutation spectra with ultra-Deep pyrosequencing: Application to HIV-1 drug resistance. Genome research 17, 1195-1201 (2007).
    • (2007) Genome Research , vol.17 , pp. 1195-1201
    • Wang, C.1    Mitsuya, Y.2    Gharizadeh, B.3    Ronaghi, M.4    Shafer, R.W.5
  • 9
    • 84861214061 scopus 로고    scopus 로고
    • Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
    • Henn, M. R. et al.Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8, e1002529 (2012).
    • (2012) PLoS Pathog , vol.8 , pp. 1002529
    • Henn, M.R.1
  • 10
    • 84870976695 scopus 로고    scopus 로고
    • High-Resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems
    • Yin, L. et al. High-Resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology 9, 108 (2012).
    • (2012) Retrovirology , vol.9 , pp. 108
    • Yin, L.1
  • 11
    • 55949095205 scopus 로고    scopus 로고
    • Keeping up with the next generation: Massively parallel sequencing in clinical diagnostics
    • ten Bosch, J. R. & Grody, W. W. Keeping up with the next generation: Massively parallel sequencing in clinical diagnostics. J Mol Diagn 10, 484-492 (2008).
    • (2008) J Mol Diagn , vol.10 , pp. 484-492
    • Ten Bosch, J.R.1    Grody, W.W.2
  • 12
    • 79959309141 scopus 로고    scopus 로고
    • Deep sequencing of patient genomes for disease diagnosis: When will it become routine?
    • Kingsmore, S. F. & Saunders, C. J. Deep sequencing of patient genomes for disease diagnosis: When will it become routine? Sci Transl Med 3, 87ps23 (2011).
    • (2011) Sci Transl Med , vol.3 , pp. 87-23
    • Kingsmore, S.F.1    Saunders, C.J.2
  • 13
    • 79956044149 scopus 로고    scopus 로고
    • Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
    • Gilles, A. et al. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12, 245 (2011).
    • (2011) BMC Genomics , vol.12 , pp. 245
    • Gilles, A.1
  • 14
    • 84858739096 scopus 로고    scopus 로고
    • Analysis of high-Depth sequence data for studying viral diversity: A comparison of next generation sequencing platforms using Segminator II
    • Archer, J. et al. Analysis of high-Depth sequence data for studying viral diversity: A comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics 13, 47 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 47
    • Archer, J.1
  • 15
    • 79959640102 scopus 로고    scopus 로고
    • Evaluation of next-Generation sequencing software in mapping and assembly
    • Bao, Set al. Evaluation of next-Generation sequencing software in mapping and assembly. J Hum Genet 56, 406-414 (2011).
    • (2011) J Hum Genet , vol.56 , pp. 406-414
    • Bao, S.1
  • 16
    • 77954383399 scopus 로고    scopus 로고
    • The RNA virus quasispecies: Fact or fiction?
    • Holmes, E. C. The RNA virus quasispecies: Fact or fiction? JMol Biol 400, 271-273 (2010).
    • (2010) JMol Biol , vol.400 , pp. 271-273
    • Holmes, E.C.1
  • 17
    • 77950020240 scopus 로고    scopus 로고
    • Unfinished stories on viral quasispecies and Darwinian views of evolution
    • Mas, A., Lopez-Galindez, C., Cacho, I., Gomez, J& Martinez, M. A. Unfinished stories on viral quasispecies and Darwinian views of evolution. J Mol Biol 397, 865-877 (2010).
    • (2010) J Mol Biol , vol.397 , pp. 865-877
    • Mas, A.1    Lopez-Galindez, C.2    Cacho, I.3    Gomez, J.4    Martinez, M.A.5
  • 18
    • 78649901946 scopus 로고    scopus 로고
    • Error correction of nextgeneration sequencing data and reliable estimation of HIV quasispecies
    • Zagordi, O., Klein, R., Daumer, M. & Beerenwinkel, N. Error correction of nextgeneration sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 38, 7400-7409 (2010).
    • (2010) Nucleic Acids Res , vol.38 , pp. 7400-7409
    • Zagordi, O.1    Klein, R.2    Daumer, M.3    Beerenwinkel, N.4
  • 19
    • 84867062073 scopus 로고    scopus 로고
    • Efficient error correction for next-Generation sequencing of viral amplicons
    • Skums, P. et al. Efficient error correction for next-Generation sequencing of viral amplicons. BMC Bioinformatics 13 Suppl 10, S6 (2012).
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL. 10
    • Skums, P.1
  • 20
    • 84861108474 scopus 로고    scopus 로고
    • Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data
    • Macalalad, A. R. et al. Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 8, e1002417 (2012).
    • (2012) PLoS Comput Biol , vol.8 , pp. 1002417
    • Macalalad, A.R.1
  • 21
    • 40549123712 scopus 로고    scopus 로고
    • Population sequencing using short reads: HIV as a case study
    • Jojic, V., Hertz, T. & Jojic, N. Population sequencing using short reads: HIV as a case study. Pac Symp Biocomput 114-125 (2008).
    • (2008) Pac Symp Biocomput , pp. 114-125
    • Jojic, V.1    Hertz, T.2    Jojic, N.3
  • 22
    • 44949250815 scopus 로고    scopus 로고
    • Viral population estimation using pyrosequencing
    • Eriksson, N. et al. Viral population estimation using pyrosequencing. PLoS Comput Biol 4, e1000074 (2008).
    • (2008) PLoS Comput Biol , vol.4 , pp. 1000074
    • Eriksson, N.1
  • 23
    • 78650798688 scopus 로고    scopus 로고
    • Combinatorial analysis and algorithms for quasispecies reconstruction using next-Generation sequencing
    • Prosperi, M. C. et al. Combinatorial analysis and algorithms for quasispecies reconstruction using next-Generation sequencing. BMC Bioinformatics 12, 5 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 5
    • Prosperi, M.C.1
  • 24
    • 81755185962 scopus 로고    scopus 로고
    • Ultra-Deep sequencing for the analysis of viral populations
    • Beerenwinkel, N. & Zagordi, O. Ultra-Deep sequencing for the analysis of viral populations. Curr Opin Virol 1, 413-418 (2011).
    • (2011) Curr Opin Virol , vol.1 , pp. 413-418
    • Beerenwinkel, N.1    Zagordi, O.2
  • 25
    • 77950840976 scopus 로고    scopus 로고
    • Deep sequencing of a genetically heterogeneous sample: Local haplotype reconstruction and read error correction
    • Zagordi, O., Geyrhofer, L., Roth, V. & Beerenwinkel, N. Deep sequencing of a genetically heterogeneous sample: Local haplotype reconstruction and read error correction. J Comput Biol 17, 417-428 (2010).
    • (2010) J Comput Biol , vol.17 , pp. 417-428
    • Zagordi, O.1    Geyrhofer, L.2    Roth, V.3    Beerenwinkel, N.4
  • 26
    • 84874964797 scopus 로고    scopus 로고
    • Challenges and opportunities in estimating viral genetic diversity from next-Generation sequencing data
    • Beerenwinkel, N., Gunthard, H. F., Roth, V. & Metzner, K. J. Challenges and opportunities in estimating viral genetic diversity from next-Generation sequencing data. Front Microbiol 3, 329 (2012).
    • (2012) Front Microbiol , vol.3 , pp. 329
    • Beerenwinkel, N.1    Gunthard, H.F.2    Roth, V.3    Metzner, K.J.4
  • 27
    • 84855993428 scopus 로고    scopus 로고
    • Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads. in Bioinformatics and Biomedicine Workshops (BIBMW) 2011
    • Mancuso, N., Tork, B., Skums, P.,Mandoiu, I. & Zelikovsky, A. Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads. in Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on 94-101 (2011).
    • (2011) IEEE International Conference on , pp. 94-101
    • Mancuso, N.1    Tork, B.2    Skums, P.3    Mandoiu, I.4    Zelikovsky, A.5
  • 28
    • 84872440314 scopus 로고    scopus 로고
    • QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-Contiguous next generation sequencing reads
    • Huang, A., Kantor, R., Delong, A., Schreier, L. & Istrail, S. QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-Contiguous next generation sequencing reads. In Silico Biol 11, 193-201 (2012).
    • (2012) In Silico Biol , vol.11 , pp. 193-201
    • Huang, A.1    Kantor, R.2    Delong, A.3    Schreier, L.4    Istrail, S.5
  • 29
    • 49949112775 scopus 로고    scopus 로고
    • HCV quasispecies assembly using network flows
    • Westbrooks, K. et al. HCV quasispecies assembly using network flows. Lect N Bioinformat 4983, 159-170 (2008).
    • (2008) Lect N Bioinformat , vol.4983 , pp. 159-170
    • Westbrooks, K.1
  • 30
    • 79955125679 scopus 로고    scopus 로고
    • ShoRAH: Estimating the genetic diversity of a mixed sample from next-Generation sequencing data
    • Zagordi, O., Bhattacharya, A., Eriksson, N. & Beerenwinkel, N. ShoRAH: Estimating the genetic diversity of a mixed sample from next-Generation sequencing data. BMC Bioinformatics 12, 119 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 119
    • Zagordi, O.1    Bhattacharya, A.2    Eriksson, N.3    Beerenwinkel, N.4
  • 31
    • 79960878783 scopus 로고    scopus 로고
    • Inferring viral quasispecies spectra from 454 pyrosequencing reads
    • Astrovskaya, I. et al. Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics 12 Suppl 6, S1 (2011).
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL.6
    • Astrovskaya, I.1
  • 32
    • 84855173088 scopus 로고    scopus 로고
    • QuRe: Software for viral quasispecies reconstruction from next-Generation sequencing data
    • Prosperi, M. C. & Salemi, M. QuRe: Software for viral quasispecies reconstruction from next-Generation sequencing data. Bioinformatics 28, 132-133 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 132-133
    • Prosperi, M.C.1    Salemi, M.2
  • 33
    • 84860819723 scopus 로고    scopus 로고
    • Probabilistic inference of viral quasispecies subject to recombination
    • ed. Chor, B. Springer Berlin Heidelberg
    • Zagordi, O. et al. Probabilistic Inference of Viral Quasispecies Subject to Recombination. in Research in Computational Molecular Biology Vol. 7262, (ed. Chor, B.) 342-354 (Springer Berlin Heidelberg, 2012).
    • (2012) Research in Computational Molecular Biology , vol.7262 , pp. 342-354
    • Zagordi, O.1
  • 34
    • 84865085855 scopus 로고    scopus 로고
    • Unexpected maintenance of hepatitis C viral diversity following liver transplantation
    • Gray, R. R. et al. Unexpected maintenance of hepatitis C viral diversity following liver transplantation. J Virol 86, 8432-8439 (2012).
    • (2012) J Virol , vol.86 , pp. 8432-8439
    • Gray, R.R.1
  • 35
    • 69449106744 scopus 로고    scopus 로고
    • Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor
    • Ho, S. K. et al. Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor. Aids 23, 1631-1640 (2009).
    • (2009) Aids , vol.23 , pp. 1631-1640
    • Ho, S.K.1
  • 36
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh, O. An improved algorithm for matching biological sequences. J Mol Biol 162, 705-708 (1982).
    • (1982) J Mol Biol , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 37
    • 0034742452 scopus 로고    scopus 로고
    • Sequence alignment: An approximation law for the Zvalue with applications to databank scanning
    • Bacro, J. N. & Comet, J. P. Sequence alignment: An approximation law for the Zvalue with applications to databank scanning. Comput Chem 25, 401-410 (2001).
    • (2001) Comput Chem , vol.25 , pp. 401-410
    • Bacro, J.N.1    Comet, J.P.2
  • 38
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K. et al. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739 (2011).
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 39
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23, 254-267 (2006).
    • (2006) Mol Biol Evol , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 40
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar, R. C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 41
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen, T. C., Philippe, H. & Bryant, D. A simple and robust statistical test for detecting the presence of recombination. Genetics 172, 2665-2681 (2006).
    • (2006) Genetics , vol.172 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.