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Volumn 2015, Issue , 2015, Pages

Utilities for High-Throughput Analysis of B-Cell Clonal Lineages

Author keywords

[No Author keywords available]

Indexed keywords

NEUTRALIZING ANTIBODY;

EID: 84945320945     PISSN: 23148861     EISSN: 23147156     Source Type: Journal    
DOI: 10.1155/2015/323506     Document Type: Article
Times cited : (9)

References (32)
  • 2
    • 78651390679 scopus 로고    scopus 로고
    • Sequencing antibody repertoires
    • N. Fischer, "Sequencing antibody repertoires," mAbs, vol. 3, no. 1, pp. 17-20, 2011.
    • (2011) MAbs , vol.3 , Issue.1 , pp. 17-20
    • Fischer, N.1
  • 3
    • 84883187027 scopus 로고    scopus 로고
    • Broadly neutralizing antibodies and the search for an HIV-1 vaccine: The end of the beginning
    • P. D. Kwong, J. R. Mascola, and G. J. Nabel, "Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning," Nature Reviews Immunology, vol. 13, no. 9, pp. 693-701, 2013.
    • (2013) Nature Reviews Immunology , vol.13 , Issue.9 , pp. 693-701
    • Kwong, P.D.1    Mascola, J.R.2    Nabel, G.J.3
  • 4
    • 84865412764 scopus 로고    scopus 로고
    • Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution
    • R. Mehr, M. Sternberg-Simon, M. Michaeli, and Y. Pickman, "Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution," Immunology Letters, vol. 148, no. 1, pp. 11-22, 2012.
    • (2012) Immunology Letters , vol.148 , Issue.1 , pp. 11-22
    • Mehr, R.1    Sternberg-Simon, M.2    Michaeli, M.3    Pickman, Y.4
  • 5
    • 79953164038 scopus 로고    scopus 로고
    • Recombination centres and the orchestration of V(D)J recombination
    • D. G. Schatz and Y. Ji, "Recombination centres and the orchestration of V(D)J recombination," Nature Reviews Immunology, vol. 11, no. 4, pp. 251-263, 2011.
    • (2011) Nature Reviews Immunology , vol.11 , Issue.4 , pp. 251-263
    • Schatz, D.G.1    Ji, Y.2
  • 6
    • 3242888974 scopus 로고    scopus 로고
    • V(D)J recombination
    • D. G. Schatz, "V(D)J recombination," Immunological Reviews, vol. 200, no. 1, pp. 5-11, 2004.
    • (2004) Immunological Reviews , vol.200 , Issue.1 , pp. 5-11
    • Schatz, D.G.1
  • 8
    • 0030006070 scopus 로고    scopus 로고
    • Clonal selection and learning in the antibody system
    • K. Rajewsky, "Clonal selection and learning in the antibody system," Nature, vol. 381, no. 6585, pp. 751-758, 1996.
    • (1996) Nature , vol.381 , Issue.6585 , pp. 751-758
    • Rajewsky, K.1
  • 9
    • 77954601328 scopus 로고    scopus 로고
    • Measurement and clinical monitoring of human lymphocyte clonality by massively parallel V-D-J pyrosequencing
    • S. D. Boyd, E. L. Marshall, J. D. Merker et al., "Measurement and clinical monitoring of human lymphocyte clonality by massively parallel V-D-J pyrosequencing," Science Translational Medicine, vol. 1, no. 12, Article ID12ra23, 2009.
    • (2009) Science Translational Medicine , vol.1 , Issue.12
    • Boyd, S.D.1    Marshall, E.L.2    Merker, J.D.3
  • 10
    • 84867350002 scopus 로고    scopus 로고
    • IMGT tools for the nucleotide analysis of immunoglobulin (IG) and t cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IGmutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS
    • E. Alamyar, P. Duroux, M.-P. Lefranc, and V. Giudicelli, "IMGT tools for the nucleotide analysis of immunoglobulin (IG) and t cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IGmutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS,"Methods inMolecular Biology, vol. 882, pp. 569-604, 2012.
    • (2012) Methods InMolecular Biology , vol.882 , pp. 569-604
    • Alamyar, E.1    Duroux, P.2    Lefranc, M.-P.3    Giudicelli, V.4
  • 12
    • 84874095196 scopus 로고    scopus 로고
    • Age-related changes in human peripheral blood IGH repertoire following vaccination
    • Y.-C. Wu, D. Kipling, and D. K. Dunn-Walters, "Age-related changes in human peripheral blood IGH repertoire following vaccination," Frontiers in Immunology, vol. 3, article 193, 2012.
    • (2012) Frontiers in Immunology , vol.3
    • Wu, Y.-C.1    Kipling, D.2    Dunn-Walters, D.K.3
  • 13
    • 77957266497 scopus 로고    scopus 로고
    • Clusteringbased identification of clonally-related immunoglobulin gene sequence sets
    • Z. Chen, A. M. Collins, Y. Wang, and B. A. Gaëta, "Clusteringbased identification of clonally-related immunoglobulin gene sequence sets," Immunome Research, vol. 6, supplement 1, article S4, 2010.
    • (2010) Immunome Research , vol.6
    • Chen, Z.1    Collins, A.M.2    Wang, Y.3    Gaëta, B.A.4
  • 14
    • 34547840205 scopus 로고    scopus 로고
    • IHMMune-align: Hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
    • B. A. Gaëta, H. R. Malming, K. J. L. Jackson, M. E. Bain, P. Wilson, and A. M. Collins, "iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences," Bioinformatics, vol. 23, no. 13, pp. 1580-1587, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 1580-1587
    • Gaëta, B.A.1    Malming, H.R.2    Jackson, K.J.L.3    Bain, M.E.4    Wilson, P.5    Collins, A.M.6
  • 15
    • 84902532520 scopus 로고    scopus 로고
    • Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing
    • M. Giraud, M. Salson, M. Duez et al., "Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing," BMC Genomics, vol. 15, no. 1, article 409, 2014.
    • (2014) BMC Genomics , vol.15 , Issue.1
    • Giraud, M.1    Salson, M.2    Duez, M.3
  • 16
    • 85000360533 scopus 로고    scopus 로고
    • Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors
    • T. B. Kepler, "Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors," F1000Research, vol. 2, article 103, 2013.
    • (2013) F1000Research , vol.2
    • Kepler, T.B.1
  • 18
    • 0030034795 scopus 로고    scopus 로고
    • A Hidden Markov Model approach to variation among sites in rate of evolution
    • J. Felsenstein and G. A. Churchill, "A Hidden Markov Model approach to variation among sites in rate of evolution," Molecular Biology and Evolution, vol. 13, no. 1, pp. 93-104, 1996.
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.1 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 19
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Z. Yang, "PAML: a program package for phylogenetic analysis by maximum likelihood," Computer Applications in the Biosciences, vol. 13, no. 5, pp. 555-556, 1997.
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.5 , pp. 555-556
    • Yang, Z.1
  • 20
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: Hypothesis testing using phylogenies
    • S. L.K. Pond, S. D.W. Frost, and S.V. Muse, "HyPhy: hypothesis testing using phylogenies," Bioinformatics, vol. 21, no. 5, pp.676-679, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.5 , pp. 676-679
    • Pond, S.L.K.1    Frost, S.D.W.2    Muse, S.V.3
  • 21
    • 0037212339 scopus 로고    scopus 로고
    • IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains
    • M.-P. Lefranc, C. Pommié, M. Ruiz et al., "IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains," Developmental and Comparative Immunology, vol. 27, no. 1, pp. 55-77, 2003.
    • (2003) Developmental and Comparative Immunology , vol.27 , Issue.1 , pp. 55-77
    • Lefranc, M.-P.1    Pommié, C.2    Ruiz, M.3
  • 23
    • 0034608480 scopus 로고    scopus 로고
    • Receptor revision of immunoglobulin heavy chain variable region genes in normal human B lymphocytes
    • P.C. Wilson, K. Wilson, Y.-J. Liu, J. Banchereau, V. Pascual, and J. D. Capra, "Receptor revision of immunoglobulin heavy chain variable region genes in normal human B lymphocytes," The Journal of Experimental Medicine, vol. 191, no. 11, pp. 1881-1894, 2000.
    • (2000) The Journal of Experimental Medicine , vol.191 , Issue.11 , pp. 1881-1894
    • Wilson, P.C.1    Wilson, K.2    Liu, Y.-J.3    Banchereau, J.4    Pascual, V.5    Capra, J.D.6
  • 24
    • 84923657453 scopus 로고    scopus 로고
    • Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin v gene segment alleles
    • D. Gadala-Maria, G. Yaari, M. Uduman, and S. H. Kleinstein, "Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles," Proceedings of the National Academy of Sciences, vol. 112, no. 8, pp. E862-E870, 2015.
    • (2015) Proceedings of the National Academy of Sciences , vol.112 , Issue.8 , pp. E862-E870
    • Gadala-Maria, D.1    Yaari, G.2    Uduman, M.3    Kleinstein, S.H.4
  • 27
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: Accelerated for clustering the next-generation sequencing data
    • L. Fu, B. Niu, Z. Zhu, S. Wu, and W. Li, "CD-HIT: accelerated for clustering the next-generation sequencing data," Bioinformatics, vol. 28, no. 23, pp. 3150-3152, 2012.
    • (2012) Bioinformatics , vol.28 , Issue.23 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 28
    • 84899991983 scopus 로고    scopus 로고
    • Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies
    • N. A. Doria-Rose, C. A. Schramm, J. Gorman et al., "Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies," Nature, vol. 509, no. 7498, pp. 55-62, 2014.
    • (2014) Nature , vol.509 , Issue.7498 , pp. 55-62
    • Doria-Rose, N.A.1    Schramm, C.A.2    Gorman, J.3
  • 29
    • 2142698665 scopus 로고    scopus 로고
    • Human immunoglobulin selection associated with class switch and possible tolerogenic origins for C delta class-switched B cells
    • N.-Y. Zheng, K. Wilson, X. Wang et al., "Human immunoglobulin selection associated with class switch and possible tolerogenic origins for C delta class-switched B cells," The Journal of Clinical Investigation, vol. 113, pp. 1188-1201, 2004.
    • (2004) The Journal of Clinical Investigation , vol.113 , pp. 1188-1201
    • Zheng, N.-Y.1    Wilson, K.2    Wang, X.3
  • 31
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available Python tools for computational molecular biology and bioinformatics
    • P. J. A. Cock, T. Antao, J. T. Chang et al., "Biopython: freely available Python tools for computational molecular biology and bioinformatics," Bioinformatics, vol. 25, no. 11, pp. 1422-1423, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.11 , pp. 1422-1423
    • Cock, P.J.A.1    Antao, T.2    Chang, J.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.