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Volumn 18, Issue 1, 2017, Pages

The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires

Author keywords

Immunology; Nonparametric methods; Repertoire sequencing

Indexed keywords

ANTIGENS; IMMUNE SYSTEM; IMMUNOLOGY;

EID: 85014633289     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-017-1556-5     Document Type: Article
Times cited : (38)

References (23)
  • 1
    • 0020534965 scopus 로고
    • Somatic generation of antibody diversity
    • Tonegawa S. Somatic generation of antibody diversity. Nature. 1983;302:575-81. Available from: https://www.ncbi.nlm.nih.gov/pubmed/?term=6300689.
    • (1983) Nature , vol.302 , pp. 575-581
    • Tonegawa, S.1
  • 2
    • 0023720148 scopus 로고
    • T-cell antigen receptor genes and T-cell recognition
    • Davis MM, Bjorkman PJ. T-cell antigen receptor genes and T-cell recognition. Nature. 1988;334:395-402.
    • (1988) Nature , vol.334 , pp. 395-402
    • Davis, M.M.1    Bjorkman, P.J.2
  • 3
    • 79953164038 scopus 로고    scopus 로고
    • Recombination centres and the orchestration of V(D)J recombination
    • [cited 2016 Aug 15]
    • Schatz DG, Ji Y. Recombination centres and the orchestration of V(D)J recombination. Nat. Rev. Immunol. [Internet]. 2011 [cited 2016 Aug 15];11:251-63. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21394103.
    • (2011) Nat. Rev. Immunol. [Internet]. , vol.11 , pp. 251-263
    • Schatz, D.G.1    Ji, Y.2
  • 5
    • 84947792008 scopus 로고    scopus 로고
    • Practical guidelines for B-cell receptor repertoire sequencing analysis
    • Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med. 2015;7:121. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4654805&tool=pmcentrez&rendertype=abstract.
    • (2015) Genome Med , vol.7 , pp. 121
    • Yaari, G.1    Kleinstein, S.H.2
  • 6
    • 84901459546 scopus 로고    scopus 로고
    • ImmPort: disseminating data to the public for the future of immunology
    • [cited 2016 Aug 15]
    • Bhattacharya S, Andorf S, Gomes L, Dunn P, Schaefer H, Pontius J, et al. ImmPort: disseminating data to the public for the future of immunology. Immunol. Res. [Internet]. 2014 [cited 2016 Aug 15];58:234-9. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24791905.
    • (2014) Immunol. Res. [Internet] , vol.58 , pp. 234-239
    • Bhattacharya, S.1    Andorf, S.2    Gomes, L.3    Dunn, P.4    Schaefer, H.5    Pontius, J.6
  • 7
    • 84990817455 scopus 로고    scopus 로고
    • VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
    • Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, et al. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics. 2016;17:333. Available from: http://dx.doi.org/10.1186/s12859-016-1214-3.
    • (2016) BMC Bioinformatics , vol.17 , pp. 333
    • Toby, I.T.1    Levin, M.K.2    Salinas, E.A.3    Christley, S.4    Bhattacharya, S.5    Breden, F.6
  • 8
    • 84946816385 scopus 로고    scopus 로고
    • Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data
    • [cited 2016 Aug 15]
    • Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics [Internet]. 2015 [cited 2016 Aug 15];31:3356-8. Available from: http://www.ncbi.nlm.nih.gov/pubmed/26069265.
    • (2015) Bioinformatics [Internet] , vol.31 , pp. 3356-3358
    • Gupta, N.T.1    Vander Heiden, J.A.2    Uduman, M.3    Gadala-Maria, D.4    Yaari, G.5    Kleinstein, S.H.6
  • 9
    • 84906835232 scopus 로고    scopus 로고
    • Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis
    • Wu YCB, James LK, Vander Heiden JA, Uduman M, Durham SR, Kleinstein SH, et al. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J Allergy Clin Immunol. 2014;134:604-12.
    • (2014) J Allergy Clin Immunol , vol.134 , pp. 604-612
    • Wu, Y.C.B.1    James, L.K.2    Vander Heiden, J.A.3    Uduman, M.4    Durham, S.R.5    Kleinstein, S.H.6
  • 10
    • 84905967681 scopus 로고    scopus 로고
    • B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes
    • Stern J, Yaari G, Vander Heiden J, Church G, Donahue W, Hintzen R, et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014;6:248ra107. Available from: https://www.ncbi.nlm.nih.gov/pubmed/?term=25100741.
    • (2014) Sci Transl Med , vol.6
    • Stern, J.1    Yaari, G.2    Vander Heiden, J.3    Church, G.4    Donahue, W.5    Hintzen, R.6
  • 11
    • 84856521514 scopus 로고    scopus 로고
    • Dirichlet multinomial mixtures: generative models for microbial metagenomics
    • [cited 2016 Aug 15]
    • Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One [Internet]. 2012 [cited 2016 Aug 15];7:e30126. Available from: http://www.ncbi.nlm.nih.gov/pubmed/22319561.
    • (2012) PLoS One [Internet] , vol.7
    • Holmes, I.1    Harris, K.2    Quince, C.3
  • 12
    • 84876427223 scopus 로고    scopus 로고
    • phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
    • [cited 2016 Aug 15]
    • McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One [Internet]. 2013 [cited 2016 Aug 15];8:e61217. Available from: http://www.ncbi.nlm.nih.gov/pubmed/23630581
    • (2013) PLoS One [Internet] , vol.8
    • McMurdie, P.J.1    Holmes, S.2
  • 13
    • 84901363655 scopus 로고    scopus 로고
    • Waste not, want not: why rarefying microbiome data is inadmissible
    • [cited 2016 Aug 15]
    • McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol. [Internet]. 2014 [cited 2016 Aug 15];10:e1003531. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24699258.
    • (2014) PLoS Comput. Biol. [Internet]. , vol.10
    • McMurdie, P.J.1    Holmes, S.2
  • 14
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • [cited 2016 Aug 15]
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. [Internet]. BioMed Central; 2010 [cited 2016 Aug 15];11:R106. Available from: http://www.ncbi.nlm.nih.gov/pubmed/20979621.
    • (2010) Genome Biol. [Internet]. BioMed Central , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 15
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Oxford University Press; [cited 2016 Aug 15]
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics [Internet]. Oxford University Press; 2010 [cited 2016 Aug 15];26:139-40. Available from: http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btp616.
    • (2010) Bioinformatics [Internet]. , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 17
    • 84867834056 scopus 로고    scopus 로고
    • IMGT/HighV-QUEST: the IMGT web portal for immunoglobulin (Ig) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing
    • Alamyar E, Giudicelli V, Li S, Duroux P, Lefranc M-P. IMGT/HighV-QUEST: the IMGT web portal for immunoglobulin (Ig) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. 2012;8:26.
    • (2012) , vol.8 , pp. 26
    • Alamyar, E.1    Giudicelli, V.2    Li, S.3    Duroux, P.4    Lefranc, M-P.5
  • 18
    • 0037083612 scopus 로고    scopus 로고
    • Cutting edge: CD4 and CD8 T cells are intrinsically different in their proliferative responses
    • Foulds KE, Zenewicz L, Shedlock DJ, Jiang J, Troy AE, Shen H. Cutting edge: CD4 and CD8 T cells are intrinsically different in their proliferative responses. J Immunol. 2002;168:1528-32. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11823476.
    • (2002) J Immunol , vol.168 , pp. 1528-1532
    • Foulds, K.E.1    Zenewicz, L.2    Shedlock, D.J.3    Jiang, J.4    Troy, A.E.5    Shen, H.6
  • 19
    • 0033873474 scopus 로고    scopus 로고
    • Functional heterogeneity and high frequencies of cytomegalovirus-specific CD8(+) T lymphocytes in healthy seropositive donors
    • Gillespie GM, Wills MR, Appay V, O'Callaghan C, Murphy M, Smith N, et al. Functional heterogeneity and high frequencies of cytomegalovirus-specific CD8(+) T lymphocytes in healthy seropositive donors. J Virol. 2000;74:8140-50.
    • (2000) J Virol , vol.74 , pp. 8140-8150
    • Gillespie, G.M.1    Wills, M.R.2    Appay, V.3    O'Callaghan, C.4    Murphy, M.5    Smith, N.6
  • 20
    • 0037442113 scopus 로고    scopus 로고
    • Memory inflation: continuous accumulation of antiviral CD8+ T cells over time
    • Karrer U, Sierro S, Wagner M, Oxenius A, Hengel H, Koszinowski UH, et al. Memory inflation: continuous accumulation of antiviral CD8+ T cells over time. J Immunol. 2003;170:2022-9.
    • (2003) J Immunol , vol.170 , pp. 2022-2029
    • Karrer, U.1    Sierro, S.2    Wagner, M.3    Oxenius, A.4    Hengel, H.5    Koszinowski, U.H.6
  • 21
    • 10344257508 scopus 로고    scopus 로고
    • Herpesvirus-Specific CD8 T Cell Immunity in Old Age: Cytomegalovirus Impairs the Response to a Coresident EBV Infection
    • Khan N, Hislop A, Gudgeon N, Cobbold M, Khanna R, Nayak L, et al. Herpesvirus-Specific CD8 T Cell Immunity in Old Age: Cytomegalovirus Impairs the Response to a Coresident EBV Infection. J Immunol. 2004;173:7481-9. Available from: http://www.jimmunol.org/content/173/12/7481.full.
    • (2004) J Immunol , vol.173 , pp. 7481-7489
    • Khan, N.1    Hislop, A.2    Gudgeon, N.3    Cobbold, M.4    Khanna, R.5    Nayak, L.6
  • 22
    • 84989906613 scopus 로고    scopus 로고
    • Cytomegalovirus Infection Leads to Development of High Frequencies of Cytotoxic Virus-Specific CD4+ T Cells Targeted to Vascular Endothelium
    • Kalejta RF, editor.
    • Pachnio A, Ciaurriz M, Begum J, Lal N, Zuo J, Beggs A, et al. Cytomegalovirus Infection Leads to Development of High Frequencies of Cytotoxic Virus-Specific CD4+ T Cells Targeted to Vascular Endothelium. Kalejta RF, editor. PLoS Pathog. [Internet]. Public Library of Science. 2016;12:e1005832. Available from: https://www.ncbi.nlm.nih.gov/pubmed/27606804.
    • (2016) PLoS Pathog. [Internet]. Public Library of Science. , vol.12
    • Pachnio, A.1    Ciaurriz, M.2    Begum, J.3    Lal, N.4    Zuo, J.5    Beggs, A.6
  • 23
    • 0030691757 scopus 로고    scopus 로고
    • Phenotypic and functional separation of memory and effector human CD8+ T cells
    • The Rockefeller University Press; [cited 2016 Aug 15]
    • Hamann D, Baars PA, Rep MH, Hooibrink B, Kerkhof-Garde SR, Klein MR, et al. Phenotypic and functional separation of memory and effector human CD8+ T cells. J. Exp. Med. [Internet]. The Rockefeller University Press; 1997 [cited 2016 Aug 15];186:1407-18. Available from: http://www.ncbi.nlm.nih.gov/pubmed/9348298.
    • (1997) J. Exp. Med. [Internet]. , vol.186 , pp. 1407-1418
    • Hamann, D.1    Baars, P.A.2    Rep, M.H.3    Hooibrink, B.4    Kerkhof-Garde, S.R.5    Klein, M.R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.