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Volumn 17, Issue 1, 2016, Pages

VDJviz: A versatile browser for immunogenomics data

Author keywords

B cell; Browser; High throughput sequencing; Immunology; Repertoire sequencing; T cell

Indexed keywords

B LYMPHOCYTE; CLONAL VARIATION; COMPUTER PROGRAM; CONTAMINATION; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOLOGIST; IMMUNOLOGY; QUALITY CONTROL; T LYMPHOCYTE; VDJ RECOMBINATION; BIOLOGY; CLONAL EVOLUTION; CLUSTER ANALYSIS; COMPLEMENTARITY DETERMINING REGION; GENETICS; METABOLISM; PROCEDURES; SOFTWARE; STANDARDS; WEB BROWSER;

EID: 84978174533     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2799-7     Document Type: Article
Times cited : (25)

References (48)
  • 2
    • 0033711628 scopus 로고    scopus 로고
    • Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities
    • Xu JL, Davis MM. Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. Immunity. 2000;13(1):37-45.
    • (2000) Immunity , vol.13 , Issue.1 , pp. 37-45
    • Xu, J.L.1    Davis, M.M.2
  • 3
    • 84856185049 scopus 로고    scopus 로고
    • Rep-Seq: uncovering the immunological repertoire through next-generation sequencing
    • Benichou J, Ben-Hamo R, Louzoun Y, Efroni S. Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology. 2012;135(3):183-91.
    • (2012) Immunology , vol.135 , Issue.3 , pp. 183-191
    • Benichou, J.1    Ben-Hamo, R.2    Louzoun, Y.3    Efroni, S.4
  • 4
    • 0025908321 scopus 로고
    • Peripheral selection of the T cell repertoire
    • Rocha B, von Boehmer H. Peripheral selection of the T cell repertoire. Science. 1991;251(4998):1225-8.
    • (1991) Science , vol.251 , Issue.4998 , pp. 1225-1228
    • Rocha, B.1    Boehmer, H.2
  • 6
    • 1142274484 scopus 로고    scopus 로고
    • The many important facets of T-cell repertoire diversity
    • Nikolich-Zugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immunol. 2004;4(2):123-32.
    • (2004) Nat Rev Immunol , vol.4 , Issue.2 , pp. 123-132
    • Nikolich-Zugich, J.1    Slifka, M.K.2    Messaoudi, I.3
  • 8
    • 48449094247 scopus 로고    scopus 로고
    • IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
    • Brochet X, Lefranc MP, Giudicelli V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 2008;36(Web Server issue):W503-8.
    • (2008) Nucleic Acids Res , vol.36 , Issue.WEB SERVER ISSUE , pp. W503-W508
    • Brochet, X.1    Lefranc, M.P.2    Giudicelli, V.3
  • 10
    • 84874671063 scopus 로고    scopus 로고
    • Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
    • Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics. 2013.
    • (2013) Bioinformatics
    • Thomas, N.1    Heather, J.2    Ndifon, W.3    Shawe-Taylor, J.4    Chain, B.5
  • 11
    • 84883563447 scopus 로고    scopus 로고
    • IgBLAST: an immunoglobulin variable domain sequence analysis tool
    • Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013;41(Web Server issue):W34-40.
    • (2013) Nucleic Acids Res , vol.41 , Issue.WEB SERVER ISSUE , pp. W34-40
    • Ye, J.1    Ma, N.2    Madden, T.L.3    Ostell, J.M.4
  • 14
    • 84960475790 scopus 로고    scopus 로고
    • LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins
    • Yu Y, Ceredig R, Seoighe C. LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins. Nucleic Acids Res. 2016;44(4):e31.
    • (2016) Nucleic Acids Res , vol.44 , Issue.4
    • Yu, Y.1    Ceredig, R.2    Seoighe, C.3
  • 17
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
    • Nicol JW, Helt GA, Blanchard Jr SG, Raja A, Loraine AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics. 2009;25(20):2730-1.
    • (2009) Bioinformatics , vol.25 , Issue.20 , pp. 2730-2731
    • Nicol, J.W.1    Helt, G.A.2    Blanchard, S.G.3    Raja, A.4    Loraine, A.E.5
  • 18
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5    Kubal, M.6
  • 19
    • 84938890197 scopus 로고    scopus 로고
    • ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data
    • Schaller S, Weinberger J, Jimenez-Heredia R, Danzer M, Oberbauer R, Gabriel C, et al. ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data. BMC Bioinformatics. 2015;16:252.
    • (2015) BMC Bioinformatics , vol.16 , pp. 252
    • Schaller, S.1    Weinberger, J.2    Jimenez-Heredia, R.3    Danzer, M.4    Oberbauer, R.5    Gabriel, C.6
  • 20
    • 84890413048 scopus 로고    scopus 로고
    • The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis
    • Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, et al. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol. 2013;4:413.
    • (2013) Front Immunol , vol.4 , pp. 413
    • Six, A.1    Mariotti-Ferrandiz, M.E.2    Chaara, W.3    Magadan, S.4    Pham, H.P.5    Lefranc, M.P.6
  • 21
    • 84903741407 scopus 로고    scopus 로고
    • pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
    • Vander Heiden JA, Yaari G, Uduman M, Stern JN, O'Connor KC, Hafler DA, et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014;30(13):1930-2.
    • (2014) Bioinformatics , vol.30 , Issue.13 , pp. 1930-1932
    • Vander Heiden, J.A.1    Yaari, G.2    Uduman, M.3    Stern, J.N.4    O'Connor, K.C.5    Hafler, D.A.6
  • 22
    • 84862908094 scopus 로고    scopus 로고
    • Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages
    • Colwell RK, Chao A, Gotelli NJ, Lin S, Mao CX, Chazdon RL, et al. Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. J Plant Ecol. 2012;5(1):3-21.
    • (2012) J Plant Ecol , vol.5 , Issue.1 , pp. 3-21
    • Colwell, R.K.1    Chao, A.2    Gotelli, N.J.3    Lin, S.4    Mao, C.X.5    Chazdon, R.L.6
  • 23
    • 84902532520 scopus 로고    scopus 로고
    • Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing
    • Giraud M, Salson M, Duez M, Villenet C, Quief S, Caillault A, et al. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics. 2014;15:409.
    • (2014) BMC Genomics , vol.15 , pp. 409
    • Giraud, M.1    Salson, M.2    Duez, M.3    Villenet, C.4    Quief, S.5    Caillault, A.6
  • 26
    • 41149170727 scopus 로고    scopus 로고
    • Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus
    • Yager EJ, Ahmed M, Lanzer K, Randall TD, Woodland DL, Blackman MA. Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus. J Exp Med. 2008;205(3):711-23.
    • (2008) J Exp Med , vol.205 , Issue.3 , pp. 711-723
    • Yager, E.J.1    Ahmed, M.2    Lanzer, K.3    Randall, T.D.4    Woodland, D.L.5    Blackman, M.A.6
  • 27
    • 84867095375 scopus 로고    scopus 로고
    • Statistical inference of the generation probability of T-cell receptors from sequence repertoires
    • Murugan A, Mora T, Walczak AM, Callan Jr CG. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc Natl Acad Sci U S A. 2012;109(40):16161-6.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , Issue.40 , pp. 16161-16166
    • Murugan, A.1    Mora, T.2    Walczak, A.M.3    Callan, C.G.4
  • 29
    • 84907553718 scopus 로고    scopus 로고
    • T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
    • Madi A, Shifrut E, Reich-Zeliger S, Gal H, Best K, Ndifon W, et al. T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity. Genome Res. 2014;24(10):1603-12.
    • (2014) Genome Res , vol.24 , Issue.10 , pp. 1603-1612
    • Madi, A.1    Shifrut, E.2    Reich-Zeliger, S.3    Gal, H.4    Best, K.5    Ndifon, W.6
  • 31
    • 84962229430 scopus 로고    scopus 로고
    • Individual heritable differences result in unique cell lymphocyte receptor repertoires of naive and antigen-experienced cells
    • Rubelt F, Bolen CR, McGuire HM, Heiden JA, Gadala-Maria D, Levin M, et al. Individual heritable differences result in unique cell lymphocyte receptor repertoires of naive and antigen-experienced cells. Nat Commun. 2016;7:11112.
    • (2016) Nat Commun , vol.7 , pp. 11112
    • Rubelt, F.1    Bolen, C.R.2    McGuire, H.M.3    Heiden, J.A.4    Gadala-Maria, D.5    Levin, M.6
  • 34
    • 84896775850 scopus 로고    scopus 로고
    • T cell repertoire following autologous stem cell transplantation for multiple sclerosis
    • Muraro PA, Robins H, Malhotra S, Howell M, Phippard D, Desmarais C, et al. T cell repertoire following autologous stem cell transplantation for multiple sclerosis. J Clin Invest. 2014;124(3):1168-72.
    • (2014) J Clin Invest , vol.124 , Issue.3 , pp. 1168-1172
    • Muraro, P.A.1    Robins, H.2    Malhotra, S.3    Howell, M.4    Phippard, D.5    Desmarais, C.6
  • 36
    • 84931446384 scopus 로고    scopus 로고
    • Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers
    • Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, et al. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. J Immunol. 2015;194(12):6155-63.
    • (2015) J Immunol , vol.194 , Issue.12 , pp. 6155-6163
    • Egorov, E.S.1    Merzlyak, E.M.2    Shelenkov, A.A.3    Britanova, O.V.4    Sharonov, G.V.5    Staroverov, D.B.6
  • 39
    • 84861120541 scopus 로고    scopus 로고
    • High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia
    • Wu D, Sherwood A, Fromm JR, Winter SS, Dunsmore KP, Loh ML, et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci Transl Med. 2012;4(134):134ra163.
    • (2012) Sci Transl Med , vol.4 , Issue.134 , pp. 134ra163
    • Wu, D.1    Sherwood, A.2    Fromm, J.R.3    Winter, S.S.4    Dunsmore, K.P.5    Loh, M.L.6
  • 41
    • 70349648171 scopus 로고    scopus 로고
    • Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
    • Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009;19(10):1817-24.
    • (2009) Genome Res , vol.19 , Issue.10 , pp. 1817-1824
    • Freeman, J.D.1    Warren, R.L.2    Webb, J.R.3    Nelson, B.H.4    Holt, R.A.5
  • 42
    • 76549090763 scopus 로고    scopus 로고
    • High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets
    • Wang C, Sanders CM, Yang Q, Schroeder Jr HW, Wang E, Babrzadeh F, et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci U S A. 2010;107(4):1518-23.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.4 , pp. 1518-1523
    • Wang, C.1    Sanders, C.M.2    Yang, Q.3    Schroeder, H.W.4    Wang, E.5    Babrzadeh, F.6
  • 43
    • 84940865012 scopus 로고    scopus 로고
    • Characteristics of tumor infiltrating lymphocyte and circulating lymphocyte repertoires in pancreatic cancer by the sequencing of T cell receptors
    • Bai X, Zhang Q, Wu S, Zhang X, Wang M, He F, et al. Characteristics of tumor infiltrating lymphocyte and circulating lymphocyte repertoires in pancreatic cancer by the sequencing of T cell receptors. Scientific Reports. 2015;5:13664.
    • (2015) Scientific Reports , vol.5 , pp. 13664
    • Bai, X.1    Zhang, Q.2    Wu, S.3    Zhang, X.4    Wang, M.5    He, F.6
  • 46
  • 48
    • 84949192008 scopus 로고    scopus 로고
    • A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance
    • Feng Y, van der Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, et al. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature. 2015;528(7580):132-6.
    • (2015) Nature , vol.528 , Issue.7580 , pp. 132-136
    • Feng, Y.1    Veeken, J.2    Shugay, M.3    Putintseva, E.V.4    Osmanbeyoglu, H.U.5    Dikiy, S.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.