메뉴 건너뛰기




Volumn 269, Issue 1, 2011, Pages 1-15

Model for comparative analysis of antigen receptor repertoires

Author keywords

Computational immunology; Lognormal distribution; Poisson abundance models; Species diversity estimation; T cell antigen receptors

Indexed keywords

IMMUNOGLOBULIN; LYMPHOCYTE ANTIGEN RECEPTOR; T LYMPHOCYTE RECEPTOR;

EID: 77958138360     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.10.001     Document Type: Article
Times cited : (28)

References (66)
  • 1
    • 0040647877 scopus 로고
    • The multivariate Poisson-log normal distribution
    • Aitchison J., Ho C. The multivariate Poisson-log normal distribution. Biometrika 1989, 76(4):643.
    • (1989) Biometrika , vol.76 , Issue.4 , pp. 643
    • Aitchison, J.1    Ho, C.2
  • 4
    • 57649205783 scopus 로고    scopus 로고
    • Bayesian estimation of the number of species using noninformative priors
    • Barger K., Bunge J. Bayesian estimation of the number of species using noninformative priors. Biometrical Journal 2008, 50(6):1064-1076.
    • (2008) Biometrical Journal , vol.50 , Issue.6 , pp. 1064-1076
    • Barger, K.1    Bunge, J.2
  • 6
    • 0022371455 scopus 로고
    • T-cell receptor beta-chain expression: dependence on relatively few variable region genes
    • Behlke M.A., Spinella D.G., Chou H.S., Sha W., Hartl D.L., Loh D.Y. T-cell receptor beta-chain expression: dependence on relatively few variable region genes. Science 1985, 229(4713):566-570.
    • (1985) Science , vol.229 , Issue.4713 , pp. 566-570
    • Behlke, M.A.1    Spinella, D.G.2    Chou, H.S.3    Sha, W.4    Hartl, D.L.5    Loh, D.Y.6
  • 7
    • 0015981751 scopus 로고
    • On fitting the Poisson lognormal distribution to species abundance data
    • Bulmer M. On fitting the Poisson lognormal distribution to species abundance data. Biometrics 1974, 30:101-110.
    • (1974) Biometrics , vol.30 , pp. 101-110
    • Bulmer, M.1
  • 8
    • 0032007065 scopus 로고    scopus 로고
    • Massive expansion of antigen-specific cd8+ t cells during an acute virus infection
    • Butz E.A., Bevan M.J. Massive expansion of antigen-specific cd8+ t cells during an acute virus infection. Immunity 1998, 8(2):167-175.
    • (1998) Immunity , vol.8 , Issue.2 , pp. 167-175
    • Butz, E.A.1    Bevan, M.J.2
  • 10
    • 28744439389 scopus 로고    scopus 로고
    • Species richness estimation
    • Wiley, New York, N. Balakrishnan, C. Read, B. Vidakovic (Eds.)
    • Chao A. Species richness estimation. Encyclopedia of Statistical Sciences 2006, Wiley, New York. N. Balakrishnan, C. Read, B. Vidakovic (Eds.).
    • (2006) Encyclopedia of Statistical Sciences
    • Chao, A.1
  • 11
    • 0344898137 scopus 로고    scopus 로고
    • Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample
    • Chao A., Shen T. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environmental and Ecological Statistics 2003, 10(4):429-443.
    • (2003) Environmental and Ecological Statistics , vol.10 , Issue.4 , pp. 429-443
    • Chao, A.1    Shen, T.2
  • 12
    • 0348223787 scopus 로고    scopus 로고
    • Conversion of peripheral cd4+cd25- naive t cells to cd4+cd25+ regulatory t cells by tgf-beta induction of transcription factor foxp3
    • Chen W., Jin W., Hardegen N., Lei K.-J., Li L., Marinos N., McGrady G., Wahl S.M. Conversion of peripheral cd4+cd25- naive t cells to cd4+cd25+ regulatory t cells by tgf-beta induction of transcription factor foxp3. Journal of Experimental Medicine 2003, 198(12):1875-1886.
    • (2003) Journal of Experimental Medicine , vol.198 , Issue.12 , pp. 1875-1886
    • Chen, W.1    Jin, W.2    Hardegen, N.3    Lei, K.-J.4    Li, L.5    Marinos, N.6    McGrady, G.7    Wahl, S.M.8
  • 13
    • 84947318637 scopus 로고
    • Locally weighted regression: an approach to regression analysis by local fitting
    • Cleveland W., Devlin S. Locally weighted regression: an approach to regression analysis by local fitting. Journal of the American Statistical Association 1988, 83(403):596-610.
    • (1988) Journal of the American Statistical Association , vol.83 , Issue.403 , pp. 596-610
    • Cleveland, W.1    Devlin, S.2
  • 14
    • 0142071148 scopus 로고    scopus 로고
    • New methods and software tools for high throughput cdr3 spectratyping. application to t lymphocyte repertoire modifications during experimental malaria
    • Collette A., Cazenave P.-A., Pied S., Six A. New methods and software tools for high throughput cdr3 spectratyping. application to t lymphocyte repertoire modifications during experimental malaria. Journal of Immunological Methods 2003, 278(1-2):105-116.
    • (2003) Journal of Immunological Methods , vol.278 , Issue.1-2 , pp. 105-116
    • Collette, A.1    Cazenave, P.-A.2    Pied, S.3    Six, A.4
  • 15
    • 0023720148 scopus 로고
    • T-cell antigen receptor genes and T-cell recognition
    • Davis M.M., Bjorkman P.J. T-cell antigen receptor genes and T-cell recognition. Nature 1988, 334(6181):395-402.
    • (1988) Nature , vol.334 , Issue.6181 , pp. 395-402
    • Davis, M.M.1    Bjorkman, P.J.2
  • 17
    • 0036084968 scopus 로고    scopus 로고
    • Analyzing spatial structure of communities using the two-dimensional Poisson lognormal species abundance model
    • Engen S., Lande R., Walla T., DeVries P. Analyzing spatial structure of communities using the two-dimensional Poisson lognormal species abundance model. The American Naturalist 2002, 160(1):60-73.
    • (2002) The American Naturalist , vol.160 , Issue.1 , pp. 60-73
    • Engen, S.1    Lande, R.2    Walla, T.3    DeVries, P.4
  • 19
    • 0002631876 scopus 로고
    • The relation between the number of species and the number of individuals in a random sample of an animal population
    • Fisher R.A., Corbet A.S., Williams C.B. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 1943, 12:42-58.
    • (1943) Journal of Animal Ecology , vol.12 , pp. 42-58
    • Fisher, R.A.1    Corbet, A.S.2    Williams, C.B.3
  • 20
    • 70349648171 scopus 로고    scopus 로고
    • Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
    • Freeman J.D., Warren R.L., Webb J.R., Nelson B.H., Holt R.A. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Research 2009, 19(10):1817-1824.
    • (2009) Genome Research , 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
  • 21
    • 67349197812 scopus 로고    scopus 로고
    • Confidence estimation via the parametric bootstrap in logistic joinpoint regression
    • Gill R., Rempala G., Czajkowski M. Confidence estimation via the parametric bootstrap in logistic joinpoint regression. Journal of Statistical Planning and Inference 2009, 139(9):3132-3141.
    • (2009) Journal of Statistical Planning and Inference , vol.139 , Issue.9 , pp. 3132-3141
    • Gill, R.1    Rempala, G.2    Czajkowski, M.3
  • 23
    • 0000803388 scopus 로고
    • The population frequencies of species and the estimation of population parameters
    • Good I. The population frequencies of species and the estimation of population parameters. Biometrika 1953, 40(3):237-264.
    • (1953) Biometrika , vol.40 , Issue.3 , pp. 237-264
    • Good, I.1
  • 25
    • 24644447794 scopus 로고    scopus 로고
    • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization
    • He M., Tomfohr J.K., Devlin B.H., Sarzotti M., Markert M.L., Kepler T.B. SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. Bioinformatics 2005, 21(18):3697-3699.
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3697-3699
    • He, M.1    Tomfohr, J.K.2    Devlin, B.H.3    Sarzotti, M.4    Markert, M.L.5    Kepler, T.B.6
  • 26
    • 84947396376 scopus 로고
    • A generalization of sampling without replacement from a finite universe
    • Horvitz D., Thompson D. A generalization of sampling without replacement from a finite universe. Journal of the American Statistical Association 1952, 47(260):663-685.
    • (1952) Journal of the American Statistical Association , vol.47 , Issue.260 , pp. 663-685
    • Horvitz, D.1    Thompson, D.2
  • 27
    • 4143066714 scopus 로고    scopus 로고
    • Recognition of the peripheral self by naturally arising cd25+ cd4+ t cell receptors
    • Hsieh C.-S., Liang Y., Tyznik A.J., Self S.G., Liggitt D., Rudensky A.Y. Recognition of the peripheral self by naturally arising cd25+ cd4+ t cell receptors. Immunity 2004, 21(2):267-277.
    • (2004) Immunity , vol.21 , Issue.2 , pp. 267-277
    • Hsieh, C.-S.1    Liang, Y.2    Tyznik, A.J.3    Self, S.G.4    Liggitt, D.5    Rudensky, A.Y.6
  • 28
    • 33645102841 scopus 로고    scopus 로고
    • An intersection between the self-reactive regulatory and nonregulatory t cell receptor repertoires
    • Hsieh C.-S., Zheng Y., Liang Y., Fontenot J.D., Rudensky A.Y. An intersection between the self-reactive regulatory and nonregulatory t cell receptor repertoires. Nature Immunology 2006, 7(4):401-410.
    • (2006) Nature Immunology , vol.7 , Issue.4 , pp. 401-410
    • Hsieh, C.-S.1    Zheng, Y.2    Liang, Y.3    Fontenot, J.D.4    Rudensky, A.Y.5
  • 30
    • 0037238291 scopus 로고    scopus 로고
    • An em algorithm for multivariate poisson distribution and related models
    • Karlis D. An em algorithm for multivariate poisson distribution and related models. Journal of Applied Statistics 2003, 30(1):63-77.
    • (2003) Journal of Applied Statistics , vol.30 , Issue.1 , pp. 63-77
    • Karlis, D.1
  • 34
    • 70349246628 scopus 로고    scopus 로고
    • Tcr repertoire and foxp3 expression define functionally distinct subsets of cd4+ regulatory t cells
    • Kuczma M., Pawlikowska I., Kopij M., Podolsky R., Rempala G.A., Kraj P. Tcr repertoire and foxp3 expression define functionally distinct subsets of cd4+ regulatory t cells. Journal of Immunology 2009, 183(5):3118-3129.
    • (2009) Journal of Immunology , vol.183 , Issue.5 , pp. 3118-3129
    • Kuczma, M.1    Pawlikowska, I.2    Kopij, M.3    Podolsky, R.4    Rempala, G.A.5    Kraj, P.6
  • 35
    • 70349310112 scopus 로고    scopus 로고
    • Foxp3-deficient regulatory t cells do not revert into conventional effector cd4+ t cells but constitute a unique cell subset
    • Kuczma M., Podolsky R., Garge N., Daniely D., Pacholczyk R., Ignatowicz L., Kraj P. Foxp3-deficient regulatory t cells do not revert into conventional effector cd4+ t cells but constitute a unique cell subset. Journal of Immunology 2009, 183(6):3731-3741.
    • (2009) Journal of Immunology , vol.183 , Issue.6 , pp. 3731-3741
    • Kuczma, M.1    Podolsky, R.2    Garge, N.3    Daniely, D.4    Pacholczyk, R.5    Ignatowicz, L.6    Kraj, P.7
  • 37
    • 78650278598 scopus 로고    scopus 로고
    • Numerical ecology. In: Developments in Environmental Modelling, English edition (Trans. and revised from the second French (1984) edition). Elsevier Science B.V., Amsterdam.
    • Legendre, P., Legendre, L., 1998. Numerical ecology. In: Developments in Environmental Modelling, vol. 20, English edition (Trans. and revised from the second French (1984) edition). Elsevier Science B.V., Amsterdam.
    • (1998) , vol.20
    • Legendre, P.1    Legendre, L.2
  • 38
    • 0021618291 scopus 로고
    • Bayesian-estimation of the number of species
    • Lewins W., Joanes D. Bayesian-estimation of the number of species. Biometrics 1984, 40(2):323-328.
    • (1984) Biometrics , vol.40 , Issue.2 , pp. 323-328
    • Lewins, W.1    Joanes, D.2
  • 39
    • 38949112965 scopus 로고    scopus 로고
    • B-cell chronic lymphocytic leukemia-derived dendritic cells stimulate allogeneic t-cell response and express chemokines involved in t-cell migration
    • Luczynski W., Stasiak-Barmuta A., Piszcz J., Ilendo E., Kowalczuk O., Krawczuk-Rybak M. B-cell chronic lymphocytic leukemia-derived dendritic cells stimulate allogeneic t-cell response and express chemokines involved in t-cell migration. Neoplasma 2007, 54(6):527-535.
    • (2007) Neoplasma , vol.54 , Issue.6 , pp. 527-535
    • Luczynski, W.1    Stasiak-Barmuta, A.2    Piszcz, J.3    Ilendo, E.4    Kowalczuk, O.5    Krawczuk-Rybak, M.6
  • 40
    • 18244403533 scopus 로고    scopus 로고
    • Biological diversity
    • Magurran A.E. Biological diversity. Current Biology 2005, 15(4):R116-R118.
    • (2005) Current Biology , vol.15 , Issue.4
    • Magurran, A.E.1
  • 41
    • 0037446522 scopus 로고    scopus 로고
    • A fractal clonotype distribution in the cd8+ memory t cell repertoire could optimize potential for immune responses
    • Naumov Y.N., Naumova E.N., Hogan K.T., Selin L.K., Gorski J. A fractal clonotype distribution in the cd8+ memory t cell repertoire could optimize potential for immune responses. Journal of Immunology 2003, 170(8):3994-4001.
    • (2003) Journal of Immunology , vol.170 , Issue.8 , pp. 3994-4001
    • Naumov, Y.N.1    Naumova, E.N.2    Hogan, K.T.3    Selin, L.K.4    Gorski, J.5
  • 42
    • 0542364567 scopus 로고
    • Estimating the number of component processes of a superimposed process
    • Nayak T. Estimating the number of component processes of a superimposed process. Biometrika 1991, 78(1):75-81.
    • (1991) Biometrika , vol.78 , Issue.1 , pp. 75-81
    • Nayak, T.1
  • 44
  • 45
    • 33747099523 scopus 로고    scopus 로고
    • Origin and t cell receptor diversity of foxp3+cd4+cd25+ t cells
    • Pacholczyk R., Ignatowicz H., Kraj P., Ignatowicz L. Origin and t cell receptor diversity of foxp3+cd4+cd25+ t cells. Immunity 2006, 25(2):249-259.
    • (2006) Immunity , vol.25 , Issue.2 , pp. 249-259
    • Pacholczyk, R.1    Ignatowicz, H.2    Kraj, P.3    Ignatowicz, L.4
  • 46
    • 34548680545 scopus 로고    scopus 로고
    • Nonself-antigens are the cognate specificities of foxp3+ regulatory t cells
    • Pacholczyk R., Kern J., Singh N., Iwashima M., Kraj P., Ignatowicz L. Nonself-antigens are the cognate specificities of foxp3+ regulatory t cells. Immunity 2007, 27(3):493-504.
    • (2007) Immunity , vol.27 , Issue.3 , pp. 493-504
    • Pacholczyk, R.1    Kern, J.2    Singh, N.3    Iwashima, M.4    Kraj, P.5    Ignatowicz, L.6
  • 47
    • 1342324593 scopus 로고    scopus 로고
    • Very diverse cd8 t cell clonotypic responses after virus infections
    • Pewe L.L., Netland J.M., Heard S.B., Perlman S. Very diverse cd8 t cell clonotypic responses after virus infections. Journal of Immunology 2004, 172(5):3151-3156.
    • (2004) Journal of Immunology , vol.172 , Issue.5 , pp. 3151-3156
    • Pewe, L.L.1    Netland, J.M.2    Heard, S.B.3    Perlman, S.4
  • 49
    • 66849098142 scopus 로고    scopus 로고
    • Application of pharmacogenomics to vaccines
    • Poland G., Ovsyannikova I., Jacobson R. Application of pharmacogenomics to vaccines. Pharmacogenomics 2009, 10(5):837-852.
    • (2009) Pharmacogenomics , vol.10 , Issue.5 , pp. 837-852
    • Poland, G.1    Ovsyannikova, I.2    Jacobson, R.3
  • 50
    • 78650269336 scopus 로고    scopus 로고
    • R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
    • R Development Core Team 2009. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
    • (2009)
  • 52
    • 0035599651 scopus 로고    scopus 로고
    • Hierarchical Bayesian estimation for the number of species
    • Rodrigues J., Milan L., Leite J. Hierarchical Bayesian estimation for the number of species. Biometrical Journal 2001, 43(6):737-746.
    • (2001) Biometrical Journal , vol.43 , Issue.6 , pp. 737-746
    • Rodrigues, J.1    Milan, L.2    Leite, J.3
  • 53
    • 77649270288 scopus 로고    scopus 로고
    • Estimation of t-cell repertoire diversity and clonal size distribution by Poisson abundance models
    • Sepúlveda N., Paulino C.D., Carneiro J. Estimation of t-cell repertoire diversity and clonal size distribution by Poisson abundance models. Journal of Immunological Methods 2010, 353(1-2):124-137.
    • (2010) Journal of Immunological Methods , vol.353 , Issue.1-2 , pp. 124-137
    • Sepúlveda, N.1    Paulino, C.D.2    Carneiro, J.3
  • 55
    • 0001359490 scopus 로고
    • Equitability indices: dependence on the species count
    • Sheldon A. Equitability indices: dependence on the species count. Ecology 1969, 50(3):466-467.
    • (1969) Ecology , vol.50 , Issue.3 , pp. 466-467
    • Sheldon, A.1
  • 56
    • 21944456057 scopus 로고    scopus 로고
    • Modelling species-abundance frequencies and species-individual functions with the generalized inverse Gaussian-Poisson distribution
    • Sichel H. Modelling species-abundance frequencies and species-individual functions with the generalized inverse Gaussian-Poisson distribution. South African Statistical Journal 1997, 31(1):13-37.
    • (1997) South African Statistical Journal , vol.31 , Issue.1 , pp. 13-37
    • Sichel, H.1
  • 57
    • 0030301933 scopus 로고    scopus 로고
    • An estimator of species overlap using a modified beta-binomial model
    • Smith W., Solow A., Preston P. An estimator of species overlap using a modified beta-binomial model. Biometrics 1996, 52(4):1472-1477.
    • (1996) Biometrics , vol.52 , Issue.4 , pp. 1472-1477
    • Smith, W.1    Solow, A.2    Preston, P.3
  • 58
    • 0028140842 scopus 로고
    • On the Bayesian-estimation of the number of species in a community
    • Solow A. On the Bayesian-estimation of the number of species in a community. Ecology 1994, 75(7):2139-2142.
    • (1994) Ecology , vol.75 , Issue.7 , pp. 2139-2142
    • Solow, A.1
  • 61
    • 34548391942 scopus 로고    scopus 로고
    • Coverage-adjusted entropy estimation
    • Vu V.Q., Yu B., Kass R.E. Coverage-adjusted entropy estimation. Statistics in Medicine 2007, 26(21):4039-4060.
    • (2007) Statistics in Medicine , vol.26 , Issue.21 , pp. 4039-4060
    • Vu, V.Q.1    Yu, B.2    Kass, R.E.3
  • 63
    • 60149109931 scopus 로고    scopus 로고
    • Profiling model T-cell metagenomes with short reads
    • Warren R., Nelson B., Holt R. Profiling model T-cell metagenomes with short reads. Bioinformatics 2009, 25(4):458.
    • (2009) Bioinformatics , vol.25 , Issue.4 , pp. 458
    • Warren, R.1    Nelson, B.2    Holt, R.3
  • 64
    • 65649122270 scopus 로고    scopus 로고
    • High-throughput sequencing of the zebrafish antibody repertoire
    • Weinstein J.A., Jiang N., White R.A., Fisher D.S., Quake S.R. High-throughput sequencing of the zebrafish antibody repertoire. Science 2009, 324(5928):807-810.
    • (2009) Science , vol.324 , Issue.5928 , pp. 807-810
    • Weinstein, J.A.1    Jiang, N.2    White, R.A.3    Fisher, D.S.4    Quake, S.R.5
  • 65
    • 34548381245 scopus 로고    scopus 로고
    • Tcr-based lineage tracing: no evidence for conversion of conventional into regulatory t cells in response to a natural self-antigen in pancreatic islets
    • Wong J., Mathis D., Benoist C. Tcr-based lineage tracing: no evidence for conversion of conventional into regulatory t cells in response to a natural self-antigen in pancreatic islets. Journal of Experimental Medicine 2007, 204(9):2039-2045.
    • (2007) Journal of Experimental Medicine , vol.204 , Issue.9 , pp. 2039-2045
    • Wong, J.1    Mathis, D.2    Benoist, C.3
  • 66
    • 77956076669 scopus 로고    scopus 로고
    • Structural biology of the t-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling
    • Wucherpfennig K.W., Gagnon E., Call M.J., Huseby E.S., Call M.E. Structural biology of the t-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling. Cold Spring Harbor Perspectives in Biology 2010, 2(4):a005140.
    • (2010) Cold Spring Harbor Perspectives in Biology , vol.2 , Issue.4
    • Wucherpfennig, K.W.1    Gagnon, E.2    Call, M.J.3    Huseby, E.S.4    Call, M.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.