-
1
-
-
84893831480
-
The promise and challenge of high-throughput sequencing of the antibody repertoire
-
G. Georgiou, G. C. Ippolito, J. Beausang, C. E. Busse, H. Wardemann, and S. R. Quake, "The promise and challenge of high-throughput sequencing of the antibody repertoire," Nature Biotechnology, vol. 32, no. 2, pp. 158-168, 2014.
-
(2014)
Nature Biotechnology
, vol.32
, Issue.2
, pp. 158-168
-
-
Georgiou, G.1
Ippolito, G.C.2
Beausang, J.3
Busse, C.E.4
Wardemann, H.5
Quake, S.R.6
-
2
-
-
78651390679
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
11
-
-
84874223925
-
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response
-
Y. Wine, D. R. Boutz, J. J. Lavinder et al., "Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 8, pp. 2993-2998, 2013.
-
(2013)
Proceedings of the National Academy of Sciences of the United States of America
, vol.110
, Issue.8
, pp. 2993-2998
-
-
Wine, Y.1
Boutz, D.R.2
Lavinder, J.J.3
-
12
-
-
84874095196
-
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
-
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
-
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
-
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
-
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
-
17
-
-
50949103123
-
IgTree: Creating immunoglobulin variable region gene lineage trees
-
M. Barak, N. S. Zuckerman, H. Edelman, R. Unger, and R. Mehr, "IgTree: creating immunoglobulin variable region gene lineage trees," Journal of Immunological Methods, vol. 338, no. 1-2, pp. 67-74, 2008.
-
(2008)
Journal of Immunological Methods
, vol.338
, Issue.1-2
, pp. 67-74
-
-
Barak, M.1
Zuckerman, N.S.2
Edelman, H.3
Unger, R.4
Mehr, R.5
-
18
-
-
0030034795
-
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
-
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
-
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
-
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
-
22
-
-
0036616218
-
The protein data bank
-
H.M. Berman, T. Battistuz, T. N. Bhat et al., "The protein data bank," Acta Crystallographica D: Biological Crystallography, vol. 58, no. 6, pp. 899-907, 2002.
-
(2002)
Acta Crystallographica D: Biological Crystallography
, vol.58
, Issue.6
, pp. 899-907
-
-
Berman, H.M.1
Battistuz, T.2
Bhat, T.N.3
-
23
-
-
0034608480
-
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
-
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
-
25
-
-
84876519306
-
Ultrafast approximation for phylogenetic bootstrap
-
B. Q. Minh, M. A. T. Nguyen, and A. von Haeseler, "Ultrafast approximation for phylogenetic bootstrap," Molecular Biology and Evolution, vol. 30, no. 5, pp. 1188-1195, 2013.
-
(2013)
Molecular Biology and Evolution
, vol.30
, Issue.5
, pp. 1188-1195
-
-
Minh, B.Q.1
Nguyen, M.A.T.2
Von Haeseler, A.3
-
26
-
-
79955109675
-
Determinism and stochasticity during maturation of the zebrafish antibody repertoire
-
N. Jiang, J. A. Weinstein, L. Penland, R. A. White, D. S. Fisherd, and S. R. Quake, "Determinism and stochasticity during maturation of the zebrafish antibody repertoire," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 13, pp. 5348-5353, 2011.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, Issue.13
, pp. 5348-5353
-
-
Jiang, N.1
Weinstein, J.A.2
Penland, L.3
White, R.A.4
Fisherd, D.S.5
Quake, S.R.6
-
27
-
-
84870431038
-
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
-
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
-
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
-
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
-
32
-
-
76749100709
-
ETE: A python environment for tree exploration
-
J. Huerta-Cepas, J. Dopazo, and T. Gabaldón, "ETE: a python environment for tree exploration," BMC Bioinformatics, vol. 11, article 24, 2010.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Huerta-Cepas, J.1
Dopazo, J.2
Gabaldón, T.3
|