-
1
-
-
0003807468
-
-
(Garland Science, New York)
-
Janeway C (2005) Immunobiology (Garland Science, New York).
-
(2005)
Immunobiology
-
-
Janeway, C.1
-
2
-
-
65649122270
-
High-throughput sequencing of the zebrafish antibody repertoire
-
Weinstein JA, Jiang N, White RA, 3rd, Fisher DS, Quake SR (2009) High-throughput sequencing of the zebrafish antibody repertoire. Science 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
-
3
-
-
84866842507
-
Chromatin conformation governs T-cell receptor Jβ gene segment usage
-
Ndifon W, et al. (2012) Chromatin conformation governs T-cell receptor Jβ gene segment usage. Proc Natl Acad Sci USA 109(39):15865-15870.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.39
, pp. 15865-15870
-
-
Ndifon, W.1
-
4
-
-
84911404755
-
Tracking global changes induced in the CD4 T cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
-
Thomas N, et al. (2014) Tracking global changes induced in the CD4 T cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. Bioinformatics 30(22):3181-3188.
-
(2014)
Bioinformatics
, vol.30
, Issue.22
, pp. 3181-3188
-
-
Thomas, N.1
-
5
-
-
84866177970
-
Shaping of human germline IgH repertoires revealed by deep sequencing
-
Larimore K, McCormick MW, Robins HS, Greenberg PD (2012) Shaping of human germline IgH repertoires revealed by deep sequencing. J Immunol 189(6):3221-3230.
-
(2012)
J Immunol
, vol.189
, Issue.6
, pp. 3221-3230
-
-
Larimore, K.1
McCormick, M.W.2
Robins, H.S.3
Greenberg, P.D.4
-
6
-
-
79960100655
-
Deep sequencing of the human TCR and TCR repertoires suggests that TCR rearranges after and T cell commitment
-
Sherwood AM, et al. (2011) Deep sequencing of the human TCR and TCR repertoires suggests that TCR rearranges after and T cell commitment. Sci Transl Med 3(90):90ra61.
-
(2011)
Sci Transl Med
, vol.3
, Issue.90
, pp. 90ra61
-
-
Sherwood, A.M.1
-
7
-
-
77950541195
-
Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells
-
Robins HS, et al. (2009) Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 114(19):4099-4107.
-
(2009)
Blood
, vol.114
, Issue.19
, pp. 4099-4107
-
-
Robins, H.S.1
-
8
-
-
84899102474
-
Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing
-
Zvyagin IV, et al. (2014) Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing. Proc Natl Acad Sci USA 111(16):5980-5985.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.16
, pp. 5980-5985
-
-
Zvyagin, I.V.1
-
9
-
-
79955554975
-
Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
-
Warren RL, et al. (2011) Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res 21(5):790-797.
-
(2011)
Genome Res
, vol.21
, Issue.5
, pp. 790-797
-
-
Warren, R.L.1
-
10
-
-
77950376484
-
Maximum entropy models for antibody diversity
-
Mora T, Walczak AM, Bialek W, Callan CG, Jr (2010) Maximum entropy models for antibody diversity. Proc Natl Acad Sci USA 107(12):5405-5410.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.12
, pp. 5405-5410
-
-
Mora, T.1
Walczak, A.M.2
Bialek, W.3
Callan, C.G.4
-
11
-
-
84892161760
-
Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire
-
Zarnitsyna VI, Evavold BD, Schoettle LN, Blattman JN, Antia R (2013) Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire. Front Immunol 4:485.
-
(2013)
Front Immunol
, vol.4
, pp. 485
-
-
Zarnitsyna, V.I.1
Evavold, B.D.2
Schoettle, L.N.3
Blattman, J.N.4
Antia, R.5
-
12
-
-
77954621832
-
Stochastic competitive exclusion in the maintenance of the naïve T cell repertoire
-
Stirk ER, Lythe G, van den Berg HA, Molina-París C (2010) Stochastic competitive exclusion in the maintenance of the naïve T cell repertoire. J Theor Biol 265(3):396-410.
-
(2010)
J Theor Biol
, vol.265
, Issue.3
, pp. 396-410
-
-
Stirk, E.R.1
Lythe, G.2
Van Den-Berg, H.A.3
Molina-París, C.4
-
13
-
-
54249123081
-
Stochastic niche structure and diversity maintenance in the T cell repertoire
-
Stirk ER, Molina-París C, van den Berg HA (2008) Stochastic niche structure and diversity maintenance in the T cell repertoire. J Theor Biol 255(2):237-249.
-
(2008)
J Theor Biol
, vol.255
, Issue.2
, pp. 237-249
-
-
Stirk, E.R.1
Molina-París, C.2
Van Den-Berg, H.A.3
-
14
-
-
0035823691
-
Resource competition determines selection of B cell repertoires
-
de Boer RJ, Freitas AA, Perelson AS (2001) Resource competition determines selection of B cell repertoires. J Theor Biol 212(3):333-343.
-
(2001)
J Theor Biol
, vol.212
, Issue.3
, pp. 333-343
-
-
De Boer, R.J.1
Freitas, A.A.2
Perelson, A.S.3
-
15
-
-
84871833659
-
Quorum-sensing in CD4(+) T cell homeostasis: A hypothesis and a model
-
Almeida ARM, et al. (2012) Quorum-sensing in CD4(+) T cell homeostasis: A hypothesis and a model. Front Immunol 3:125.
-
(2012)
Front Immunol
, vol.3
, pp. 125
-
-
Almeida, A.R.M.1
-
16
-
-
84890389129
-
A mechanistic model for naive CD4 T cell homeostasis in healthy adults and children
-
Hapuarachchi T, Lewis J, Callard RE (2013) A mechanistic model for naive CD4 T cell homeostasis in healthy adults and children. Front Immunol 4:366.
-
(2013)
Front Immunol
, vol.4
, pp. 366
-
-
Hapuarachchi, T.1
Lewis, J.2
Callard, R.E.3
-
17
-
-
84859171784
-
Deterministic and stochastic naïve T cell population dynamics: Symmetric and asymmetric cell division
-
Reynolds J, Coles M, Lythe G, Molina-París C (2012) Deterministic and stochastic naïve T cell population dynamics: Symmetric and asymmetric cell division. Dyn Syst 27:75-103.
-
(2012)
Dyn Syst
, vol.27
, pp. 75-103
-
-
Reynolds, J.1
Coles, M.2
Lythe, G.3
Molina-París, C.4
-
18
-
-
0037438341
-
Cutting edge: Homeostatic proliferation of peripheral T lymphocytes is regulated by clonal competition
-
Troy AE, Shen H (2003) Cutting edge: Homeostatic proliferation of peripheral T lymphocytes is regulated by clonal competition. J Immunol 170:672-676.
-
(2003)
J Immunol
, vol.170
, pp. 672-676
-
-
Troy, A.E.1
Shen, H.2
-
20
-
-
0027934814
-
T cell repertoires and competitive exclusion
-
de Boer RJ, Perelson AS (1994) T cell repertoires and competitive exclusion. J Theor Biol 169(4):375-390.
-
(1994)
J Theor Biol
, vol.169
, Issue.4
, pp. 375-390
-
-
De Boer, R.J.1
Perelson, A.S.2
-
21
-
-
0029049941
-
The role of cellular competition in B cell survival and selection of B cell repertoires
-
Freitas AA, Rosado MM, Viale AC, Grandien A (1995) The role of cellular competition in B cell survival and selection of B cell repertoires. Eur J Immunol 25(6):1729-1738.
-
(1995)
Eur J Immunol
, vol.25
, Issue.6
, pp. 1729-1738
-
-
Freitas, A.A.1
Rosado, M.M.2
Viale, A.C.3
Grandien, A.4
-
22
-
-
67049167214
-
Quantifying the development of the peripheral naive CD4+ T-cell pool in humans
-
Bains I, Antia R, Callard R, Yates AJ (2009) Quantifying the development of the peripheral naive CD4+ T-cell pool in humans. Blood 113(22):5480-5487.
-
(2009)
Blood
, vol.113
, Issue.22
, pp. 5480-5487
-
-
Bains, I.1
Antia, R.2
Callard, R.3
Yates, A.J.4
-
23
-
-
84867095375
-
Statistical inference of the generation probability of T-cell receptors from sequence repertoires
-
Murugan A, Mora T, Walczak AM, Callan CG, Jr (2012) Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc Natl Acad Sci USA 109(40):16161-16166.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.40
, pp. 16161-16166
-
-
Murugan, A.1
Mora, T.2
Walczak, A.M.3
Callan, C.G.4
-
24
-
-
55949095006
-
How the thymus designs antigen-specific and self-tolerant T cell receptor sequences
-
Kosmrlj A, Jha AK, Huseby ES, Kardar M, Chakraborty AK (2008) How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc Natl Acad Sci USA 105(43):16671-16676.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.43
, pp. 16671-16676
-
-
Kosmrlj, A.1
Jha, A.K.2
Huseby, E.S.3
Kardar, M.4
Chakraborty, A.K.5
-
25
-
-
77952742298
-
Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection
-
Kosmrlj A, et al. (2010) Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465(7296):350-354.
-
(2010)
Nature
, vol.465
, Issue.7296
, pp. 350-354
-
-
Kosmrlj, A.1
-
26
-
-
0032005477
-
Counting antigen-specific CD8 T cells: A reevaluation of bystander activation during viral infection
-
Murali-Krishna K, et al. (1998) Counting antigen-specific CD8 T cells: A reevaluation of bystander activation during viral infection. Immunity 8(2):177-187.
-
(1998)
Immunity
, vol.8
, Issue.2
, pp. 177-187
-
-
Murali-Krishna, K.1
-
27
-
-
0036550559
-
Effector and memory T-cell differentiation: Implications for vaccine development
-
Kaech SM, Wherry EJ, Ahmed R (2002) Effector and memory T-cell differentiation: implications for vaccine development. Nat Rev Immunol 2(4):251-262.
-
(2002)
Nat Rev Immunol
, vol.2
, Issue.4
, pp. 251-262
-
-
Kaech, S.M.1
Wherry, E.J.2
Ahmed, R.3
-
28
-
-
84882279791
-
Principles of maximum entropy and maximum caliber in statistical physics
-
Pressé S, Ghosh K, Lee J, Dill KA (2013) Principles of maximum entropy and maximum caliber in statistical physics. Rev Mod Phys 85:1115-1141.
-
(2013)
Rev Mod Phys
, vol.85
, pp. 1115-1141
-
-
Pressé, S.1
Ghosh, K.2
Lee, J.3
Dill, K.A.4
-
29
-
-
84899751182
-
Dynamical maximum entropy approach to flocking
-
Cavagna A, et al. (2014) Dynamical maximum entropy approach to flocking. Phys Rev E Stat Nonlin Soft Matter Phys 89(4):042707.
-
(2014)
Phys Rev e Stat Nonlin Soft Matter Phys
, vol.89
, Issue.4
, pp. 042707
-
-
Cavagna, A.1
-
30
-
-
65549085067
-
Power-law distributions in empirical data
-
Clauset A, Shalizi CR, Newman MJ (2009) Power-law distributions in empirical data. SIAM Rev 51:661-703.
-
(2009)
SIAM Rev
, vol.51
, pp. 661-703
-
-
Clauset, A.1
Shalizi, C.R.2
Newman, M.J.3
-
31
-
-
84930802799
-
Assessing T cell clonal size distribution: A non-parametric approach
-
Bolkhovskaya OV, Zorin DY, Ivanchenko MV (2014) Assessing T cell clonal size distribution: A non-parametric approach. PLoS One 9(9):e108658.
-
(2014)
PLoS One
, vol.9
, Issue.9
, pp. e108658
-
-
Bolkhovskaya, O.V.1
Zorin, D.Y.2
Ivanchenko, M.V.3
-
32
-
-
0034332403
-
Interleukin-7 mediates the homeostasis of naïve and memory CD8 T cells in vivo
-
Schluns KS, Kieper WC, Jameson SC, Lefrançois L (2000) Interleukin-7 mediates the homeostasis of naïve and memory CD8 T cells in vivo. Nat Immunol 1(5):426-432.
-
(2000)
Nat Immunol
, vol.1
, Issue.5
, pp. 426-432
-
-
Schluns, K.S.1
Kieper, W.C.2
Jameson, S.C.3
Lefrançois, L.4
-
33
-
-
0035902513
-
IL-7 is critical for homeostatic proliferation and survival of naive T cells
-
Tan JT, et al. (2001) IL-7 is critical for homeostatic proliferation and survival of naive T cells. Proc Natl Acad Sci USA 98(15):8732-8737.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.15
, pp. 8732-8737
-
-
Tan, J.T.1
-
34
-
-
84876093634
-
Quantifying T lymphocyte turnover
-
de Boer RJ, Perelson AS (2013) Quantifying T lymphocyte turnover. J Theor Biol 327:45-87.
-
(2013)
J Theor Biol
, vol.327
, pp. 45-87
-
-
De Boer, R.J.1
Perelson, A.S.2
-
35
-
-
0037105615
-
TCR signals mediated by Src family kinases are essential for the survival of naive T cells
-
Seddon B, Zamoyska R (2002) TCR signals mediated by Src family kinases are essential for the survival of naive T cells. J Immunol 169(6):2997-3005.
-
(2002)
J Immunol
, vol.169
, Issue.6
, pp. 2997-3005
-
-
Seddon, B.1
Zamoyska, R.2
-
36
-
-
0030873556
-
Differential requirements for survival and proliferation of CD8 naïve or memory T cells
-
Tanchot C, Lemonnier FA, Pérarnau B, Freitas AA, Rocha B (1997) Differential requirements for survival and proliferation of CD8 naïve or memory T cells. Science 276(5321):2057-2062.
-
(1997)
Science
, vol.276
, Issue.5321
, pp. 2057-2062
-
-
Tanchot, C.1
Lemonnier, F.A.2
Pérarnau, B.3
Freitas, A.A.4
Rocha, B.5
-
37
-
-
2642714166
-
MHC class I is required for peripheral accumulation of CD8+ thymic emigrants
-
Nesić D, Vukmanović S (1998) MHC class I is required for peripheral accumulation of CD8+ thymic emigrants. J Immunol 160(8):3705-3712.
-
(1998)
J Immunol
, vol.160
, Issue.8
, pp. 3705-3712
-
-
Nesić, D.1
Vukmanović, S.2
-
38
-
-
84954496851
-
Sequence and primer independent stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding
-
dx.doi.org/10.1101/011411
-
Best K, Oakes T, Heather JM, Taylor JS, Chain B (2014) Sequence and primer independent stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding. bio Rxiv. Available at dx.doi.org/10.1101/011411.
-
(2014)
Bio Rxiv
-
-
Best, K.1
Oakes, T.2
Heather, J.M.3
Taylor, J.S.4
Chain, B.5
-
39
-
-
84882432416
-
Genetic measurement of memory B-cell recall using antibody repertoire sequencing
-
Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR (2013) Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci USA 110(33):13463-13468.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.33
, pp. 13463-13468
-
-
Vollmers, C.1
Sit, R.V.2
Weinstein, J.A.3
Dekker, C.L.4
Quake, S.R.5
-
40
-
-
84925284996
-
In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire
-
De Kosky BJ, et al. (2015) In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire. Nat Med 21(1):86-91.
-
(2015)
Nat Med
, vol.21
, Issue.1
, pp. 86-91
-
-
De Kosky, B.J.1
-
41
-
-
0031099956
-
Convergent multiplicative processes repelled from zero: Power laws and truncated power laws
-
Sornette D, Cont R (1997) Convergent multiplicative processes repelled from zero: Power laws and truncated power laws. Journal de Physique I, EDP Sciences 7(3):431-434.
-
(1997)
Journal de Physique I, EDP Sciences
, vol.7
, Issue.3
, pp. 431-434
-
-
Sornette, D.1
Cont, R.2
-
42
-
-
0032069506
-
Dynamical optimization theory of a diversified portfolio
-
Marsili M, Maslov S, Zhang YC (1998) Dynamical optimization theory of a diversified portfolio. Physica A 253:9.
-
(1998)
Physica A
, vol.253
, pp. 9
-
-
Marsili, M.1
Maslov, S.2
Zhang, Y.C.3
-
43
-
-
79960601554
-
A brief history of generative models for power law and lognormal distributions
-
Mitzenmacher M (2004) A brief history of generative models for power law and lognormal distributions. Internet Math 1:226-251.
-
(2004)
Internet Math
, vol.1
, pp. 226-251
-
-
Mitzenmacher, M.1
-
46
-
-
84945237305
-
The impact of environmental fluctuations on evolutionary fitness functions
-
Melbinger A, Vergassola M (2015) The impact of environmental fluctuations on evolutionary fitness functions. Scientific Reports 5:15211.
-
(2015)
Scientific Reports
, vol.5
, pp. 15211
-
-
Melbinger, A.1
Vergassola, M.2
-
47
-
-
77955608576
-
Individual histories and selection in heterogeneous populations
-
Leibler S, Kussell E (2010) Individual histories and selection in heterogeneous populations. Proc Natl Acad Sci USA 107(29):13183-13188.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.29
, pp. 13183-13188
-
-
Leibler, S.1
Kussell, E.2
-
48
-
-
77749254888
-
Fitness flux and ubiquity of adaptive evolution
-
Mustonen V, Lässig M (2010) Fitness flux and ubiquity of adaptive evolution. Proc Natl Acad Sci USA 107(9):4248-4253.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.9
, pp. 4248-4253
-
-
Mustonen, V.1
Lässig, M.2
-
49
-
-
84900506575
-
A model for the generation and transmission of variations in evolution
-
Rivoire O, Leibler S (2014) A model for the generation and transmission of variations in evolution. Proc Natl Acad Sci USA 111(19):E1940-E1949.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.19
, pp. E1940-E1949
-
-
Rivoire, O.1
Leibler, S.2
|