P. Moss and J. Bell, Sequence analysis of the human ?? T-cell receptor CDR3 region, Immunogenetics, vol.173, issue.1, pp.10-18, 1995.
DOI : 10.1007/BF00164982

P. Moss and J. Bell, Comparative sequence analysis of the human T cell receptor TCRA and TCRB CDR3 regions, Human Immunology, vol.48, issue.1-2, pp.32-40, 1996.
DOI : 10.1016/0198-8859(96)00084-5

C. Pannetier, S. Delassus, S. Darche, C. Saucier, and P. Kourilsky, Quantitative titration of nucleic acids by enzymatic amplification reactions run to saturation, Nucleic Acids Research, vol.21, issue.3, pp.577-83, 1993.
DOI : 10.1093/nar/21.3.577

B. Manfras, W. Rudert, M. Trucco, and O. Boehm, Analysis of the ?? T-cell receptor repertoire by competitive and quantitative family-specific PCR with exogenous standards and high resolution fluorescence based CDR3 size imaging, J Immunol Methods, vol.21097, pp.235-284, 1997.

A. Vanderborght, A. Van-der-aa, P. Geusens, C. Vandevyver, J. Raus et al., Identification of overrepresented T cell receptor genes in blood and tissue biopsies by PCR-ELISA, Journal of Immunological Methods, vol.223, issue.1, pp.47-61, 1999.
DOI : 10.1016/S0022-1759(98)00201-4

A. Lim, V. Baron, L. Ferradini, M. Bonneville, P. Kourilsky et al., Combination of MHC???peptide multimer-based T cell sorting with the Immunoscope permits sensitive ex vivo quantitation and follow-up of human CD8+ T cell immune responses, Journal of Immunological Methods, vol.261, issue.1-2, pp.177-94, 2002.
DOI : 10.1016/S0022-1759(02)00004-2

A. Casrouge, E. Beaudoing, S. Dalle, C. Pannetier, J. Kanellopoulos et al., Size Estimate of the ???? TCR Repertoire of Naive Mouse Splenocytes, The Journal of Immunology, vol.164, issue.11, pp.5782-5789, 2000.
DOI : 10.4049/jimmunol.164.11.5782

A. Gallard, G. Foucras, C. Coureau, and J. Guery, Tracking T cell clonotypes in complex T lymphocyte populations by real-time quantitative PCR using fluorogenic complementarity-determining region-3-specific probes, Journal of Immunological Methods, vol.270, issue.2, pp.269-80, 2002.
DOI : 10.1016/S0022-1759(02)00336-8

D. Liu, J. Callahan, and P. Dau, Intrafamily fragment analysis of the T cell receptor ?? chain CDR3 region, Journal of Immunological Methods, vol.187, issue.1, pp.139-5010, 1995.
DOI : 10.1016/0022-1759(95)00178-D

E. Mugnaini, T. Egeland, A. Syversen, A. Spurkland, and J. Brinchmann, Molecular analysis of the complementarity determining region 3 of the human T cell receptor ?? chain. Establishment of a reference panel of CDR3 lengths from phytohaemagglutinin activated lymphocytes, Journal of Immunological Methods, vol.223, issue.2, pp.207-223, 1999.
DOI : 10.1016/S0022-1759(99)00004-6

T. Matsutani, T. Yoshioka, Y. Tsuruta, S. Iwagami, and R. Suzuki, Analysis of TCRAV and TCRBV Repertoires in Healthy Individuals by Microplate Hybridization Assay, Human Immunology, vol.56, issue.1-2, pp.57-69, 1997.
DOI : 10.1016/S0198-8859(97)00102-X

T. Matsutani, T. Yoshioka, Y. Tsuruta, S. Iwagami, T. Toyosaki-maeda et al., Restricted usage of T-cell receptor alpha-chain variable region (TCRAV) and T-cell receptor beta-chain variable region (TCRBV) repertoires after human allogeneic haematopoietic transplantation, British Journal of Haematology, vol.21, issue.4, pp.759-69, 2000.
DOI : 10.1016/S0022-1759(96)00221-9

R. Yoshida, T. Yoshioka, S. Yamane, T. Matsutani, T. Toyosaki-maeda et al., A new method for quantitative analysis of the mouse T-cell receptor V region repertoires: comparison of repertoires among strains, Immunogenetics, vol.52, issue.1-2, pp.35-4510, 1007.
DOI : 10.1007/s002510000248

G. Du, L. Qiu, L. Shen, P. Sehgal, Y. Shen et al., Combined megaplex TCR isolation and SMART-based real-time quantitation methods for quantitating antigen-specific T cell clones in mycobacterial infection, Journal of Immunological Methods, vol.308, issue.1-2, pp.19-35, 2006.
DOI : 10.1016/j.jim.2005.09.009

B. Ogle, M. Cascalho, J. C. Taylor, W. West, L. Platt et al., Direct measurement of lymphocyte receptor diversity, Nucleic Acids Research, vol.31, issue.22, 2003.
DOI : 10.1093/nar/gng139

C. Joao, B. Ogle, C. Gay-rabinstein, J. Platt, and M. Cascalho, B Cell-Dependent TCR Diversification, The Journal of Immunology, vol.172, issue.8, pp.4709-4725, 2004.
DOI : 10.4049/jimmunol.172.8.4709

C. Joao, Immunoglobulin is a highly diverse self-molecule that improves cellular diversity and function during immune reconstitution, Medical Hypotheses, vol.68, issue.1, pp.158-61, 2007.
DOI : 10.1016/j.mehy.2006.05.062

H. Bonarius, F. Baas, E. Remmerswaal, R. Van-lier, I. Ten-berge et al., Monitoring the T-Cell Receptor Repertoire at Single-Clone Resolution, PLoS ONE, vol.8, issue.1, 2006.
DOI : 10.1371/journal.pone.0000055.s007
URL : http://doi.org/10.1371/journal.pone.0000055

C. Pannetier, M. Cochet, S. Darche, A. Casrouge, M. Zöller et al., The sizes of the CDR3 hypervariable regions of the murine T-cell receptor beta chains vary as a function of the recombined germ-line segments., Proceedings of the National Academy of Sciences, vol.90, issue.9, pp.4319-4342, 1993.
DOI : 10.1073/pnas.90.9.4319

C. Pannetier, J. Even, and P. Kourilsky, T-cell repertoire diversity and clonal expansions in normal and clinical samples, Immunology Today, vol.16, issue.4, pp.176-8110, 1995.
DOI : 10.1016/0167-5699(95)80117-0

C. Pannetier, J. Levraud, A. Lim, J. Even, and P. Kourilsky, The immunoscope approach for the analysis of T-cell repertoires. In: Oksenberg J editor. The Human Antigen T Cell Receptor. Selected Protocols and Applications, pp.287-325, 1997.

M. Cochet, C. Pannetier, S. Darche, C. Leclerc, and P. Kourilsky, Molecular detection andin vivo analysis of the specific T cell response to a protein antigen, European Journal of Immunology, vol.79, issue.10, pp.2639-2686, 1992.
DOI : 10.1146/annurev.iy.09.040191.003525

A. Regnault, A. Cumano, P. Vassalli, D. Guy-grand, and P. Kourilsky, Oligoclonal repertoire of the CD8 alpha alpha and the CD8 alpha beta TCR-alpha/beta murine intestinal intraepithelial T lymphocytes: evidence for the random emergence of T cells, Journal of Experimental Medicine, vol.180, issue.4, pp.1345-58, 1994.
DOI : 10.1084/jem.180.4.1345

A. Regnault, J. Levraud, A. Lim, A. Six, C. Moreau et al., The expansion and selection of T cell receptor ???? intestinal intraepithelial T cell clones, European Journal of Immunology, vol.180, issue.4, pp.914-935, 1996.
DOI : 10.1002/eji.1830260429

H. Ema, A. Cumano, and P. Kourilsky, TCR? repertoire development in the mouse embryo, J Immunol, vol.159, pp.4227-4259, 1997.

T. Arstila, A. Casrouge, V. Baron, J. Even, J. Kanellopoulos et al., A Direct Estimate of the Human T Cell Receptor Diversity, Science, vol.286, issue.5441, pp.958-61, 1999.
DOI : 10.1126/science.286.5441.958

P. Bousso, F. Lemaître, D. Laouini, J. Kanellopoulos, and P. Kourilsky, The peripheral CD8 T cell repertoire is largely independent of the presence of intestinal flora, International Immunology, vol.12, issue.4, 2000.
DOI : 10.1093/intimm/12.4.425

T. Arstila and J. Even, D??veloppement et taille du r??pertoire T ???? humain., m??decine/sciences, vol.16, issue.11, pp.1257-60, 2000.
DOI : 10.4267/10608/1566

J. Cabaniols, N. Fazilleau, A. Casrouge, P. Kourilsky, and J. Kanellopoulos, Most ??/?? T Cell Receptor Diversity Is Due to Terminal Deoxynucleotidyl Transferase, The Journal of Experimental Medicine, vol.161, issue.9, 2001.
DOI : 10.1084/jem.192.12.1719
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2195970/pdf

N. Fazilleau, J. Cabaniols, F. Lemaitre, I. Motta, P. Kourilsky et al., V?? and V?? Public Repertoires Are Highly Conserved in Terminal Deoxynucleotidyl Transferase-Deficient Mice, The Journal of Immunology, vol.174, issue.1, pp.345-55, 2005.
DOI : 10.4049/jimmunol.174.1.345

R. Cibotti, J. Cabaniols, C. Pannetier, C. Delarbre, I. Vergnon et al., Public and private V beta T cell receptor repertoires against hen egg white lysozyme (HEL) in nontransgenic versus HEL transgenic mice, Journal of Experimental Medicine, vol.180, issue.3, pp.861-72, 1994.
DOI : 10.1084/jem.180.3.861
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2191659/pdf

L. Gapin, Y. Fukui, J. Kanellopoulos, T. Sano, A. Casrouge et al., Quantitative Analysis of the T Cell Repertoire Selected by a Single Peptide???Major Histocompatibility Complex, The Journal of Experimental Medicine, vol.8, issue.11, pp.1871-83, 1998.
DOI : 10.1016/S0065-2776(08)60630-6

C. Bouneaud, P. Kourilsky, and P. Bousso, Impact of Negative Selection on the T Cell Repertoire Reactive to a Self-Peptide, Immunity, vol.13, issue.6, pp.829-869, 2000.
DOI : 10.1016/S1074-7613(00)00080-7

Y. Fukui, T. Oono, J. Cabaniols, K. Nakao, K. Hirokawa et al., Diversity of T cell repertoire shaped by a single peptide ligand is critically affected by its amino acid residue at a T cell receptor contact, Proceedings of the National Academy of Sciences, vol.380, issue.6574, pp.13760-13765, 2000.
DOI : 10.1038/380495a0

P. Musette, J. Bureau, G. Gachelin, P. Kourilsky, and M. Brahic, T lymphocyte repertoire in Theiler's virus encephalomyelitis: the nonspecific infiltration of the central nervous system of infected SJL/J mice is associated with a selective local T cell expansion, European Journal of Immunology, vol.54, issue.6, pp.1589-93, 1995.
DOI : 10.1002/eji.1830250618

D. Sourdive, K. Murali-krishna, J. Altman, A. Zajac, J. Whitmire et al., Conserved T Cell Receptor Repertoire in Primary and Memory CD8 T Cell Responses to an Acute Viral Infection, The Journal of Experimental Medicine, vol.151, issue.1, pp.71-82, 1998.
DOI : 10.1073/pnas.93.9.4102

P. Musette, D. Bequet, C. Delarbre, G. Gachelin, P. Kourilsky et al., Expansion of a recurrent V beta 5.3+ T-cell population in newly diagnosed and untreated HLA-DR2 multiple sclerosis patients., Proceedings of the National Academy of Sciences, vol.93, issue.22, pp.12461-12467, 1996.
DOI : 10.1073/pnas.93.22.12461

N. Fazilleau, C. Delarasse, C. Sweenie, S. Anderton, S. Fillatreau et al., Persistence of autoreactive myelin oligodendrocyte glycoprotein (MOG)-specific T???cell repertoires in MOG-expressing mice, European Journal of Immunology, vol.31, issue.3, pp.533-576, 2006.
DOI : 10.1002/eji.200535021

P. Musette, H. Bachelez, B. Flageul, C. Delarbre, P. Kourilsky et al., Immune-mediated destruction of melanocytes in halo nevi is associated with the local expansion of a limited number of T cell clones, J Immunol, vol.162, pp.1789-94, 1999.

P. Douillard, C. Pannetier, R. Josien, S. Menoret, P. Kourilsky et al., Donor-specific blood transfusion-induced tolerance in adult rats with a dominant TCR-V? rearrangement in heart allografts, J Immunol, vol.157, pp.1250-60, 1996.

H. Pilch, H. Höhn, K. Freitag, C. Neukirch, A. Necker et al., Improved Assessment of T-Cell Receptor (TCR) VB Repertoire in Clinical Specimens: Combination of TCR-CDR3 Spectratyping with Flow Cytometry-Based TCR VB Frequency Analysis, Clinical and Vaccine Immunology, vol.9, issue.2, pp.257-66, 2002.
DOI : 10.1128/CDLI.9.2.257-266.2002

I. Messaoudi, J. Lemaoult, J. Guevara-patino, B. Metzner, and J. Nikolich-zugich, Age-related CD8 T Cell Clonal Expansions Constrict CD8 T Cell Repertoire and Have the Potential to Impair Immune Defense, The Journal of Experimental Medicine, vol.157, issue.10, pp.1347-58, 2004.
DOI : 10.4049/jimmunol.170.2.672
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211915

F. Hakim, S. Memon, R. Cepeda, E. Jones, C. Chow et al., Age-dependent incidence, time course, and consequences of thymic renewal in adults, Journal of Clinical Investigation, vol.115, issue.4, pp.930-939, 2005.
DOI : 10.1172/JCI200522492

I. Messaoudi, J. Warner, M. Fischer, B. Park, B. Hill et al., Delay of T cell senescence by caloric restriction in aged long-lived nonhuman primates, Proceedings of the National Academy of Sciences, vol.42, issue.1, pp.19448-53, 2006.
DOI : 10.2307/2531248

P. Boudinot, S. Boubekeur, and A. Benmansour, Rhabdovirus Infection Induces Public and Private T Cell Responses in Teleost Fish, The Journal of Immunology, vol.167, issue.11, pp.6202-6211, 2001.
DOI : 10.4049/jimmunol.167.11.6202

P. Boudinot, S. Boubekeur, and A. Benmansour, Primary Structure and Complementarity-Determining Region (CDR) 3 Spectratyping of Rainbow Trout TCR?? Transcripts Identify Ten V?? Families with V??6 Displaying Unusual CDR2 and Differently Spliced Forms, The Journal of Immunology, vol.169, issue.11, pp.6244-52, 2002.
DOI : 10.4049/jimmunol.169.11.6244

P. Boudinot, D. Bernard, S. Boubekeur, M. Thoulouze, M. Bremont et al., The glycoprotein of a fish rhabdovirus profiles the virus-specific T-cell repertoire in rainbow trout, Journal of General Virology, vol.85, issue.10, pp.3099-108, 2004.
DOI : 10.1099/vir.0.80135-0

S. Desravines and E. Hsu, Measuring CDR3 length variability in individuals during ontogeny, Journal of Immunological Methods, vol.168, issue.2, pp.219-244, 1994.
DOI : 10.1016/0022-1759(94)90058-2

J. Gorski, M. Yassai, X. Zhu, B. Kissella, C. Keever et al., Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 spectratyping, J Immunol, vol.152, pp.5109-5128, 1994.

K. Maslanka, T. Piatek, J. Gorski, and M. Yassai, Molecular analysis of T cell repertoires, Human Immunology, vol.44, issue.1, pp.28-34, 1995.
DOI : 10.1016/0198-8859(95)00056-A

C. Lue, Y. Mitani, M. Crew, J. George, L. Fink et al., An Automated Method for the Analysis of T-Cell Receptor Repertoires: Rapid RT-PCR Fragment Length Analysis of the T-Cell Receptor ?? Chain Complementarity-Determining Region 3, American Journal of Clinical Pathology, vol.111, issue.5, pp.683-90, 1999.
DOI : 10.1093/ajcp/111.5.683

K. Yamamoto, K. Masuko-hongo, A. Tanaka, M. Kurokawa, T. Hoeger et al., Establishment and application of a novel T cell clonality analysis using single-strand conformation polymorphism of T cell receptor messenger signals, Human Immunology, vol.48, issue.1-2, pp.23-31, 1996.
DOI : 10.1016/0198-8859(96)00080-8

S. Shiokawa, J. Nishimura, K. Ohshima, N. Uike, and K. Yamamoto, Establishment of a Novel B Cell Clonality Analysis Using Single-Strand Conformation Polymorphism of Immunoglobulin Light Chain Messenger Signals, The American Journal of Pathology, vol.153, issue.5, pp.1393-400, 1998.
DOI : 10.1016/S0002-9440(10)65726-4

F. Raaphorst, E. Gokmen, and J. Teale, Analysis of clonal diversity in mouse immunoglobulin heavy chain genes selected for size of the antigen combining site, Immunological Investigations, vol.178, issue.6, pp.355-65, 1998.
DOI : 10.1084/jem.178.3.951

A. Sottini, Q. Roldan, E. Albertini, A. Primi, D. Imberti et al., Assessment of T-Cell receptor ??-chain diversity by heteroduplex analysis, Human Immunology, vol.48, issue.1-2, pp.12-22, 1996.
DOI : 10.1016/0198-8859(96)00087-0

A. Wack, D. Montagna, P. Dellabona, and G. Casorati, An improved PCR-heteroduplex method permits high-sensitivity detection of clonal expansions in complex T cell populations, Journal of Immunological Methods, vol.196, issue.2, pp.181-92, 1996.
DOI : 10.1016/0022-1759(96)00114-7

D. Shen, L. Doukhan, S. Kalam, and E. Delwart, High-resolution analysis of T-cell receptor ??-chain repertoires using DNA heteroduplex tracking: generally stable, clonal CD8+ expansions in all healthy young adults, Journal of Immunological Methods, vol.215, issue.1-2, pp.113-134, 1998.
DOI : 10.1016/S0022-1759(98)00066-0

L. Wedderburn, M. Maini, A. Patel, P. Beverley, and P. Woo, Molecular fingerprinting reveals non-overlapping T cell oligoclonality between an inflamed site and peripheral blood, International Immunology, vol.11, issue.4, pp.535-578, 1999.
DOI : 10.1093/intimm/11.4.535

P. Bouffard, C. Gagnon, D. Cloutier, S. Maclean, A. Souleimani et al., Analysis of T cell receptor ?? chain expression by isoelectric focusing following gene amplification and in vitro translation, Journal of Immunological Methods, vol.187, issue.1, pp.9-21, 1995.
DOI : 10.1016/0022-1759(95)00161-3

D. Sant-'angelo, B. Lucas, P. Waterbury, B. Cohen, T. Brabb et al., A molecular map of T cell development, Immunity, vol.9, issue.00, pp.179-86, 1998.

M. Correia-neves, C. Waltzinger, D. Mathis, and C. Benoist, The Shaping of the T Cell Repertoire, Immunity, vol.14, issue.1, pp.21-3210, 2001.
DOI : 10.1016/S1074-7613(01)00086-3

C. Hsieh, Y. Liang, A. Tyznik, S. Self, D. Liggitt et al., Recognition of the Peripheral Self by Naturally Arising CD25+ CD4+ T Cell Receptors, Immunity, vol.21, issue.2, pp.267-77, 2004.
DOI : 10.1016/j.immuni.2004.07.009

C. Hsieh, Y. Zheng, Y. Liang, J. Fontenot, and A. Rudensky, An intersection between the self-reactive regulatory and nonregulatory T cell receptor repertoires, Nature Immunology, vol.164, issue.4, pp.401-1010, 1038.
DOI : 10.4049/jimmunol.164.11.5782

R. Pacholczyk, H. Ignatowicz, P. Kraj, and L. Ignatowicz, Origin and T Cell Receptor Diversity of Foxp3+CD4+CD25+ T Cells, Immunity, vol.25, issue.2, pp.249-59, 2006.
DOI : 10.1016/j.immuni.2006.05.016

R. Pacholczyk, J. Kern, N. Singh, M. Iwashima, P. Kraj et al., Nonself-Antigens Are the Cognate Specificities of Foxp3+ Regulatory T Cells, Immunity, vol.27, issue.3, pp.493-504, 2007.
DOI : 10.1016/j.immuni.2007.07.019

J. Wong, R. Obst, M. Correia-neves, G. Losyev, D. Mathis et al., Adaptation of TCR Repertoires to Self-Peptides in Regulatory and Nonregulatory CD4+ T Cells, The Journal of Immunology, vol.178, issue.11, pp.7032-7073, 2007.
DOI : 10.4049/jimmunol.178.11.7032

J. Kang, M. Mohindru, B. Kang, S. Park, and B. Kim, Clonal Expansion of Infiltrating T Cells in the Spinal Cords of SJL/J Mice Infected with Theiler's Virus, The Journal of Immunology, vol.165, issue.1, pp.583-90, 2000.
DOI : 10.4049/jimmunol.165.1.583

I. Apostolou, A. Cumano, G. Gachelin, and P. Kourilsky, Evidence for Two Subgroups of CD4-CD8- NKT Cells with Distinct TCR???? Repertoires and Differential Distribution in Lymphoid Tissues, The Journal of Immunology, vol.165, issue.5, pp.2481-90, 2000.
DOI : 10.4049/jimmunol.165.5.2481

D. Bernard, A. Six, L. Rigottier-gois, S. Messiaen, S. Chilmonczyk et al., Phenotypic and Functional Similarity of Gut Intraepithelial and Systemic T Cells in a Teleost Fish, The Journal of Immunology, vol.176, issue.7, pp.3942-3951, 2006.
DOI : 10.4049/jimmunol.176.7.3942

S. Mancini, S. Candéias, H. Fehling, H. Von-boehmer, E. Jouvin-marche et al., TCR ?-chain repertoire in pT?-deficient mice is diverse and developmentally regulated: implications for pre-TCR functions and TCRA gene rearrangement, J Immunol, vol.163, pp.6053-6062, 1999.

E. Halapi, A. Werner, J. Wahlström, A. Österborg, M. Jeddi-tehrani et al., T cell repertoire in patients with multiple myeloma and monoclonal gammopathy of undetermined significance: Clonal CD8+ T cell expansions are found preferentially in patients with a low tumor burden, European Journal of Immunology, vol.1, issue.9, pp.2245-52, 1997.
DOI : 10.1111/j.1365-2141.1995.tb08902.x

P. Brawand, J. Cerottini, and H. Macdonald, Hierarchal utilization of different T-cell receptor V? gene segments in the CD8 + -T-cell response to an immunodominant Moloney leukemia virus-encoded epitope in vivo, J Virol, vol.73, pp.9161-9170, 1999.

G. Matsuzaki, H. Takada, and K. Nomoto, Escherichia coli infection induces only fetal thymus-derived ?? T cells at the infected site, 12<3877::AID- IMMU3877>3.3.CO, pp.3877-861521, 1999.
DOI : 10.1002/(sici)1521-4141(199912)29:12<3877::aid-immu3877>3.3.co;2-3

A. Collette, S. Bagot, M. Ferrandiz, P. Cazenave, A. Six et al., A Profound Alteration of Blood TCRB Repertoire Allows Prediction of Cerebral Malaria, The Journal of Immunology, vol.173, issue.7, pp.4568-75, 2004.
DOI : 10.4049/jimmunol.173.7.4568

D. Douek, M. Betts, J. Brenchley, B. Hill, D. Ambrozak et al., A Novel Approach to the Analysis of Specificity, Clonality, and Frequency of HIV-Specific T Cell Responses Reveals a Potential Mechanism for Control of Viral Escape, The Journal of Immunology, vol.168, issue.6, pp.3099-104, 2002.
DOI : 10.4049/jimmunol.168.6.3099

A. Lim, B. Lemercier, X. Wertz, S. Pottier, F. Huetz et al., Many human peripheral VH5-expressing IgM+ B cells display a unique heavy-chain rearrangement, International Immunology, vol.20, issue.1, pp.105-121, 2008.
DOI : 10.1093/intimm/dxm125
URL : https://hal.archives-ouvertes.fr/pasteur-00319682

K. Voelkerding, S. Dames, and J. Durtschi, Next-Generation Sequencing: From Basic Research to Diagnostics, Clinical Chemistry, vol.55, issue.4, pp.641-58112789, 2008.
DOI : 10.1373/clinchem.2008.112789

S. Mcginn and I. Gut, DNA sequencing ??? spanning the generations, New Biotechnology, vol.30, issue.4, pp.366-72, 2013.
DOI : 10.1016/j.nbt.2012.11.012

J. Weinstein, N. Jiang, R. White, . Iii, D. Fisher et al., High-Throughput Sequencing of the Zebrafish Antibody Repertoire, Science, vol.88, issue.3, pp.807-817, 2009.
DOI : 10.1146/annurev.es.05.110174.001441

H. Robins, P. Campregher, S. Srivastava, A. Wacher, C. Turtle et al., Comprehensive assessment of T-cell receptor ??-chain diversity in ???? T cells, Blood, vol.114, issue.19, pp.4099-107, 2009.
DOI : 10.1182/blood-2009-04-217604

J. Freeman, R. Warren, J. Webb, B. Nelson, and R. Holt, Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing, Genome Research, vol.19, issue.10, pp.1817-1841, 2009.
DOI : 10.1101/gr.092924.109
URL : http://genome.cshlp.org/content/19/10/1817.full.pdf

C. Wang, C. Sanders, Q. Yang, H. Schroeder, E. Wang et al., High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets, Proceedings of the National Academy of Sciences, vol.17, issue.8, pp.1518-1541, 2010.
DOI : 10.1101/gr.6468307

R. Warren, J. Freeman, T. Zeng, G. Choe, S. Munro et al., 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 Research, vol.21, issue.5, pp.790-797, 2011.
DOI : 10.1101/gr.115428.110

V. Venturi, M. Quigley, H. Greenaway, P. Ng, Z. Ende et al., A Mechanism for TCR Sharing between T Cell Subsets and Individuals Revealed by Pyrosequencing, The Journal of Immunology, vol.186, issue.7, pp.4285-94, 2011.
DOI : 10.4049/jimmunol.1003898

D. Wu, A. Sherwood, J. Fromm, S. Winter, K. Dunsmore et al., High-Throughput Sequencing Detects Minimal Residual Disease in Acute T Lymphoblastic Leukemia, Science Translational Medicine, vol.20, issue.suppl_1, 2012.
DOI : 10.1093/bioinformatics/bth945

L. Föhse, J. Suffner, K. Suhre, B. Wahl, C. Lindner et al., High TCR diversity ensures optimal function and homeostasis of Foxp3 + regulatory T cells

A. Sherwood, C. Desmarais, R. Livingston, J. Andriesen, M. Haussler et al., Deep sequencing of the human TCR? and TCR? repertoires suggests that TCR? rearranges after ?? and ?? T cell commitment, Sci Transl Med, 2011.

A. Cebula, M. Seweryn, G. Rempala, S. Pabla, R. Mcindoe et al., Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota, Nature, vol.1, issue.7448, pp.258-6210, 1038.
DOI : 10.1007/978-1-61737-979-6_3
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711137

R. Bashford-rogers, A. Palser, B. Huntly, R. Rance, G. Vassiliou et al., Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations, Genome Research, vol.23, issue.11, pp.1874-84, 2013.
DOI : 10.1101/gr.154815.113

S. Srivastava and H. Robins, Palindromic Nucleotide Analysis in Human T Cell Receptor Rearrangements, PLoS ONE, vol.20, issue.19, 2012.
DOI : 10.1371/journal.pone.0052250.s007
URL : http://doi.org/10.1371/journal.pone.0052250

A. Murugan, T. Mora, A. Walczak, and C. Callan, Statistical inference of the generation probability of T-cell receptors from sequence repertoires, Proceedings of the National Academy of Sciences, vol.20, issue.suppl_1, pp.16161-16167, 2012.
DOI : 10.1093/bioinformatics/bth945

W. Ndifon, H. Gal, E. Shifrut, R. Aharoni, N. Yissachar et al., Chromatin conformation governs T-cell receptor J?? gene segment usage, Proceedings of the National Academy of Sciences, vol.3, issue.11, pp.15865-70, 2012.
DOI : 10.1016/0893-6080(90)90029-K
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465372

H. Robins, S. Srivastava, P. Campregher, C. Turtle, J. Andriesen et al., Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire, Science Translational Medicine, vol.20, issue.suppl_1, 2010.
DOI : 10.1093/bioinformatics/bth945

P. Prabakaran, W. Chen, M. Singarayan, C. Stewart, E. Streaker et al., Expressed antibody repertoires in human cord blood cells: 454 sequencing and IMGT/HighV-QUEST analysis of germline gene usage, junctional diversity, and somatic mutations, Immunogenetics, vol.85, issue.Suppl 1, pp.337-50, 2012.
DOI : 10.1128/JVI.05312-11

J. Van-heijst, I. Ceberio, L. Lipuma, D. Samilo, G. Wasilewski et al., Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation, Nature Medicine, vol.8, issue.3, pp.372-73100, 2013.
DOI : 10.1128/AEM.01541-09

J. Meier, C. Roberts, K. Avent, A. Hazlett, J. Berrie et al., Fractal Organization of the Human T Cell Repertoire in Health and after Stem Cell Transplantation, Biology of Blood and Marrow Transplantation, vol.19, issue.3, pp.366-77, 2013.
DOI : 10.1016/j.bbmt.2012.12.004

A. Ademokun, Y. Wu, V. Martin, R. Mitra, U. Sack et al., Vaccination-induced changes in human B-cell repertoire and pneumococcal IgM and IgA antibody at different ages, Aging Cell, vol.116, issue.6, pp.922-952, 2011.
DOI : 10.1182/blood-2010-03-275859
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264704

P. Bousso, A. Casrouge, J. Altman, M. Haury, J. Kanellopoulos et al., Individual Variations in the Murine T Cell Response to a Specific Peptide Reflect Variability in Naive Repertoires, Immunity, vol.9, issue.2, pp.169-78, 1998.
DOI : 10.1016/S1074-7613(00)80599-3

M. Lin and R. Welsh, Stability and Diversity of ???T Cell Receptor Repertoire Usage during Lymphocytic Choriomeningitis Virus Infection of Mice, The Journal of Experimental Medicine, vol.71, issue.11, 1993.
DOI : 10.1073/pnas.84.7.1992

M. Metzker, Sequencing technologies ??? the next generation, Nature Reviews Genetics, vol.37, issue.1, pp.31-46, 2010.
DOI : 10.1016/j.tig.2007.12.006

M. Margulies, M. Egholm, W. Altman, S. Attiya, J. Bader et al., Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, pp.376-80, 2005.
DOI : 10.1016/0888-7543(88)90007-9
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464427

J. Rothberg, W. Hinz, T. Rearick, J. Schultz, W. Mileski et al., An integrated semiconductor device enabling non-optical genome sequencing, Nature, vol.32, issue.7, pp.348-5210, 1038.
DOI : 10.1002/humu.21382

D. Bolotin, I. Mamedov, O. Britanova, I. Zvyagin, D. Shagin et al., Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms, European Journal of Immunology, vol.107, issue.11, pp.3073-83, 2012.
DOI : 10.1073/pnas.0913939107

L. Bragg, G. Stone, M. Butler, P. Hugenholtz, and G. Tyson, Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data, PLoS Computational Biology, vol.6, issue.4, 2013.
DOI : 10.1371/journal.pcbi.1003031.s014

J. Shendure and E. Aiden, The expanding scope of DNA sequencing, Nature Biotechnology, vol.30, issue.11, 2012.
DOI : 10.1038/nature06293

P. Dash, J. Mcclaren, T. Oguin, . Iii, W. Rothwell et al., Paired analysis of TCR?? and TCR?? chains at the single-cell level in mice, Journal of Clinical Investigation, vol.121, issue.1, pp.288-95, 2011.
DOI : 10.1172/JCI44752DS1

B. Dekosky, G. Ippolito, R. Deschner, J. Lavinder, Y. Wine et al., High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire, Nature Biotechnology, vol.31, issue.2, pp.166-175, 2013.
DOI : 10.1093/nar/gkn316

M. Turchaninova, O. Britanova, D. Bolotin, M. Shugay, E. Putintseva et al., Pairing of T-cell receptor chains via emulsion PCR, European Journal of Immunology, vol.19, issue.9, pp.2507-2522, 2013.
DOI : 10.1101/gr.092759.109

C. Plessy, L. Desbois, T. Fujii, and P. Carninci, Population transcriptomics with single-cell resolution: A new field made possible by microfluidics, BioEssays, vol.9, issue.2, pp.131-171, 2013.
DOI : 10.1002/cbic.200700536
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583089

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, issue.1, pp.11-22, 2012.
DOI : 10.1016/j.imlet.2012.08.002

Z. Pancer, C. Amemiya, G. Ehrhardt, J. Ceitlin, G. Gartland et al., Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey, Nature, vol.147, issue.6996, pp.174-80, 2004.
DOI : 10.1093/bioinformatics/17.12.1244

M. Lefranc, V. Giudicelli, C. Ginestoux, J. Jabado-michaloud, G. Folch et al., IMGT(R), the international ImMunoGeneTics information system(R), Nucleic Acids Research, vol.37, issue.Database, pp.1006-1018, 2009.
DOI : 10.1093/nar/gkn838
URL : https://hal.archives-ouvertes.fr/hal-00357158

V. Giudicelli and M. Lefranc, IMGT-ONTOLOGY 2012, Frontiers in Genetics, vol.3, 2012.
DOI : 10.3389/fgene.2012.00079
URL : https://hal.archives-ouvertes.fr/hal-00723101

E. Alamyar, V. Giudicelli, S. Li, P. Duroux, and M. Lefranc, IMGT/HighV-QUEST: the IMGT(R) web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing, Immunome Res, vol.8, pp.26-36, 2012.

F. Watson, R. Puttmann-holgado, F. Thomas, D. Lamar, M. Hughes et al., Extensive Diversity of Ig-Superfamily Proteins in the Immune System of Insects, Science, vol.309, issue.5742, pp.1874-1882, 2005.
DOI : 10.1126/science.1116887

D. Pasquier and L. , IMMUNOLOGY: Insects Diversify One Molecule to Serve Two Systems, Science, vol.309, issue.5742, pp.1826-1833, 2005.
DOI : 10.1126/science.1118828

S. Zhang, C. Adema, T. Kepler, and E. Loker, Diversification of Ig Superfamily Genes in an Invertebrate, Science, vol.305, issue.5681, pp.251-255, 2004.
DOI : 10.1126/science.1088069

E. Philipp, L. Kraemer, F. Melzner, A. Poustka, S. Thieme et al., Massively Parallel RNA Sequencing Identifies a Complex Immune Gene Repertoire in the lophotrochozoan Mytilus edulis, PLoS ONE, vol.44, issue.3, 2012.
DOI : 10.1371/journal.pone.0033091.s014

N. Matsushima, T. Tanaka, P. Enkhbayar, T. Mikami, M. Taga et al., Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors, BMC Genomics, vol.8, issue.1, pp.124-134, 2007.
DOI : 10.1186/1471-2164-8-124

N. Matsushima, H. Miyashita, T. Mikami, and Y. Kuroki, A nested leucine rich repeat (LRR) domain: The precursor of LRRs is a ten or eleven residue motif, BMC Microbiology, vol.10, issue.1, pp.235-245, 2010.
DOI : 10.1186/1471-2180-10-235

Q. Kaas, F. Ehrenmann, M. Lefranc, . Ig, . Igsf et al., IG, TR and IgSF, MHC and MhcSF: what do we learn from the IMGT Colliers de Perles?, Briefings in Functional Genomics and Proteomics, vol.6, issue.4, pp.253-64, 2007.
DOI : 10.1093/bfgp/elm032
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.531.4515

C. Bomberger, M. Singh-jairam, G. Rodey, A. Guerriero, A. Yeager et al., Lymphoid reconstitution after autologous PBSC transplantation with FACS-sorted CD34+ hematopoietic progenitors, Blood, vol.91, pp.2588-600, 1998.

G. Gorochov, A. Neumann, A. Kereveur, C. Parizot, T. Li et al., Perturbation of CD4+ and CD8+ T-cell repertoires during progression to AIDS and regulation of the CD4+ repertoire during antiviral therapy, Nature Medicine, vol.83, issue.2, pp.215-2110, 1038.
DOI : 10.1038/373123a0

C. Wu, A. Chillemi, E. Alyea, E. Orsini, D. Neuberg et al., Reconstitution of T-cell receptor repertoire diversity following T-cell depleted allogeneic bone marrow transplantation is related to hematopoietic chimerism, Blood, vol.95, pp.352-361, 2000.

S. Hori, A. Collette, J. Demengeot, and J. Stewart, A new statistical method for quantitative analyses: application to the precise quantification of T cell receptor repertoires, Journal of Immunological Methods, vol.268, issue.2, pp.159-70, 2002.
DOI : 10.1016/S0022-1759(02)00187-4

A. Collette and A. Six, ISEApeaks: an Excel platform for GeneScan and Immunoscope data retrieval, management and analysis, Bioinformatics, vol.18, issue.2, 2002.
DOI : 10.1093/bioinformatics/18.2.329

M. Guillet, S. Brouard, K. Gagne, F. Sebille, M. Cuturi et al., Different Qualitative and Quantitative Regulation of V?? TCR Transcripts During Early Acute Allograft Rejection and Tolerance Induction, The Journal of Immunology, vol.168, issue.10, pp.5088-95, 2002.
DOI : 10.4049/jimmunol.168.10.5088

K. Peggs, S. Verfuerth, D. Sa, S. Yong, K. Mackinnon et al., Assessing diversity: immune reconstitution and T-cell receptor BV spectratype analysis following stem cell transplantation, British Journal of Haematology, vol.95, issue.1, pp.154-65, 2003.
DOI : 10.1046/j.1365-2141.2003.04036.x

S. Long, J. Khalili, J. Ashe, R. Berenson, C. Ferrand et al., Standardized analysis for the quantification of Vbeta CDR3 T-cell receptor diversity, J Immunol Methods, vol.317, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00473465

P. Miqueu, M. Guillet, N. Degauque, J. Dore, J. Soulillou et al., Statistical analysis of CDR3 length distributions for the assessment of T and B cell repertoire biases, Molecular Immunology, vol.44, issue.6, 2007.
DOI : 10.1016/j.molimm.2006.06.026

M. Guillet, F. Sebille, and J. Soulillou, TCR usage in naive and committed alloreactive cells: implications for the understanding of TCR biases in transplantation, Current Opinion in Immunology, vol.13, issue.5, pp.566-71, 2001.
DOI : 10.1016/S0952-7915(00)00260-0

A. Collette, P. Cazenave, S. Pied, and A. Six, New methods and software tools for high throughput CDR3 spectratyping. Application to T lymphocyte repertoire modifications during experimental malaria, Journal of Immunological Methods, vol.278, issue.1-2, pp.105-121, 2003.
DOI : 10.1016/S0022-1759(03)00225-4

A. Sassi, B. Largueche-darwaz, A. Collette, A. Six, D. Laouini et al., Mechanisms of the Natural Reactivity of Lymphocytes from Noninfected Individuals to Membrane-Associated Leishmania infantum Antigens, The Journal of Immunology, vol.174, issue.6, pp.3598-607, 2005.
DOI : 10.4049/jimmunol.174.6.3598
URL : https://hal.archives-ouvertes.fr/pasteur-00874327

R. Castro, F. Takizawa, W. Chaara, A. Lunazzi, T. Dang et al., Contrasted TCR?? Diversity of CD8+ and CD8??? T Cells in Rainbow Trout, PLoS ONE, vol.85, issue.4, 2013.
DOI : 10.1371/journal.pone.0060175.s002

T. Kepler, M. He, J. Tomfohr, B. Devlin, M. Sarzotti et al., Statistical analysis of antigen receptor spectratype data, Bioinformatics, vol.21, issue.16, pp.3394-400, 2005.
DOI : 10.1093/bioinformatics/bti539

M. He, J. Tomfohr, B. Devlin, M. Sarzotti, M. Markert et al., SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization, Bioinformatics, vol.21, issue.18, pp.3697-3706, 2005.
DOI : 10.1093/bioinformatics/bti600
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.4807

C. Liu, M. He, B. Rooney, T. Kepler, and N. Chao, Longitudinal Analysis of T-Cell Receptor Variable ?? Chain Repertoire in Patients with Acute Graft-versus-Host Disease after Allogeneic Stem Cell Transplantation, Biology of Blood and Marrow Transplantation, vol.12, issue.3, pp.335-380, 2006.
DOI : 10.1016/j.bbmt.2005.09.019

M. Lefranc, I. From, and . Classification, Axiom to IMGT standardized gene and allele nomenclature: for immunoglobulins (IG) and T cell receptors (TR), Cold Spring Harb Protoc, vol.2011, pp.627-659, 2011.
DOI : 10.1101/pdb.ip84
URL : https://hal.archives-ouvertes.fr/hal-00616556

M. Lefranc, From IMGT-ONTOLOGY DESCRIPTION Axiom to IMGT Standardized Labels: For Immunoglobulin (IG) and T Cell Receptor (TR) Sequences and Structures, Cold Spring Harbor Protocols, vol.2011, issue.6, pp.614-640, 2011.
DOI : 10.1101/pdb.ip83
URL : https://hal.archives-ouvertes.fr/hal-00616486

M. Lefranc, From IMGT-ONTOLOGY IDENTIFICATION Axiom to IMGT Standardized Keywords: For Immunoglobulins (IG), T Cell Receptors (TR), and Conventional Genes, Cold Spring Harbor Protocols, vol.2011, issue.6, pp.604-617, 2011.
DOI : 10.1101/pdb.ip82
URL : https://hal.archives-ouvertes.fr/hal-00616485

M. Lefranc, . Mh, and M. Igsf, IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, Cold Spring Harb Protoc, vol.2011, pp.633-675, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00616559

V. Giudicelli, D. Chaume, and M. Lefranc, IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis, Nucleic Acids Research, vol.32, issue.Web Server, pp.435-475, 2004.
DOI : 10.1093/nar/gkh412
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441550

X. Brochet, M. Lefranc, V. Giudicelli, and . Imgt-/-v-quest, IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis, Nucleic Acids Research, vol.36, issue.Web Server, pp.503-511, 2008.
DOI : 10.1093/nar/gkn316
URL : https://hal.archives-ouvertes.fr/hal-00322389

B. Gaëta, H. Malming, K. Jackson, M. Bain, P. Wilson et al., iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences, Bioinformatics, vol.23, issue.13, pp.1580-1587, 2007.
DOI : 10.1093/bioinformatics/btm147

T. Rogosch, S. Kerzel, K. Hoi, Z. Zhang, R. Maier et al., Immunoglobulin Analysis Tool: A Novel Tool for the Analysis of Human and Mouse Heavy and Light Chain Transcripts, Frontiers in Immunology, vol.3, 2012.
DOI : 10.3389/fimmu.2012.00176

J. Ye, N. Ma, T. Madden, and J. Ostell, IgBLAST: an immunoglobulin variable domain sequence analysis tool, Nucleic Acids Research, vol.41, issue.W1, pp.34-40, 2013.
DOI : 10.1093/nar/gkt382
URL : http://doi.org/10.1093/nar/gkt382

N. Thomas, J. Heather, W. Ndifon, J. Shawe-taylor, and B. Chain, Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine, Bioinformatics, vol.29, issue.5, pp.542-50, 2013.
DOI : 10.1093/bioinformatics/btt004

H. Pham, M. Manuel, N. Petit, D. Klatzmann, S. Cohen-kaminsky et al., Half of the T-cell repertoire combinatorial diversity is genetically determined in humans and humanized mice, European Journal of Immunology, vol.196, issue.3, pp.760-70, 2012.
DOI : 10.1084/jem.20021074

M. Eisenstein, Personalized, sequencing-based immune profiling spurs startups, Nature Biotechnology, vol.31, issue.3, pp.184-190, 2013.
DOI : 10.1038/nbt.2492

D. Stahl, S. Lacroix-desmazes, C. Barreau, W. Sibrowski, M. Kazatchkine et al., Altered antibody repertoires of plasma IgM and IgG toward nonself antigens in patients with warm autoimmune hemolytic anemia, Human Immunology, vol.62, issue.4, pp.348-61, 2001.
DOI : 10.1016/S0198-8859(01)00225-7

A. Magurran, Measuring Biological Diversity, 2004.

R. Colwell and . Estimates, Statistical Estimation of Species Richness and Shared Species from Samples. [Version 9]. User's Guide and application (2013) Available from

T. Wu and E. Kabat, AN ANALYSIS OF THE SEQUENCES OF THE VARIABLE REGIONS OF BENCE JONES PROTEINS AND MYELOMA LIGHT CHAINS AND THEIR IMPLICATIONS FOR ANTIBODY COMPLEMENTARITY, Journal of Experimental Medicine, vol.132, issue.2, 1970.
DOI : 10.1084/jem.132.2.211

R. Jores, P. Alzari, and T. Meo, Resolution of hypervariable regions in T-cell receptor beta chains by a modified Wu-Kabat index of amino acid diversity., Proceedings of the National Academy of Sciences, vol.87, issue.23, pp.9138-9180, 1990.
DOI : 10.1073/pnas.87.23.9138

J. Stewart, C. Lee, I. S. Watts, P. Shlomchik, M. Weigert et al., A Shannon entropy analysis of immunoglobulin and T cell receptor, Molecular Immunology, vol.34, issue.15, pp.1067-82, 1997.
DOI : 10.1016/S0161-5890(97)00130-2

P. Thomas, A. Handel, P. Doherty, L. Gruta, and N. , Ecological analysis of antigen-specific CTL repertoires defines the relationship between naive and immune T-cell populations, Proceedings of the National Academy of Sciences, vol.186, issue.7, pp.1839-1883, 2013.
DOI : 10.4049/jimmunol.1003898

S. Li, M. Lefranc, J. Miles, E. Alamyar, V. Giudicelli et al., IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling, Nature Communications, vol.175, 2013.
DOI : 10.1172/JCI28277
URL : https://hal.archives-ouvertes.fr/hal-00875260

J. Conrad, R. Ramalingam, C. Duncan, R. Smith, J. Wei et al., Antiretroviral therapy reduces the magnitude and T cell receptor repertoire Frontiers in Immunology | T Cell Biology 195. Perelson AS, Weisbuch G. Immunology for physicist, Rev Mod Phys, vol.69, pp.1219-67, 1997.

A. Perelson and G. Oster, Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination, Journal of Theoretical Biology, vol.81, issue.4, pp.645-70, 1979.
DOI : 10.1016/0022-5193(79)90275-3

J. Percus, O. Percus, and A. Perelson, Predicting the size of the T-cell receptor and antibody combining region from consideration of efficient self-nonself discrimination., Proceedings of the National Academy of Sciences, vol.90, issue.5, pp.1691-1696, 1993.
DOI : 10.1073/pnas.90.5.1691

C. Bergstrom and R. Antia, How do adaptive immune systems control pathogens while avoiding autoimmunity?, Trends in Ecology & Evolution, vol.21, issue.1, pp.22-30, 2006.
DOI : 10.1016/j.tree.2005.11.008

A. Perelson, MODELLING VIRAL AND IMMUNE SYSTEM DYNAMICS, Nature Reviews Immunology, vol.284, issue.1, pp.28-36, 2002.
DOI : 10.1006/bulm.1997.0035

R. Antia, V. Ganusov, and R. Ahmed, The role of models in understanding CD8+ T-cell memory, Nature Reviews Immunology, vol.4, issue.2, pp.101-112, 1550.
DOI : 10.1038/nri1355

V. Thomas-vaslin, A. Six, B. Bellier, D. Klatzmann, W. Dubitzky et al., Lymphocyte Dynamics and Repertoires, Modeling, Encyclopedia of Systems Biology, pp.1149-52, 2013.
DOI : 10.1007/978-1-4419-9863-7_96

D. Boer, R. Homann, D. Perelson, and A. , Different Dynamics of CD4+ and CD8+ T Cell Responses During and After Acute Lymphocytic Choriomeningitis Virus Infection, The Journal of Immunology, vol.171, issue.8, pp.3928-3963, 2003.
DOI : 10.4049/jimmunol.171.8.3928

L. Verkoczy, A. Martensson, and D. Nemazee, The scope of receptor editing and its association with autoimmunity, Current Opinion in Immunology, vol.16, issue.6, pp.808-822, 2004.
DOI : 10.1016/j.coi.2004.09.017

K. Wucherpfennig, P. Allen, F. Celada, I. Cohen, B. De et al., Polyspecificity of T cell and B cell receptor recognition, Seminars in Immunology, vol.19, issue.4, pp.216-240, 2007.
DOI : 10.1016/j.smim.2007.02.012

R. Germain, M. Meier-schellersheim, A. Nita-lazar, and I. Fraser, Systems Biology in Immunology: A Computational Modeling Perspective, Annual Review of Immunology, vol.29, issue.1, pp.527-85, 2011.
DOI : 10.1146/annurev-immunol-030409-101317

T. Emonet and G. Altan-bonnet, Systems immunology: a primer for biophysicists, Comprehensive Biophysics, pp.389-413, 2012.

M. Quigley, H. Greenaway, V. Venturi, R. Lindsay, K. Quinn et al., Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire, Proceedings of the National Academy of Sciences, vol.27, issue.1, pp.19414-19423, 2010.
DOI : 10.1093/nar/27.1.209

V. Martins, E. Ruggiero, S. Schlenner, V. Madan, M. Schmidt et al., Thymus-autonomous T cell development in the absence of progenitor import, The Journal of Experimental Medicine, vol.209, issue.8, pp.1409-1426, 2012.
DOI : 10.1038/23287

J. Farmer, N. Packard, and A. Perelson, The immune system, adaptation, and machine learning, Physica D: Nonlinear Phenomena, vol.22, issue.1-3, pp.187-204, 1986.
DOI : 10.1016/0167-2789(86)90240-X

D. Boer, R. Perelson, and A. , Size and connectivity as emergent properties of a developing immune network, Journal of Theoretical Biology, vol.149, issue.3, pp.381-42410, 1991.
DOI : 10.1016/S0022-5193(05)80313-3

F. Celada and P. Seiden, A computer model of cellular interactions in the immune system, Immunology Today, vol.13, issue.2, pp.56-62, 1992.
DOI : 10.1016/0167-5699(92)90135-T

B. Goldstein, J. Faeder, and W. Hlavacek, Mathematical and computational models of immune-receptor signalling, Nature Reviews Immunology, vol.91, issue.6, pp.445-56, 1374.
DOI : 10.1038/ni0303-217

A. Chao, R. Chazdon, R. Colwell, and T. Shen, A new statistical approach for assessing similarity of species composition with incidence and abundance data, Ecology Letters, vol.50, issue.2, pp.148-59, 2005.
DOI : 10.1111/j.1461-0248.2004.00707.x

A. Kosmrlj, A. Jha, E. Huseby, M. Kardar, and A. Chakraborty, How the thymus designs antigen-specific and self-tolerant T cell receptor sequences, Proceedings of the National Academy of Sciences, vol.1, issue.9, pp.16671-16677, 2008.
DOI : 10.1016/S1074-7613(94)80013-8
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575478

A. Kosmrlj, A. Chakraborty, M. Kardar, and E. Shakhnovich, Thymic Selection of T-Cell Receptors as an Extreme Value Problem, Physical Review Letters, vol.5, issue.6, 2009.
DOI : 10.1103/PhysRevLett.51.523

J. Verhagen, R. Genolet, G. Britton, B. Stevenson, C. Sabatos-peyton et al., CTLA-4 controls the thymic development of both conventional and regulatory T cells through modulation of the TCR repertoire, Proceedings of the National Academy of Sciences, vol.106, issue.9, pp.221-251, 2013.
DOI : 10.1073/pnas.0803186106

T. Mora, A. Walczak, W. Bialek, and C. Callan, Maximum entropy models for antibody diversity, Proceedings of the National Academy of Sciences, vol.62, issue.23, pp.5405-5415, 2010.
DOI : 10.1103/RevModPhys.62.251
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851784

P. Baum, V. Venturi, and D. Price, Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors, European Journal of Immunology, vol.4, issue.11, pp.2834-2843, 2012.
DOI : 10.1126/scitranslmed.3003656

H. Robins, C. Desmarais, J. Matthis, R. Livingston, J. Andriesen et al., Ultra-sensitive detection of rare T cell clones, Journal of Immunological Methods, vol.375, issue.1-2, 2012.
DOI : 10.1016/j.jim.2011.09.001

G. Zipf, Human Behaviour and the Principle of Least Effort: An Introduction to Human Ecology, 1949.

N. Sepulveda, C. Paulino, and J. Carneiro, Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models, Journal of Immunological Methods, vol.353, issue.1-2, pp.124-161, 2009.
DOI : 10.1016/j.jim.2009.11.009

G. Rempala, M. Seweryn, and L. Ignatowicz, Model for comparative analysis of antigen receptor repertoires, Journal of Theoretical Biology, vol.269, issue.1, pp.1-15, 2011.
DOI : 10.1016/j.jtbi.2010.10.001

R. Ben-hamo and S. Efroni, The whole-organism heavy chain B cell repertoire from Zebrafish self-organizes into distinct network features, BMC Systems Biology, vol.5, issue.1, pp.27-37, 2011.
DOI : 10.1093/nar/gkh435
URL : http://doi.org/10.1186/1752-0509-5-27

K. Bleakley, M. Lefranc, and G. Biau, Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools, BMC Bioinformatics, vol.9, issue.1, pp.408-418, 2008.
DOI : 10.1186/1471-2105-9-408
URL : https://hal.archives-ouvertes.fr/hal-00331710

S. Kleinstein, Y. Louzoun, and M. Shlomchik, Estimating Hypermutation Rates from Clonal Tree Data, The Journal of Immunology, vol.171, issue.9, pp.4639-4688, 2003.
DOI : 10.4049/jimmunol.171.9.4639

S. Anderson, A. Khalil, M. Uduman, U. Hershberg, Y. Louzoun et al., Taking Advantage: High-Affinity B Cells in the Germinal Center Have Lower Death Rates, but Similar Rates of Division, Compared to Low-Affinity Cells, The Journal of Immunology, vol.183, issue.11, pp.7314-7339, 2009.
DOI : 10.4049/jimmunol.0902452

M. Uduman, G. Yaari, U. Hershberg, J. Stern, M. Shlomchik et al., Detecting selection in immunoglobulin sequences, Nucleic Acids Research, vol.39, issue.suppl, pp.499-504, 2011.
DOI : 10.1093/nar/gkr413
URL : http://doi.org/10.1093/nar/gkr413

G. Yaari, M. Uduman, and S. Kleinstein, Quantifying selection in high-throughput Immunoglobulin sequencing data sets, Nucleic Acids Research, vol.40, issue.17, 2012.
DOI : 10.1093/nar/gks457
URL : http://doi.org/10.1093/nar/gks457

E. Rock, P. Sibbald, M. Davis, and Y. Chien, CDR3 length in antigen-specific immune receptors, Journal of Experimental Medicine, vol.179, issue.1, 1994.
DOI : 10.1084/jem.179.1.323
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2191339/pdf

G. Hyatt, R. Melamed, R. Park, R. Seguritan, C. Laplace et al., Gene expression microarrays: glimpses of the immunological genome, Nature Immunology, vol.3, issue.7, pp.686-91, 2006.
DOI : 10.4049/jimmunol.171.1.47

Q. Han, N. Bagheri, E. Bradshaw, D. Hafler, D. Lauffenburger et al., Polyfunctional responses by human T cells result from sequential release of cytokines, Proceedings of the National Academy of Sciences, vol.6, issue.7, pp.1607-1619, 2012.
DOI : 10.1038/msb.2010.90

S. Bendall, E. Simonds, P. Qiu, E. Amir, P. Krutzik et al., Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum, Science, vol.3, issue.5, pp.687-96, 2011.
DOI : 10.1038/nmeth872

E. Newell, N. Sigal, S. Bendall, G. Nolan, and M. Davis, Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes, Immunity, vol.36, issue.1, pp.142-52, 2012.
DOI : 10.1016/j.immuni.2012.01.002

K. Schepers, E. Swart, J. Van-heijst, C. Gerlach, M. Castrucci et al., Dissecting T cell lineage relationships by cellular barcoding, The Journal of Experimental Medicine, vol.161, issue.10, pp.2309-2327, 2008.
DOI : 10.1093/nar/30.4.e15
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556794

C. Sumen, T. Mempel, I. Mazo, and U. Von-andrian, Intravital Microscopy, Immunity, vol.21, issue.3, pp.315-344, 2004.
DOI : 10.1016/j.immuni.2004.08.006
URL : http://doi.org/10.1016/j.immuni.2004.08.006

F. Marangoni, T. Murooka, T. Manzo, E. Kim, E. Carrizosa et al., The Transcription Factor NFAT Exhibits Signal Memory during Serial T Cell Interactions with Antigen-Presenting Cells, Immunity, vol.38, issue.2, pp.237-286, 2013.
DOI : 10.1016/j.immuni.2012.09.012

L. Flatz, R. Roychoudhuri, M. Honda, A. Filali-mouhim, J. Goulet et al., Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines, Proceedings of the National Academy of Sciences, vol.458, issue.7239, pp.5724-5733, 2011.
DOI : 10.1038/nature07733
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078363

R. Mehr, Modeling and analysis of the meta-population dynamics of lymphocyte repertoires, Journal of Computational and Applied Mathematics, vol.184, issue.1, pp.223-264, 2005.
DOI : 10.1016/j.cam.2004.07.033

S. Ciupe, B. Devlin, M. Markert, and T. Kepler, The Dynamics of T-Cell Receptor Repertoire Diversity Following Thymus Transplantation for DiGeorge Anomaly, PLoS Computational Biology, vol.180, issue.6, 2009.
DOI : 10.1371/journal.pcbi.1000396.s001

E. Stirk, C. Molina-paris, and H. Van-den-berg, Stochastic niche structure and diversity maintenance in the T cell repertoire, Journal of Theoretical Biology, vol.255, issue.2, pp.237-286, 2008.
DOI : 10.1016/j.jtbi.2008.07.017

C. Benoist, R. Germain, and D. Mathis, A Plaidoyer for 'Systems Immunology', Immunological Reviews, vol.210, issue.1, pp.229-263, 2006.
DOI : 10.1111/j.0105-2896.2006.00374.x

I. Cohen, Autoantibody repertoires, natural biomarkers, and system controllers, Trends in Immunology, vol.34, issue.12, 2013.
DOI : 10.1016/j.it.2013.05.003

U. Petrausch, D. Haley, W. Miller, K. Floyd, W. Urba et al., Polychromatic flow cytometry: A rapid method for the reduction and analysis of complex multiparameter data, Cytometry Part A, vol.128, issue.12, pp.1162-73, 2006.
DOI : 10.1002/cyto.a.20114

M. Hofmann and H. Zerwes, Identification of organ-specific T cell populations by analysis of multiparameter flow cytometry data using DNA-chip analysis software, Cytometry Part A, vol.118, issue.6, pp.533-573, 2006.
DOI : 10.4049/jimmunol.166.7.4697

E. Lugli, M. Pinti, L. Troiano, M. Nasi, V. Patsekin et al., Subject classification obtained by cluster analysis and principal component analysis applied to flow cytometric data, Cytometry Part A, vol.26, issue.5, pp.334-378, 2007.
DOI : 10.4049/jimmunol.167.6.3231