@article{bib1,
	author = {Akkaya, M and Kwak, K and Pierce, SK},
	journal = {Nature Reviews. Immunology},
	year = {2020},
	pages = {229--238},
	title = {B cell memory: building two walls of protection against pathogens},
	volume = {20},
}

@article{bib2,
	author = {Bashford-Rogers, RJM and Bergamaschi, L and McKinney, EF and Pombal, DC and Mescia, F and Lee, JC and Thomas, DC and Flint, SM and Kellam, P and Jayne, DRW and Lyons, PA and Smith, KGC},
	journal = {Nature},
	year = {2019},
	pages = {122--126},
	title = {Analysis of the {B} cell receptor repertoire in six immune-mediated diseases},
	volume = {574},
}

@article{bib3,
	author = {Bolotin, DA and Poslavsky, S and Mitrophanov, I and Shugay, M and Mamedov, IZ and Putintseva, EV and Chudakov, DM},
	journal = {Nature Methods},
	year = {2015},
	pages = {380--381},
	title = {MiXCR: software for comprehensive adaptive immunity profiling},
	volume = {12},
}

@article{bib4,
	author = {Bonsignori, M and Liao, HX and Gao, F and Williams, WB and Alam, SM and Montefiori, DC and Haynes, BF},
	journal = {Immunological Reviews},
	year = {2017},
	pages = {145--160},
	title = {Antibody-virus co-evolution in {HIV} infection: paths for {HIV} vaccine development},
	volume = {275},
}

@article{bib5,
	author = {Briney, B and Inderbitzin, A and Joyce, C and Burton, DR},
	journal = {Nature},
	year = {2019},
	pages = {393--397},
	title = {Commonality despite exceptional diversity in the baseline human antibody repertoire},
	volume = {566},
}

@article{bib6,
	author = {Chaudhary, N and Wesemann, DR},
	journal = {Frontiers in Immunology},
	year = {2018},
	title = {Analyzing immunoglobulin repertoires},
	volume = {9},
}

@article{bib7,
	author = {Davydov, AN and Obraztsova, AS and Lebedin, MY and Turchaninova, MA and Staroverov, DB and Merzlyak, EM and Sharonov, GV and Kladova, O and Shugay, M and Britanova, OV and Chudakov, DM},
	journal = {Frontiers in Immunology},
	year = {2018},
	title = {Comparative analysis of {B}-cell receptor repertoires induced by live yellow fever vaccine in young and middle-age donors},
	volume = {9},
}

@article{bib8,
	author = {de Bourcy, CFA and Angel, CJL and Vollmers, C and Dekker, CL and Davis, MM and Quake, SR},
	journal = {PNAS},
	year = {2017},
	pages = {1105--1110},
	title = {Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging},
	volume = {114},
}

@article{bib9,
	author = {De Silva, NS and Klein, U},
	journal = {Nature Reviews. Immunology},
	year = {2015},
	pages = {137--148},
	title = {Dynamics of {B} cells in germinal centres},
	volume = {15},
}

@article{bib10,
	author = {Edgar, RC},
	journal = {Nucleic Acids Research},
	year = {2004},
	pages = {1792--1797},
	title = {Muscle: multiple sequence alignment with high accuracy and high throughput},
	volume = {32},
}

@article{bib11,
	author = {Gadala-Maria, D and Yaari, G and Uduman, M and Kleinstein, SH},
	journal = {PNAS},
	year = {2015},
	title = {Automated analysis of high-throughput {B}-cell sequencing data reveals a high frequency of novel immunoglobulin {V} gene segment alleles},
	volume = {112},
}

@article{bib12,
	author = {Gaebler, C and Wang, Z and Lorenzi, JCC and Muecksch, F and Finkin, S and Tokuyama, M and Cho, A and Jankovic, M and Schaefer-Babajew, D and Oliveira, TY and Cipolla, M and Viant, C and Barnes, CO and Bram, Y and Breton, G and H{\" a}ggl{\" o}f, T and Mendoza, P and Hurley, A and Turroja, M and Gordon, K and Millard, KG and Ramos, V and Schmidt, F and Weisblum, Y and Jha, D and Tankelevich, M and Martinez-Delgado, G and Yee, J and Patel, R and Dizon, J and Unson-O\textquoteright{}Brien, C and Shimeliovich, I and Robbiani, DF and Zhao, Z and Gazumyan, A and Schwartz, RE and Hatziioannou, T and Bjorkman, PJ and Mehandru, S and Bieniasz, PD and Caskey, M and Nussenzweig, MC},
	journal = {Nature},
	year = {2021},
	pages = {639--644},
	title = {Evolution of antibody immunity to {SARS}-cov-2},
	volume = {591},
}

@article{bib13,
	author = {Galson, JD and Clutterbuck, EA and Tr{\" u}ck, J and Ramasamy, MN and M{\" u}nz, M and Fowler, A and Cerundolo, V and Pollard, AJ and Lunter, G and Kelly, DF},
	journal = {Immunology and Cell Biology},
	year = {2015},
	pages = {885--895},
	title = {Bcr repertoire sequencing: different patterns of {B}-cell activation after two meningococcal vaccines},
	volume = {93},
}

@article{bib14,
	author = {Garimalla, S and Nguyen, DC and Halliley, JL and Tipton, C and Rosenberg, AF and Fucile, CF and Saney, CL and Kyu, S and Kaminski, D and Qian, Y and Scheuermann, RH and Gibson, G and Sanz, I and Lee, FEH},
	journal = {JCI Insight},
	year = {2019},
	title = {Differential transcriptome and development of human peripheral plasma cell subsets},
	volume = {4},
}

@article{bib15,
	author = {Ghraichy, M and von Niederh{\" a}usern, V and Kovaltsuk, A and Galson, JD and Deane, CM and Tr{\" u}ck, J},
	journal = {eLife},
	year = {2021},
	title = {Different {B} cell subpopulations show distinct patterns in their {IgH} repertoire metrics},
	volume = {10},
}

@article{bib16,
	author = {Gidoni, M and Snir, O and Peres, A and Polak, P and Lindeman, I and Mikocziova, I and Sarna, VK and Lundin, KEA and Clouser, C and Vigneault, F and Collins, AM and Sollid, LM and Yaari, G},
	journal = {Nature Communications},
	year = {2019},
	title = {Mosaic deletion patterns of the human antibody heavy chain gene locus shown by {Bayesian} haplotyping},
	volume = {10},
}

@article{bib17,
	author = {Ginestet, C},
	journal = {Journal of the Royal Statistical Society},
	year = {2011},
	pages = {245--246},
	title = {Ggplot2: elegant graphics for data analysis},
	volume = {174},
}

@article{bib18,
	author = {Grimsholm, O and Piano Mortari, E and Davydov, AN and Shugay, M and Obraztsova, AS and Bocci, C and Marasco, E and Marcellini, V and Aranburu, A and Farroni, C and Silvestris, DA and Cristofoletti, C and Giorda, E and Scarsella, M and Cascioli, S and Barresi, S and Lougaris, V and Plebani, A and Cancrini, C and Finocchi, A and Moschese, V and Valentini, D and Vallone, C and Signore, F and de Vincentiis, G and Zaffina, S and Russo, G and Gallo, A and Locatelli, F and Tozzi, AE and Tartaglia, M and Chudakov, DM and Carsetti, R},
	journal = {Cell Reports},
	year = {2011},
	pages = {2963--2977},
	title = {The interplay between cd27dull and cd27bright {B} cells ensures the flexibility, stability, and resilience of human {B} cell memory},
	volume = {30},
}

@article{bib19,
	author = {Gupta, NT and Vander Heiden, JA and Uduman, M and Gadala-Maria, D and Yaari, G and Kleinstein, SH},
	journal = {Bioinformatics},
	year = {2015},
	pages = {3356--3358},
	title = {Change-{O}: a toolkit for analyzing large-scale {B} cell immunoglobulin repertoire sequencing data},
	volume = {31},
}

@article{bib20,
	author = {Hoehn, KB and Turner, JS and Miller, FI and Jiang, R and Pybus, OG and Ellebedy, AH and Kleinstein, SH},
	journal = {eLife},
	year = {2021},
	title = {Human {B} cell lineages associated with germinal centers following influenza vaccination are measurably evolving},
	volume = {10},
}

@article{bib21,
	author = {Horns, F and Vollmers, C and Dekker, CL and Quake, SR},
	journal = {PNAS},
	year = {2019},
	pages = {1261--1266},
	title = {Signatures of selection in the human antibody repertoire: selective sweeps, competing subclones, and neutral drift},
	volume = {116},
}

@article{bib22,
	author = {Laserson, U and Vigneault, F and Gadala-Maria, D and Yaari, G and Uduman, M and Vander Heiden, JA and Kelton, W and Taek Jung, S and Liu, Y and Laserson, J and Chari, R and Lee, JH and Bachelet, I and Hickey, B and Lieberman-Aiden, E and Hanczaruk, B and Simen, BB and Egholm, M and Koller, D and Georgiou, G and Kleinstein, SH and Church, GM},
	journal = {PNAS},
	year = {2014},
	pages = {4928--4933},
	title = {High-{Resolution} antibody dynamics of vaccine-induced immune responses},
	volume = {111},
}

@article{bib23,
	author = {Mandric, I and Rotman, J and Yang, HT and Strauli, N and Montoya, DJ and Van Der Wey, W and Ronas, JR and Statz, B and Yao, D and Petrova, V and Zelikovsky, A and Spreafico, R and Shifman, S and Zaitlen, N and Rossetti, M and Ansel, KM and Eskin, E and Mangul, S},
	journal = {Nature Communications},
	year = {2020},
	title = {Profiling immunoglobulin repertoires across multiple human tissues using {RNA} sequencing},
	volume = {11},
}

@article{bib24,
	author = {McDonald, JH and Kreitman, M},
	journal = {Nature},
	year = {1991},
	pages = {652--654},
	title = {Adaptive protein evolution at the {Adh} locus in {Drosophila}},
	volume = {351},
}

@article{bib25,
	author = {Mitsunaga, EM and Snyder, MP},
	journal = {Molecular & Cellular Proteomics},
	year = {2020},
	pages = {278--293},
	title = {Deep characterization of the human antibody response to natural infection using longitudinal immune repertoire sequencing},
	volume = {19},
}

@article{bib26,
	author = {Neher, RA and Hallatschek, O},
	journal = {PNAS},
	year = {2013},
	pages = {437--442},
	title = {Genealogies of rapidly adapting populations},
	volume = {110},
}

@article{bib27,
	author = {Nei, M and Gojobori, T},
	journal = {Molecular Biology and Evolution},
	year = {1986},
	pages = {418--426},
	title = {Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions},
	volume = {3},
}

@article{bib28,
	address = {Oxford ; New York},
	author = {Nei, M and Kumar, S},
	year = {2000},
	publisher = {Oxford University Press},
	title = {Molecular {Evolution} and {Phylogenetics}},
}

@article{bib29,
	author = {Nielsen, R},
	journal = {Annual Review of Genetics},
	year = {2005},
	pages = {197--218},
	title = {Molecular signatures of natural selection},
	volume = {39},
}

@article{bib30,
	author = {Nielsen, SCA and Yang, F and Jackson, KJL and Hoh, RA and R{\" o}ltgen, K and Jean, GH and Stevens, BA and Lee, JY and Rustagi, A and Rogers, AJ and Powell, AE and Hunter, M and Najeeb, J and Otrelo-Cardoso, AR and Yost, KE and Daniel, B and Nadeau, KC and Chang, HY and Satpathy, AT and Jardetzky, TS and Kim, PS and Wang, TT and Pinsky, BA and Blish, CA and Boyd, SD},
	journal = {Cell Host & Microbe},
	year = {2020},
	pages = {516--525},
	title = {Human {B} cell clonal expansion and convergent antibody responses to {SARS}-cov-2},
	volume = {28},
}

@article{bib31,
	author = {Nourmohammad, A and Otwinowski, J and \L{}uksza, M and Mora, T and Walczak, AM},
	journal = {Molecular Biology and Evolution},
	year = {2019},
	pages = {2184--2194},
	title = {Fierce selection and interference in {B}-cell repertoire response to chronic {HIV}-1},
	volume = {36},
}

@article{bib32,
	author = {Peng, W and Liu, S and Meng, J and Huang, J and Huang, J and Tang, D and Dai, Y},
	journal = {Scientific Reports},
	year = {2019},
	title = {Profiling the {TRB} and {IgH} repertoire of patients with {H5N6} avian influenza virus infection by high-throughput sequencing},
	volume = {9},
}

@article{bib33,
	author = {Perez-Andres, M and Paiva, B and Nieto, WG and Caraux, A and Schmitz, A and Almeida, J and Vogt, RF and Marti, GE and Rawstron, AC and Van Zelm, MC and Van Dongen, JJM and Johnsen, HE and Klein, B and Orfao, A and {Primary Health Care Group of Salamanca for the Study of MBL}},
	journal = {Cytometry. Part B, Clinical Cytometry},
	year = {2010},
	title = {Human peripheral blood {B}-cell compartments: a crossroad in {B}-cell traffic},
	volume = {78},
}

@article{bib34,
	author = {Phad, GE and Pinto, D and Foglierini, M and Akhmedov, M and Rossi, RL and Malvicini, E and Cassotta, A and Fregni, CS and Bruno, L and Sallusto, F and Lanzavecchia, A},
	journal = {Nature Immunology},
	year = {2022},
	pages = {1--10},
	title = {Clonal structure, stability and dynamics of human memory {B} cells and circulating plasmablasts},
	volume = {23},
}

@article{bib35,
	address = {Vienna, Austria},
	author = {{R Development Core Team}},
	year = {2018},
	publisher = {R Foundation for Statistical Computing},
	title = {R: a language and environment for statistical computing. {R} foundation for statistical computing},
}

@article{bib36,
	author = {Robinson, MD and McCarthy, DJ and Smyth, GK},
	journal = {Bioinformatics},
	year = {2010},
	pages = {139--140},
	title = {EdgeR: a {Bioconductor} package for differential expression analysis of digital gene expression data},
	volume = {26},
}

@article{bib37,
	author = {Robinson, MD and Oshlack, A},
	journal = {Genome Biology},
	year = {2010},
	title = {A scaling normalization method for differential expression analysis of {RNA}-{Seq} data},
	volume = {11},
}

@article{bib38,
	author = {Sakharkar, M and Rappazzo, CG and Wieland-Alter, WF and Hsieh, CL and Wrapp, D and Esterman, ES and Kaku, CI and Wec, AZ and Geoghegan, JC and McLellan, JS and Connor, RI and Wright, PF and Walker, LM},
	journal = {Science Immunology},
	year = {2021},
	title = {Prolonged evolution of the human {B} cell response to {SARS}-cov-2 infection},
	volume = {6},
}

@article{bib39,
	author = {Sethna, Z and Elhanati, Y and Callan, CG and Walczak, AM and Mora, T},
	journal = {Bioinformatics},
	year = {2019},
	pages = {2974--2981},
	title = {OLGA: fast computation of generation probabilities of {B}- and {T}-cell receptor amino acid sequences and motifs},
	volume = {35},
}

@article{bib40,
	author = {Shah, HB and Smith, K and Wren, JD and Webb, CF and Ballard, JD and Bourn, RL and James, JA and Lang, ML},
	journal = {Frontiers in Immunology},
	year = {2018},
	title = {Insights from analysis of human antigen-specific memory {B} cell repertoires},
	volume = {9},
}

@article{bib41,
	author = {Shugay, M and Britanova, OV and Merzlyak, EM and Turchaninova, MA and Mamedov, IZ and Tuganbaev, TR and Bolotin, DA and Staroverov, DB and Putintseva, EV and Plevova, K and Linnemann, C and Shagin, D and Pospisilova, S and Lukyanov, S and Schumacher, TN and Chudakov, DM},
	journal = {Nature Methods},
	year = {2014},
	pages = {653--655},
	title = {Towards error-free profiling of immune repertoires},
	volume = {11},
}

@article{bib42,
	author = {Soto, C and Bombardi, RG and Branchizio, A and Kose, N and Matta, P and Sevy, AM and Sinkovits, RS and Gilchuk, P and Finn, JA and Crowe, JE},
	journal = {Nature},
	year = {2019},
	pages = {398--402},
	title = {High frequency of shared clonotypes in human {B} cell receptor repertoires},
	volume = {566},
}

@article{bib43,
	author = {Stamatakis, A},
	journal = {Bioinformatics},
	year = {2014},
	pages = {1312--1313},
	title = {RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
	volume = {30},
}

@article{bib44,
	author = {Stavnezer, J and Guikema, JEJ and Schrader, CE},
	journal = {Annual Review of Immunology},
	year = {2008},
	pages = {261--292},
	title = {Mechanism and regulation of class switch recombination},
	volume = {26},
}

@article{bib45,
	author = {Turchaninova, MA and Davydov, A and Britanova, OV and Shugay, M and Bikos, V and Egorov, ES and Kirgizova, VI and Merzlyak, EM and Staroverov, DB and Bolotin, DA and Mamedov, IZ and Izraelson, M and Logacheva, MD and Kladova, O and Plevova, K and Pospisilova, S and Chudakov, DM},
	journal = {Nature Protocols},
	year = {2016},
	pages = {1599--1616},
	title = {High-{Quality} full-length immunoglobulin profiling with unique molecular barcoding},
	volume = {11},
}

@article{bib46,
	author = {Vidarsson, G and Dekkers, G and Rispens, T},
	journal = {Frontiers in Immunology},
	year = {2014},
	title = {Igg subclasses and allotypes: from structure to effector functions},
	volume = {5},
}

@article{bib47,
	author = {Wu, YC and Kipling, D and Leong, HS and Martin, V and Ademokun, AA and Dunn-Walters, DK},
	journal = {Blood},
	year = {2010},
	pages = {1070--1078},
	title = {High-{Throughput} immunoglobulin repertoire analysis distinguishes between human {IgM} memory and switched memory {B}-cell populations},
	volume = {116},
}

@article{bib48,
	author = {Yang, X and Wang, M and Wu, J and Shi, D and Zhang, Y and Zeng, H and Zhu, Y and Lan, C and Deng, Y and Guo, S and Xu, L and Ma, C and Zhang, Y and Ou, J and Liu, CJ and Chen, Y and Wang, Q and Xie, W and Guan, J and Ding, J and Wang, Z and Chang, C and Yang, W and Zhang, H and Chen, J and Qin, L and Zhou, H and Bei, JX and Wei, L and Cao, G and Yu, X and Zhang, Z},
	journal = {Cell Reports},
	year = {2021},
	title = {Large-{Scale} analysis of 2,152 ig-seq datasets reveals key features of {B} cell biology and the antibody repertoire},
	volume = {35},
}

@article{bib49,
	author = {Yu, G and Smith, DK and Zhu, H and Guan, Y and Tommy, TYL and McInerny, Greg},
	journal = {Methods in Ecology and Evolution},
	year = {2017},
	pages = {28--36},
	publisher = {British ecological society},
	title = {Ggtree: package for visualization and annotation of phylogenetic trees with their covariates and other associated data},
}

@article{bib50,
	author = {Zvyagin, IV and Mamedov, IZ and Tatarinova, OV and Komech, EA and Kurnikova, EE and Boyakova, EV and Brilliantova, V and Shelikhova, LN and Balashov, DN and Shugay, M and Sycheva, AL and Kasatskaya, SA and Lebedev, YB and Maschan, AA and Maschan, MA and Chudakov, DM},
	journal = {Leukemia},
	year = {2017},
	pages = {1145--1153},
	title = {Tracking {T}-cell immune reconstitution after {TCR}\alpha{}\beta{}/{CD19}-depleted hematopoietic cells transplantation in children},
	volume = {31},
}