references.bib

@article{Maynard2020,
  doi       = {10.1016/j.cell.2020.07.017},
  url       = {https://doi.org/10.1016/j.cell.2020.07.017},
  year      = {2020},
  month     = sep,
  publisher = {Elsevier {BV}},
  volume    = {182},
  number    = {5},
  pages     = {1232--1251.e22},
  author    = {Ashley Maynard and Caroline E. McCoach and Julia K. Rotow and Lincoln Harris and Franziska Haderk and D. Lucas Kerr and Elizabeth A. Yu and Erin L. Schenk and Weilun Tan and Alexander Zee and Michelle Tan and Philippe Gui and Tasha Lea and Wei Wu and Anatoly Urisman and Kirk Jones and Rene Sit and Pallav K. Kolli and Eric Seeley and Yaron Gesthalter and Daniel D. Le and Kevin A. Yamauchi and David M. Naeger and Sourav Bandyopadhyay and Khyati Shah and Lauren Cech and Nicholas J. Thomas and Anshal Gupta and Mayra Gonzalez and Hien Do and Lisa Tan and Bianca Bacaltos and Rafael Gomez-Sjoberg and Matthew Gubens and Thierry Jahan and Johannes R. Kratz and David Jablons and Norma Neff and Robert C. Doebele and Jonathan Weissman and Collin M. Blakely and Spyros Darmanis and Trever G. Bivona},
  title     = {Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell {RNA} Sequencing},
  journal   = {Cell}
}
@article{Stephenson.2021,
 author = {Stephenson, Emily and Reynolds, Gary and Botting, Rachel A. and Calero-Nieto, Fernando J. and Morgan, Michael D. and Tuong, Zewen Kelvin and Bach, Karsten and Sungnak, Waradon and Worlock, Kaylee B. and Yoshida, Masahiro and Kumasaka, Natsuhiko and Kania, Katarzyna and Engelbert, Justin and Olabi, Bayanne and Spegarova, Jarmila Stremenova and Wilson, Nicola K. and Mende, Nicole and Jardine, Laura and Gardner, Louis C. S. and Goh, Issac and others},
 year = {2021},
 title = {Single-cell multi-omics analysis of the immune response in COVID-19},
 pages = {904--916},
 volume = {27},
 number = {5},
 issn = {1078-8956},
 journal = {Nature medicine},
 doi = {10.1038/s41591-021-01329-2}
}

@article{Balashova.2024,
 author = {Balashova, Daria and {van Schaik}, Barbera D. C. and Stratigopoulou, Maria and Guikema, Jeroen E. J. and Caniels, Tom G. and Claireaux, Mathieu and {van Gils}, Marit J. and Musters, Anne and Anang, Dornatien C. and de Vries, Niek and Greiff, Victor and {van Kampen}, Antoine H. C.},
 year = {2024},
 title = {Systematic evaluation of B-cell clonal family inference approaches},
 pages = {13},
 volume = {25},
 number = {1},
 issn = {1471-2172},
 journal = {BMC Immunology},
 doi = {10.1186/s12865-024-00600-8}
}

@article{Ralph.2016,
 author = {Ralph, Duncan K. and Matsen, 4th., Frederick A.},
 year = {2016},
 title = {Likelihood-Based Inference of B Cell Clonal Families},
 keywords = {0 (Receptors, Antigen, B-Cell);B-Lymphocytes/immunology;Clone Cells/immunology;Computer Simulation;Gene Rearrangement, B-Lymphocyte/genetics/immunology;High-Throughput Nucleotide Sequencing/methods;Models, Genetic;Models, Immunological;Models, Statistical;Receptors, Antigen, B-Cell/genetics/immunology;Sequence Analysis, DNA},
 pages = {e1005086},
 volume = {12},
 number = {10},
 issn = {1553-734X},
 journal = {PLoS computational biology},
 doi = {10.1371/journal.pcbi.1005086}
}

@article{Nouri.2018,
 author = {Nouri, Nima and Kleinstein, Steven H.},
 year = {2018},
 title = {A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data},
 keywords = {B-Lymphocytes;Clone Cells;Cluster Analysis;DNA/methods;High-Throughput Nucleotide Sequencing;Models;Sequence Analysis;Software;Statistical},
 pages = {i341-i349},
 volume = {34},
 number = {13},
 issn = {1367-4803},
 journal = {Bioinformatics},
 doi = {10.1093/bioinformatics/bty235}
}

@article{Lindenbaum.2021,
 author = {Lindenbaum, Ofir and Nouri, Nima and Kluger, Yuval and Kleinstein, Steven H.},
 year = {2021},
 title = {Alignment free identification of clones in B cell receptor repertoires},
 keywords = {Clone Cells;DNA/methods;Genes;Immunoglobulin;Sequence Analysis;VDJ Exons},
 pages = {e21},
 volume = {49},
 number = {4},
 issn = {0305-1048},
 journal = {Nucleic acids research},
 doi = {10.1093/nar/gkaa1160}
}

@article{BashfordRogers.2013,
 author = {Bashford-Rogers, Rachael J. M. and Palser, Anne L. and Huntly, Brian J. and Rance, Richard and Vassiliou, George S. and Follows, George A. and Kellam, Paul},
 year = {2013},
 title = {Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations},
 keywords = {0 (Receptors, Antigen, B-Cell);Adaptive Immunity;Adult;Aged;Aged, 80 and over;B-Lymphocytes/immunology;Case-Control Studies;Cell Line, Tumor;Clone Cells;Computational Biology;Female;Genes, Immunoglobulin Heavy Chain;High-Throughput Nucleotide Sequencing;Humans;Leukemia, Lymphocytic, Chronic, B-Cell/immunology/pathology;Male;Middle Aged;Receptors, Antigen, B-Cell/genetics/immunology;Reverse Transcriptase Polymerase Chain Reaction;Sequence Analysis, DNA;Young Adult},
 pages = {1874--1884},
 volume = {23},
 number = {11},
 issn = {1088-9051},
 journal = {Genome research},
 doi = {10.1101/gr.154815.113}
}

@article{Yaari.2015,
 author = {Yaari, Gur and Kleinstein, Steven H.},
 year = {2015},
 title = {Practical guidelines for B-cell receptor repertoire sequencing analysis},
 pages = {121},
 volume = {7},
 number = {1},
 issn = {1756-994X},
 journal = {Genome Medicine},
 doi = {10.1186/s13073-015-0243-2}
}

@article{Kleinstein.2003,
 author = {Kleinstein, Steven H. and Louzoun, Yoram and Shlomchik, Mark J.},
 year = {2003},
 title = {Estimating Hypermutation Rates from Clonal Tree Data 1},
 pages = {4639--4649},
 volume = {171},
 number = {9},
 issn = {0022-1767},
 journal = {Journal of immunology (Baltimore, Md. : 1950)},
 doi = {10.4049/jimmunol.171.9.4639}
}

@article{Wilson.1998,
 author = {Wilson, Patrick C. and de Bouteiller, Odette and Liu, Yong-Jun and Potter, Kathleen and Banchereau, Jacques and Capra, J. Donald and Pascual, Virginia},
 year = {1998},
 title = {Somatic Hypermutation Introduces Insertions and Deletions into Immunoglobulin V Genes},
 pages = {59--70},
 volume = {187},
 number = {1},
 issn = {0022-1007},
 journal = {Journal of Experimental Medicine},
 doi = {10.1084/jem.187.1.59}
}

@article{Schramm.2018,
 author = {Schramm, Chaim A. and Douek, Daniel C.},
 year = {2018},
 title = {Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design},
 url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2018.01876},
 volume = {9},
 issn = {1664-3224},
 journal = {Frontiers in immunology},
 doi = {10.3389/fimmu.2018.01876}
}



@article{TabulaSapiens.2022,
author = {{Robert C. Jones} and {Jim Karkanias} and {Mark A. Krasnow} and {Angela Oliveira Pisco} and {Stephen R. Quake} and {Julia Salzman} and {Nir Yosef} and {Bryan Bulthaup} and {Phillip Brown} and {William Harper} and {Marisa Hemenez} and {Ravikumar Ponnusamy} and {Ahmad Salehi} and {Bhavani A. Sanagavarapu} and {Eileen Spallino} and {Ksenia A. Aaron} and {Waldo Concepcion} and {James M. Gardner} and {Burnett Kelly} and {Nikole Neidlinger} and others},
 year = {2022},
 title = {The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans},
 pages = {eabl4896},
 volume = {376},
 number = {6594},
 issn = {0036-8075},
 journal = {Science (New York, N.Y.)},
 doi = {10.1126/science.abl4896}
}

@article{Suo.2023,
author = {Suo, Chenqu and Polanski, Krzysztof and Dann, Emma and Lindeboom, Rik G. H. and Vilarrasa-Blasi, Roser and Vento-Tormo, Roser and Haniffa, Muzlifah and Meyer, Kerstin B. and Dratva, Lisa M. and Tuong, Zewen Kelvin and Clatworthy, Menna R. and Teichmann, Sarah A.},
 year = {2023},
 title = {Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins},
 issn = {1546-1696},
 journal = {Nature Biotechnology},
 doi = {10.1038/s41587-023-01734-7}
}

@article{Lefranc.2003,
author = {Lefranc, Marie-Paule and Pommi{\'e}, Christelle and Ruiz, Manuel and Giudicelli, V{\'e}ronique and Foulquier, Elodie and Truong, Lisa and Thouvenin-Contet, Val{\'e}rie and Lefranc, G{\'e}rard},
 year = {2003},
 title = {IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains},
 pages = {55--77},
 volume = {27},
 number = {1},
 issn = {0145-305X},
 journal = {Developmental and comparative immunology},
 doi = {10.1016/s0145-305x(02)00039-3}
}

@article{Zhu.2023,
 author = {Zhu, Lanwei and Peng, Qi and Wu, Yingjie and Yao, Xinsheng},
 year = {2023},
 title = {scBCR-seq revealed a special and novel IG H{\&}L V(D)J allelic inclusion rearrangement and the high proportion dual BCR expressing B cells},
 pages = {319},
 volume = {80},
 number = {11},
 issn = {1420-9071},
 journal = {Cellular and Molecular Life Sciences},
 doi = {10.1007/s00018-023-04973-8}
}

@article{RobertaPelanda.2014,
 author = {{Roberta Pelanda}},
 year = {2014},
 title = {Dual immunoglobulin light chain B cells: Trojan horses of autoimmunity?},
 url = {https://www.sciencedirect.com/science/article/pii/S095279151400020X},
 pages = {53--59},
 volume = {27},
 issn = {0952-7915},
 journal = {Current Opinion in Immunology},
 doi = {10.1016/j.coi.2014.01.012}
}


@article{Shi.2019,
author = {Shi, Zhan and Zhang, Qingyang and Yan, Huige and Yang, Ying and Wang, Pingzhang and Zhang, Yixiao and Deng, Zhenling and Yu, Meng and Zhou, Wenjing and Wang, Qianqian and Yang, Xi and Mo, Xiaoning and Zhang, Chi and Huang, Jing and Dai, Hui and Sun, Baofa and Zhao, Yongliang and Zhang, Liang and Yang, Yun-Gui and Qiu, Xiaoyan},
 year = {2019},
 title = {More than one antibody of individual B cells revealed by single-cell immune profiling},
 pages = {64},
 volume = {5},
 number = {1},
 issn = {2056-5968},
 journal = {Cell Discovery},
 doi = {10.1038/s41421-019-0137-3}
}

@article{Gupta.2017,
 author = {Gupta, Namita T. and Adams, Kristofor D. and Briggs, Adrian W. and Timberlake, Sonia C. and Vigneault, Francois and Kleinstein, Steven H.},
 year = {2017},
 title = {Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data},
 pages = {2489--2499},
 volume = {198},
 number = {6},
 issn = {0022-1767},
 journal = {Journal of immunology (Baltimore, Md. : 1950)},
 doi = {10.4049/jimmunol.1601850}
}

@article{Clauset.2004,
 author = {Clauset, Aaron and Newman, M. E. J. and Moore, Cristopher},
 year = {2004},
 title = {Finding community structure in very large networks},
 url = {https://link.aps.org/doi/10.1103/PhysRevE.70.066111},
 pages = {066111},
 volume = {70},
 number = {6},
 journal = {Phys. Rev. E},
 doi = {10.1103/PhysRevE.70.066111}
}
@article{Kepler.2014,
 author = {Kepler, Thomas B. and Liao, Hua-Xin and Alam, S. Munir and Bhaskarabhatla, Rekha and Zhang, Ruijun and Yandava, Chandri and Stewart, Shelley and Anasti, Kara and Kelsoe, Garnett and Parks, Robert and Lloyd, Krissey E. and Stolarchuk, Christina and Pritchett, Jamie and Solomon, Erika and Friberg, Emma and Morris, Lynn and Karim, Salim S. Abdool and Cohen, Myron S. and Walter, Emmanuel and Moody, M. Anthony and Wu, Xueling and Altae-Tran, Han R. and Georgiev, Ivelin S. and Kwong, Peter D. and Boyd, Scott D. and Fire, Andrew Z. and Mascola, John R. and Haynes, Barton F.},
 year = {2014},
 title = {Immunoglobulin Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly Reactive Neutralizing Antibodies},
 pages = {304--313},
 volume = {16},
 number = {3},
 issn = {1931-3128},
 journal = {Cell Host {\&} Microbe},
 doi = {10.1016/j.chom.2014.08.006}
}

@article{DeKosky.2013,
author = {DeKosky, Brandon J. and Ippolito, Gregory C. and Deschner, Ryan P. and Lavinder, Jason J. and Wine, Yariv and Rawlings, Brandon M. and Varadarajan, Navin and Giesecke, Claudia and D{\"o}rner, Thomas and Andrews, Sarah F. and Wilson, Patrick C. and Hunicke-Smith, Scott P. and Willson, C. Grant and Ellington, Andrew D. and Georgiou, George},
 year = {2013},
 title = {High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire},
 pages = {166--169},
 volume = {31},
 number = {2},
 issn = {1546-1696},
 journal = {Nature Biotechnology},
 doi = {10.1038/nbt.2492}
}

@article{Adams.2020,
 author = {Adams, Nicholas M. and Grassmann, Simon and Sun, Joseph C.},
 year = {2020},
 title = {Clonal expansion of innate and adaptive lymphocytes},
 pages = {694--707},
 volume = {20},
 number = {11},
 issn = {1474-1741},
 journal = {Nature Reviews Immunology},
 doi = {10.1038/s41577-020-0307-4}
}

@article{Nutt.2015,
 author = {Nutt, Stephen L. and Hodgkin, Philip D. and Tarlinton, David M. and Corcoran, Lynn M.},
 year = {2015},
 title = {The generation of antibody-secreting plasma cells},
 keywords = {0 (Antibodies);Antibodies/immunology;Antibody Formation/immunology;B-Lymphocytes/immunology;Cell Differentiation/immunology;Humans;Plasma Cells/immunology/metabolism},
 pages = {160--171},
 volume = {15},
 number = {3},
 issn = {1474-1741},
 journal = {Nature Reviews Immunology},
 doi = {10.1038/nri3795}
}

@article{Finotello.2016,
 author = {Finotello, Francesca and Mastrorilli, Eleonora and {Di Camillo}, Barbara},
 year = {2016},
 title = {Measuring the diversity of the human microbiota with targeted next-generation sequencing},
 pages = {679--692},
 volume = {19},
 number = {4},
 issn = {1477-4054},
 journal = {Briefings in Bioinformatics},
 doi = {10.1093/bib/bbw119}
}

@article{Pelissier.2023,
 author = {Pelissier, Aurelien and Luo, Siyuan and Stratigopoulou, Maria and Guikema, Jeroen E. J. and {Rodr{\'i}guez Mart{\'i}nez}, Mar{\'i}a},
 year = {2023},
 title = {Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires},
 url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.1123968},
 volume = {14},
 issn = {1664-3224},
 journal = {Frontiers in immunology},
 doi = {10.3389/fimmu.2023.1123968}
}

@article{Jost.2010,
 author = {Jost, Lou},
 year = {2010},
 title = {The Relation between Evenness and Diversity},
 url = {https://www.mdpi.com/1424-2818/2/2/207},
 pages = {207--232},
 volume = {2},
 number = {2},
 issn = {1424-2818},
 journal = {Diversity},
 doi = {10.3390/d2020207}
}

@book{Kenneth.2017,
 author = {Murphy, Kenneth M. and Weaver, Casey},
 year = {2017},
 title = {Janeway's immunobiology},
 address = {New York and London},
 edition = {9th edition},
 publisher = {{GS Garland Science Taylor {\&} Francis Group}},
 isbn = {978-0-8153-4551-0},
 institution = {{Taylor {\&} Francis Group}}
}

@article{Chao.2014,
 author = {Chao, Anne and Gotelli, Nicholas J. and Hsieh, T. C. and Sander, Elizabeth L. and Ma, K. H. and Colwell, Robert K. and Ellison, Aaron M.},
 year = {2014},
 title = {Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies},
 keywords = {abundance data;diversity;extrapolation;Hill numbers;incidence data;interpolation;prediction;rarefaction;sample coverage;species richness},
 pages = {45--67},
 volume = {84},
 number = {1},
 journal = {Ecological Monographs},
 doi = {10.1890/13-0133.1}
}

@article{Vettermann2010,
  doi       = {10.1111/j.1600-065x.2010.00935.x},
  url       = {https://doi.org/10.1111/j.1600-065x.2010.00935.x},
  year      = {2010},
  month     = aug,
  publisher = {Wiley},
  volume    = {237},
  number    = {1},
  pages     = {22--42},
  author    = {Christian Vettermann and Mark S. Schlissel},
  title     = {Allelic exclusion of immunoglobulin genes: models and mechanisms},
  journal   = {Immunological Reviews}
}

@article{Wu2020,
  doi       = {10.1038/s41586-020-2056-8},
  url       = {https://doi.org/10.1038/s41586-020-2056-8},
  year      = {2020},
  month     = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {579},
  number    = {7798},
  pages     = {274--278},
  author    = {Thomas D. Wu and Shravan Madireddi and Patricia E. de Almeida and Romain Banchereau and Ying-Jiun J. Chen and Avantika S. Chitre and Eugene Y. Chiang and Hina Iftikhar and William E. O'Gorman and Amelia Au-Yeung and Chikara Takahashi and Leonard D. Goldstein and Chungkee Poon and Shilpa Keerthivasan and Denise E. de Almeida Nagata and Xiangnan Du and Hyang-Mi Lee and Karl L. Banta and Sanjeev Mariathasan and Meghna Das Thakur and Mahrukh A. Huseni and Marcus Ballinger and Ivette Estay and Patrick Caplazi and Zora Modrusan and L{\'{e}}lia Delamarre and Ira Mellman and Richard Bourgon and Jane L. Grogan},
  title     = {Peripheral T cell expansion predicts tumour infiltration and clinical response},
  journal   = {Nature}
}

@article{Schuldt2019,
  doi       = {10.4049/jimmunol.1800904},
  url       = {https://doi.org/10.4049/jimmunol.1800904},
  year      = {2019},
  month     = jan,
  publisher = {The American Association of Immunologists},
  volume    = {202},
  number    = {3},
  pages     = {637--644},
  author    = {Nathaniel J. Schuldt and Bryce A. Binstadt},
  title     = {Dual {TCR} T Cells: Identity Crisis or Multitaskers?},
  journal   = {The Journal of Immunology}
}

@article{TCRdist,
  doi       = {10.1038/nature22383},
  url       = {https://doi.org/10.1038/nature22383},
  year      = {2017},
  month     = jun,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {547},
  number    = {7661},
  pages     = {89--93},
  author    = {Pradyot Dash and Andrew J. Fiore-Gartland and Tomer Hertz and George C. Wang and Shalini Sharma and Aisha Souquette and Jeremy Chase Crawford and E. Bridie Clemens and Thi H. O. Nguyen and Katherine Kedzierska and Nicole L. La Gruta and Philip Bradley and Paul G. Thomas},
  title     = {Quantifiable predictive features define epitope-specific T cell receptor repertoires},
  journal   = {Nature}
}

@article{TCRBLOSUM,
  doi       = {10.1093/bib/bbae602},
  url       = {https://doi.org/10.1093/bib/bbae602},
  year      = {2024},
  month     = nov,
  publisher = {Oxford University Press ({OUP})},
  volume    = {26},
  number    = {1},
  pages     = {bbae602},
  author    = {Anna Postovskaya and Koen Vercauteren and Pieter Meysman and Kris Laukens},
  title     = {{tcrBLOSUM}: an amino acid substitution matrix for sensitive alignment of distant epitope-specific {TCRs}},
  journal   = {Briefings in Bioinformatics}
}

@article{Brady2010-gh,
  title    = {Antigen receptor allelic exclusion: an update and reappraisal},
  author   = {Brady, Brenna L and Steinel, Natalie C and Bassing, Craig H},
  abstract = {Most lymphocytes express cell surface Ag receptor chains from
              single alleles of distinct Ig or TCR loci. Since the
              identification of Ag receptor allelic exclusion, the importance
              of this process and the precise molecular mechanisms by which it
              is achieved have remained enigmatic. This brief review summarizes
              current knowledge of the extent to which Ig and TCR loci are
              subject to allelic exclusion. Recent progress in studying and
              defining mechanistic steps and molecules that may control the
              monoallelic initiation and subsequent inhibition of V-to-(D)-J
              recombination is outlined using the mouse TCR$\beta$ locus as a
              model with frequent comparisons to the mouse IgH and Ig$\kappa$
              loci. Potential consequences of defects in mechanisms that
              control Ag receptor allelic exclusion and a reappraisal of the
              physiologic relevance of this immunologic process also are
              discussed.},
  journal  = {J. Immunol.},
  volume   = 185,
  number   = 7,
  pages    = {3801--3808},
  month    = oct,
  year     = 2010,
  language = {en}
}

@article{Afik2017-sg,
  title    = {Targeted reconstruction of {T} cell receptor sequence from single
              cell {RNA-seq} links {CDR3} length to {T} cell differentiation
              state},
  author   = {Afik, Shaked and Yates, Kathleen B and Bi, Kevin and Darko,
              Samuel and Godec, Jernej and Gerdemann, Ulrike and Swadling, Leo
              and Douek, Daniel C and Klenerman, Paul and Barnes, Eleanor J and
              Sharpe, Arlene H and Haining, W Nicholas and Yosef, Nir},
  abstract = {The T cell compartment must contain diversity in both T cell
              receptor (TCR) repertoire and cell state to provide effective
              immunity against pathogens. However, it remains unclear how
              differences in the TCR contribute to heterogeneity in T cell
              state. Single cell RNA-sequencing (scRNA-seq) can allow
              simultaneous measurement of TCR sequence and global
              transcriptional profile from single cells. However, current
              methods for TCR inference from scRNA-seq are limited in their
              sensitivity and require long sequencing reads, thus increasing
              the cost and decreasing the number of cells that can be feasibly
              analyzed. Here we present TRAPeS, a publicly available tool that
              can efficiently extract TCR sequence information from short-read
              scRNA-seq libraries. We apply it to investigate heterogeneity in
              the CD8+ T cell response in humans and mice, and show that it is
              accurate and more sensitive than existing approaches. Coupling
              TRAPeS with transcriptome analysis of CD8+ T cells specific for a
              single epitope from Yellow Fever Virus (YFV), we show that the
              recently described 'naive-like' memory population have
              significantly longer CDR3 regions and greater divergence from
              germline sequence than do effector-memory phenotype cells. This
              suggests that TCR usage is associated with the differentiation
              state of the CD8+ T cell response to YFV.},
  journal  = {Nucleic Acids Res.},
  volume   = 45,
  number   = 16,
  pages    = {e148},
  month    = sep,
  year     = 2017,
  language = {en}
}

@article{Fischer2019,
  doi       = {10.1101/734053},
  url       = {https://doi.org/10.1101/734053},
  year      = {2019},
  month     = aug,
  publisher = {Cold Spring Harbor Laboratory},
  author    = {David S. Fischer and Yihan Wu and Benjamin Schubert and Fabian J. Theis},
  title     = {Predicting antigen-specificity of single T-cells based on {TCR} {CDR}3 regions},
  journal   = {BioRxiv}
}

@article{Zhang2018-ip,
  title    = {Lineage tracking reveals dynamic relationships of {T} cells in
              colorectal cancer},
  author   = {Zhang, Lei and Yu, Xin and Zheng, Liangtao and Zhang, Yuanyuan
              and Li, Yansen and Fang, Qiao and Gao, Ranran and Kang, Boxi and
              Zhang, Qiming and Huang, Julie Y and Konno, Hiroyasu and Guo,
              Xinyi and Ye, Yingjiang and Gao, Songyuan and Wang, Shan and Hu,
              Xueda and Ren, Xianwen and Shen, Zhanlong and Ouyang, Wenjun and
              Zhang, Zemin},
  abstract = {T cells are key elements of cancer immunotherapy1 but certain
              fundamental properties, such as the development and migration of
              T cells within tumours, remain unknown. The enormous T cell
              receptor (TCR) repertoire, which is required for the recognition
              of foreign and self-antigens2, could serve as lineage tags to
              track these T cells in tumours3. Here we obtained transcriptomes
              of 11,138 single T cells from 12 patients with colorectal cancer,
              and developed single T cell analysis by RNA sequencing and TCR
              tracking (STARTRAC) indices to quantitatively analyse the dynamic
              relationships among 20 identified T cell subsets with distinct
              functions and clonalities. Although both CD8+ effector and
              'exhausted' T cells exhibited high clonal expansion, they were
              independently connected with tumour-resident CD8+ effector memory
              cells, implicating a TCR-based fate decision. Of the CD4+ T
              cells, most tumour-infiltrating T regulatory (Treg) cells showed
              clonal exclusivity, whereas certain Treg cell clones were
              developmentally linked to several T helper (TH) cell clones.
              Notably, we identified two IFNG+ TH1-like cell clusters in
              tumours that were associated with distinct IFN$\gamma$-regulating
              transcription factors -the GZMK+ effector memory T cells, which
              were associated with EOMES and RUNX3, and CXCL13+BHLHE40+
              TH1-like cell clusters, which were associated with BHLHE40. Only
              CXCL13+BHLHE40+ TH1-like cells were preferentially enriched in
              patients with microsatellite-instable tumours, and this might
              explain their favourable responses to immune-checkpoint blockade.
              Furthermore, IGFLR1 was highly expressed in both CXCL13+BHLHE40+
              TH1-like cells and CD8+ exhausted T cells and possessed
              co-stimulatory functions. Our integrated STARTRAC analyses
              provide a powerful approach to dissect the T cell properties in
              colorectal cancer comprehensively, and could provide insights
              into the dynamic relationships of T cells in other cancers.},
  journal  = {Nature},
  volume   = 564,
  number   = 7735,
  pages    = {268--272},
  month    = dec,
  year     = 2018,
  language = {en}
}

@article{Ji2010-bn,
  title    = {Viral infection triggers central nervous system autoimmunity via
              activation of {CD8+} {T} cells expressing dual {TCRs}},
  author   = {Ji, Qingyong and Perchellet, Antoine and Goverman, Joan M},
  abstract = {Multiple sclerosis is an inflammatory, demyelinating, central
              nervous system disease mediated by myelin-specific T cells.
              Environmental triggers that cause the breakdown of
              myelin-specific T cell tolerance are unknown. Here we found that
              CD8(+) myelin basic protein (MBP)-specific T cell tolerance was
              broken and autoimmunity was induced by infection with a virus
              that did not express MBP cross-reactive epitopes and did not
              depend on bystander activation. Instead, the virus activated T
              cells expressing dual T cell antigen receptors (TCRs) that were
              able to recognize both MBP and viral antigens. Our results
              demonstrate the importance of dual TCR-expressing T cells in
              autoimmunity and suggest a mechanism by which a ubiquitous viral
              infection could trigger autoimmunity in a subset of infected
              people, as suggested by the etiology of multiple sclerosis.},
  journal  = {Nat. Immunol.},
  volume   = 11,
  number   = 7,
  pages    = {628--634},
  month    = jul,
  year     = 2010,
  language = {en}
}

@article{Stubbington2016-kh,
  title    = {{T} cell fate and clonality inference from single-cell
              transcriptomes},
  author   = {Stubbington, Michael J T and L{\"o}nnberg, Tapio and Proserpio,
              Valentina and Clare, Simon and Speak, Anneliese O and Dougan,
              Gordon and Teichmann, Sarah A},
  abstract = {We developed TraCeR, a computational method to reconstruct
              full-length, paired T cell receptor (TCR) sequences from T
              lymphocyte single-cell RNA sequence data. TraCeR links T cell
              specificity with functional response by revealing clonal
              relationships between cells alongside their transcriptional
              profiles. We found that T cell clonotypes in a mouse Salmonella
              infection model span early activated CD4(+) T cells as well as
              mature effector and memory cells.},
  journal  = {Nat. Methods},
  volume   = 13,
  number   = 4,
  pages    = {329--332},
  month    = apr,
  year     = 2016,
  language = {en}
}

@article{Glanville2017-ay,
  title    = {Identifying specificity groups in the {T} cell receptor
              repertoire},
  author   = {Glanville, Jacob and Huang, Huang and Nau, Allison and Hatton,
              Olivia and Wagar, Lisa E and Rubelt, Florian and Ji, Xuhuai and
              Han, Arnold and Krams, Sheri M and Pettus, Christina and Haas,
              Nikhil and Arlehamn, Cecilia S Lindestam and Sette, Alessandro
              and Boyd, Scott D and Scriba, Thomas J and Martinez, Olivia M and
              Davis, Mark M},
  abstract = {T cell receptor (TCR) sequences are very diverse, with many more
              possible sequence combinations than T cells in any one
              individual. Here we define the minimal requirements for TCR
              antigen specificity, through an analysis of TCR sequences using a
              panel of peptide and major histocompatibility complex
              (pMHC)-tetramer-sorted cells and structural data. From this
              analysis we developed an algorithm that we term GLIPH (grouping
              of lymphocyte interactions by paratope hotspots) to cluster TCRs
              with a high probability of sharing specificity owing to both
              conserved motifs and global similarity of
              complementarity-determining region 3 (CDR3) sequences. We show
              that GLIPH can reliably group TCRs of common specificity from
              different donors, and that conserved CDR3 motifs help to define
              the TCR clusters that are often contact points with the antigenic
              peptides. As an independent validation, we analysed 5,711
              TCR$\beta$ chain sequences from reactive CD4 T cells from 22
              individuals with latent Mycobacterium tuberculosis infection. We
              found 141 TCR specificity groups, including 16 distinct groups
              containing TCRs from multiple individuals. These TCR groups
              typically shared HLA alleles, allowing prediction of the likely
              HLA restriction, and a large number of M. tuberculosis T cell
              epitopes enabled us to identify pMHC ligands for all five of the
              groups tested. Mutagenesis and de novo TCR design confirmed that
              the GLIPH-identified motifs were critical and sufficient for
              shared-antigen recognition. Thus the GLIPH algorithm can analyse
              large numbers of TCR sequences and define TCR specificity groups
              shared by TCRs and individuals, which should greatly accelerate
              the analysis of T cell responses and expedite the identification
              of specific ligands.},
  journal  = {Nature},
  volume   = 547,
  number   = 7661,
  pages    = {94--98},
  month    = jul,
  year     = 2017,
  language = {en}
}


@article{Attaf2015,
  doi       = {10.1038/cmi.2014.134},
  url       = {https://doi.org/10.1038/cmi.2014.134},
  year      = {2015},
  month     = jan,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {12},
  number    = {4},
  pages     = {391--399},
  author    = {Meriem Attaf and Eric Huseby and Andrew K Sewell},
  title     = {$\upalpha$$\upbeta$ T cell receptors as predictors of health and disease},
  journal   = {Cellular {\&} Molecular Immunology}
}

@article{Ilicic2016,
  doi       = {10.1186/s13059-016-0888-1},
  url       = {https://doi.org/10.1186/s13059-016-0888-1},
  year      = {2016},
  month     = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {17},
  number    = {1},
  author    = {Tomislav Ilicic and Jong Kyoung Kim and Aleksandra A. Kolodziejczyk and Frederik Otzen Bagger and Davis James McCarthy and John C. Marioni and Sarah A. Teichmann},
  title     = {Classification of low quality cells from single-cell {RNA}-seq data},
  journal   = {Genome Biology}
}

@article{Setliff2018,
  doi       = {10.1016/j.chom.2018.05.001},
  url       = {https://doi.org/10.1016/j.chom.2018.05.001},
  year      = {2018},
  month     = jun,
  publisher = {Elsevier {BV}},
  volume    = {23},
  number    = {6},
  pages     = {845--854.e6},
  author    = {Ian Setliff and Wyatt J. McDonnell and Nagarajan Raju and Robin G. Bombardi and Amyn A. Murji and Cathrine Scheepers and Rutendo Ziki and Charissa Mynhardt and Bryan E. Shepherd and Alusha A. Mamchak and Nigel Garrett and Salim Abdool Karim and Simon A. Mallal and James E. Crowe and Lynn Morris and Ivelin S. Georgiev},
  title     = {Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in {HIV}-1 Infection},
  journal   = {Cell Host {\&} Microbe}
}

@article{Daily2016,
  doi       = {10.1186/s12859-016-0930-z},
  url       = {https://doi.org/10.1186/s12859-016-0930-z},
  year      = {2016},
  month     = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {17},
  number    = {1},
  author    = {Jeff Daily},
  title     = {Parasail: {SIMD} C library for global,  semi-global,  and local pairwise sequence alignments},
  journal   = {{BMC} Bioinformatics}
}

@article{Liao2020,
  doi       = {10.1038/s41591-020-0901-9},
  url       = {https://doi.org/10.1038/s41591-020-0901-9},
  year      = {2020},
  month     = may,
  publisher = {Springer Science and Business Media {LLC}},
  author    = {Mingfeng Liao and Yang Liu and Jing Yuan and Yanling Wen and Gang Xu and Juanjuan Zhao and Lin Cheng and Jinxiu Li and Xin Wang and Fuxiang Wang and Lei Liu and Ido Amit and Shuye Zhang and Zheng Zhang},
  title     = {Single-cell landscape of bronchoalveolar immune cells in patients with {COVID}-19},
  journal   = {Nature Medicine}
}

@article{Chung2017,
  doi       = {10.1038/ncomms15081},
  url       = {https://doi.org/10.1038/ncomms15081},
  year      = {2017},
  month     = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {8},
  number    = {1},
  author    = {Woosung Chung and Hye Hyeon Eum and Hae-Ock Lee and Kyung-Min Lee and Han-Byoel Lee and Kyu-Tae Kim and Han Suk Ryu and Sangmin Kim and Jeong Eon Lee and Yeon Hee Park and Zhengyan Kan and Wonshik Han and Woong-Yang Park},
  title     = {Single-cell {RNA}-seq enables comprehensive tumour and immune cell profiling in primary breast cancer},
  journal   = {Nature Communications}
}

@article{Weber2020,
  doi       = {10.1093/bioinformatics/btaa158},
  url       = {https://doi.org/10.1093/bioinformatics/btaa158},
  year      = {2020},
  month     = apr,
  publisher = {Oxford University Press ({OUP})},
  author    = {C{\'{e}}dric R Weber and Rahmad Akbar and Alexander Yermanos and Milena Pavlovi{\'{c}} and Igor Snapkov and Geir K Sandve and Sai T Reddy and Victor Greiff},
  editor    = {Russell Schwartz},
  title     = {{immuneSIM}: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking},
  journal   = {Bioinformatics}
}

@article{Venturi2006,
  doi       = {10.1073/pnas.0608907103},
  url       = {https://doi.org/10.1073/pnas.0608907103},
  year      = {2006},
  month     = nov,
  publisher = {Proceedings of the National Academy of Sciences},
  volume    = {103},
  number    = {49},
  pages     = {18691--18696},
  author    = {V. Venturi and K. Kedzierska and D. A. Price and P. C. Doherty and D. C. Douek and S. J. Turner and M. P. Davenport},
  title     = {Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination},
  journal   = {Proceedings of the National Academy of Sciences}
}

@article{Lindeman2018,
  doi       = {10.1038/s41592-018-0082-3},
  url       = {https://doi.org/10.1038/s41592-018-0082-3},
  year      = {2018},
  month     = jul,
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {15},
  number    = {8},
  pages     = {563--565},
  author    = {Ida Lindeman and Guy Emerton and Lira Mamanova and Omri Snir and Krzysztof Polanski and Shuo-Wang Qiao and Ludvig M. Sollid and Sarah A. Teichmann and Michael J. T. Stubbington},
  title     = {{BraCeR}: B-cell-receptor reconstruction and clonality inference from single-cell {RNA}-seq},
  journal   = {Nature Methods}
}

@article{Stephenson2021,
  doi       = {10.1038/s41591-021-01329-2},
  url       = {https://www.nature.com/articles/s41591-021-01329-2},
  year      = {2021},
  month     = apr,
  publisher = {Springer Science and Business Media {LLC}},
  author    = {Emily Stephenson and Gary Reynolds and Rachel A Botting and Fernando J Calero-Nieto and Michael Morgan and Zewen Kelvin Tuong and Karsten Bach and Waradon Sungnak and Kaylee B Worlock and Masahiro Yoshida and Natsuhiko Kumasaka and Katarzyna Kania and Justin Engelbert and Bayanne Olabi and Jarmila Stremenova Spegarova and Nicola K Wilson and Nicole Mende and Laura Jardine and Louis CS Gardner and Issac Goh and Dave Horsfall and Jim McGrath and Simone Webb and Michael W. Mather and Rik GH Lindeboom and Emma Dann and Ni Huang and Krzysztof Polanski and Elena Prigmore and Florian Gothe and Jonathan Scott and Rebecca P Payne and Kenneth F Baker and Aidan T Hanrath and Ina CD Schim van der Loeff and Andrew S Barr and Amada Sanchez-Gonzalez and Laura Bergamaschi and Federica Mescia and Josephine L Barnes and Eliz Kilich and Angus de Wilton and Anita Saigal and Aarash Saleh and Sam M Janes and Claire M Smith and Nusayhah Gopee and Caroline Wilson and Paul Coupland and Jonathan M Coxhead and Vladimir Y Kiselev and Stijn van Dongen and Jaume Bacardit and Hamish W King and Anthony J Rostron and A John Simpson and Sophie Hambleton and Elisa Laurenti and Paul A Lyons and Kerstin B Meyer and Marko Z Nikolic and Christopher JA Duncan and Ken Smith and Sarah A Teichmann and Menna R Clatworthy and John C Marioni and Berthold Gottgens and Muzlifah Haniffa and},
  title     = {Single-cell multi-omics analysis of the immune response in {COVID}-19},
  journal   = {Nature Medicine}
}

@article{Schattgen2021,
  author   = {Schattgen, Stefan A.  and Guion, Kate and Crawford, Jeremy Chase and Souquette, Aisha and Barrio, Alvaro Martinez and Stubbington, Michael J. T.  and Thomas, Paul G.  and Bradley, Philip},
  title    = {Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA)},
  journal  = {Nature Biotechnology},
  year     = {2021},
  month    = {Aug},
  day      = {23},
  abstract = {Links between T cell clonotypes, as defined by T cell receptor (TCR) sequences, and phenotype, as reflected in gene expression (GEX) profiles, surface protein expression and peptide:major histocompatibility complex binding, can reveal functional relationships beyond the features shared by clonally related cells. Here we present clonotype neighbor graph analysis (CoNGA), a graph theoretic approach that identifies correlations between GEX profile and TCR sequence through statistical analysis of GEX and TCR similarity graphs. Using CoNGA, we uncovered associations between TCR sequence and GEX profiles that include a previously undescribed `natural lymphocyte' population of human circulating CD8+ T cells and a set of TCR sequence determinants of differentiation in thymocytes. These examples show that CoNGA might help elucidate complex relationships between TCR sequence and T cell phenotype in large, heterogeneous, single-cell datasets.},
  issn     = {1546-1696},
  doi      = {10.1038/s41587-021-00989-2},
  url      = {https://doi.org/10.1038/s41587-021-00989-2}
}

@article{vdjdb,
  doi       = {10.1093/nar/gkz874},
  url       = {https://doi.org/10.1093/nar/gkz874},
  year      = {2019},
  month     = oct,
  publisher = {Oxford University Press ({OUP})},
  volume    = {48},
  number    = {D1},
  pages     = {D1057--D1062},
  author    = {Dmitry V Bagaev and Renske M A Vroomans and Jerome Samir and Ulrik Stervbo and Cristina Rius and Garry Dolton and Alexander Greenshields-Watson and Meriem Attaf and Evgeny S Egorov and Ivan V Zvyagin and Nina Babel and David K Cole and Andrew J Godkin and Andrew K Sewell and Can Kesmir and Dmitriy M Chudakov and Fabio Luciani and Mikhail Shugay},
  title     = {{VDJdb} in 2019: database extension,  new analysis infrastructure and a T-cell receptor motif compendium},
  journal   = {Nucleic Acids Research}
}

@article{iedb,
  doi       = {10.1093/nar/gky1006},
  url       = {https://doi.org/10.1093/nar/gky1006},
  year      = {2019},
  month     = jan,
  publisher = {Oxford University Press ({OUP})},
  volume    = {47},
  number    = {D1},
  pages     = {D339–D343},
  author    = {Randi Vita and Swapnil Mahajan and James A Overton and Sandeep Kumar Dhanda and Sheridan Martini and Jason R Cantrell and Daniel K Wheeler and Alessandro Sette and Bjoern Peters},
  title     = {The Immune Epitope Database (IEDB): 2018 update},
  journal   = {Nucleic Acids Research}
}

@article{Virshup_2023,
  doi       = {10.1038/s41587-023-01733-8},
  url       = {https://doi.org/10.1038%2Fs41587-023-01733-8},
  year      = 2023,
  month     = {apr},
  publisher = {Springer Science and Business Media {LLC}},
  author    = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
  title     = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
  journal   = {Nature Biotechnology}
}

@article{Gabernet2024,
  title = {nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework},
  volume = {20},
  ISSN = {1553-7358},
  url = {http://dx.doi.org/10.1371/journal.pcbi.1012265},
  DOI = {10.1371/journal.pcbi.1012265},
  number = {7},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Gabernet,  Gisela and Marquez,  Susanna and Bjornson,  Robert and Peltzer,  Alexander and Meng,  Hailong and Aron,  Edel and Lee,  Noah Y. and Jensen,  Cole G. and Ladd,  David and Polster,  Mark and Hanssen,  Friederike and Heumos,  Simon and Yaari,  Gur and Kowarik,  Markus C. and Nahnsen,  Sven and Kleinstein,  Steven H.},
  editor = {Niarakis,  Anna},
  year = {2024},
  month = jul,
  pages = {e1012265}
}