Bibliography#
Nicholas M. Adams, Simon Grassmann, and Joseph C. Sun. Clonal expansion of innate and adaptive lymphocytes. Nature Reviews Immunology, 20(11):694–707, 2020. doi:10.1038/s41577-020-0307-4.
Shaked Afik, Kathleen B Yates, Kevin Bi, Samuel Darko, Jernej Godec, Ulrike Gerdemann, Leo Swadling, Daniel C Douek, Paul Klenerman, Eleanor J Barnes, Arlene H Sharpe, W Nicholas Haining, and Nir Yosef. Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. Nucleic Acids Res., 45(16):e148, September 2017.
Meriem Attaf, Eric Huseby, and Andrew K Sewell. $\upalpha $$\upbeta $ t cell receptors as predictors of health and disease. Cellular & Molecular Immunology, 12(4):391–399, January 2015. URL: https://doi.org/10.1038/cmi.2014.134, doi:10.1038/cmi.2014.134.
Dmitry V Bagaev, Renske M A Vroomans, Jerome Samir, Ulrik Stervbo, Cristina Rius, Garry Dolton, Alexander Greenshields-Watson, Meriem Attaf, Evgeny S Egorov, Ivan V Zvyagin, Nina Babel, David K Cole, Andrew J Godkin, Andrew K Sewell, Can Kesmir, Dmitriy M Chudakov, Fabio Luciani, and Mikhail Shugay. VDJdb in 2019: database extension, new analysis infrastructure and a t-cell receptor motif compendium. Nucleic Acids Research, 48(D1):D1057–D1062, October 2019. URL: https://doi.org/10.1093/nar/gkz874, doi:10.1093/nar/gkz874.
Daria Balashova, Barbera D. C. van Schaik, Maria Stratigopoulou, Jeroen E. J. Guikema, Tom G. Caniels, Mathieu Claireaux, Marit J. van Gils, Anne Musters, Dornatien C. Anang, Niek de Vries, Victor Greiff, and Antoine H. C. van Kampen. Systematic evaluation of b-cell clonal family inference approaches. BMC Immunology, 25(1):13, 2024. doi:10.1186/s12865-024-00600-8.
Rachael J. M. Bashford-Rogers, Anne L. Palser, Brian J. Huntly, Richard Rance, George S. Vassiliou, George A. Follows, and Paul Kellam. Network properties derived from deep sequencing of human b-cell receptor repertoires delineate b-cell populations. Genome research, 23(11):1874–1884, 2013. doi:10.1101/gr.154815.113.
Brenna L Brady, Natalie C Steinel, and Craig H Bassing. Antigen receptor allelic exclusion: an update and reappraisal. J. Immunol., 185(7):3801–3808, October 2010.
Woosung Chung, Hye Hyeon Eum, Hae-Ock Lee, Kyung-Min Lee, Han-Byoel Lee, Kyu-Tae Kim, Han Suk Ryu, Sangmin Kim, Jeong Eon Lee, Yeon Hee Park, Zhengyan Kan, Wonshik Han, and Woong-Yang Park. Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. Nature Communications, May 2017. URL: https://doi.org/10.1038/ncomms15081, doi:10.1038/ncomms15081.
Aaron Clauset, M. E. J. Newman, and Cristopher Moore. Finding community structure in very large networks. Phys. Rev. E, 70(6):066111, 2004. URL: https://link.aps.org/doi/10.1103/PhysRevE.70.066111, doi:10.1103/PhysRevE.70.066111.
Jeff Daily. Parasail: SIMD c library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, February 2016. URL: https://doi.org/10.1186/s12859-016-0930-z, doi:10.1186/s12859-016-0930-z.
Pradyot Dash, Andrew J. Fiore-Gartland, Tomer Hertz, George C. Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E. Bridie Clemens, Thi H. O. Nguyen, Katherine Kedzierska, Nicole L. La Gruta, Philip Bradley, and Paul G. Thomas. Quantifiable predictive features define epitope-specific t cell receptor repertoires. Nature, 547(7661):89–93, June 2017. URL: https://doi.org/10.1038/nature22383, doi:10.1038/nature22383.
Brandon J. DeKosky, Gregory C. Ippolito, Ryan P. Deschner, Jason J. Lavinder, Yariv Wine, Brandon M. Rawlings, Navin Varadarajan, Claudia Giesecke, Thomas Dörner, Sarah F. Andrews, Patrick C. Wilson, Scott P. Hunicke-Smith, C. Grant Willson, Andrew D. Ellington, and George Georgiou. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nature Biotechnology, 31(2):166–169, 2013. doi:10.1038/nbt.2492.
David S. Fischer, Yihan Wu, Benjamin Schubert, and Fabian J. Theis. Predicting antigen-specificity of single t-cells based on TCR CDR3 regions. BioRxiv, August 2019. URL: https://doi.org/10.1101/734053, doi:10.1101/734053.
Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, and Steven H. Kleinstein. Nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the immcantation framework. PLOS Computational Biology, 20(7):e1012265, July 2024. URL: http://dx.doi.org/10.1371/journal.pcbi.1012265, doi:10.1371/journal.pcbi.1012265.
Jacob Glanville, Huang Huang, Allison Nau, Olivia Hatton, Lisa E Wagar, Florian Rubelt, Xuhuai Ji, Arnold Han, Sheri M Krams, Christina Pettus, Nikhil Haas, Cecilia S Lindestam Arlehamn, Alessandro Sette, Scott D Boyd, Thomas J Scriba, Olivia M Martinez, and Mark M Davis. Identifying specificity groups in the T cell receptor repertoire. Nature, 547(7661):94–98, July 2017.
Namita T. Gupta, Kristofor D. Adams, Adrian W. Briggs, Sonia C. Timberlake, Francois Vigneault, and Steven H. Kleinstein. Hierarchical clustering can identify b cell clones with high confidence in ig repertoire sequencing data. Journal of immunology (Baltimore, Md. : 1950), 198(6):2489–2499, 2017. doi:10.4049/jimmunol.1601850.
Tomislav Ilicic, Jong Kyoung Kim, Aleksandra A. Kolodziejczyk, Frederik Otzen Bagger, Davis James McCarthy, John C. Marioni, and Sarah A. Teichmann. Classification of low quality cells from single-cell RNA-seq data. Genome Biology, February 2016. URL: https://doi.org/10.1186/s13059-016-0888-1, doi:10.1186/s13059-016-0888-1.
Qingyong Ji, Antoine Perchellet, and Joan M Goverman. Viral infection triggers central nervous system autoimmunity via activation of CD8+ T cells expressing dual TCRs. Nat. Immunol., 11(7):628–634, July 2010.
Steven H. Kleinstein, Yoram Louzoun, and Mark J. Shlomchik. Estimating hypermutation rates from clonal tree data 1. Journal of immunology (Baltimore, Md. : 1950), 171(9):4639–4649, 2003. doi:10.4049/jimmunol.171.9.4639.
Marie-Paule Lefranc, Christelle Pommié, Manuel Ruiz, Véronique Giudicelli, Elodie Foulquier, Lisa Truong, Valérie Thouvenin-Contet, and Gérard Lefranc. Imgt unique numbering for immunoglobulin and t cell receptor variable domains and ig superfamily v-like domains. Developmental and comparative immunology, 27(1):55–77, 2003. doi:10.1016/s0145-305x(02)00039-3.
Mingfeng Liao, Yang Liu, Jing Yuan, Yanling Wen, Gang Xu, Juanjuan Zhao, Lin Cheng, Jinxiu Li, Xin Wang, Fuxiang Wang, Lei Liu, Ido Amit, Shuye Zhang, and Zheng Zhang. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nature Medicine, May 2020. URL: https://doi.org/10.1038/s41591-020-0901-9, doi:10.1038/s41591-020-0901-9.
Ida Lindeman, Guy Emerton, Lira Mamanova, Omri Snir, Krzysztof Polanski, Shuo-Wang Qiao, Ludvig M. Sollid, Sarah A. Teichmann, and Michael J. T. Stubbington. BraCeR: b-cell-receptor reconstruction and clonality inference from single-cell RNA-seq. Nature Methods, 15(8):563–565, July 2018. URL: https://doi.org/10.1038/s41592-018-0082-3, doi:10.1038/s41592-018-0082-3.
Ofir Lindenbaum, Nima Nouri, Yuval Kluger, and Steven H. Kleinstein. Alignment free identification of clones in b cell receptor repertoires. Nucleic acids research, 49(4):e21, 2021. doi:10.1093/nar/gkaa1160.
Ashley Maynard, Caroline E. McCoach, Julia K. Rotow, Lincoln Harris, Franziska Haderk, D. Lucas Kerr, Elizabeth A. Yu, Erin L. Schenk, Weilun Tan, Alexander Zee, Michelle Tan, Philippe Gui, Tasha Lea, Wei Wu, Anatoly Urisman, Kirk Jones, Rene Sit, Pallav K. Kolli, Eric Seeley, Yaron Gesthalter, Daniel D. Le, Kevin A. Yamauchi, David M. Naeger, Sourav Bandyopadhyay, Khyati Shah, Lauren Cech, Nicholas J. Thomas, Anshal Gupta, Mayra Gonzalez, Hien Do, Lisa Tan, Bianca Bacaltos, Rafael Gomez-Sjoberg, Matthew Gubens, Thierry Jahan, Johannes R. Kratz, David Jablons, Norma Neff, Robert C. Doebele, Jonathan Weissman, Collin M. Blakely, Spyros Darmanis, and Trever G. Bivona. Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing. Cell, 182(5):1232–1251.e22, September 2020. URL: https://doi.org/10.1016/j.cell.2020.07.017, doi:10.1016/j.cell.2020.07.017.
Kenneth M. Murphy and Casey Weaver. Janeway's immunobiology. GS Garland Science Taylor & Francis Group, New York and London, 9th edition edition, 2017. ISBN 978-0-8153-4551-0.
Nima Nouri and Steven H. Kleinstein. A spectral clustering-based method for identifying clones from high-throughput b cell repertoire sequencing data. Bioinformatics, 34(13):i341–i349, 2018. doi:10.1093/bioinformatics/bty235.
Stephen L. Nutt, Philip D. Hodgkin, David M. Tarlinton, and Lynn M. Corcoran. The generation of antibody-secreting plasma cells. Nature Reviews Immunology, 15(3):160–171, 2015. doi:10.1038/nri3795.
Duncan K. Ralph and Frederick A. Matsen, 4th. Likelihood-based inference of b cell clonal families. PLoS computational biology, 12(10):e1005086, 2016. doi:10.1371/journal.pcbi.1005086.
Stefan A. Schattgen, Kate Guion, Jeremy Chase Crawford, Aisha Souquette, Alvaro Martinez Barrio, Michael J. T. Stubbington, Paul G. Thomas, and Philip Bradley. Integrating t cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (conga). Nature Biotechnology, Aug 2021. URL: https://doi.org/10.1038/s41587-021-00989-2, doi:10.1038/s41587-021-00989-2.
Chaim A. Schramm and Daniel C. Douek. Beyond hot spots: biases in antibody somatic hypermutation and implications for vaccine design. Frontiers in immunology, 2018. URL: https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2018.01876, doi:10.3389/fimmu.2018.01876.
Nathaniel J. Schuldt and Bryce A. Binstadt. Dual TCR t cells: identity crisis or multitaskers? The Journal of Immunology, 202(3):637–644, January 2019. URL: https://doi.org/10.4049/jimmunol.1800904, doi:10.4049/jimmunol.1800904.
Ian Setliff, Wyatt J. McDonnell, Nagarajan Raju, Robin G. Bombardi, Amyn A. Murji, Cathrine Scheepers, Rutendo Ziki, Charissa Mynhardt, Bryan E. Shepherd, Alusha A. Mamchak, Nigel Garrett, Salim Abdool Karim, Simon A. Mallal, James E. Crowe, Lynn Morris, and Ivelin S. Georgiev. Multi-donor longitudinal antibody repertoire sequencing reveals the existence of public antibody clonotypes in HIV-1 infection. Cell Host & Microbe, 23(6):845–854.e6, June 2018. URL: https://doi.org/10.1016/j.chom.2018.05.001, doi:10.1016/j.chom.2018.05.001.
Zhan Shi, Qingyang Zhang, Huige Yan, Ying Yang, Pingzhang Wang, Yixiao Zhang, Zhenling Deng, Meng Yu, Wenjing Zhou, Qianqian Wang, Xi Yang, Xiaoning Mo, Chi Zhang, Jing Huang, Hui Dai, Baofa Sun, Yongliang Zhao, Liang Zhang, Yun-Gui Yang, and Xiaoyan Qiu. More than one antibody of individual b cells revealed by single-cell immune profiling. Cell Discovery, 5(1):64, 2019. doi:10.1038/s41421-019-0137-3.
Emily Stephenson, Gary Reynolds, Rachel A Botting, Fernando J Calero-Nieto, Michael Morgan, Zewen Kelvin Tuong, Karsten Bach, Waradon Sungnak, Kaylee B Worlock, Masahiro Yoshida, Natsuhiko Kumasaka, Katarzyna Kania, Justin Engelbert, Bayanne Olabi, Jarmila Stremenova Spegarova, Nicola K Wilson, Nicole Mende, Laura Jardine, Louis CS Gardner, Issac Goh, Dave Horsfall, Jim McGrath, Simone Webb, Michael W. Mather, Rik GH Lindeboom, Emma Dann, Ni Huang, Krzysztof Polanski, Elena Prigmore, Florian Gothe, Jonathan Scott, Rebecca P Payne, Kenneth F Baker, Aidan T Hanrath, Ina CD Schim van der Loeff, Andrew S Barr, Amada Sanchez-Gonzalez, Laura Bergamaschi, Federica Mescia, Josephine L Barnes, Eliz Kilich, Angus de Wilton, Anita Saigal, Aarash Saleh, Sam M Janes, Claire M Smith, Nusayhah Gopee, Caroline Wilson, Paul Coupland, Jonathan M Coxhead, Vladimir Y Kiselev, Stijn van Dongen, Jaume Bacardit, Hamish W King, Anthony J Rostron, A John Simpson, Sophie Hambleton, Elisa Laurenti, Paul A Lyons, Kerstin B Meyer, Marko Z Nikolic, Christopher JA Duncan, Ken Smith, Sarah A Teichmann, Menna R Clatworthy, John C Marioni, Berthold Gottgens, and Muzlifah Haniffa and. Single-cell multi-omics analysis of the immune response in COVID-19. Nature Medicine, April 2021. URL: https://www.nature.com/articles/s41591-021-01329-2, doi:10.1038/s41591-021-01329-2.
Michael J T Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, and Sarah A Teichmann. T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods, 13(4):329–332, April 2016.
Chenqu Suo, Krzysztof Polanski, Emma Dann, Rik G. H. Lindeboom, Roser Vilarrasa-Blasi, Roser Vento-Tormo, Muzlifah Haniffa, Kerstin B. Meyer, Lisa M. Dratva, Zewen Kelvin Tuong, Menna R. Clatworthy, and Sarah A. Teichmann. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nature Biotechnology, 2023. doi:10.1038/s41587-023-01734-7.
V. Venturi, K. Kedzierska, D. A. Price, P. C. Doherty, D. C. Douek, S. J. Turner, and M. P. Davenport. Sharing of t cell receptors in antigen-specific responses is driven by convergent recombination. Proceedings of the National Academy of Sciences, 103(49):18691–18696, November 2006. URL: https://doi.org/10.1073/pnas.0608907103, doi:10.1073/pnas.0608907103.
Christian Vettermann and Mark S. Schlissel. Allelic exclusion of immunoglobulin genes: models and mechanisms. Immunological Reviews, 237(1):22–42, August 2010. URL: https://doi.org/10.1111/j.1600-065x.2010.00935.x, doi:10.1111/j.1600-065x.2010.00935.x.
Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis and. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, apr 2023. URL: https://doi.org/10.1038%2Fs41587-023-01733-8, doi:10.1038/s41587-023-01733-8.
Randi Vita, Swapnil Mahajan, James A Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R Cantrell, Daniel K Wheeler, Alessandro Sette, and Bjoern Peters. The immune epitope database (iedb): 2018 update. Nucleic Acids Research, 47(D1):D339–D343, January 2019. URL: https://doi.org/10.1093/nar/gky1006, doi:10.1093/nar/gky1006.
Cédric R Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlović, Igor Snapkov, Geir K Sandve, Sai T Reddy, and Victor Greiff. immuneSIM: tunable multi-feature simulation of b- and t-cell receptor repertoires for immunoinformatics benchmarking. Bioinformatics, April 2020. URL: https://doi.org/10.1093/bioinformatics/btaa158, doi:10.1093/bioinformatics/btaa158.
Patrick C. Wilson, Odette de Bouteiller, Yong-Jun Liu, Kathleen Potter, Jacques Banchereau, J. Donald Capra, and Virginia Pascual. Somatic hypermutation introduces insertions and deletions into immunoglobulin v genes. Journal of Experimental Medicine, 187(1):59–70, 1998. doi:10.1084/jem.187.1.59.
Thomas D. Wu, Shravan Madireddi, Patricia E. de Almeida, Romain Banchereau, Ying-Jiun J. Chen, Avantika S. Chitre, Eugene Y. Chiang, Hina Iftikhar, William E. O'Gorman, Amelia Au-Yeung, Chikara Takahashi, Leonard D. Goldstein, Chungkee Poon, Shilpa Keerthivasan, Denise E. de Almeida Nagata, Xiangnan Du, Hyang-Mi Lee, Karl L. Banta, Sanjeev Mariathasan, Meghna Das Thakur, Mahrukh A. Huseni, Marcus Ballinger, Ivette Estay, Patrick Caplazi, Zora Modrusan, Lélia Delamarre, Ira Mellman, Richard Bourgon, and Jane L. Grogan. Peripheral t cell expansion predicts tumour infiltration and clinical response. Nature, 579(7798):274–278, February 2020. URL: https://doi.org/10.1038/s41586-020-2056-8, doi:10.1038/s41586-020-2056-8.
Gur Yaari and Steven H. Kleinstein. Practical guidelines for b-cell receptor repertoire sequencing analysis. Genome Medicine, 7(1):121, 2015. doi:10.1186/s13073-015-0243-2.
Lei Zhang, Xin Yu, Liangtao Zheng, Yuanyuan Zhang, Yansen Li, Qiao Fang, Ranran Gao, Boxi Kang, Qiming Zhang, Julie Y Huang, Hiroyasu Konno, Xinyi Guo, Yingjiang Ye, Songyuan Gao, Shan Wang, Xueda Hu, Xianwen Ren, Zhanlong Shen, Wenjun Ouyang, and Zemin Zhang. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature, 564(7735):268–272, December 2018.
Lanwei Zhu, Qi Peng, Yingjie Wu, and Xinsheng Yao. 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. Cellular and Molecular Life Sciences, 80(11):319, 2023. doi:10.1007/s00018-023-04973-8.
Roberta Pelanda. Dual immunoglobulin light chain b cells: trojan horses of autoimmunity? Current Opinion in Immunology, 27:53–59, 2014. URL: https://www.sciencedirect.com/science/article/pii/S095279151400020X, doi:10.1016/j.coi.2014.01.012.