{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T16:05:30Z","timestamp":1788969930338,"version":"build-2803163510"},"reference-count":117,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2021,2,8]],"date-time":"2021-02-08T00:00:00Z","timestamp":1612742400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,2,8]],"date-time":"2021-02-08T00:00:00Z","timestamp":1612742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100008530","name":"EC | European Regional Development Fund","doi-asserted-by":"publisher","award":["CZ.02.2.69\/0.0\/0.0\/19_074\/0012727"],"award-info":[{"award-number":["CZ.02.2.69\/0.0\/0.0\/19_074\/0012727"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["1935\/17"],"award-info":[{"award-number":["1935\/17"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["16-15-00149"],"award-info":[{"award-number":["16-15-00149"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003443","name":"Ministry of Education and Science of the Russian Federation","doi-asserted-by":"publisher","award":["14.W03.31.0005"],"award-info":[{"award-number":["14.W03.31.0005"]}],"id":[{"id":"10.13039\/501100003443","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Aging"],"DOI":"10.1038\/s43587-021-00029-3","type":"journal-article","created":{"date-parts":[[2021,2,8]],"date-time":"2021-02-08T19:43:01Z","timestamp":1612813381000},"page":"179-189","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Distinct organization of adaptive immunity in the long-lived rodent Spalax galili"],"prefix":"10.1038","volume":"1","author":[{"given":"M.","family":"Izraelson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9722-0533","authenticated-orcid":false,"given":"M.","family":"Metsger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. N.","family":"Davydov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I. A.","family":"Shagina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. A.","family":"Dronina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. S.","family":"Obraztsova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. A.","family":"Miskevich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I. Z.","family":"Mamedov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. N.","family":"Volchkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T. O.","family":"Nakonechnaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Shugay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8484-6067","authenticated-orcid":false,"given":"D. A.","family":"Bolotin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. B.","family":"Staroverov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. V.","family":"Sharonov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. Y.","family":"Kondratyuk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. V.","family":"Zagaynova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Lukyanov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I.","family":"Shams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6295-1392","authenticated-orcid":false,"given":"O. V.","family":"Britanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0430-790X","authenticated-orcid":false,"given":"D. M.","family":"Chudakov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,2,8]]},"reference":[{"key":"29_CR1","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.immuni.2018.02.010","volume":"48","author":"SC Jameson","year":"2018","unstructured":"Jameson, S. C. & Masopust, D. Understanding subset diversity in T cell memory. Immunity 48, 214\u2013226 (2018).","journal-title":"Immunity"},{"key":"29_CR2","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1615\/CritRevImmunol.2014010373","volume":"34","author":"DJ Gasper","year":"2014","unstructured":"Gasper, D. J., Tejera, M. M. & Suresh, M. CD4 T-cell memory generation and maintenance. Crit. Rev. Immunol. 34, 121\u2013146 (2014).","journal-title":"Crit. Rev. Immunol."},{"key":"29_CR3","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/nri3802","volume":"15","author":"T Kurosaki","year":"2015","unstructured":"Kurosaki, T., Kometani, K. & Ise, W. Memory B cells. Nat. Rev. Immunol. 15, 149\u2013159 (2015).","journal-title":"Nat. Rev. Immunol."},{"key":"29_CR4","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nri3128","volume":"12","author":"M McHeyzer-Williams","year":"2011","unstructured":"McHeyzer-Williams, M., Okitsu, S., Wang, N. & McHeyzer-Williams, L. Molecular programming of B cell memory. Nat. Rev. Immunol. 12, 24\u201334 (2011).","journal-title":"Nat. Rev. Immunol."},{"key":"29_CR5","doi-asserted-by":"publisher","first-page":"2963","DOI":"10.1016\/j.celrep.2020.02.022","volume":"30","author":"O Grimsholm","year":"2020","unstructured":"Grimsholm, O. et al. The interplay between CD27(dull) and CD27(bright) B cells ensures the flexibility, stability, and resilience of human B cell memory. Cell Rep. 30, 2963\u20132977 (2020).","journal-title":"Cell Rep."},{"key":"29_CR6","doi-asserted-by":"publisher","first-page":"5005","DOI":"10.4049\/jimmunol.1600005","volume":"196","author":"OV Britanova","year":"2016","unstructured":"Britanova, O. V. et al. Dynamics of individual T cell repertoires: from cord blood to centenarians. J. Immunol. 196, 5005\u20135013 (2016).","journal-title":"J. Immunol."},{"key":"29_CR7","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1172\/JCI12673","volume":"107","author":"NR Rose","year":"2001","unstructured":"Rose, N. R. Infection, mimics, and autoimmune disease. J. Clin. Invest. 107, 943\u2013944 (2001).","journal-title":"J. Clin. Invest."},{"key":"29_CR8","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1016\/j.it.2009.05.005","volume":"30","author":"S Kivity","year":"2009","unstructured":"Kivity, S., Agmon-Levin, N., Blank, M. & Shoenfeld, Y. Infections and autoimmunity\u2014friends or foes? Trends Immunol. 30, 409\u2013414 (2009).","journal-title":"Trends Immunol."},{"key":"29_CR9","doi-asserted-by":"publisher","first-page":"245","DOI":"10.3184\/003685011X13139280383942","volume":"94","author":"HA Van Den Berg","year":"2011","unstructured":"Van Den Berg, H. A., Molina-Paris, C. & Sewell, A. K. Specific T-cell activation in an unspecific T-cell repertoire. Sci. Prog. 94, 245\u2013264 (2011).","journal-title":"Sci. Prog."},{"key":"29_CR10","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1016\/j.immuni.2017.03.010","volume":"46","author":"JJ Goronzy","year":"2017","unstructured":"Goronzy, J. J. & Weyand, C. M. Successful and maladaptive T cell aging. Immunity 46, 364\u2013378 (2017).","journal-title":"Immunity"},{"key":"29_CR11","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1093\/intimm\/dxaa006","volume":"32","author":"N Minato","year":"2020","unstructured":"Minato, N., Hattori, M. & Hamazaki, Y. Physiology and pathology of T-cell aging. Int. Immunol. 32, 223\u2013231 (2020).","journal-title":"Int. Immunol."},{"key":"29_CR12","doi-asserted-by":"publisher","first-page":"331","DOI":"10.3389\/fimmu.2014.00331","volume":"5","author":"DL Turner","year":"2014","unstructured":"Turner, D. L. & Farber, D. L. Mucosal resident memory CD4 T cells in protection and immunopathology. Front. Immunol. 5, 331 (2014).","journal-title":"Front. Immunol."},{"key":"29_CR13","doi-asserted-by":"publisher","first-page":"D1083","DOI":"10.1093\/nar\/gkx1042","volume":"46","author":"R Tacutu","year":"2018","unstructured":"Tacutu, R. et al. Human ageing genomic resources: new and updated databases. Nucleic Acids Res. 46, D1083\u2013D1090 (2018).","journal-title":"Nucleic Acids Res."},{"key":"29_CR14","doi-asserted-by":"publisher","first-page":"e31157","DOI":"10.7554\/eLife.31157","volume":"7","author":"JG Ruby","year":"2018","unstructured":"Ruby, J. G., Smith, M. & Buffenstein, R. Naked mole-rat mortality rates defy gompertzian laws by not increasing with age. eLife 7, e31157 (2018).","journal-title":"eLife"},{"key":"29_CR15","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1093\/ilar.52.1.41","volume":"52","author":"YH Edrey","year":"2011","unstructured":"Edrey, Y. H., Hanes, M., Pinto, M., Mele, J. & Buffenstein, R. Successful aging and sustained good health in the naked mole rat: a long-lived mammalian model for biogerontology and biomedical research. ILAR J. 52, 41\u201353 (2011).","journal-title":"ILAR J."},{"key":"29_CR16","doi-asserted-by":"publisher","first-page":"19392","DOI":"10.1073\/pnas.1217211109","volume":"109","author":"V Gorbunova","year":"2012","unstructured":"Gorbunova, V. et al. Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism. Proc. Natl Acad. Sci. USA 109, 19392\u201319396 (2012).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR17","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1038\/nature12234","volume":"499","author":"X Tian","year":"2013","unstructured":"Tian, X. et al. High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat. Nature 499, 346\u2013349 (2013).","journal-title":"Nature"},{"key":"29_CR18","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7007-11-91","volume":"11","author":"I Manov","year":"2013","unstructured":"Manov, I. et al. Pronounced cancer resistance in a subterranean rodent, the blind mole-rat, Spalax: in vivo and in vitro evidence. BMC Biol. 11, 91 (2013).","journal-title":"BMC Biol."},{"key":"29_CR19","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1038\/nrg3728","volume":"15","author":"V Gorbunova","year":"2014","unstructured":"Gorbunova, V., Seluanov, A., Zhang, Z., Gladyshev, V. N. & Vijg, J. Comparative genetics of longevity and cancer: insights from long-lived rodents. Nat. Rev. Genet. 15, 531\u2013540 (2014).","journal-title":"Nat. Rev. Genet."},{"key":"29_CR20","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-13905-z","volume":"7","author":"H Schmidt","year":"2017","unstructured":"Schmidt, H. et al. Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax\u2014a liver transcriptomics approach. Sci. Rep. 7, 14348 (2017).","journal-title":"Sci. Rep."},{"key":"29_CR21","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5417-z","volume":"20","author":"R Altwasser","year":"2019","unstructured":"Altwasser, R. et al. The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: insights into cancer resistance mechanisms. BMC Genomics 20, 17 (2019).","journal-title":"BMC Genomics"},{"key":"29_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4966","volume":"5","author":"X Fang","year":"2014","unstructured":"Fang, X. et al. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat. Commun. 5, 3966 (2014).","journal-title":"Nat. Commun."},{"key":"29_CR23","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1038\/nmeth.3364","volume":"12","author":"DA Bolotin","year":"2015","unstructured":"Bolotin, D. A. et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods 12, 380\u2013381 (2015).","journal-title":"Nat. Methods"},{"key":"29_CR24","doi-asserted-by":"publisher","first-page":"e0182029","DOI":"10.1371\/journal.pone.0182029","volume":"12","author":"DK Lanning","year":"2017","unstructured":"Lanning, D. K., Esteves, P. J. & Knight, K. L. The remnant of the European rabbit (Oryctolagus cuniculus) IgD gene. PLoS ONE 12, e0182029 (2017).","journal-title":"PLoS ONE"},{"key":"29_CR25","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1111\/imm.12857","volume":"153","author":"M Izraelson","year":"2018","unstructured":"Izraelson, M. et al. Comparative analysis of murine T-cell receptor repertoires. Immunology 153, 133\u2013144 (2018).","journal-title":"Immunology"},{"key":"29_CR26","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1084\/jem.179.2.609","volume":"179","author":"DN Posnett","year":"1994","unstructured":"Posnett, D. N., Sinha, R., Kabak, S. & Russo, C. Clonal populations of T cells in normal elderly humans: the T cell equivalent to \u201cbenign monoclonal gammapathy\u201d. J. Exp. Med. 179, 609\u2013618 (1994).","journal-title":"J. Exp. Med."},{"key":"29_CR27","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1084\/jem.20040437","volume":"200","author":"I Messaoudi","year":"2004","unstructured":"Messaoudi, I., Lemaoult, J., Guevara-Patino, J. A., Metzner, B. M. & Nikolich-Zugich, J. Age-related CD8 T cell clonal expansions constrict CD8 T cell repertoire and have the potential to impair immune defense. J. Exp. Med. 200, 1347\u20131358 (2004).","journal-title":"J. Exp. Med."},{"key":"29_CR28","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.immuni.2020.11.005","volume":"54","author":"DA Mogilenko","year":"2020","unstructured":"Mogilenko, D. A. et al. Comprehensive profiling of an aging immune system reveals clonal GZMK+ CD8+ T cells as conserved hallmark of inflammaging. Immunity 54, 99\u2013115 (2020).","journal-title":"Immunity"},{"key":"29_CR29","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1002\/eji.201445277","volume":"45","author":"D Franckaert","year":"2015","unstructured":"Franckaert, D. et al. Premature thymic involution is independent of structural plasticity of the thymic stroma. Eur. J. Immunol. 45, 1535\u20131547 (2015).","journal-title":"Eur. J. Immunol."},{"key":"29_CR30","first-page":"280","volume":"3","author":"J Gui","year":"2012","unstructured":"Gui, J., Mustachio, L. M., Su, D. M. & Craig, R. W. Thymus size and age-related thymic involution: early programming, sexual dimorphism, progenitors and stroma. Aging Dis. 3, 280\u2013290 (2012).","journal-title":"Aging Dis."},{"key":"29_CR31","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1182\/blood.V79.6.1472.1472","volume":"79","author":"A Bonati","year":"1992","unstructured":"Bonati, A. et al. T-cell receptor beta-chain gene rearrangement and expression during human thymic ontogenesis. Blood 79, 1472\u20131483 (1992).","journal-title":"Blood"},{"key":"29_CR32","doi-asserted-by":"publisher","first-page":"16161","DOI":"10.1073\/pnas.1212755109","volume":"109","author":"A Murugan","year":"2012","unstructured":"Murugan, A., Mora, T., Walczak, A. M. & Callan, C. G. Jr. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc. Natl Acad. Sci. USA 109, 16161\u201316166 (2012).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR33","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.4049\/jimmunol.1003898","volume":"186","author":"V Venturi","year":"2011","unstructured":"Venturi, V. et al. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J. Immunol. 186, 4285\u20134294 (2011).","journal-title":"J. Immunol."},{"key":"29_CR34","doi-asserted-by":"publisher","first-page":"19414","DOI":"10.1073\/pnas.1010586107","volume":"107","author":"MF Quigley","year":"2010","unstructured":"Quigley, M. F. et al. Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire. Proc. Natl Acad. Sci. USA 107, 19414\u201319419 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR35","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1007\/BF00345618","volume":"20","author":"D Nizetic","year":"1984","unstructured":"Nizetic, D. et al. Major histocompatibility complex of the mole-rat. I. Serological and biochemical analysis. Immunogenetics 20, 443\u2013451 (1984).","journal-title":"Immunogenetics"},{"key":"29_CR36","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/s12979-020-00195-9","volume":"17","author":"C Krishna","year":"2020","unstructured":"Krishna, C., Chowell, D., Gonen, M., Elhanati, Y. & Chan, T. A. Genetic and environmental determinants of human TCR repertoire diversity. Immun. Ageing 17, 26 (2020).","journal-title":"Immun. Ageing"},{"key":"29_CR37","doi-asserted-by":"publisher","first-page":"5980","DOI":"10.1073\/pnas.1319389111","volume":"111","author":"IV Zvyagin","year":"2014","unstructured":"Zvyagin, I. V. et al. Distinctive properties of identical twins\u2019 TCR repertoires revealed by high-throughput sequencing. Proc. Natl Acad. Sci. USA 111, 5980\u20135985 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR38","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1073\/pnas.1915008117","volume":"117","author":"H Tanno","year":"2020","unstructured":"Tanno, H. et al. Determinants governing T cell receptor alpha\/beta-chain pairing in repertoire formation of identical twins. Proc. Natl Acad. Sci. USA 117, 532\u2013540 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR39","doi-asserted-by":"publisher","first-page":"13659","DOI":"10.1073\/pnas.2003170117","volume":"117","author":"NN Logunova","year":"2020","unstructured":"Logunova, N. N. et al. MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naive CD4+ T cells. Proc. Natl Acad. Sci. USA 117, 13659\u201313669 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR40","doi-asserted-by":"publisher","first-page":"1618","DOI":"10.3389\/fimmu.2018.01618","volume":"9","author":"ES Egorov","year":"2018","unstructured":"Egorov, E. S. et al. The changing landscape of naive T cell receptor repertoire with human aging. Front. Immunol. 9, 1618 (2018).","journal-title":"Front. Immunol."},{"key":"29_CR41","doi-asserted-by":"publisher","first-page":"1478","DOI":"10.3389\/fimmu.2018.01478","volume":"9","author":"LC Garner","year":"2018","unstructured":"Garner, L. C., Klenerman, P. & Provine, N. M. Insights into mucosal-associated invariant T cell biology from studies of invariant natural killer T cells. Front. Immunol. 9, 1478 (2018).","journal-title":"Front. Immunol."},{"key":"29_CR42","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02540-x","volume":"9","author":"LJ Howson","year":"2018","unstructured":"Howson, L. J. et al. MAIT cell clonal expansion and TCR repertoire shaping in human volunteers challenged with Salmonella Paratyphi A. Nat. Commun. 9, 253 (2018).","journal-title":"Nat. Commun."},{"key":"29_CR43","doi-asserted-by":"publisher","first-page":"2305","DOI":"10.1084\/jem.20130958","volume":"210","author":"R Reantragoon","year":"2013","unstructured":"Reantragoon, R. et al. Antigen-loaded MR1 tetramers define T cell receptor heterogeneity in mucosal-associated invariant T cells. J. Exp. Med. 210, 2305\u20132320 (2013).","journal-title":"J. Exp. Med."},{"key":"29_CR44","doi-asserted-by":"publisher","first-page":"e22057","DOI":"10.7554\/eLife.22057","volume":"6","author":"A Madi","year":"2017","unstructured":"Madi, A. et al. T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences. eLife 6, e22057 (2017).","journal-title":"eLife"},{"key":"29_CR45","doi-asserted-by":"publisher","first-page":"D419","DOI":"10.1093\/nar\/gkx760","volume":"46","author":"MEA Shugay","year":"2017","unstructured":"Shugay, M. E. A. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Res. 46, D419\u2013D427 (2017).","journal-title":"Nucleic Acids Res."},{"key":"29_CR46","doi-asserted-by":"publisher","first-page":"E119","DOI":"10.1073\/pnas.1320777110","volume":"111","author":"R Bedel","year":"2014","unstructured":"Bedel, R. et al. Effective functional maturation of invariant natural killer T cells is constrained by negative selection and T-cell antigen receptor affinity. Proc. Natl Acad. Sci. USA 111, E119\u2013E128 (2014).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10198-w","volume":"10","author":"HF Koay","year":"2019","unstructured":"Koay, H. F. et al. Diverse MR1-restricted T cells in mice and humans. Nat. Commun. 10, 2243 (2019).","journal-title":"Nat. Commun."},{"key":"29_CR48","doi-asserted-by":"publisher","first-page":"e38358","DOI":"10.7554\/eLife.38358","volume":"7","author":"WS DeWitt 3rd","year":"2018","unstructured":"DeWitt, W. S. 3rd et al. Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. eLife 7, e38358 (2018).","journal-title":"eLife"},{"key":"29_CR49","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-42120-1","volume":"9","author":"DKJ Pieren","year":"2019","unstructured":"Pieren, D. K. J., Smits, N. A. M., van de Garde, M. D. B. & Guichelaar, T. Response kinetics reveal novel features of ageing in murine T cells. Sci. Rep. 9, 5587 (2019).","journal-title":"Sci. Rep."},{"key":"29_CR50","doi-asserted-by":"publisher","first-page":"1861","DOI":"10.1084\/jem.20170494","volume":"214","author":"D Fang","year":"2017","unstructured":"Fang, D. & Zhu, J. Dynamic balance between master transcription factors determines the fates and functions of CD4 T cell and innate lymphoid cell subsets. J. Exp. Med. 214, 1861\u20131876 (2017).","journal-title":"J. Exp. Med."},{"key":"29_CR51","doi-asserted-by":"publisher","first-page":"eaaw8330","DOI":"10.1126\/sciadv.aaw8330","volume":"5","author":"Y Elyahu","year":"2019","unstructured":"Elyahu, Y. et al. Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes. Sci. Adv. 5, eaaw8330 (2019).","journal-title":"Sci. Adv."},{"key":"29_CR52","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9570","volume":"6","author":"MJ Peters","year":"2015","unstructured":"Peters, M. J. et al. The transcriptional landscape of age in human peripheral blood. Nat. Commun. 6, 8570 (2015).","journal-title":"Nat. Commun."},{"key":"29_CR53","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14396-9","volume":"11","author":"EJ Marquez","year":"2020","unstructured":"Marquez, E. J. et al. Sexual-dimorphism in human immune system aging. Nat. Commun. 11, 751 (2020).","journal-title":"Nat. Commun."},{"key":"29_CR54","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1038\/ni1022","volume":"5","author":"G Eberl","year":"2004","unstructured":"Eberl, G. et al. An essential function for the nuclear receptor ROR\u03b3t in the generation of fetal lymphoid tissue inducer cells. Nat. Immunol. 5, 64\u201373 (2004).","journal-title":"Nat. Immunol."},{"key":"29_CR55","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1111\/acel.12191","volume":"13","author":"SK Garg","year":"2014","unstructured":"Garg, S. K. et al. Aging is associated with increased regulatory T-cell function. Aging Cell 13, 441\u2013448 (2014).","journal-title":"Aging Cell"},{"key":"29_CR56","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1016\/j.mad.2009.08.006","volume":"130","author":"R Channappanavar","year":"2009","unstructured":"Channappanavar, R., Twardy, B. S., Krishna, P. & Suvas, S. Advancing age leads to predominance of inhibitory receptor expressing CD4 T cells. Mech. Ageing Dev. 130, 709\u2013712 (2009).","journal-title":"Mech. Ageing Dev."},{"key":"29_CR57","doi-asserted-by":"publisher","first-page":"280","DOI":"10.4049\/jimmunol.178.1.280","volume":"178","author":"MA Burchill","year":"2007","unstructured":"Burchill, M. A., Yang, J., Vogtenhuber, C., Blazar, B. R. & Farrar, M. A. IL-2 receptor \u03b2-dependent STAT5 activation is required for the development of Foxp3+ regulatory T cells. J. Immunol. 178, 280\u2013290 (2007).","journal-title":"J. Immunol."},{"key":"29_CR58","doi-asserted-by":"publisher","first-page":"890","DOI":"10.1038\/nature04790","volume":"441","author":"MA Williams","year":"2006","unstructured":"Williams, M. A., Tyznik, A. J. & Bevan, M. J. Interleukin-2 signals during priming are required for secondary expansion of CD8+ memory T cells. Nature 441, 890\u2013893 (2006).","journal-title":"Nature"},{"key":"29_CR59","doi-asserted-by":"publisher","first-page":"224","DOI":"10.12688\/f1000research.7634.1","volume":"5","author":"WJ Leonard","year":"2016","unstructured":"Leonard, W. J. & Wan, C. K. IL-21 signaling in immunity. F1000Res 5, 224 (2016).","journal-title":"F1000Res"},{"key":"29_CR60","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1111\/j.1365-2567.2007.02730.x","volume":"123","author":"K Skak","year":"2008","unstructured":"Skak, K., Frederiksen, K. S. & Lundsgaard, D. Interleukin-21 activates human natural killer cells and modulates their surface receptor expression. Immunology 123, 575\u2013583 (2008).","journal-title":"Immunology"},{"key":"29_CR61","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1016\/j.immuni.2008.11.002","volume":"29","author":"CD Surh","year":"2008","unstructured":"Surh, C. D. & Sprent, J. Homeostasis of naive and memory T cells. Immunity 29, 848\u2013862 (2008).","journal-title":"Immunity"},{"key":"29_CR62","doi-asserted-by":"publisher","first-page":"4965","DOI":"10.4049\/jimmunol.171.10.4965","volume":"171","author":"EA Lynch","year":"2003","unstructured":"Lynch, E. A., Heijens, C. A., Horst, N. F., Center, D. M. & Cruikshank, W. W. Cutting edge: IL-16\/CD4 preferentially induces Th1 cell migration: requirement of CCR5. J. Immunol. 171, 4965\u20134968 (2003).","journal-title":"J. Immunol."},{"key":"29_CR63","doi-asserted-by":"publisher","DOI":"10.1186\/1742-2094-3-13","volume":"3","author":"DS Skundric","year":"2006","unstructured":"Skundric, D. S., Cai, J., Cruikshank, W. W. & Gveric, D. Production of IL-16 correlates with CD4+ Th1 inflammation and phosphorylation of axonal cytoskeleton in multiple sclerosis lesions. J. Neuroinflammation 3, 13 (2006).","journal-title":"J. Neuroinflammation"},{"key":"29_CR64","doi-asserted-by":"publisher","first-page":"2081","DOI":"10.1084\/jem.170.6.2081","volume":"170","author":"DF Fiorentino","year":"1989","unstructured":"Fiorentino, D. F., Bond, M. W. & Mosmann, T. R. Two types of mouse T helper cell. IV. Th2 clones secrete a factor that inhibits cytokine production by Th1 clones. J. Exp. Med. 170, 2081\u20132095 (1989).","journal-title":"J. Exp. Med."},{"key":"29_CR65","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1146\/annurev.immunol.19.1.683","volume":"19","author":"KW Moore","year":"2001","unstructured":"Moore, K. W., de Waal Malefyt, R., Coffman, R. L. & O\u2019Garra, A. Interleukin-10 and the interleukin-10 receptor. Annu. Rev. Immunol. 19, 683\u2013765 (2001).","journal-title":"Annu. Rev. Immunol."},{"key":"29_CR66","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1159\/000447692","volume":"170","author":"D Bagnasco","year":"2016","unstructured":"Bagnasco, D., Ferrando, M., Varricchi, G., Passalacqua, G. & Canonica, G. W. A critical evaluation of anti-IL-13 and anti-IL-4 strategies in severe asthma. Int. Arch. Allergy Immunol. 170, 122\u2013131 (2016).","journal-title":"Int. Arch. Allergy Immunol."},{"key":"29_CR67","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1038\/ni1261","volume":"6","author":"H Park","year":"2005","unstructured":"Park, H. et al. A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat. Immunol. 6, 1133\u20131141 (2005).","journal-title":"Nat. Immunol."},{"key":"29_CR68","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1016\/j.cell.2006.07.035","volume":"126","author":"II Ivanov","year":"2006","unstructured":"Ivanov, I. I. et al. The orphan nuclear receptor ROR\u03b3t directs the differentiation program of proinflammatory IL-17+ T helper cells. Cell 126, 1121\u20131133 (2006).","journal-title":"Cell"},{"key":"29_CR69","doi-asserted-by":"crossref","first-page":"5909","DOI":"10.4049\/jimmunol.161.11.5909","volume":"161","author":"MV Soares","year":"1998","unstructured":"Soares, M. V. et al. IL-7-dependent extrathymic expansion of CD45RA+ T cells enables preservation of a naive repertoire. J. Immunol. 161, 5909\u20135917 (1998).","journal-title":"J. Immunol."},{"key":"29_CR70","doi-asserted-by":"publisher","first-page":"4807853","DOI":"10.1155\/2017\/4807853","volume":"2017","author":"V Nguyen","year":"2017","unstructured":"Nguyen, V., Mendelsohn, A. & Larrick, J. W. Interleukin-7 and immunosenescence. J. Immunol. Res. 2017, 4807853 (2017).","journal-title":"J. Immunol. Res."},{"key":"29_CR71","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s12979-015-0048-6","volume":"12","author":"WM Passtoors","year":"2015","unstructured":"Passtoors, W. M. et al. IL7R gene expression network associates with human healthy ageing. Immun. Ageing 12, 21 (2015).","journal-title":"Immun. Ageing"},{"key":"29_CR72","doi-asserted-by":"publisher","first-page":"e16578","DOI":"10.7554\/eLife.16578","volume":"5","author":"F Horns","year":"2016","unstructured":"Horns, F. et al. Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. eLife 5, e16578 (2016).","journal-title":"eLife"},{"key":"29_CR73","doi-asserted-by":"publisher","DOI":"10.1186\/s12948-017-0077-0","volume":"15","author":"MT Ventura","year":"2017","unstructured":"Ventura, M. T., Casciaro, M., Gangemi, S. & Buquicchio, R. Immunosenescence in aging: between immune cells depletion and cytokines up-regulation. Clin. Mol. Allergy 15, 21 (2017).","journal-title":"Clin. Mol. Allergy"},{"key":"29_CR74","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1111\/j.1365-2249.1992.tb07954.x","volume":"90","author":"R Paganelli","year":"1992","unstructured":"Paganelli, R. et al. Changes in circulating B cells and immunoglobulin classes and subclasses in a healthy aged population. Clin. Exp. Immunol. 90, 351\u2013354 (1992).","journal-title":"Clin. Exp. Immunol."},{"key":"29_CR75","doi-asserted-by":"publisher","first-page":"5449","DOI":"10.4049\/jimmunol.1103347","volume":"189","author":"T Rogosch","year":"2012","unstructured":"Rogosch, T. et al. IgA response in preterm neonates shows little evidence of antigen-driven selection. J. Immunol. 189, 5449\u20135456 (2012).","journal-title":"J. Immunol."},{"key":"29_CR76","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1038\/icb.2017.43","volume":"95","author":"BG de Jong","year":"2017","unstructured":"de Jong, B. G. et al. Human IgG2- and IgG4-expressing memory B cells display enhanced molecular and phenotypic signs of maturity and accumulate with age. Immunol. Cell Biol. 95, 744\u2013752 (2017).","journal-title":"Immunol. Cell Biol."},{"key":"29_CR77","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.3389\/fimmu.2020.01734","volume":"11","author":"M Ghraichy","year":"2020","unstructured":"Ghraichy, M. et al. Maturation of the human immunoglobulin heavy chain repertoire with age. Front. Immunol. 11, 1734 (2020).","journal-title":"Front. Immunol."},{"key":"29_CR78","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1002\/eji.201141890","volume":"42","author":"YS Choi","year":"2012","unstructured":"Choi, Y. S., Dieter, J. A., Rothaeusler, K., Luo, Z. & Baumgarth, N. B-1 cells in the bone marrow are a significant source of natural IgM. Eur. J. Immunol. 42, 120\u2013129 (2012).","journal-title":"Eur. J. Immunol."},{"key":"29_CR79","doi-asserted-by":"publisher","first-page":"3387","DOI":"10.4049\/jimmunol.1700943","volume":"199","author":"N Baumgarth","year":"2017","unstructured":"Baumgarth, N. A Hard(y) look at B-1 cell development and function. J. Immunol. 199, 3387\u20133394 (2017).","journal-title":"J. Immunol."},{"key":"29_CR80","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1111\/nyas.12825","volume":"1362","author":"NE Holodick","year":"2015","unstructured":"Holodick, N. E. & Rothstein, T. L. B cells in the aging immune system: time to consider B-1 cells. Ann. N. Y. Acad. Sci. 1362, 176\u2013187 (2015).","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"29_CR81","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.4049\/jimmunol.1700568","volume":"200","author":"TA Prohaska","year":"2018","unstructured":"Prohaska, T. A. et al. Massively parallel sequencing of peritoneal and splenic B cell repertoires highlights unique properties of B-1 cell antibodies. J. Immunol. 200, 1702\u20131717 (2018).","journal-title":"J. Immunol."},{"key":"29_CR82","doi-asserted-by":"publisher","first-page":"16671","DOI":"10.1073\/pnas.0808081105","volume":"105","author":"A Kosmrlj","year":"2008","unstructured":"Kosmrlj, A., Jha, A. K., Huseby, E. S., Kardar, M. & Chakraborty, A. K. How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc. Natl Acad. Sci. USA 105, 16671\u201316676 (2008).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR83","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1038\/nature08997","volume":"465","author":"A Kosmrlj","year":"2010","unstructured":"Kosmrlj, A. et al. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465, 350\u2013354 (2010).","journal-title":"Nature"},{"key":"29_CR84","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1038\/ni.3491","volume":"17","author":"BD Stadinski","year":"2016","unstructured":"Stadinski, B. D. et al. Hydrophobic CDR3 residues promote the development of self-reactive T cells. Nat. Immunol. 17, 946\u2013955 (2016).","journal-title":"Nat. Immunol."},{"key":"29_CR85","doi-asserted-by":"publisher","first-page":"1806","DOI":"10.4049\/jimmunol.181.3.1806","volume":"181","author":"AL Tang","year":"2008","unstructured":"Tang, A. L. et al. CTLA4 expression is an indicator and regulator of steady-state CD4+ FoxP3+ T cell homeostasis. J. Immunol. 181, 1806\u20131813 (2008).","journal-title":"J. Immunol."},{"key":"29_CR86","doi-asserted-by":"publisher","first-page":"E2383","DOI":"10.1073\/pnas.1603892113","volume":"113","author":"K Klocke","year":"2016","unstructured":"Klocke, K., Sakaguchi, S., Holmdahl, R. & Wing, K. Induction of autoimmune disease by deletion of CTLA-4 in mice in adulthood. Proc. Natl Acad. Sci. USA 113, E2383\u2013E2392 (2016).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"29_CR87","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.imlet.2017.02.007","volume":"184","author":"LSK Walker","year":"2017","unstructured":"Walker, L. S. K. EFIS lecture: understanding the CTLA-4 checkpoint in the maintenance of immune homeostasis. Immunol. Lett. 184, 43\u201350 (2017).","journal-title":"Immunol. Lett."},{"key":"29_CR88","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1016\/j.immuni.2012.02.006","volume":"36","author":"I den Braber","year":"2012","unstructured":"den Braber, I. et al. Maintenance of peripheral naive T cells is sustained by thymus output in mice but not humans. Immunity 36, 288\u2013297 (2012).","journal-title":"Immunity"},{"key":"29_CR89","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/nature10533","volume":"479","author":"EB Kim","year":"2011","unstructured":"Kim, E. B. et al. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 479, 223\u2013227 (2011).","journal-title":"Nature"},{"key":"29_CR90","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s00335-016-9648-5","volume":"27","author":"KN Lewis","year":"2016","unstructured":"Lewis, K. N. et al. Unraveling the message: insights into comparative genomics of the naked mole-rat. Mamm. Genome 27, 259\u2013278 (2016).","journal-title":"Mamm. Genome"},{"key":"29_CR91","doi-asserted-by":"publisher","DOI":"10.1038\/srep38624","volume":"6","author":"A Malik","year":"2016","unstructured":"Malik, A. et al. Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome. Sci. Rep. 6, 38624 (2016).","journal-title":"Sci. Rep."},{"key":"29_CR92","doi-asserted-by":"publisher","first-page":"1558","DOI":"10.1093\/nar\/27.6.1558","volume":"27","author":"M Matz","year":"1999","unstructured":"Matz, M. et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27, 1558\u20131560 (1999).","journal-title":"Nucleic Acids Res."},{"key":"29_CR93","doi-asserted-by":"publisher","first-page":"6155","DOI":"10.4049\/jimmunol.1500215","volume":"194","author":"ES Egorov","year":"2015","unstructured":"Egorov, E. S. et al. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. J. Immunol. 194, 6155\u20136163 (2015).","journal-title":"J. Immunol."},{"key":"29_CR94","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1038\/nprot.2016.093","volume":"11","author":"MA Turchaninova","year":"2016","unstructured":"Turchaninova, M. A. et al. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat. Protoc. 11, 1599\u20131616 (2016).","journal-title":"Nat. Protoc."},{"key":"29_CR95","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09180-3","volume":"10","author":"J Weber","year":"2019","unstructured":"Weber, J. et al. PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice. Nat. Commun. 10, 1415 (2019).","journal-title":"Nat. Commun."},{"key":"29_CR96","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1038\/nmeth.1778","volume":"9","author":"T Kivioja","year":"2012","unstructured":"Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72\u201374 (2012).","journal-title":"Nat. Methods"},{"key":"29_CR97","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows\u2013Wheeler transform. Bioinformatics 26, 589\u2013595 (2010).","journal-title":"Bioinformatics"},{"key":"29_CR98","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4230","volume":"5","author":"Y Yu","year":"2014","unstructured":"Yu, Y. et al. A rat RNA-seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat. Commun. 5, 3230 (2014).","journal-title":"Nat. Commun."},{"key":"29_CR99","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/nmeth.2960","volume":"11","author":"M Shugay","year":"2014","unstructured":"Shugay, M. et al. Towards error-free profiling of immune repertoires. Nat. Methods 11, 653\u2013655 (2014).","journal-title":"Nat. Methods"},{"key":"29_CR100","doi-asserted-by":"publisher","first-page":"e1004503","DOI":"10.1371\/journal.pcbi.1004503","volume":"11","author":"M Shugay","year":"2015","unstructured":"Shugay, M. et al. VDJtools: unifying post-analysis of T cell receptor repertoires. PLoS Comput. Biol. 11, e1004503 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"29_CR101","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1038\/nature13954","volume":"515","author":"PC Tumeh","year":"2014","unstructured":"Tumeh, P. C. et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568\u2013571 (2014).","journal-title":"Nature"},{"key":"29_CR102","doi-asserted-by":"publisher","first-page":"908","DOI":"10.1038\/nbt.3979","volume":"35","author":"DA Bolotin","year":"2017","unstructured":"Bolotin, D. A. et al. Antigen receptor repertoire profiling from RNA-seq data. Nat. Biotechnol. 35, 908\u2013911 (2017).","journal-title":"Nat. Biotechnol."},{"key":"29_CR103","doi-asserted-by":"publisher","first-page":"4399","DOI":"10.1128\/AEM.67.10.4399-4406.2001","volume":"67","author":"JB Hughes","year":"2001","unstructured":"Hughes, J. B., Hellmann, J. J., Ricketts, T. H. & Bohannan, B. J. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67, 4399\u20134406 (2001).","journal-title":"Appl. Environ. Microbiol."},{"key":"29_CR104","doi-asserted-by":"publisher","first-page":"e1634","DOI":"10.7717\/peerj.1634","volume":"4","author":"CH Chiu","year":"2016","unstructured":"Chiu, C. H. & Chao, A. Estimating and comparing microbial diversity in the presence of sequencing errors. PeerJ 4, e1634 (2016).","journal-title":"PeerJ"},{"key":"29_CR105","doi-asserted-by":"publisher","first-page":"466","DOI":"10.3389\/fimmu.2013.00466","volume":"4","author":"M Shugay","year":"2013","unstructured":"Shugay, M. et al. Huge overlap of individual TCR beta repertoires. Front. Immunol. 4, 466 (2013).","journal-title":"Front. Immunol."},{"key":"29_CR106","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-09334-7","volume":"7","author":"J Mamrot","year":"2017","unstructured":"Mamrot, J. et al. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). Sci. Rep. 7, 8996 (2017).","journal-title":"Sci. Rep."},{"key":"29_CR107","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"29_CR108","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giz100","volume":"8","author":"E Bushmanova","year":"2019","unstructured":"Bushmanova, E., Antipov, D., Lapidus, A. & Prjibelski, A. D. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-seq data. Gigascience 8, giz100 (2019).","journal-title":"Gigascience"},{"key":"29_CR109","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","volume":"29","author":"MG Grabherr","year":"2011","unstructured":"Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644\u2013652 (2011).","journal-title":"Nat. Biotechnol."},{"key":"29_CR110","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Simao","year":"2015","unstructured":"Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210\u20133212 (2015).","journal-title":"Bioinformatics"},{"key":"29_CR111","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).","journal-title":"BMC Bioinformatics"},{"key":"29_CR112","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","volume":"42","author":"RD Finn","year":"2014","unstructured":"Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222\u2013D230 (2014).","journal-title":"Nucleic Acids Res."},{"key":"29_CR113","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/978-1-4939-7015-5_6","volume":"1611","author":"H Nielsen","year":"2017","unstructured":"Nielsen, H. Predicting secretory proteins with SignalP. Methods Mol. Biol. 1611, 59\u201373 (2017).","journal-title":"Methods Mol. Biol."},{"key":"29_CR114","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","volume":"305","author":"A Krogh","year":"2001","unstructured":"Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567\u2013580 (2001).","journal-title":"J. Mol. Biol."},{"key":"29_CR115","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"29_CR116","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).","journal-title":"BMC Bioinformatics"},{"key":"29_CR117","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1038\/nprot.2009.97","volume":"4","author":"S Durinck","year":"2009","unstructured":"Durinck, S., Spellman, P. T., Birney, E. & Huber, W. Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt. Nat. Protoc. 4, 1184\u20131191 (2009).","journal-title":"Nat. Protoc."}],"container-title":["Nature Aging"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43587-021-00029-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43587-021-00029-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43587-021-00029-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,20]],"date-time":"2023-10-20T14:40:51Z","timestamp":1697812851000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43587-021-00029-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,8]]},"references-count":117,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2]]}},"alternative-id":["29"],"URL":"https:\/\/doi.org\/10.1038\/s43587-021-00029-3","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/259374","asserted-by":"object"}]},"ISSN":["2662-8465"],"issn-type":[{"value":"2662-8465","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,8]]},"assertion":[{"value":"24 July 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 January 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 February 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}