{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T11:56:02Z","timestamp":1772711762251,"version":"3.50.1"},"reference-count":40,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T00:00:00Z","timestamp":1556841600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010198","name":"Ministerio de Econom\u00eda, Industria y Competitividad, Gobierno de Espa\u00f1a","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010198","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"DOI":"10.3389\/fimmu.2019.01002","type":"journal-article","created":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T09:54:01Z","timestamp":1556877241000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Linking Cell Dynamics With Gene Coexpression Networks to Characterize Key Events in Chronic Virus Infections"],"prefix":"10.3389","volume":"10","author":[{"given":"Mireia","family":"Pedragosa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graciela","family":"Riera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Casella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Esteve-Codina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yael","family":"Steuerman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Celina","family":"Seth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gennady","family":"Bocharov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Heath","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irit","family":"Gat-Viks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jordi","family":"Argilaguet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Meyerhans","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2019,5,3]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1101\/476077","article-title":"Time-resolved systems analysis reveals a critical role of XCR1+ dendritic cells in the maintenance of effector T cells during chronic viral infection","author":"Argilaguet","year":"2018","journal-title":"bioRxiv"},{"key":"B2","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1016\/j.cell.2017.08.024","article-title":"Organism-level analysis of vaccination reveals networks of protection across tissues","volume":"171","author":"Kadoki","year":"2017","journal-title":"Cell"},{"key":"B3","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1016\/j.chom.2013.05.014","article-title":"Networking at the level of host immunity: immune cell interactions during persistent viral infections","volume":"13","author":"Ng","year":"2013","journal-title":"Cell Host Microbe"},{"key":"B4","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1016\/j.immuni.2018.04.026","article-title":"Epigenomic-guided mass cytometry profiling reveals disease-specific features of exhausted CD8 T cells","volume":"48","author":"Bengsch","year":"2018","journal-title":"Immunity"},{"key":"B5","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1016\/j.cell.2016.04.019","article-title":"Mass cytometry: single cells, many features","volume":"165","author":"Spitzer","year":"2016","journal-title":"Cell"},{"key":"B6","doi-asserted-by":"publisher","first-page":"4638","DOI":"10.1038\/s41467-018-06214-0","article-title":"A deadly dance: the choreography of host\u2013pathogen interactions, as revealed by single-cell technologies","volume":"9","author":"Chattopadhyay","year":"2018","journal-title":"Nat Commun"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1130","DOI":"10.1016\/j.immuni.2012.08.021","article-title":"Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory","volume":"37","author":"Doering","year":"2012","journal-title":"Immunity"},{"key":"B8","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1016\/j.cell.2016.09.031","article-title":"L-arginine modulates T cell metabolism and enhances survival and anti-tumor activity","volume":"167","author":"Geiger","year":"2016","journal-title":"Cell"},{"key":"B9","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.immuni.2018.02.010","article-title":"Understanding subset diversity in T cell memory","volume":"48","author":"Jameson","year":"2018","journal-title":"Immunity"},{"key":"B10","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1126\/science.1247651","article-title":"Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types","volume":"343","author":"Jaitin","year":"2014","journal-title":"Science"},{"key":"B11","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1002\/msb.134947","article-title":"Digital cell quantification identifies global immune cell dynamics during influenza infection","volume":"10","author":"Altboum","year":"2014","journal-title":"Mol Syst Biol"},{"key":"B12","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/0166-0934(91)90018-U","article-title":"Quantification of lymphocytic choriomeningitis virus with an immunological focus assay in 24- or 96-well plates","volume":"33","author":"Battegay","year":"1991","journal-title":"J Virol Methods"},{"key":"B13","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/0022-1759(94)90012-4","article-title":"Liposome mediated depletion of macrophages: mechanism of action, preparation of liposomes and applications","volume":"174","author":"Van Rooijen","year":"1994","journal-title":"J Immunol Methods"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization paths for generalized linear models via coordinate descent","volume":"33","author":"Friedman","year":"2010","journal-title":"J Stat Softw"},{"key":"B15","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"B17","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"B18","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat Protoc"},{"key":"B19","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.virol.2005.09.028","article-title":"Viral persistence: parameters, mechanisms and future predictions","volume":"344","author":"Oldstone","year":"2006","journal-title":"Virology"},{"key":"B20","doi-asserted-by":"publisher","first-page":"e1003362","DOI":"10.1371\/journal.ppat.1003362","article-title":"IL-21 restricts virus-driven Treg cell expansion in chronic LCMV infection","volume":"9","author":"Schmitz","year":"2013","journal-title":"PLoS Pathog"},{"key":"B21","doi-asserted-by":"publisher","first-page":"23505","DOI":"10.1038\/srep23505","article-title":"Crucial roles of XCR1-expressing dendritic cells and the XCR1-XCL1 chemokine axis in intestinal immune homeostasis","volume":"6","author":"Ohta","year":"2016","journal-title":"Sci Rep"},{"key":"B22","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1016\/j.immuni.2012.10.022","article-title":"Chronic but not acute virus infection induces sustained expansion of myeloid suppressor cell numbers that inhibit viral-specific T cell immunity","volume":"38","author":"Norris","year":"2013","journal-title":"Immunity"},{"key":"B23","doi-asserted-by":"publisher","first-page":"e123","DOI":"10.1371\/journal.ppat.0030123","article-title":"Natural killer cells promote early CD8 T cell responses against cytomegalovirus","volume":"3","author":"Robbins","year":"2007","journal-title":"PLoS Pathog"},{"key":"B24","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1038\/nature10624","article-title":"Natural killer cells act as rheostats modulating antiviral T cells","volume":"481","author":"Waggoner","year":"2011","journal-title":"Nature"},{"key":"B25","doi-asserted-by":"publisher","first-page":"5488","DOI":"10.1182\/blood-2008-10-187179","article-title":"Maturation of mouse NK cells is a 4-stage developmental program","volume":"113","author":"Chiossone","year":"2009","journal-title":"Blood"},{"key":"B26","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1189\/jlb.4HI1214-594R","article-title":"NK cells inhibit humoral immunity by reducing the abundance of CD4+ T follicular helper cells during a chronic virus infection","volume":"98","author":"Cook","year":"2015","journal-title":"J Leukoc Biol"},{"key":"B27","doi-asserted-by":"publisher","first-page":"eaah6817","DOI":"10.1126\/sciimmunol.aah6817","article-title":"Interferon-driven deletion of antiviral B cells at the onset of chronic infection","volume":"1","author":"Fallet","year":"2016","journal-title":"Sci Immunol"},{"key":"B28","doi-asserted-by":"publisher","first-page":"6375","DOI":"10.1038\/ncomms7375","article-title":"Generation of cellular immune memory and B-cell immunity is impaired by natural killer cells","volume":"6","author":"Rydyznski","year":"2015","journal-title":"Nat Commun"},{"key":"B29","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nature19330","article-title":"Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy","volume":"537","author":"Im","year":"2016","journal-title":"Nature"},{"key":"B30","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1038\/nature19317","article-title":"Follicular CXCR5- expressing CD8(+) T cells curtail chronic viral infection","volume":"537","author":"He","year":"2016","journal-title":"Nature"},{"key":"B31","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/j.immuni.2018.08.002","article-title":"CD8+ T cell priming in established chronic viral infection preferentially directs differentiation of memory-like cells for sustained immunity","volume":"49","author":"Snell","year":"2018","journal-title":"Immunity"},{"key":"B32","doi-asserted-by":"publisher","first-page":"3635809","DOI":"10.1155\/2016\/3635809","article-title":"CCR9 is a key regulator of early phases of allergic airway inflammation","volume":"2016","author":"L\u00f3pez-Pacheco","year":"2016","journal-title":"Mediators Inflamm"},{"key":"B33","doi-asserted-by":"publisher","first-page":"4613","DOI":"10.4049\/jimmunol.1600339","article-title":"The analysis of CD83 expression on human immune cells identifies a unique CD83+-activated T cell population","volume":"197","author":"Ju","year":"2016","journal-title":"J Immunol"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1286","DOI":"10.3389\/fimmu.2018.01286","article-title":"seq-ImmuCC: cell-centric view of tissue transcriptome measuring cellular compositions of immune microenvironment from mouse RNA-Seq data","volume":"9","author":"Chen","year":"2018","journal-title":"Front Immunol"},{"key":"B35","doi-asserted-by":"publisher","first-page":"3961","DOI":"10.1093\/bioinformatics\/btv498","article-title":"CoD: inferring immune-cell quantities related to disease states","volume":"31","author":"Frishberg","year":"2015","journal-title":"Bioinformatics"},{"key":"B36","doi-asserted-by":"publisher","first-page":"2780","DOI":"10.4049\/jimmunol.1502582","article-title":"Dendritic cells are dispensable for T cell priming and control of acute lymphocytic choriomeningitis virus infection","volume":"197","author":"Hilpert","year":"2016","journal-title":"J Immunol"},{"key":"B37","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.4049\/jimmunol.121.4.1262","article-title":"Interactions between viruses and lymphocytes. I. in vivo replication of lymphocytic choriomeningitis virus in mononuclear cells during both chronic and acute viral infections","volume":"121","author":"Doyle","year":"1978","journal-title":"J Immunol"},{"key":"B38","doi-asserted-by":"publisher","first-page":"6239","DOI":"10.4049\/jimmunol.172.10.6239","article-title":"Visualizing the viral burden: phenotypic and functional alterations of T cells and APCs during persistent infection","volume":"172","author":"Homann","year":"2004","journal-title":"J Immunol"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1084\/jem.192.9.1249","article-title":"Immunosuppression and resultant viral persistence by specific viral targeting of dendritic cells","volume":"192","author":"Sevilla","year":"2000","journal-title":"J Exp Med"},{"key":"B40","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1016\/j.chom.2016.01.002","article-title":"Integrated omics analysis of pathogenic host responses during pandemic H1N1 influenza virus infection: the crucial role of lipid metabolism","volume":"19","author":"Tisoncik-Go","year":"2016","journal-title":"Cell Host Microbe"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fimmu.2019.01002\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T07:51:01Z","timestamp":1694850661000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fimmu.2019.01002\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,3]]},"references-count":40,"alternative-id":["10.3389\/fimmu.2019.01002"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2019.01002","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,3]]},"article-number":"1002"}}