{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T01:14:33Z","timestamp":1792718073187,"version":"4.5.0"},"reference-count":98,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000349","name":"National Institute of Academic Anaesthesia","doi-asserted-by":"publisher","award":["WKRO-2018-0047"],"award-info":[{"award-number":["WKRO-2018-0047"]}],"id":[{"id":"10.13039\/501100000349","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000659","name":"NIHR Trainees Coordinating Centre","doi-asserted-by":"publisher","award":["CS-2016-16-011"],"award-info":[{"award-number":["CS-2016-16-011"]}],"id":[{"id":"10.13039\/501100000659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001297","name":"Royal College of Anaesthetists","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001297","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Immunity"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.immuni.2026.08.003","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T15:08:18Z","timestamp":1787929698000},"page":"2580-2598.e7","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["Temporal analyses of immune responses in sepsis reveal asynchrony between clinical stage of illness and immune states"],"prefix":"10.1016","volume":"59","author":[{"given":"Matthew","family":"Fish","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Rynne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Timms","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aislinn","family":"Jennings","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolynn","family":"Lam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gill","family":"Arbane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neus","family":"Novellas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Campos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barney","family":"Sanderson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Bosco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gianluca","family":"Lucchese","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Ellis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cynthia","family":"Bishop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina","family":"Todd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasmeen","family":"Ghnewa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mervyn","family":"Singer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chad","family":"Swanson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5338-2538","authenticated-orcid":false,"given":"Manu","family":"Shankar-Hari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.immuni.2026.08.003_bib1","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1001\/jama.2016.0287","article-title":"The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3)","volume":"315","author":"Singer","year":"2016","journal-title":"JAMA"},{"key":"10.1016\/j.immuni.2026.08.003_bib2","doi-asserted-by":"crossref","first-page":"2450","DOI":"10.1016\/j.immuni.2021.10.012","article-title":"The immunology of sepsis","volume":"54","author":"van der Poll","year":"2021","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2026.08.003_bib3","doi-asserted-by":"crossref","first-page":"e2013","DOI":"10.1016\/S2214-109X(25)00356-0","article-title":"Global, regional, and national sepsis incidence and mortality, 1990\u20132021: a systematic analysis","volume":"13","year":"2025","journal-title":"Lancet Glob. Health"},{"key":"10.1016\/j.immuni.2026.08.003_bib4","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.molmed.2014.01.007","article-title":"Why have clinical trials in sepsis failed?","volume":"20","author":"Marshall","year":"2014","journal-title":"Trends Mol. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib5","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/S2213-2600(23)00468-X","article-title":"Reframing sepsis immunobiology for translation: towards informative subtyping and targeted immunomodulatory therapies","volume":"12","author":"Shankar-Hari","year":"2024","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib6","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1097\/CCM.0000000000003084","article-title":"Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters","volume":"46","author":"Sweeney","year":"2018","journal-title":"Crit. Care Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib7","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S2213-2600(16)00046-1","article-title":"Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study","volume":"4","author":"Davenport","year":"2016","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib8","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1016\/S2213-2600(17)30294-1","article-title":"Classification of patients with sepsis according to blood genomic endotype: a prospective cohort study","volume":"5","author":"Scicluna","year":"2017","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib9","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.abq4433","article-title":"An immune dysfunction score for stratification of patients with acute infection based on whole-blood gene expression","volume":"14","author":"Cano-Gamez","year":"2022","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib10","doi-asserted-by":"crossref","first-page":"2003","DOI":"10.1001\/jama.2019.5791","article-title":"Derivation, Validation, and Potential Treatment Implications of Novel Clinical Phenotypes for Sepsis","volume":"321","author":"Seymour","year":"2019","journal-title":"JAMA"},{"key":"10.1016\/j.immuni.2026.08.003_bib11","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1016\/S2213-2600(23)00237-0","article-title":"Identifying molecular phenotypes in sepsis: an analysis of two prospective observational cohorts and secondary analysis of two randomised controlled trials","volume":"11","author":"Sinha","year":"2023","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib12","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1126\/science.abi5200","article-title":"The spectrum of inflammatory responses","volume":"374","author":"Medzhitov","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.immuni.2026.08.003_bib13","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1016\/j.cels.2022.11.004","article-title":"Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection","volume":"13","author":"Cohn","year":"2022","journal-title":"Cell Syst."},{"key":"10.1016\/j.immuni.2026.08.003_bib14","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1038\/s41590-022-01309-9","article-title":"A guide to systems-level immunomics","volume":"23","author":"Bonaguro","year":"2022","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib15","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nri3158","article-title":"Standardizing immunophenotyping for the Human Immunology Project","volume":"12","author":"Maecker","year":"2012","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib16","doi-asserted-by":"crossref","first-page":"e149","DOI":"10.1016\/j.bja.2021.01.006","article-title":"Utilising mass cytometry with CD45 barcoding and standardised leucocyte phenotyping for immune trajectory assessment in critically ill patients","volume":"126","author":"Fish","year":"2021","journal-title":"Br. J. Anaesth."},{"key":"10.1016\/j.immuni.2026.08.003_bib17","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1177\/1751143720966286","article-title":"Cellular and molecular mechanisms of IMMunE dysfunction and Recovery from SEpsis-related critical illness in adults: An observational cohort study (IMMERSE) protocol paper","volume":"23","author":"Fish","year":"2022","journal-title":"J. Intensive Care Soc."},{"key":"10.1016\/j.immuni.2026.08.003_bib18","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-023-38238-6","article-title":"Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection","volume":"14","author":"Ahuja","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2026.08.003_bib19","doi-asserted-by":"crossref","first-page":"2581","DOI":"10.1084\/jem.20111354","article-title":"A genomic storm in critically injured humans","volume":"208","author":"Xiao","year":"2011","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib20","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1038\/s41591-022-01843-x","article-title":"Redefining critical illness","volume":"28","author":"Maslove","year":"2022","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib21","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1097\/CCM.0000000000005357","article-title":"Executive Summary: Surviving Sepsis Campaign: International Guidelines for the Management of Sepsis and Septic Shock 2021","volume":"49","author":"Evans","year":"2021","journal-title":"Crit. Care Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib22","unstructured":"Gencode. Human. Release 50 (GRCh38.p14). https:\/\/www.gencodegenes.org\/human\/."},{"key":"10.1016\/j.immuni.2026.08.003_bib23","doi-asserted-by":"crossref","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":"10.1016\/j.immuni.2026.08.003_bib24","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3009701","article-title":"Clinical recovery from surgery correlates with single-cell immune signatures","volume":"6","author":"Gaudilli\u00e8re","year":"2014","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib25","doi-asserted-by":"crossref","first-page":"4119","DOI":"10.1038\/s41591-025-03964-5","article-title":"A consensus blood transcriptomic framework for sepsis","volume":"31","author":"Scicluna","year":"2025","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib26","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-018-04696-6","article-title":"Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data","volume":"9","author":"Campbell","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2026.08.003_bib27","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1038\/s41587-019-0336-3","article-title":"Visualizing structure and transitions in high-dimensional biological data","volume":"37","author":"Moon","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.immuni.2026.08.003_bib28","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/s13054-015-0778-z","article-title":"The diagnostic and prognostic significance of monitoring blood levels of immature neutrophils in patients with systemic inflammation","volume":"19","author":"Mare","year":"2015","journal-title":"Crit. Care"},{"key":"10.1016\/j.immuni.2026.08.003_bib29","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/s41590-023-01490-5","article-title":"Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis","volume":"24","author":"Kwok","year":"2023","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib30","doi-asserted-by":"crossref","first-page":"4084","DOI":"10.1038\/s41591-025-03956-5","article-title":"A consensus immune dysregulation framework for sepsis and critical illnesses","volume":"31","author":"Moore","year":"2025","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib31","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."},{"key":"10.1016\/j.immuni.2026.08.003_bib32","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.immuni.2015.12.006","article-title":"Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation","volume":"44","author":"Godec","year":"2016","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2026.08.003_bib33","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41392-021-00762-6","article-title":"Wnt\/beta-catenin signalling: function, biological mechanisms, and therapeutic opportunities","volume":"7","author":"Liu","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.immuni.2026.08.003_bib34","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1186\/s12859-021-04461-5","article-title":"GeneTonic: an R\/Bioconductor package for streamlining the interpretation of RNA-seq data","volume":"22","author":"Marini","year":"2021","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.immuni.2026.08.003_bib35","doi-asserted-by":"crossref","DOI":"10.1002\/cpz1.90","article-title":"Gene Set Knowledge Discovery with Enrichr","volume":"1","author":"Xie","year":"2021","journal-title":"Curr. Protoc."},{"key":"10.1016\/j.immuni.2026.08.003_bib36","doi-asserted-by":"crossref","first-page":"W338","DOI":"10.1093\/nar\/gkaf373","article-title":"L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine","volume":"53","author":"Marino","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2026.08.003_bib37","doi-asserted-by":"crossref","first-page":"1736","DOI":"10.3389\/fimmu.2018.01736","article-title":"Immune Effects of Corticosteroids in Sepsis","volume":"9","author":"Heming","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib38","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/s41586-024-07282-7","article-title":"Metabolic rewiring promotes anti-inflammatory effects of glucocorticoids","volume":"629","author":"Auger","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.immuni.2026.08.003_bib39","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1164\/rccm.201807-1419OC","article-title":"Transcriptomic Signatures in Sepsis and a Differential Response to Steroids. From the VANISH Randomized Trial","volume":"199","author":"Antcliffe","year":"2019","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib40","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1016\/j.immuni.2013.08.039","article-title":"Anthracyclines induce DNA damage response-mediated protection against severe sepsis","volume":"39","author":"Figueiredo","year":"2013","journal-title":"Immunity"},{"key":"10.1016\/j.immuni.2026.08.003_bib41","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2023-075158","article-title":"Epirubicin for the Treatment of Sepsis and Septic Shock (EPOS-1): study protocol for a randomised, placebo-controlled phase IIa dose-escalation trial","volume":"14","author":"Thomas-R\u00fcddel","year":"2024","journal-title":"BMJ Open"},{"key":"10.1016\/j.immuni.2026.08.003_bib42","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1016\/j.cell.2017.05.031","article-title":"Metabolic Adaptation Establishes Disease Tolerance to Sepsis","volume":"169","author":"Weis","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.immuni.2026.08.003_bib43","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1097\/SHK.0000000000000520","article-title":"A PPARgamma AGONIST ENHANCES BACTERIAL CLEARANCE THROUGH NEUTROPHIL EXTRACELLULAR TRAP FORMATION AND IMPROVES SURVIVAL IN SEPSIS","volume":"45","author":"Ara\u00fajo","year":"2016","journal-title":"Shock"},{"key":"10.1016\/j.immuni.2026.08.003_bib44","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1002\/cyto.a.22625","article-title":"FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data","volume":"87","author":"Van Gassen","year":"2015","journal-title":"Cytometry A"},{"key":"10.1016\/j.immuni.2026.08.003_bib45","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/S2213-2600(23)00330-2","article-title":"Profiling the dysregulated immune response in sepsis: overcoming challenges to achieve the goal of precision medicine","volume":"12","author":"Cajander","year":"2024","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib46","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/ni.3123","article-title":"Control of adaptive immunity by the innate immune system","volume":"16","author":"Iwasaki","year":"2015","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib47","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nri2297","article-title":"CCR7 and its ligands: balancing immunity and tolerance","volume":"8","author":"F\u00f6rster","year":"2008","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib48","doi-asserted-by":"crossref","first-page":"3549","DOI":"10.4049\/jimmunol.1401138","article-title":"CXCL1 contributes to host defense in polymicrobial sepsis via modulating T cell and neutrophil functions","volume":"193","author":"Jin","year":"2014","journal-title":"J. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib49","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1111\/imcb.12644","article-title":"CCL17\/TARC in autoimmunity and inflammation-not just a T-cell chemokine","volume":"101","author":"Lupancu","year":"2023","journal-title":"Immunol. Cell Biol."},{"key":"10.1016\/j.immuni.2026.08.003_bib50","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107602","article-title":"Histones, DNA, and Citrullination Promote Neutrophil Extracellular Trap Inflammation by Regulating the Localization and Activation of TLR4","volume":"31","author":"Tsourouktsoglou","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.immuni.2026.08.003_bib51","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1038\/nm.2053","article-title":"Extracellular histones are major mediators of death in sepsis","volume":"15","author":"Xu","year":"2009","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib52","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1146\/annurev-biodatasci-012420-122454","article-title":"Data Integration for Immunology","volume":"3","author":"Pineda","year":"2020","journal-title":"Annu. Rev. Biomed. Data Sci."},{"key":"10.1016\/j.immuni.2026.08.003_bib53","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"10.1016\/j.immuni.2026.08.003_bib54","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1038\/s41392-021-00780-4","article-title":"KRAS mutation: from undruggable to druggable in cancer","volume":"6","author":"Huang","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.immuni.2026.08.003_bib55","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/s11908-016-0544-7","article-title":"Understanding Long-Term Outcomes Following Sepsis: Implications and Challenges","volume":"18","author":"Shankar-Hari","year":"2016","journal-title":"Curr. Infect. Dis. Rep."},{"key":"10.1016\/j.immuni.2026.08.003_bib56","doi-asserted-by":"crossref","DOI":"10.1001\/jamanetworkopen.2020.13580","article-title":"Development, Validation, and Clinical Utility Assessment of a Prognostic Score for 1-Year Unplanned Rehospitalization or Death of Adult Sepsis Survivors","volume":"3","author":"Shankar-Hari","year":"2020","journal-title":"JAMA Netw. Open"},{"key":"10.1016\/j.immuni.2026.08.003_bib57","doi-asserted-by":"crossref","DOI":"10.1001\/jamanetworkopen.2019.8686","article-title":"Long-term Host Immune Response Trajectories Among Hospitalized Patients With Sepsis","volume":"2","author":"Yende","year":"2019","journal-title":"JAMA Netw. Open"},{"key":"10.1016\/j.immuni.2026.08.003_bib58","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/s41584-020-0419-z","article-title":"Translating IL-6 biology into effective treatments","volume":"16","author":"Choy","year":"2020","journal-title":"Nat. Rev. Rheumatol."},{"key":"10.1016\/j.immuni.2026.08.003_bib59","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1004174","article-title":"Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: A Mendelian randomisation study","volume":"20","author":"Hamilton","year":"2023","journal-title":"PLoS Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib60","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1038\/s41586-023-06034-3","article-title":"GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19","volume":"617","author":"Pairo-Castineira","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.immuni.2026.08.003_bib61","doi-asserted-by":"crossref","DOI":"10.1136\/bmj.m3379","article-title":"A living WHO guideline on drugs for covid-19","volume":"370","author":"Agarwal","year":"2020","journal-title":"BMJ"},{"key":"10.1016\/j.immuni.2026.08.003_bib62","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1038\/s41591-020-1038-6","article-title":"A dynamic COVID-19 immune signature includes associations with poor prognosis","volume":"26","author":"Laing","year":"2020","journal-title":"Nat. Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib63","doi-asserted-by":"crossref","DOI":"10.1126\/science.abc8511","article-title":"Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications","volume":"369","author":"Mathew","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.immuni.2026.08.003_bib64","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1038\/s41590-022-01329-5","article-title":"Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination","volume":"23","author":"Fourati","year":"2022","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib65","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1038\/s41592-024-02351-1","article-title":"Unlocking human immune system complexity through AI","volume":"21","author":"Berson","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2026.08.003_bib66","doi-asserted-by":"crossref","first-page":"748","DOI":"10.1097\/CCM.0000000000004842","article-title":"Sepsis Subclasses: A Framework for Development and Interpretation","volume":"49","author":"DeMerle","year":"2021","journal-title":"Crit. Care Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib67","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1097\/00003246-198510000-00009","article-title":"APACHE II: a severity of disease classification system","volume":"13","author":"Knaus","year":"1985","journal-title":"Crit. Care Med."},{"key":"10.1016\/j.immuni.2026.08.003_bib68","doi-asserted-by":"crossref","first-page":"e3","DOI":"10.1158\/0008-5472.CAN-17-0387","article-title":"The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research","volume":"77","author":"Lau","year":"2017","journal-title":"Cancer Res."},{"key":"10.1016\/j.immuni.2026.08.003_bib69","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2026.08.003_bib70","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.immuni.2026.08.003_bib71","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2026.08.003_bib72","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","author":"Soneson","year":"2015","journal-title":"F1000Res"},{"key":"10.1016\/j.immuni.2026.08.003_bib73","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2026.08.003_bib74","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1186\/s12864-018-4772-0","article-title":"Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics","volume":"19","author":"Street","year":"2018","journal-title":"BMC Genomics"},{"key":"10.1016\/j.immuni.2026.08.003_bib75","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.immuni.2026.08.003_bib76","author":"Alboukadel"},{"key":"10.1016\/j.immuni.2026.08.003_bib77","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006899","article-title":"Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)","volume":"15","author":"Meng","year":"2019","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.immuni.2026.08.003_bib78","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkt660","article-title":"Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations","volume":"41","author":"Yaari","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2026.08.003_bib79","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-24584-w","article-title":"Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data","volume":"12","author":"Altman","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.immuni.2026.08.003_bib80","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","article-title":"The Gene Ontology resource: enriching a gold mine","volume":"49","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.immuni.2026.08.003_bib81","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"10.1016\/j.immuni.2026.08.003_bib82","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.immuni.2026.08.003_bib83","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.immuni.2026.08.003_bib84","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.immuni.2026.08.003_bib85","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1093\/bioinformatics\/btq048","article-title":"Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks","volume":"26","author":"Gao","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.immuni.2026.08.003_bib86","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1002\/cyto.a.22271","article-title":"Normalization of mass cytometry data with bead standards","volume":"83","author":"Finck","year":"2013","journal-title":"Cytometry A"},{"key":"10.1016\/j.immuni.2026.08.003_bib87","unstructured":"Crowell, H.L., Zanotelli, V., Chevrier, S., and Robinson, M. (2022). CATALYST: Cytometry dATa anALYSis Tools. https:\/\/bioc.r-universe.dev\/CATALYST."},{"key":"10.1016\/j.immuni.2026.08.003_bib88","first-page":"Unit10.17","article-title":"Web-based analysis and publication of flow cytometry experiments","volume":"Chapter 10","author":"Kotecha","year":"2010","journal-title":"Curr. Protoc. Cytom."},{"key":"10.1016\/j.immuni.2026.08.003_bib89","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1002\/cyto.a.23926","article-title":"Automated Data Cleanup for Mass Cytometry","volume":"97","author":"Bagwell","year":"2020","journal-title":"Cytometry A"},{"key":"10.1016\/j.immuni.2026.08.003_bib90","doi-asserted-by":"crossref","first-page":"864","DOI":"10.4049\/jimmunol.1901530","article-title":"A Comprehensive Workflow for Applying Single-Cell Clustering and Pseudotime Analysis to Flow Cytometry Data","volume":"205","author":"Melsen","year":"2020","journal-title":"J. Immunol."},{"key":"10.1016\/j.immuni.2026.08.003_bib91","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005112","article-title":"Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline","volume":"12","author":"Chen","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.immuni.2026.08.003_bib92","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1002\/cyto.a.23030","article-title":"Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data","volume":"89","author":"Weber","year":"2016","journal-title":"Cytometry A"},{"key":"10.1016\/j.immuni.2026.08.003_bib93","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1186\/s13059-019-1917-7","article-title":"A comparison framework and guideline of clustering methods for mass cytometry data","volume":"20","author":"Liu","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.immuni.2026.08.003_bib94","doi-asserted-by":"crossref","first-page":"861","DOI":"10.21105\/joss.00861","article-title":"Umap: Uniform manifold approximation and projection for dimension reduction","volume":"3","author":"McInnes","year":"2018","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.immuni.2026.08.003_bib95","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.immuni.2026.08.003_bib96","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Hadley","year":"2016"},{"key":"10.1016\/j.immuni.2026.08.003_bib97","author":"Kolde"},{"key":"10.1016\/j.immuni.2026.08.003_bib98","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Immunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1074761326003250?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1074761326003250?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T12:12:10Z","timestamp":1789733530000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1074761326003250"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":98,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S1074761326003250"],"URL":"https:\/\/doi.org\/10.1016\/j.immuni.2026.08.003","relation":{},"ISSN":["1074-7613"],"issn-type":[{"value":"1074-7613","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Temporal analyses of immune responses in sepsis reveal asynchrony between clinical stage of illness and immune states","name":"articletitle","label":"Article Title"},{"value":"Immunity","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.immuni.2026.08.003","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}