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Immunol."},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.108954_bib77","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1182\/blood.2019000553","article-title":"Overexpression of wild-type IL-7R\u03b1 promotes T-cell acute lymphoblastic leukaemia\/lymphoma","volume":"138","author":"Silva","year":"2021","journal-title":"Blood"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108954_bib78","doi-asserted-by":"crossref","DOI":"10.4110\/in.2021.21.e13","article-title":"CD11B deficiency exacerbates methicillin-resistant staphylococcus aureus-Induced sepsis by upregulating inflammatory responses of macrophages","volume":"21","author":"Sim","year":"2021","journal-title":"Immune Netw."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108954_bib79","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1038\/s41590-018-0225-9","article-title":"The value of transcriptomics in advancing knowledge of the immune response and diagnosis in tuberculosis","volume":"19","author":"Singhania","year":"2018","journal-title":"Nat. Immunol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108954_bib80","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-018-04579-w","article-title":"A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection","volume":"9","author":"Singhania","year":"2018","journal-title":"Nat. Commun."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108954_bib81","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1038\/s41590-018-0225-9","article-title":"The value of transcriptomics in advancing knowledge of the immune response and diagnosis in tuberculosis","volume":"19","author":"Singhania","year":"2018","journal-title":"Nat. Immunol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108954_bib82","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-018-04579-w","article-title":"A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection","volume":"9","author":"Singhania","year":"2018","journal-title":"Nat. Commun."},{"issue":"6977","key":"10.1016\/j.compbiolchem.2026.108954_bib83","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1038\/nature02343","article-title":"The cytoplasmic body component TRIM5\u03b1 restricts HIV-1 infection in Old World monkeys","volume":"427","author":"Stremlau","year":"2004","journal-title":"Nature"},{"issue":"6121","key":"10.1016\/j.compbiolchem.2026.108954_bib84","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1126\/science.1232458","article-title":"Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway","volume":"339","author":"Sun","year":"2012","journal-title":"Science"},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.108954_bib85","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/S2213-2600(16)00048-5","article-title":"Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis","volume":"4","author":"Sweeney","year":"2016","journal-title":"Lancet Respir. Med."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2026.108954_bib86","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gku1003","article-title":"STRING v10: protein-protein interaction networks integrated over the Tree of Life","volume":"43","author":"Szklarczyk","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2026.108954_bib87","unstructured":"TB incidence. (n.d.). \u3008https:\/\/www.who.int\/teams\/global-programme-on-tuberculosis-and-lung-health\/tb-reports\/global-tuberculosis-report-2024\/tb-disease-burden\/1-1-tb-incidence\u3009."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108954_bib88","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.1016\/j.bbamcr.2012.03.017","article-title":"Ubiquitination and phosphorylation in the regulation of NOD2 signalling and NOD2-mediated disease","volume":"1823","author":"Tigno-Aranjuez","year":"2012","journal-title":"Biochimica Et Biophysica Acta (BBA) Molecular Cell Research"},{"issue":"3_part_1","key":"10.1016\/j.compbiolchem.2026.108954_bib89","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1212\/WNL.44.3_Part_1.481","article-title":"HIV-1 infection of subcortical astrocytes in the pediatric central nervous system","volume":"44","author":"Tornatore","year":"1994","journal-title":"Neurology"},{"key":"10.1016\/j.compbiolchem.2026.108954_bib90","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/978-1-4614-6111-1_7","article-title":"Cytokines in the balance of protection and pathology during mycobacterial infections","author":"Torrado","year":"2013","journal-title":"Adv. Exp. Med. Biol."},{"key":"10.1016\/j.compbiolchem.2026.108954_bib91","unstructured":"UNAIDS. (n.d.). 2024 global AIDS report \u2014 The Urgency of Now: AIDS at a Crossroads. \u3008https:\/\/www.unaids.org\/en\/resources\/documents\/2024\/global-aids-update-2024\u3009."},{"key":"10.1016\/j.compbiolchem.2026.108954_bib92","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/978-1-4615-0059-9_20","article-title":"Innate immunity to Mycobacterium tuberculosis","author":"Van Crevel","year":"2003","journal-title":"Adv. Exp. Med. Biol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108954_bib93","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-36696-3","article-title":"Immune cell characteristics and cytokine responses in adult HIV-negative tuberculous meningitis: an observational cohort study","volume":"9","author":"Van Laarhoven","year":"2019","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108954_bib94","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1080\/08830185.2017.1380200","article-title":"Toll-like receptors: significance, ligands, signalling pathways, and functions in mammals","volume":"37","author":"Vidya","year":"2017","journal-title":"Int. Rev. Immunol."},{"key":"10.1016\/j.compbiolchem.2026.108954_bib95","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2023.106865","article-title":"scJVAE: a novel method for integrative analysis of multimodal single-cell data","volume":"158","author":"Wani","year":"2023","journal-title":"Comput. Biol. Med."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108954_bib96","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1002786","article-title":"Host-response-based gene signatures for tuberculosis diagnosis: a systematic comparison of 16 signatures","volume":"16","author":"Warsinske","year":"2019","journal-title":"PLoS Med."},{"key":"10.1016\/j.compbiolchem.2026.108954_bib97","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","article-title":"ggplot2","author":"Wickham","year":"2016","journal-title":"Use R. !"},{"key":"10.1016\/j.compbiolchem.2026.108954_bib98","series-title":"Global Tuberculosis Report 2022","author":"World Health Organization","year":"2022"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108954_bib99","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02233-17","article-title":"Interactions between the Hepatitis C virus nonstructural 2 protein and host adaptor proteins 1 and 4 orchestrate virus release","volume":"9","author":"Xiao","year":"2018","journal-title":"mBio"},{"key":"10.1016\/j.compbiolchem.2026.108954_bib100","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.1008653","article-title":"Blood transcriptome analysis revealed the crosstalk between COVID-19 and HIV","volume":"13","author":"Yan","year":"2022","journal-title":"Front. Immunol."},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.108954_bib101","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1038\/ni.3279","article-title":"PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signalling and control viral infection","volume":"16","author":"Zhang","year":"2015","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.compbiolchem.2026.108954_bib102","article-title":"Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression","volume":"15","author":"Zhang","year":"2024","journal-title":"Front. Immunol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108954_bib103","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. 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