Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses

A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections

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Concise whole blood transcriptional signatures for incipient tuberculosis: a systematic review and patient-level pooled meta-analysis

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Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients

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Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure

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Blood transcriptional biomarkers for active pulmonary tuberculosis in a high-burden setting: a prospective, observational, diagnostic accuracy study

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Severe COVID-19 is marked by a dysregulated myeloid cell compartment

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Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19

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A single-cell atlas of the peripheral immune response in patients with severe COVID-19

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Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients

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Emerging Pandemic Diseases: How We Got to COVID-19

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Efficacy of Tocilizumab in Patients Hospitalized with Covid-19

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Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans

(2020) Prabhu S. Arunachalam et al.   SCIENCE

Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections

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Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections

(2019) Xuesen Zhao et al.   Frontiers in Microbiology

Functional Involvement of Interferon-Inducible Transmembrane Proteins in Antiviral Immunity

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Neutrophils-related host factors associated with severe disease and fatality in patients with influenza infection

(2019) Benjamin M. Tang et al.   Nature Communications

Systems analysis of subjects acutely infected with the Chikungunya virus

(2019) Alessandra Soares-Schanoski et al.   PLoS Pathogens

Induction of PGRN by influenza virus inhibits the antiviral immune responses through downregulation of type I interferons signaling

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Reduction of respiratory infections in asthma patients supplemented with vitamin D is related to increased serum IL-10 and IFNγ levels and cathelicidin expression

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Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza

(2018) Jake Dunning et al.   NATURE IMMUNOLOGY

Whole blood transcriptional profiles as a prognostic tool in complete and incomplete Kawasaki Disease

(2018) Preeti Jaggi et al.   PLoS One

KLRD1-expressing natural killer cells predict influenza susceptibility

(2018) Erika Bongen et al.   Genome Medicine

Phosphoinositide-3-Kinase Signaling in Human Natural Killer Cells: New Insights from Primary Immunodeficiency

(2018) Emily M. Mace   Frontiers in Immunology

Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases

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A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes

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Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection

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Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases

(2018) Francesco Vallania et al.   Nature Communications

Thioredoxin a novel biomarker of post-injury sepsis

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Respiratory Syncytial Virus Genotypes, Host Immune Profiles, and Disease Severity in Young Children Hospitalized With Bronchiolitis

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Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

BCAT1 controls metabolic reprogramming in activated human macrophages and is associated with inflammatory diseases

(2017) Adonia E. Papathanassiu et al.   Nature Communications

Rhinovirus Detection in Symptomatic and Asymptomatic Children: Value of Host Transcriptome Analysis

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Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection

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An individualized predictor of health and disease using paired reference and target samples

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Stroke-induced immunodepression and dysphagia independently predict stroke-associated pneumonia – The PREDICT study

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Robust classification of bacterial and viral infections via integrated host gene expression diagnostics

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Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis

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Transcriptome assists prognosis of disease severity in respiratory syncytial virus infected infants

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Orosomucoid 1 drives opportunistic infections through the polarization of monocytes to the M2b phenotype

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Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses

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Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Combating emerging viral threats

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Vitamin D–dependent induction of cathelicidin in human macrophages results in cytotoxicity against high-grade B cell lymphoma

(2015) Heiko Bruns et al.   Science Translational Medicine

A comprehensive time-course–based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set

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Host Transcriptional Response to Influenza and Other Acute Respiratory Viral Infections – A Prospective Cohort Study

(2015) Yijie Zhai et al.   PLoS Pathogens

Transcriptomic profiling facilitates classification of response to influenza challenge

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Patient-Based Transcriptome-Wide Analysis Identify Interferon and Ubiquination Pathways as Potential Predictors of Influenza A Disease Severity

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Identification of a human neonatal immune-metabolic network associated with bacterial infection

(2014) Claire L. Smith et al.   Nature Communications

IFITM-Family Proteins: The Cell's First Line of Antiviral Defense

(2014) Charles C. Bailey et al.   Annual Review of Virology

Whole Blood Gene Expression Profiles to Assess Pathogenesis and Disease Severity in Infants with Respiratory Syncytial Virus Infection

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Qualimap: evaluating next-generation sequencing alignment data

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STAR: ultrafast universal RNA-seq aligner

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Demand-adapted regulation of early hematopoiesis in infection and inflammation

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Excessive innate immune response and mutant D222G/N in severe A (H1N1) pandemic influenza

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Aberrant Cell Cycle and Apoptotic Changes Characterise Severe Influenza A Infection – A Meta-Analysis of Genomic Signatures in Circulating Leukocytes

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Gene Expression Signatures Diagnose Influenza and Other Symptomatic Respiratory Viral Infections in Humans

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Interleukin-8 as a Stratification Tool for Interventional Trials Involving Pediatric Septic Shock

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