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

[1]  Eric A. Meyerowitz,et al.  Efficacy of Tocilizumab in Patients Hospitalized with Covid-19 , 2020, The New England journal of medicine.

[2]  A. Fauci,et al.  Emerging Pandemic Diseases: How We Got to COVID-19 , 2020, Cell.

[3]  Madeleine K. D. Scott,et al.  Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans , 2020, Science.

[4]  I. Amit,et al.  Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19 , 2020, Cell.

[5]  Alexander Sczyrba,et al.  Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment , 2020, Cell.

[6]  Raphael Gottardo,et al.  Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories , 2020, bioRxiv.

[7]  Nicolas Carlier,et al.  Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients , 2020, Science.

[8]  B. Brando,et al.  Decrease of Non‐Classical and Intermediate Monocyte Subsets in Severe Acute SARS‐CoV‐2 Infection , 2020, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[9]  Yudong D. He,et al.  Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections , 2020, iScience.

[10]  Aaron J. Wilk,et al.  A single-cell atlas of the peripheral immune response in patients with severe COVID-19 , 2020, Nature Medicine.

[11]  Jie Dong,et al.  Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients , 2020, Cell Host & Microbe.

[12]  M. Netea,et al.  Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure , 2020, Cell Host & Microbe.

[13]  F. Venet,et al.  Myeloid cells in sepsis‐acquired immunodeficiency , 2020, Annals of the New York Academy of Sciences.

[14]  Carolin T. Turner,et al.  Blood transcriptional biomarkers for active pulmonary tuberculosis in a high-burden setting: a prospective, observational, diagnostic accuracy study , 2020, The Lancet. Respiratory medicine.

[15]  Michael B. Mayhew,et al.  A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections , 2020, Nature Communications.

[16]  Eugene C. Butcher,et al.  Exploration of Cell Development Pathways through High-Dimensional Single Cell Analysis in Trajectory Space , 2020, iScience.

[17]  G. Gao,et al.  Induction of PGRN by influenza virus inhibits the antiviral immune responses through downregulation of type I interferons signaling , 2019, PLoS pathogens.

[18]  Stephen J. Huang,et al.  Neutrophils-related host factors associated with severe disease and fatality in patients with influenza infection , 2019, Nature Communications.

[19]  Carolin T. Turner,et al.  Concise whole blood transcriptional signatures for incipient tuberculosis: a systematic review and patient-level pooled meta-analysis , 2019, bioRxiv.

[20]  Madeleine K. D. Scott,et al.  Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study , 2019, The Lancet. Respiratory medicine.

[21]  J. Choi,et al.  The Prevalence of Low Plasma Neutrophil Gelatinase-Associated Lipocalin Level in Systemic Inflammation and its Relationship with Proinflammatory Cytokines, Procalcitonin, Nutritional Status, and Leukocyte Profiles. , 2019, Clinical Laboratory.

[22]  H. Nakaya,et al.  Systems analysis of subjects acutely infected with the Chikungunya virus , 2019, PLoS pathogens.

[23]  Ji-Long Chen,et al.  Functional Involvement of Interferon-Inducible Transmembrane Proteins in Antiviral Immunity , 2019, Front. Microbiol..

[24]  T. Roger,et al.  Myeloid-Derived Suppressor Cells in Sepsis , 2019, Front. Immunol..

[25]  C. Winkler,et al.  IFITM Genes, Variants, and Their Roles in the Control and Pathogenesis of Viral Infections , 2019, Front. Microbiol..

[26]  A. Butte,et al.  Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage , 2018, Nature Immunology.

[27]  Francesco Vallania,et al.  Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases , 2018, Nature Communications.

[28]  Derick R. Peterson,et al.  Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection , 2018, The Journal of infectious diseases.

[29]  Madeleine K. D. Scott,et al.  Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response , 2018, JAMA network open.

[30]  Leland McInnes,et al.  UMAP: Uniform Manifold Approximation and Projection , 2018, J. Open Source Softw..

[31]  E. Amir,et al.  Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases , 2018, Molecular systems biology.

[32]  Mark M. Davis,et al.  A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes , 2018, Nature.

[33]  J. Rojas-Serrano,et al.  Reduction of respiratory infections in asthma patients supplemented with vitamin D is related to increased serum IL‐10 and IFN&ggr; levels and cathelicidin expression , 2018, Cytokine.

[34]  Francesco Vallania,et al.  KLRD1-expressing natural killer cells predict influenza susceptibility , 2018, Genome Medicine.

[35]  Avi Srivastava,et al.  Alevin efficiently estimates accurate gene abundances from dscRNA-seq data , 2018, Genome Biology.

[36]  V. Pascual,et al.  Whole blood transcriptional profiles as a prognostic tool in complete and incomplete Kawasaki Disease , 2018, PloS one.

[37]  J. Banchereau,et al.  Progression of whole blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in patients with severe influenza , 2018, Nature Immunology.

[38]  E. Mace Phosphoinositide-3-Kinase Signaling in Human Natural Killer Cells: New Insights from Primary Immunodeficiency , 2018, Front. Immunol..

[39]  Charlotte Soneson,et al.  Bias, robustness and scalability in single-cell differential expression analysis , 2018, Nature Methods.

[40]  B. Mackert,et al.  Stroke-induced immunodepression and dysphagia independently predict stroke-associated pneumonia – The PREDICT study , 2017, Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism.

[41]  P. Srivastava,et al.  BCAT1 controls metabolic reprogramming in activated human macrophages and is associated with inflammatory diseases , 2017, Nature Communications.

[42]  Rob Patro,et al.  Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.

[43]  E. Larsson,et al.  Thioredoxin a novel biomarker of post‐injury sepsis , 2017, Free radical biology & medicine.

[44]  John G Kenny,et al.  Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus , 2017, Genome Biology.

[45]  A. Elkahloun,et al.  The TCF1-Bcl6 axis counteracts type I interferon to repress exhaustion and maintain T cell stemness , 2016, Science Immunology.

[46]  Aldert L. Zomer,et al.  Transcriptome assists prognosis of disease severity in respiratory syncytial virus infected infants , 2016, Scientific Reports.

[47]  O. Ramilo,et al.  Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection. , 2016, American journal of respiratory and critical care medicine.

[48]  Winston Haynes,et al.  Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility , 2016, bioRxiv.

[49]  P. Khatri,et al.  Robust classification of bacterial and viral infections via integrated host gene expression diagnostics , 2016, Science Translational Medicine.

[50]  V. Pascual,et al.  Rhinovirus Detection in Symptomatic and Asymptomatic Children: Value of Host Transcriptome Analysis. , 2016, American journal of respiratory and critical care medicine.

[51]  Purvesh Khatri,et al.  Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. , 2016, The Lancet. Respiratory medicine.

[52]  Alfred O. Hero,et al.  An individualized predictor of health and disease using paired reference and target samples , 2016, BMC Bioinformatics.

[53]  Purvesh Khatri,et al.  Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses , 2015, Immunity.

[54]  C. Shaw,et al.  Host Transcriptional Response to Influenza and Other Acute Respiratory Viral Infections – A Prospective Cohort Study , 2015, PLoS pathogens.

[55]  Purvesh Khatri,et al.  A comprehensive time-course–based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set , 2015, Science Translational Medicine.

[56]  D. Herndon,et al.  Orosomucoid 1 drives opportunistic infections through the polarization of monocytes to the M2b phenotype. , 2015, Cytokine.

[57]  Elena Bekerman,et al.  Combating emerging viral threats , 2015, Science.

[58]  A. Mackensen,et al.  Vitamin D–dependent induction of cathelicidin in human macrophages results in cytotoxicity against high-grade B cell lymphoma , 2015, Science Translational Medicine.

[59]  A. Regev,et al.  Spatial reconstruction of single-cell gene expression , 2015, Nature Biotechnology.

[60]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[61]  H. Wertheim,et al.  Patient-Based Transcriptome-Wide Analysis Identify Interferon and Ubiquination Pathways as Potential Predictors of Influenza A Disease Severity , 2014, PloS one.

[62]  J. Knight,et al.  Transcriptomic profiling facilitates classification of response to influenza challenge , 2014, Journal of Molecular Medicine.

[63]  M. Farzan,et al.  IFITM-Family Proteins: The Cell's First Line of Antiviral Defense. , 2014, Annual review of virology.

[64]  Peter Ghazal,et al.  Identification of a human neonatal immune-metabolic network associated with bacterial infection , 2014, Nature Communications.

[65]  J. Banchereau,et al.  Whole Blood Gene Expression Profiles to Assess Pathogenesis and Disease Severity in Infants with Respiratory Syncytial Virus Infection , 2013, PLoS medicine.

[66]  H. Wong,et al.  Interleukin-27 is a novel candidate diagnostic biomarker for bacterial infection in critically ill children , 2012, Critical Care.

[67]  Joaquín Dopazo,et al.  Qualimap: evaluating next-generation sequencing alignment data , 2012, Bioinform..

[68]  Stephen J. Huang,et al.  A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia , 2012, Critical Care.

[69]  M. Manz,et al.  Demand-adapted regulation of early hematopoiesis in infection and inflammation. , 2012, Blood.

[70]  J. Laake,et al.  Excessive innate immune response and mutant D222G/N in severe A (H1N1) pandemic influenza. , 2011, The Journal of infection.

[71]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[72]  Stephen Huang,et al.  Aberrant Cell Cycle and Apoptotic Changes Characterise Severe Influenza A Infection – A Meta-Analysis of Genomic Signatures in Circulating Leukocytes , 2011, PloS one.

[73]  J. Rello,et al.  Pandemic Influenza , 2018, Emergency Medicine.

[74]  L. Carin,et al.  Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. , 2009, Cell host & microbe.

[75]  H. Wong,et al.  Interleukin-8 as a stratification tool for interventional trials involving pediatric septic shock. , 2008, American journal of respiratory and critical care medicine.

[76]  Michael G. Barnes,et al.  Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome. , 2007, Physiological genomics.

[77]  J. Banchereau,et al.  Gene expression patterns in blood leukocytes discriminate patients with acute infections. , 2007, Blood.

[78]  R. Glass,et al.  Rotavirus Infection Alters Peripheral T-Cell Homeostasis in Children with Acute Diarrhea , 2007, Journal of Virology.

[79]  N. Voirin,et al.  Persisting low monocyte human leukocyte antigen-DR expression predicts mortality in septic shock , 2006, Intensive Care Medicine.

[80]  R. Tibshirani,et al.  Empirical bayes methods and false discovery rates for microarrays , 2002, Genetic epidemiology.

[81]  P. Ghezzi,et al.  Thioredoxin, a Redox Enzyme Released in Infection and Inflammation, Is a Unique Chemoattractant for Neutrophils, Monocytes, and T Cells , 1999, The Journal of experimental medicine.

[82]  Carla Garcia,et al.  Respiratory Syncytial Virus Genotypes, Host Immune Profiles, and Disease Severity in Young Children Hospitalized With Bronchiolitis , 2017, The Journal of infectious diseases.

[83]  R. A. KtJNKLE,et al.  Infectious disease. , 2015, Clinical privilege white paper.

[84]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[85]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.