Mouse transcriptome reveals potential signatures of protection and pathogenesis in human tuberculosis

The cis-Regulatory Atlas of the Mouse Immune System

(2019) Hideyuki Yoshida et al.   CELL

Transcriptional profiling unveils type I and II interferon networks in blood and tissues across diseases

(2019) Akul Singhania et al.   Nature Communications

Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by IL-1Ra

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Type I interferons in tuberculosis: Foe and occasionally friend

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Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis

(2018) Hanif Esmail et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection

(2018) Akul Singhania et al.   Nature Communications

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

(2018) Roshni Roy Chowdhury et al.   NATURE

T Cell–Derived IL-10 Impairs Host Resistance toMycobacterium tuberculosisInfection

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Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease

(2017) Thomas J. Scriba et al.   PLoS Pathogens

Concordant and discordant gene expression patterns in mouse strains identify best-fit animal model for human tuberculosis

(2017) Teresa Domaszewska et al.   Scientific Reports

MultiQC: summarize analysis results for multiple tools and samples in a single report

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A Functional Role for Antibodies in Tuberculosis

(2016) Lenette L. Lu et al.   CELL

A 380-gene meta-signature of active tuberculosis compared with healthy controls

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A blood RNA signature for tuberculosis disease risk: a prospective cohort study

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The Transcriptional Signature of Active Tuberculosis Reflects Symptom Status in Extra-Pulmonary and Pulmonary Tuberculosis

(2016) Simon Blankley et al.   PLoS One

Presence of multiple lesion types with vastly different microenvironments in C3HeB/FeJ mice following aerosol infection with Mycobacterium tuberculosis

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B cells and antibodies in the defense againstMycobacterium tuberculosisinfection

(2015) Jacqueline M. Achkar et al.   IMMUNOLOGICAL REVIEWS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Mouse models of human TB pathology: roles in the analysis of necrosis and the development of host-directed therapies

(2015) Igor Kramnik et al.   Seminars in Immunopathology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Type I IFN signaling triggers immunopathology in tuberculosis-susceptible mice by modulating lung phagocyte dynamics

(2014) Anca Dorhoi et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk

(2014) Katrin D. Mayer-Barber et al.   NATURE

S100A8/A9 Proteins Mediate Neutrophilic Inflammation and Lung Pathology during Tuberculosis

(2013) Radha Gopal et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

The Immune Response in Tuberculosis

(2013) Anne O'Garra et al.   Annual Review of Immunology

TPL-2-ERK1/2 Signaling Promotes Host Resistance against Intracellular Bacterial Infection by Negative Regulation of Type I IFN Production

(2013) F. W. McNab et al.   JOURNAL OF IMMUNOLOGY

Influenza A Virus Impairs Control of Mycobacterium tuberculosis Coinfection Through a Type I Interferon Receptor–Dependent Pathway

(2013) Paul S. Redford et al.   JOURNAL OF INFECTIOUS DISEASES

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations

(2013) Gur Yaari et al.   NUCLEIC ACIDS RESEARCH

Mycobacterium tuberculosis Strains Are Differentially Recognized by TLRs with an Impact on the Immune Response

(2013) Jenny Carmona et al.   PLoS One

Transcriptional Blood Signatures Distinguish Pulmonary Tuberculosis, Pulmonary Sarcoidosis, Pneumonias and Lung Cancers

(2013) Chloe I. Bloom et al.   PLoS One

A Helicopter Perspective on TB Biomarkers: Pathway and Process Based Analysis of Gene Expression Data Provides New Insight into TB Pathogenesis

(2013) Simone A. Joosten et al.   PLoS One

Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study

(2013) Myrsini Kaforou et al.   PLOS MEDICINE

Is Passive Diagnosis Enough?

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Mycobacterial Disease and Impaired IFN-  Immunity in Humans with Inherited ISG15 Deficiency

(2012) D. Bogunovic et al.   SCIENCE

Regulation of neutrophils by interferon-γ limits lung inflammation during tuberculosis infection

(2011) Bisweswar Nandi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Role of innate cytokines in mycobacterial infection

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Human gene expression profiles of susceptibility and resistance in tuberculosis

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Intranasal Poly-IC treatment exacerbates tuberculosis in mice through the pulmonary recruitment of a pathogen-permissive monocyte/macrophage population

(2010) Lis R.V. Antonelli et al.   JOURNAL OF CLINICAL INVESTIGATION

The adaptor molecule CARD9 is essential for tuberculosis control

(2010) Anca Dorhoi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

(2010) Matthew P. R. Berry et al.   NATURE

Evasion of innate immunity by Mycobacterium tuberculosis: is death an exit strategy?

(2010) Samuel M. Behar et al.   NATURE REVIEWS MICROBIOLOGY

Dominant Role of the sst1 Locus in Pathogenesis of Necrotizing Lung Granulomas during Chronic Tuberculosis Infection and Reactivation in Genetically Resistant Hosts

(2009) Alexander V. Pichugin et al.   AMERICAN JOURNAL OF PATHOLOGY

Neutrophils Are the Predominant Infected Phagocytic Cells in the Airways of Patients With Active Pulmonary TB

(2009) Seok-Yong Eum et al.   CHEST

The spectrum of latent tuberculosis: rethinking the biology and intervention strategies

(2009) Clifton E. Barry et al.   NATURE REVIEWS MICROBIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY