Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq

Microarray analysis ofMycobacterium tuberculosis-infected monocytes revealsIL26as a new candidate gene for tuberculosis susceptibility

(2015) José M. Guerra-Laso et al.   IMMUNOLOGY

A new role for LOX and LOXL2 proteins in transcription regulation

(2014) Ane Iturbide et al.   FEBS Journal

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Macrophage immunoregulatory pathways in tuberculosis

(2014) Murugesan V.S. Rajaram et al.   SEMINARS IN IMMUNOLOGY

Perspectives on host adaptation in response to Mycobacterium tuberculosis: Modulation of inflammation

(2014) Anca Dorhoi et al.   SEMINARS IN IMMUNOLOGY

Innate cytokine profiling of bovine alveolar macrophages reveals commonalities and divergence in the response to Mycobacterium bovis and Mycobacterium tuberculosis infection

(2014) David A. Magee et al.   TUBERCULOSIS

Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis

(2014) Kate E. Killick et al.   Frontiers in Immunology

Comparative Functional Genomics and the Bovine Macrophage Response to Strains of the Mycobacterium Genus

(2014) Kévin Rue-Albrecht et al.   Frontiers in Immunology

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis

(2014) Kirsten E. McLoughlin et al.   Frontiers in Immunology

The Immune Response in Tuberculosis

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

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

(2013) Nicolas C Nalpas et al.   BMC GENOMICS

Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection

(2013) Elise A Lamont et al.   BMC GENOMICS

Receptor-mediated recognition of mycobacterial pathogens

(2013) Kate E. Killick et al.   CELLULAR MICROBIOLOGY

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Systems approaches to studying the immune response in tuberculosis

(2013) Matthew Paul Reddoch Berry et al.   CURRENT OPINION IN IMMUNOLOGY

Global gene expression profiling of monocyte-derived macrophages from red deer (Cervus elaphus) genotypically resistant or susceptible to Mycobacterium avium subspecies paratuberculosis infection

(2013) Brooke J. Marfell et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

No Holes Barred: Invasion of the Intestinal Mucosa by Mycobacterium avium subsp. paratuberculosis

(2013) John P. Bannantine et al.   INFECTION AND IMMUNITY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Mannosylated Lipoarabinomannans from Mycobacterium Avium Subsp. Paratuberculosis Alters the Inflammatory Response by Bovine Macrophages and Suppresses Killing of Mycobacterium Avium Subsp. Avium Organisms

(2013) Cleverson Souza et al.   PLoS One

Mycobacterium tuberculosis and the host cell inflammasome: a complex relationship

(2013) Volker Briken et al.   Frontiers in Cellular and Infection Microbiology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Estimating RNA-quality using GeneChip microarrays

(2012) Mario Fasold et al.   BMC GENOMICS

Regulatory T cells in cattle and their potential role in bovine paratuberculosis

(2012) Paul M. Coussens et al.   COMPARATIVE IMMUNOLOGY MICROBIOLOGY AND INFECTIOUS DISEASES

A commentary on current perspectives onMycobacterium aviumsubsp.paratuberculosis, Johne’s disease and Crohn’s disease: A review by Over et al. (2011)

(2012) Ros Robertson et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Caspase-8 Blocks Kinase RIPK3-Mediated Activation of the NLRP3 Inflammasome

(2012) Tae-Bong Kang et al.   IMMUNITY

Infection with Mycobacterium avium subsp. paratuberculosis Results in Rapid Interleukin-1β Release and Macrophage Transepithelial Migration

(2012) Elise A. Lamont et al.   INFECTION AND IMMUNITY

Mycobacterium avium subsp. paratuberculosis Inhibits Gamma Interferon-Induced Signaling in Bovine Monocytes: Insights into the Cellular Mechanisms of Johne's Disease

(2012) Ryan J. Arsenault et al.   INFECTION AND IMMUNITY

Enabling biomarkers for tuberculosis control [State of the Art Series. New tools. Number 3 in the series]

(2012) J. Maertzdorf et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

Economic analysis of Mycobacterium avium subspecies paratuberculosis vaccines in dairy herds

(2012) J. Cho et al.   JOURNAL OF DAIRY SCIENCE

Caspase-4 Is Required for Activation of Inflammasomes

(2012) G. Sollberger et al.   JOURNAL OF IMMUNOLOGY

Nitric oxide controls the immunopathology of tuberculosis by inhibiting NLRP3 inflammasome–dependent processing of IL-1β

(2012) Bibhuti B Mishra et al.   NATURE IMMUNOLOGY

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Global Gene Expression and Systems Biology Analysis of Bovine Monocyte-Derived Macrophages in Response to In Vitro Challenge with Mycobacterium bovis

(2012) David A. Magee et al.   PLoS One

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

(2012) Zhide Fang et al.   Cell and Bioscience

Linking the Transcriptional Profiles and the Physiological States of Mycobacterium tuberculosis during an Extended Intracellular Infection

(2012) Kyle H. Rohde et al.   PLoS Pathogens

Infection of Primary Bovine Macrophages with Mycobacterium avium Subspecies paratuberculosis Suppresses Host Cell Apoptosis

(2012) Edward Kabara et al.   Frontiers in Microbiology

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

(2011) Alessandro Guida et al.   BMC GENOMICS

A large-scale study of differential gene expression in monocyte-derived macrophages infected with several strains of Mycobacterium avium subspecies paratuberculosis

(2011) E. Kabara et al.   Briefings in Functional Genomics

A comparison of analog and Next-Generation transcriptomic tools for mammalian studies

(2011) N. C. Roy et al.   Briefings in Functional Genomics

Current perspectives onMycobacterium aviumsubsp.paratuberculosis,Johne’s disease, and Crohn’s disease: a Review

(2011) Ken Over et al.   CRITICAL REVIEWS IN MICROBIOLOGY

A delicate dance: host response to mycobacteria

(2011) Kassidy K Huynh et al.   CURRENT OPINION IN IMMUNOLOGY

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

For better or for worse: the immune response against Mycobacterium tuberculosis balances pathology and protection

(2011) Anca Dorhoi et al.   IMMUNOLOGICAL REVIEWS

Serum Amyloid A Activates the NLRP3 Inflammasome and Promotes Th17 Allergic Asthma in Mice

(2011) J. L. Ather et al.   JOURNAL OF IMMUNOLOGY

Risk Factors Associated with Transmission of Mycobacterium avium subsp. paratuberculosis to Calves within Dairy Herd: A Systematic Review

(2011) E. Doré et al.   JOURNAL OF VETERINARY INTERNAL MEDICINE

The role of IL-10 in immune regulation during M. tuberculosis infection

(2011) P S Redford et al.   Mucosal Immunology

Pathogenesis of Paratuberculosis

(2011) Raymond W. Sweeney   VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE

Epidemiology and Economics of Paratuberculosis

(2011) Jason E. Lombard   VETERINARY CLINICS OF NORTH AMERICA-FOOD ANIMAL PRACTICE

Crohn's disease and Mycobacterium avium subsp. paratuberculosis: The need for a study is long overdue

(2011) William C. Davis et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

The Inflammasomes

(2010) Kate Schroder et al.   CELL

NLR-containing inflammasomes: Central mediators of host defense and inflammation

(2010) Katherine A. Fitzgerald   EUROPEAN JOURNAL OF IMMUNOLOGY

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Genomic and transcriptomic studies in Mycobacterium avium subspecies paratuberculosis

(2010) John P. Bannantine et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

Transcriptional profiling of immune genes in bovine monocyte-derived macrophages exposed to bacterial antigens

(2010) Maria Taraktsoglou et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Macrophage CD40 signaling: A pivotal regulator of disease protection and pathogenesis

(2009) Jill Suttles et al.   SEMINARS IN IMMUNOLOGY

Gene Expression Profiling of the Host Response toMycobacterium bovisInfection in Cattle

(2009) D. E. MacHugh et al.   Transboundary and Emerging Diseases

A whole-genome assembly of the domestic cow, Bos taurus

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Mycobacterium tuberculosis Prevents Inflammasome Activation

(2008) Sharon S. Master et al.   Cell Host & Microbe

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Mycobacterium avium subspecies paratuberculosis suppresses expression of IL-12p40 and iNOS genes induced by signalling through CD40 in bovine monocyte-derived macrophages

(2008) Sandra Sommer et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

Review Paper: Modulation of Mononuclear Phagocyte Function by Mycobacterium avium subsp. paratuberculosis

(2008) D. J. Weiss et al.   VETERINARY PATHOLOGY