Bacterial and viral pathogen-associated molecular patterns induce divergent early transcriptomic landscapes in a bovine macrophage cell line

Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry

(2017) Lisa E. Pomeranz et al.   JOURNAL OF NEUROSCIENCE

Selective immuno-modulatory effect of prolactin upon pro-inflammatory response in human fetal membranes

(2017) Pilar Flores-Espinosa et al.   JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Roles of M1 and M2 Macrophages in Herpes Simplex Virus 1 Infectivity

(2017) Dhong Hyun Lee et al.   JOURNAL OF VIROLOGY

Autoimmune disease variants regulateGSDMBgene expression in human immune cells and whole blood

(2017) Yang Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene polymorphism linked to increased asthma and IBD risk alters gasdermin-B structure, a sulfatide and phosphoinositide binding protein

(2017) Kinlin L. Chao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innate Immune Gene Transcript Level Associated with the Infection of Macrophages with Ectromelia Virus in Two Different Mouse Strains

(2017) Patryk Dolega et al.   VIRAL IMMUNOLOGY

IFN regulatory factor 1 restricts hepatitis E virus replication by activating STAT1 to induce antiviral IFN-stimulated genes

(2016) Lei Xu et al.   FASEB JOURNAL

Identification of Interferon-Stimulated Gene Proteins That Inhibit Human Parainfluenza Virus Type 3

(2016) M. A. G. Rabbani et al.   JOURNAL OF VIROLOGY

Genome Wide Host Gene Expression Analysis in Chicken Lungs Infected with Avian Influenza Viruses

(2016) Pradip B. Ranaware et al.   PLoS One

Non-classical effects of prolactin on the innate immune response of bovine mammary epithelial cells: Implications during Staphylococcus aureus internalization

(2015) Ivan Medina-Estrada et al.   MICROBIAL PATHOGENESIS

Tumor necrosis factor–related apoptosis-inducing ligand induces the expression of proinflammatory cytokines in macrophages and re-educates tumor-associated macrophages to an antitumor phenotype

(2015) Jing Gao et al.   MOLECULAR BIOLOGY OF THE CELL

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

The Rheumatoid Arthritis Risk GeneLBHRegulates Growth in Fibroblast-like Synoviocytes

(2015) Anna-Karin H. Ekwall et al.   Arthritis & Rheumatology

Immune response to bovine viral diarrhea virus—looking at newly defined targets

(2015) Christopher C. L. Chase et al.   ANIMAL HEALTH RESEARCH REVIEWS

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

(2015) Maura E. Casey et al.   Frontiers in Immunology

Toll-Like Receptor Signaling Pathways

(2014) Takumi Kawasaki et al.   Frontiers in Immunology

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

(2013) Y. Liao et al.   BIOINFORMATICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The early phase transcriptome of bovine monocyte-derived macrophages infected with Staphylococcus aureus in vitro

(2013) Anna Lewandowska-Sabat et al.   BMC GENOMICS

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

Toll-like receptor 3 in viral pathogenesis: friend or foe?

(2013) Renzo Perales-Linares et al.   IMMUNOLOGY

CXCL5 limits macrophage foam cell formation in atherosclerosis

(2013) Anthony Rousselle et al.   JOURNAL OF CLINICAL INVESTIGATION

RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA

(2013) Cherilyn M. Sirois et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Loss of T Regulatory Cell Suppression following Signaling through Glucocorticoid-induced Tumor Necrosis Receptor (GITR) Is Dependent on c-Jun N-terminal Kinase Activation

(2012) Anthony Joetham et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Systematic identification of type I and type II interferon-induced antiviral factors

(2012) S.-Y. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NR4A1 (Nur77) Deletion Polarizes Macrophages Toward an Inflammatory Phenotype and Increases Atherosclerosis

(2011) Richard N. Hanna et al.   CIRCULATION RESEARCH

Proliferative lesions and metalloproteinase activity in murine lupus nephritis mediated by type I interferons and macrophages

(2010) A. Triantafyllopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

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

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

Cytochrome P450 CYP1A1: wider roles in cancer progression and prevention

(2009) Vasilis P Androutsopoulos et al.   BMC CANCER

S100A8/A9 induces autophagy and apoptosis via ROS-mediated cross-talk between mitochondria and lysosomes that involves BNIP3

(2009) Saeid Ghavami et al.   CELL RESEARCH

Distinct Antiviral Roles for Human 2',5'-Oligoadenylate Synthetase Family Members against Dengue Virus Infection

(2009) R.-J. Lin et al.   JOURNAL OF IMMUNOLOGY

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Signalling pathways leading to IFN-α production in human plasmacytoid dendritic cell and the possible use of agonists or antagonists of TLR7 and TLR9 in clinical indications

(2008) C. Guiducci et al.   JOURNAL OF INTERNAL MEDICINE