Signal Integration of IFN-I and IFN-II With TLR4 Involves Sequential Recruitment of STAT1-Complexes and NFκB to Enhance Pro-inflammatory Transcription

A Positive Feedback Amplifier Circuit That Regulates Interferon (IFN)-Stimulated Gene Expression and Controls Type I and Type II IFN Responses

(2018) Agata Michalska et al.   Frontiers in Immunology

The unique role of STAT2 in constitutive and IFN-induced transcription and antiviral responses

(2016) Katarzyna Blaszczyk et al.   CYTOKINE & GROWTH FACTOR REVIEWS

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Noncanonical Effects of IRF9 in Intestinal Inflammation: More than Type I and Type III Interferons

(2015) Isabella Rauch et al.   MOLECULAR AND CELLULAR BIOLOGY

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex

(2015) Sebastian Wienerroither et al.   Cell Reports

Data Mining of Atherosclerotic Plaque Transcriptomes Predicts STAT1-Dependent Inflammatory Signal Integration in Vascular Disease

(2014) Krzysztof Sikorski et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

STAT1-Dependent Signal Integration between IFNγ and TLR4 in Vascular Cells Reflect Pro-Atherogenic Responses in Human Atherosclerosis

(2014) Stefan Chmielewski et al.   PLoS One

Extensive Cooperation of Immune Master Regulators IRF3 and NFκB in RNA Pol II Recruitment and Pause Release in Human Innate Antiviral Transcription

(2013) Jonathan E. Freaney et al.   Cell Reports

Type I interferons modulate vascular function, repair, thrombosis, and plaque progression in murine models of lupus and atherosclerosis

(2012) Seth G. Thacker et al.   ARTHRITIS AND RHEUMATISM

Inhibiting autophagy potentiates the anticancer activity of IFN1@/IFNα in chronic myeloid leukemia cells

(2012) Shan Zhu et al.   Autophagy

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

TLR4 antagonist reduces early-stage atherosclerosis in diabetic apolipoprotein E-deficient mice

(2012) Zhongyang Lu et al.   JOURNAL OF ENDOCRINOLOGY

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor   in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

(2012) M. S. Siersbaek et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes

(2011) N. A. S. Rao et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nonconventional Initiation Complex Assembly by STAT and NF-κB Transcription Factors Regulates Nitric Oxide Synthase Expression

(2010) Matthias Farlik et al.   IMMUNITY

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

(2010) Luca Giorgetti et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors

(2010) Taro Kawai et al.   NATURE IMMUNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Uncovering an IL-10-dependent NF-κB recruitment to the IL-1ra promoter that is impaired in STAT3 functionally defective patients

(2009) Nicola Tamassia et al.   FASEB JOURNAL

Cross-regulation of Signaling Pathways by Interferon-γ: Implications for Immune Responses and Autoimmune Diseases

(2009) Xiaoyu Hu et al.   IMMUNITY

Regulation of interferon and Toll-like receptor signaling during macrophage activation by opposing feedforward and feedback inhibition mechanisms

(2009) Xiaoyu Hu et al.   IMMUNOLOGICAL REVIEWS

Synergistic Induction of Endothelin-1 by Tumor Necrosis Factor α and Interferon γ Is due to Enhanced NF-κB Binding and Histone Acetylation at Specific κB Sites

(2009) Stephen J. Wort et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Standardization of real-time PCR gene expression data from independent biological replicates

(2008) Erik Willems et al.   ANALYTICAL BIOCHEMISTRY

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY