Systems biology approaches to toll-like receptor signaling

Structural Basis of TLR5-Flagellin Recognition and Signaling

(2012) S.-i. Yoon et al.   SCIENCE

Structural analysis of the intracellular domain of (pro)renin receptor fused to maltose-binding protein

(2011) Yanfeng Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

Toll-like receptors

(2011) Eva Marie Y. Moresco et al.   CURRENT BIOLOGY

Mapping a Dynamic Innate Immunity Protein Interaction Network Regulating Type I Interferon Production

(2011) Shitao Li et al.   IMMUNITY

Macrophages.com: An on-line community resource for innate immunity research

(2011) Christelle Robert et al.   IMMUNOBIOLOGY

Identification of Interaction Sites for Dimerization and Adapter Recruitment in Toll/Interleukin-1 Receptor (TIR) Domain of Toll-like Receptor 4

(2011) Celia Bovijn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations

(2011) Shunsuke Teraguchi et al.   PHYSICAL REVIEW E

Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection

(2011) E. Valkov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of template based protein structure predictions in CASP9

(2011) Valerio Mariani et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

What the Myddosome structure tells us about the initiation of innate immunity

(2011) Nicholas J. Gay et al.   TRENDS IN IMMUNOLOGY

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

(2010) Sobia Raza et al.   BMC Systems Biology

A peptidoglycan monomer with the glutamine to serine change and basic peptides bind in silico to TLR-2 (403–455)

(2010) Yufeng Li et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Selective Transcription in Response to an Inflammatory Stimulus

(2010) Stephen T. Smale   CELL

Pattern Recognition Receptors and Inflammation

(2010) Osamu Takeuchi et al.   CELL

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Human TLRs 10 and 1 Share Common Mechanisms of Innate Immune Sensing but Not Signaling

(2010) Y. Guan et al.   JOURNAL OF IMMUNOLOGY

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

(2010) Luca Giorgetti et al.   MOLECULAR CELL

The phosphoproteome of toll-like receptor-activated macrophages

(2010) Gabriele Weintz et al.   Molecular Systems Biology

Helical assembly in the MyD88–IRAK4–IRAK2 complex in TLR/IL-1R signalling

(2010) Su-Chang Lin et al.   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

(2010) Takashi Satoh et al.   NATURE IMMUNOLOGY

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

Evidence that tricyclic small molecules may possess toll-like receptor and myeloid differentiation protein 2 activity

(2010) M.R. Hutchinson et al.   NEUROSCIENCE

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Epigenetic regulation of the alternatively activated macrophage phenotype

(2009) M. Ishii et al.   BLOOD

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

(2009) Diana C. Hargreaves et al.   CELL

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

(2009) Francesca De Santa et al.   EMBO JOURNAL

Recognition of Lipopeptide Patterns by Toll-like Receptor 2-Toll-like Receptor 6 Heterodimer

(2009) Jin Young Kang et al.   IMMUNITY

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Kinetic control of negative feedback regulators of NF- B/RelA determines their pathogen- and cytokine-receptor signaling specificity

(2009) V. F.-S. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling

(2009) H. Ohnishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling

(2009) Fan Li et al.   PLoS Computational Biology

The Crystal Structure of the Human Toll-like Receptor 10 Cytoplasmic Domain Reveals a Putative Signaling Dimer

(2008) Tomas Nyman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Understanding NF-κB signaling via mathematical modeling

(2008) Raymond Cheong et al.   Molecular Systems Biology

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

(2008) David J Lynn et al.   Molecular Systems Biology

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

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

Structural Basis of Toll-Like Receptor 3 Signaling with Double-Stranded RNA

(2008) L. Liu et al.   SCIENCE

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

(2008) Stephen A. Ramsey et al.   PLoS Computational Biology