Aging disrupts circadian gene regulation and function in macrophages

The clock gene Bmal1 inhibits macrophage motility, phagocytosis, and impairs defense against pneumonia

(2020) Gareth B. Kitchen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Daily Variation in Macrophage Phagocytosis is Clock-independent and Dispensable for Cytokine Production

(2019) Sarah S. Geiger et al.   IMMUNOLOGY

Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity

(2019) Qingkun Liu et al.   NATURE IMMUNOLOGY

KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

(2019) Dafne Campigli Di Giammartino et al.   NATURE CELL BIOLOGY

Genomic variants in members of the Krüppel-like factor gene family are associated with disease severity and hydroxyurea treatment efficacy in β-hemoglobinopathies patients

(2019) Apostolos Stratopoulos et al.   PHARMACOGENOMICS

Effective In Vivo Gene Modification in Mouse Tissue-Resident Peritoneal Macrophages by Intraperitoneal Delivery of Lentiviral Vectors

(2019) Natacha Ipseiz et al.   Molecular Therapy-Methods & Clinical Development

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

The Circadian Clock Controls Immune Checkpoint Pathway in Sepsis

(2018) Wenjun Deng et al.   Cell Reports

Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data

(2018) Alan L. Hutchison et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Circadian Expression of Migratory Factors Establishes Lineage-Specific Signatures that Guide the Homing of Leukocyte Subsets to Tissues

(2018) Wenyan He et al.   IMMUNITY

Macrophage de novo NAD+ synthesis specifies immune function in aging and inflammation

(2018) Paras S. Minhas et al.   NATURE IMMUNOLOGY

Myeloid Bmal1 deletion increases monocyte recruitment and worsens atherosclerosis

(2017) Mingyu Huo et al.   FASEB JOURNAL

The chromatin accessibility signature of human immune aging stems from CD8+T cells

(2017) Duygu Ucar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Evolution of circadian rhythms: from bacteria to human

(2017) Utpal Bhadra et al.   SLEEP MEDICINE

MetaCycle: an integrated R package to evaluate periodicity in large scale data

(2016) Gang Wu et al.   BIOINFORMATICS

Endogenous circadian regulation of pro-inflammatory cytokines and chemokines in the presence of bacterial lipopolysaccharide in humans

(2015) Shadab A. Rahman et al.   BRAIN BEHAVIOR AND IMMUNITY

Microglia inflammatory responses are controlled by an intrinsic circadian clock

(2015) Laura K. Fonken et al.   BRAIN BEHAVIOR AND IMMUNITY

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Irf6 directly regulates Klf17 in zebrafish periderm and Klf4 in murine oral epithelium, and dominant-negative KLF4 variants are present in patients with cleft lip and palate

(2015) Huan Liu et al.   HUMAN MOLECULAR GENETICS

Transcription Factors STAT6 and KLF4 Implement Macrophage Polarization via the Dual Catalytic Powers of MCPIP

(2015) Nidhi Kapoor et al.   JOURNAL OF IMMUNOLOGY

Genetic variants associated with colorectal brain metastases susceptibility and survival

(2015) S Stremitzer et al.   PHARMACOGENOMICS JOURNAL

Circadian control of innate immunity in macrophages by miR-155 targetingBmal1

(2015) Anne M. Curtis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crosstalk between circadian rhythmicity, mitochondrial dynamics and macrophage bactericidal activity

(2014) Jacqueline Oliva-Ramírez et al.   IMMUNOLOGY

Detecting Rhythms in Time Series with RAIN

(2014) Paul F. Thaben et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Kruppel-Like Factor 4 Is Essential for Inflammatory Monocyte Differentiation In Vivo

(2014) J. K. Alder et al.   JOURNAL OF IMMUNOLOGY

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circadian Gene Bmal1 Regulates Diurnal Oscillations of Ly6Chi Inflammatory Monocytes

(2013) K. D. Nguyen et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Role of Proinflammatory Cytokines on Lipopolysaccharide-Induced Phase Shifts in Locomotor Activity Circadian Rhythm

(2012) M. Juliana Leone et al.   CHRONOBIOLOGY INTERNATIONAL

Adrenergic Nerves Govern Circadian Leukocyte Recruitment to Tissues

(2012) Christoph Scheiermann et al.   IMMUNITY

Eosinophil contamination of thioglycollate-elicited peritoneal macrophage cultures skews the functional readouts of in vitro assays

(2012) Alexander V. Misharin et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways

(2011) Michela Palmieri et al.   HUMAN MOLECULAR GENETICS

Krüppel-like factor 4 regulates macrophage polarization

(2011) Xudong Liao et al.   JOURNAL OF CLINICAL INVESTIGATION

Clonal analysis reveals multiple functional defects of aged murine hematopoietic stem cells

(2011) Brad Dykstra et al.   JOURNAL OF EXPERIMENTAL MEDICINE

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

A circadian clock in macrophages controls inflammatory immune responses

(2009) Maren Keller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Gene Network Regulating Lysosomal Biogenesis and Function

(2009) Marco Sardiello et al.   SCIENCE

Stems Cells and the Pathways to Aging and Cancer

(2008) Derrick J. Rossi et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL