Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits

Lactobacillus paracasei-derived extracellular vesicles attenuate the intestinal inflammatory response by augmenting the endoplasmic reticulum stress pathway

(2020) Ji Hyun Choi et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Determining sequencing depth in a single-cell RNA-seq experiment

(2020) Martin Jinye Zhang et al.   Nature Communications

Prediction of condition-specific regulatory genes using machine learning

(2020) Qi Song et al.   NUCLEIC ACIDS RESEARCH

TICAM2-related pathway mediates neutrophil exhaustion

(2020) RuiCi Lin et al.   Scientific Reports

Frontline Science: Monocytes sequentially rewire metabolism and bioenergetics during an acute inflammatory response

(2019) Xuewei Zhu et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Novel reprogramming of neutrophils modulates inflammation resolution during atherosclerosis

(2019) Shuo Geng et al.   Science Advances

The cis-Regulatory Atlas of the Mouse Immune System

(2019) Hideyuki Yoshida et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Signals trigger state-specific transcriptional programs to support diversity and homeostasis in immune cells

(2019) Cornelius Fischer et al.   Science Signaling

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

(2019) Geng Chen et al.   Frontiers in Genetics

Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders

(2019) Marina Spörrer et al.   EBioMedicine

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

(2019) Evan D Tarbell et al.   NUCLEIC ACIDS RESEARCH

Human Monocyte Subsets and Phenotypes in Major Chronic Inflammatory Diseases

(2019) Theodore S. Kapellos et al.   Frontiers in Immunology

Phenylbutyrate facilitates homeostasis of non-resolving inflammatory macrophages

(2019) Allison Rahtes et al.   Innate Immunity

ShinyGO: a graphical gene-set enrichment tool for animals and plants

(2019) Steven Xijin Ge et al.   BIOINFORMATICS

The impact of interferon-regulatory factors to macrophage differentiation and polarization into M1 and M2

(2018) Dimitry A. Chistiakov et al.   IMMUNOBIOLOGY

Using single‐cell genomics to understand developmental processes and cell fate decisions

(2018) Jonathan A Griffiths et al.   Molecular Systems Biology

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Points of Significance: Statistics versus machine learning

(2018) Danilo Bzdok et al.   NATURE METHODS

Human Monocyte Heterogeneity as Revealed by High-Dimensional Mass Cytometry

(2018) Anouk A.J. Hamers et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Regulatory Networks Involving STATs, IRFs, and NFκB in Inflammation

(2018) Ekaterini Platanitis et al.   Frontiers in Immunology

Inflammatory monocytes require type I interferon receptor signaling to activate NK cells via IL-18 during a mucosal viral infection

(2017) Amanda J. Lee et al.   JOURNAL OF EXPERIMENTAL MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

4-PBA inhibits LPS-induced inflammation through regulating ER stress and autophagy in acute lung injury models

(2017) Meichun Zeng et al.   TOXICOLOGY LETTERS

Beneficial Effects of Sodium Phenylbutyrate Administration during Infection with Salmonella enterica Serovar Typhimurium

(2016) Stefan Jellbauer et al.   INFECTION AND IMMUNITY

TRIF-dependent TLR signaling, its functions in host defense and inflammation, and its potential as a therapeutic target

(2016) M. Obayed Ullah et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Low-grade inflammatory polarization of monocytes impairs wound healing

(2016) Ruoxi Yuan et al.   JOURNAL OF PATHOLOGY

4-Phenylbutyric Acid Attenuates Pancreatic Beta-Cell Injury in Rats with Experimental Severe Acute Pancreatitis

(2016) Yu-pu Hong et al.   International Journal of Endocrinology

The persistence of low-grade inflammatory monocytes contributes to aggravated atherosclerosis

(2016) Shuo Geng et al.   Nature Communications

The “Intermediate” CD14++CD16+ monocyte subset increases in severe peripheral artery disease in humans

(2016) Moritz Wildgruber et al.   Scientific Reports

Molecular Mechanisms That Underlie the Dynamic Adaptation of Innate Monocyte Memory to Varying Stimulant Strength of TLR Ligands

(2016) Ruoxi Yuan et al.   Frontiers in Immunology

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The therapeutic effects of 4-phenylbutyric acid in maintaining proteostasis

(2015) P.S. Kolb et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Naturally Occurring Subclinical Endotoxemia in Humans Alters Adaptive and Innate Immune Functions through Reduced MAPK and Increased STAT1 Phosphorylation

(2015) Christine D. Palmer et al.   JOURNAL OF IMMUNOLOGY

Innate Immune Programing by Endotoxin and Its Pathological Consequences

(2015) Matthew C. Morris et al.   Frontiers in Immunology

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Dynamic Modulation of Innate Immune Response by Varying Dosages of Lipopolysaccharide (LPS) in Human Monocytic Cells

(2014) Matthew C. Morris et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular and Cellular Mechanisms Responsible for Cellular Stress and Low-grade Inflammation Induced by a Super-low Dose of Endotoxin

(2014) Bianca Baker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptional Control of Macrophage Polarization

(2013) Derin Tugal et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Gene selection with guided regularized random forest

(2013) Houtao Deng et al.   PATTERN RECOGNITION

Inhibition of endoplasmic reticulum stress alleviates lipopolysaccharide-induced lung inflammation through modulation of NF-κB/HIF-1α signaling pathway

(2013) Hee Jung Kim et al.   Scientific Reports

The three human monocyte subsets: implications for health and disease

(2012) Kok Loon Wong et al.   IMMUNOLOGIC RESEARCH

Molecular Mechanism Responsible for the Priming of Macrophage Activation

(2012) Hui Deng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Mechanisms Responsible for the Selective and Low-Grade Induction of Proinflammatory Mediators in Murine Macrophages by Lipopolysaccharide

(2012) U. Maitra et al.   JOURNAL OF IMMUNOLOGY

Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells

(2012) Yan Fu et al.   PLoS Computational Biology

Molecular Mechanisms and Pathological Consequences of Endotoxin Tolerance and Priming

(2011) Matthew Morris et al.   ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS

The CD14bright CD16+ monocyte subset is expanded in rheumatoid arthritis and promotes expansion of the Th17 cell population

(2011) Manuela Rossol et al.   ARTHRITIS AND RHEUMATISM

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Examining Associations of Circulating Endotoxin With Nutritional Status, Inflammation, and Mortality in Hemodialysis Patients

(2011) Usama Feroze et al.   JOURNAL OF RENAL NUTRITION

Reduction in endotoxemia, oxidative and inflammatory stress, and insulin resistance after Roux-en-Y gastric bypass surgery in patients with morbid obesity and type 2 diabetes mellitus

(2011) Scott V. Monte et al.   SURGERY

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

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Pharmacological Inhibition of C-C Chemokine Receptor 2 Decreases Macrophage Infiltration in the Aortic Root of the Human C-C Chemokine Receptor 2/Apolipoprotein E −/− Mouse: Magnetic Resonance Imaging Assessment

(2009) Alan R. Olzinski et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

CX3CR1 is required for monocyte homeostasis and atherogenesis by promoting cell survival

(2008) L. Landsman et al.   BLOOD