Impaired expression of metallothioneins contributes to allergen-induced inflammation in patients with atopic dermatitis

Transcriptional programming of immunoregulatory responses in human Langerhans cells

(2022) James Davies et al.   Frontiers in Immunology

Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes

(2021) Evgeny Kiner et al.   NATURE IMMUNOLOGY

Developmental cell programs are co-opted in inflammatory skin disease

(2021) Gary Reynolds et al.   SCIENCE

Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering

(2021) Andres F. Vallejo et al.   iScience

CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks

(2021) James S Nagai et al.   BIOINFORMATICS

An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells

(2021) James Davies et al.   Frontiers in Immunology

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Genomic programming of IRF4-expressing human Langerhans cells

(2020) Sofia Sirvent et al.   Nature Communications

Machine learning applied to atopic dermatitis transcriptome reveals distinct therapy‐dependent modification of the keratinocyte immunophenotype

(2020) K. Clayton et al.   BRITISH JOURNAL OF DERMATOLOGY

Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning

(2020) Nicholas J. Bernstein et al.   Cell Systems

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Antigen presentation and adaptive immune responses in skin

(2019) Tetsuya Honda et al.   INTERNATIONAL IMMUNOLOGY

Choreographing Immunity in the Skin Epithelial Barrier

(2019) Tetsuro Kobayashi et al.   IMMUNITY

GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data

(2019) E. Mossotto et al.   BMC BIOINFORMATICS

Self-Renewal and Toll-like Receptor Signaling Sustain Exhausted Plasmacytoid Dendritic Cells during Chronic Viral Infection

(2018) Monica Macal et al.   IMMUNITY

The immunology of atopic dermatitis and its reversibility with broad-spectrum and targeted therapies

(2017) Patrick M. Brunner et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Aeroallergens Induce Reactive Oxygen Species Production and DNA Damage and Dampen Antioxidant Responses in Bronchial Epithelial Cells

(2017) Tze Khee Chan et al.   JOURNAL OF IMMUNOLOGY

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Maxed out macs: physiologic cell clearance as a function of macrophage phagocytic capacity

(2016) Clive S. Zent et al.   FEBS Journal

T Follicular Helper Cell Plasticity Shapes Pathogenic T Helper 2 Cell-Mediated Immunity to Inhaled House Dust Mite

(2016) André Ballesteros-Tato et al.   IMMUNITY

Early-onset pediatric atopic dermatitis is T H 2 but also T H 17 polarized in skin

(2016) Hitokazu Esaki et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

House dust mite–induced asthma causes oxidative damage and DNA double-strand breaks in the lungs

(2016) Tze Khee Chan et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Enrichment of Inflammatory IL-17 and TNF-α Secreting CD4+ T Cells within Colorectal Tumors despite the Presence of Elevated CD39+ T Regulatory Cells and Increased Expression of the Immune Checkpoint Molecule, PD-1

(2016) Margaret R. Dunne et al.   Frontiers in Oncology

IgE Sensitization Profiles Differ between Adult Patients with Severe and Moderate Atopic Dermatitis

(2016) Irene Mittermann et al.   PLoS One

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Exacerbation of atopic dermatitis on grass pollen exposure in an environmental challenge chamber

(2015) Thomas Werfel et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Regulation of T Cell Immunity in Atopic Dermatitis by Microbes: The Yin and Yang of Cutaneous Inflammation

(2015) Tilo Biedermann et al.   Frontiers in Immunology

TNF-α and Th2 Cytokines Induce Atopic Dermatitis–Like Features on Epidermal Differentiation Proteins and Stratum Corneum Lipids in Human Skin Equivalents

(2014) Mogbekeloluwa O. Danso et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Nickel allergy from adolescence to adulthood in the TOACS cohort

(2013) Charlotte G. Mortz et al.   CONTACT DERMATITIS

Adult eczema prevalence and associations with asthma and other health and demographic factors: A US population–based study

(2013) Jonathan I. Silverberg et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Intrinsic atopic dermatitis shows similar TH2 and higher TH17 immune activation compared with extrinsic atopic dermatitis

(2013) Mayte Suárez-Fariñas et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Sensitization via Healthy Skin Programs Th2 Responses in Individuals with Atopic Dermatitis

(2013) Louise Newell et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Distinct Molecular Signature of Human Skin Langerhans Cells Denotes Critical Differences in Cutaneous Dendritic Cell Immune Regulation

(2013) Marta E. Polak et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Psoriasis Severity and the Prevalence of Major Medical Comorbidity

(2013) Howa Yeung et al.   JAMA Dermatology

Human Epidermal Langerhans Cells Maintain Immune Homeostasis in Skin by Activating Skin Resident Regulatory T Cells

(2012) Julien Seneschal et al.   IMMUNITY

CD70–CD27 Interaction Augments CD8+ T-Cell Activation by Human Epidermal Langerhans Cells

(2012) Marta E. Polak et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Management of Difficult-to-Treat Atopic Dermatitis

(2012) Peter D. Arkwright et al.   Journal of Allergy and Clinical Immunology-In Practice

Nonlesional atopic dermatitis skin is characterized by broad terminal differentiation defects and variable immune abnormalities

(2011) Mayte Suárez-Fariñas et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Langerhans cells are precommitted to immune tolerance induction

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Quantifying human susceptibility to contact sensitization; risk assessments now and in the future

(2010) Peter S. Friedmann et al.   CONTACT DERMATITIS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Heme oxygenase 1 attenuates the development of atopic dermatitis–like lesions in mice: Implications for human disease

(2008) Mio Kirino et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Filaggrin null mutations are associated with atopic dermatitis and elevated levels of IgE in the Japanese population: a family and case–control study

(2008) Hisako Enomoto et al.   JOURNAL OF HUMAN GENETICS