Commensal microbiota modulate gene expression in the skin

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

(2017) James M. Davison et al.   GENOME RESEARCH

Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year

(2017) Elizabeth A. Kennedy et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The Molecular Revolution in Cutaneous Biology: EDC and Locus Control

(2017) Inez Y. Oh et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

IL-27 Facilitates Skin Wound Healing through Induction of Epidermal Proliferation and Host Defense

(2017) Bin Yang et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Cathepsin S is the major activator of the psoriasis-associated proinflammatory cytokine IL-36γ

(2017) Joseph S. Ainscough et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis

(2017) Teruaki Nakatsuji et al.   Science Translational Medicine

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis

(2017) Adrian Tett et al.   npj Biofilms and Microbiomes

The gut-skin axis in health and disease: A paradigm with therapeutic implications

(2016) Catherine A. O'Neill et al.   BIOESSAYS

DGCA: A comprehensive R package for Differential Gene Correlation Analysis

(2016) Andrew T. McKenzie et al.   BMC Systems Biology

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

(2016) Qi Zheng et al.   PLoS Computational Biology

Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota

(2016) Allison L. Richards et al.   mSystems

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

(2015) Andrey Morgun et al.   GUT

A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes

(2015) Tiffany C. Scharschmidt et al.   IMMUNITY

Dysbiosis and Staphylococcus aureus Colonization Drives Inflammation in Atopic Dermatitis

(2015) Tetsuro Kobayashi et al.   IMMUNITY

IL-33 impacts on the skin barrier by downregulating the expression of filaggrin

(2015) Jenny Seltmann et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

IL-36γ (IL-1F9) Is a Biomarker for Psoriasis Skin Lesions

(2015) Angelo Massimiliano D'Erme et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

Commensal–dendritic-cell interaction specifies a unique protective skin immune signature

(2015) Shruti Naik et al.   NATURE

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome

(2015) Geoffrey D. Hannigan et al.   mBio

The biology and regulation of corneodesmosomes

(2014) Akemi Ishida-Yamamoto et al.   CELL AND TISSUE RESEARCH

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

(2014) J. Gray Camp et al.   GENOME RESEARCH

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne

(2013) Sorel Fitz-Gibbon et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Keratin 16 regulates innate immunity in response to epidermal barrier breach

(2013) J. C. Lessard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Skin-specific expression of IL-33 activates group 2 innate lymphoid cells and elicits atopic dermatitis-like inflammation in mice

(2013) Yasutomo Imai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complement modulates the cutaneous microbiome and inflammatory milieu

(2013) C. Chehoud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

Community differentiation of the cutaneous microbiota in psoriasis

(2013) Alexander V Alekseyenko et al.   Microbiome

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

Neutralisation of the interleukin-33/ST2 pathway ameliorates experimental colitis through enhancement of mucosal healing in mice

(2012) Mamdouh A K Sedhom et al.   GUT

Compartmentalized Control of Skin Immunity by Resident Commensals

(2012) S. Naik et al.   SCIENCE

Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription

(2012) J. Gray Camp et al.   PLoS Genetics

ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments

(2011) M. j. Nueda et al.   BIOSTATISTICS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

(2011) Erik Larsson et al.   GUT

A Novel Role for Interleukin-27 (IL-27) as Mediator of Intestinal Epithelial Barrier Protection Mediated via Differential Signal Transducer and Activator of Transcription (STAT) Protein Signaling and Induction of Antibacterial and Anti-inflammatory Proteins

(2011) Julia Diegelmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A milieu of regulatory elements in the epidermal differentiation complex syntenic block: implications for atopic dermatitis and psoriasis

(2010) Cristina de Guzman Strong et al.   HUMAN MOLECULAR GENETICS

Epithelial-derived IL-33 and its receptor ST2 are dysregulated in ulcerative colitis and in experimental Th1/Th2 driven enteritis

(2010) Luca Pastorelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Commensal bacteria regulate Toll-like receptor 3–dependent inflammation after skin injury

(2009) Yuping Lai et al.   NATURE MEDICINE

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Genetic interplays between Msx2 and Foxn1 are required for Notch1 expression and hair shaft differentiation

(2008) Jing Cai et al.   DEVELOPMENTAL BIOLOGY