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

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis

(2016) Gitte J. M. Christensen et al.   BMC GENOMICS

Microbiology: the road to strain-level identification

(2016) Vivien Marx   NATURE METHODS

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

(2016) Moreno Zolfo et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare

(2016) Kern Rei Chng et al.   Nature Microbiology

Psoriasis

(2015) Wolf-Henning Boehncke et al.   LANCET

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

(2015) Shruti Naik et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

(2015) Guangxi Wu et al.   PLoS Genetics

Inter-individual differences in the gene content of human gut bacterial species

(2015) Ana Zhu et al.   GENOME BIOLOGY

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Bacterial diversity and Clostridia abundance decrease with increasing severity of necrotizing enterocolitis

(2015) Valarie E McMurtry et al.   Microbiome

Immunology of Psoriasis

(2014) Michelle A. Lowes et al.   Annual Review of Immunology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Psoriasis is not an autoimmune disease?

(2014) Lionel Fry et al.   EXPERIMENTAL DERMATOLOGY

Molecular characterization of the skin fungal microbiome in patients with psoriasis

(2014) Akemi Takemoto et al.   JOURNAL OF DERMATOLOGY

Association ofMalasseziaspecies with psoriatic lesions

(2014) Shivaprakash M. Rudramurthy et al.   MYCOSES

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Recent advances in genomic DNA sequencing of microbial species from single cells

(2014) Roger S. Lasken et al.   NATURE REVIEWS GENETICS

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

The antimicrobial peptide LL37 is a T-cell autoantigen in psoriasis

(2014) Roberto Lande et al.   Nature Communications

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease

(2014) Jose U. Scher et al.   Arthritis & Rheumatology

Microbiome and skin diseases

(2013) Patrick L.J.M. Zeeuwen et al.   Current Opinion in Allergy and Clinical Immunology

Responsiveness to Change and Interpretability of the Simplified Psoriasis Index

(2013) Leena Chularojanamontri et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison

(2013) Alexander Statnikov et al.   Scientific Reports

Community differentiation of the cutaneous microbiota in psoriasis

(2013) Alexander V Alekseyenko et al.   Microbiome

The Malassezia Genus in Skin and Systemic Diseases

(2012) G. Gaitanis et al.   CLINICAL MICROBIOLOGY REVIEWS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An Expanded Multilocus Sequence Typing Scheme for Propionibacterium acnes: Investigation of ‘Pathogenic’, ‘Commensal’ and Antibiotic Resistant Strains

(2012) Andrew McDowell et al.   PLoS One

Compartmentalized Control of Skin Immunity by Resident Commensals

(2012) S. Naik et al.   SCIENCE

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates

(2012) Sean Conlan et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin

(2011) Annika Fahlén et al.   ARCHIVES OF DERMATOLOGICAL RESEARCH

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens

(2011) A. McDowell et al.   MICROBIOLOGY-SGM

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Activation of TLR2 by a Small Molecule Produced by Staphylococcus epidermidis Increases Antimicrobial Defense against Bacterial Skin Infections

(2010) Yuping Lai et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Yuping Lai et al.   NATURE MEDICINE

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

A diversity profile of the human skin microbiota

(2008) E. A. Grice et al.   GENOME RESEARCH

Substantial Alterations of the Cutaneous Bacterial Biota in Psoriatic Lesions

(2008) Zhan Gao et al.   PLoS One