Our natural “makeup” reveals more than it hides: Modeling the skin and its microbiome

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Mathematical modelling of contact dermatitis from nickel and chromium

(2019) J. P. Ward et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Neuromodulation of metabolic functions: from pharmaceuticals to bioelectronics to biocircuits

(2019) Benjamin J. Seicol et al.   Journal of Biological Engineering

A QSP Model for Predicting Clinical Responses to Monotherapy, Combination and Sequential Therapy Following CTLA-4, PD-1, and PD-L1 Checkpoint Blockade

(2019) Oleg Milberg et al.   Scientific Reports

Toward a Common Coordinate Framework for the Human Body

(2019) Jennifer E. Rood et al.   CELL

Unraveling the Complex Interplay Between T Cell Metabolism and Function

(2018) Ramon I. Klein Geltink et al.   Annual Review of Immunology

Integrated Approaches to Testing and Assessment: OECD Activities on the Development and Use of Adverse Outcome Pathways and Case Studies

(2018) Yuki Sakuratani et al.   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair

(2018) Jonathan L. Linehan et al.   CELL

S. aureus endocarditis: Clinical aspects and experimental approaches

(2018) V. Hoerr et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Contextual control of skin immunity and inflammation byCorynebacterium

(2018) Vanessa K. Ridaura et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis

(2018) Mark Lyte et al.   PLoS One

Redefining the Role of Langerhans Cells As Immune Regulators within the Skin

(2018) Heather C. West et al.   Frontiers in Immunology

The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing

(2018) Taylor Johnson et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Modelling skin wound healing angiogenesis: A review

(2018) Ana Guerra et al.   JOURNAL OF THEORETICAL BIOLOGY

Expanded skin virome in DOCK8-deficient patients

(2018) Osnat Tirosh et al.   NATURE MEDICINE

Genomes OnLine database (GOLD) v.7: updates and new features

(2018) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Regulation of Monospecies and Mixed Biofilms Formation of Skin Staphylococcus aureus and Cutibacterium acnes by Human Natriuretic Peptides

(2018) Andrei Vladislavovich Gannesen et al.   Frontiers in Microbiology

Gut microbiota functions: metabolism of nutrients and other food components

(2017) Ian Rowland et al.   EUROPEAN JOURNAL OF NUTRITION

Neuroendocrine-immune circuits, phenotypes, and interactions

(2017) Noah T. Ashley et al.   HORMONES AND BEHAVIOR

White Adipose Tissue Is a Reservoir for Memory T Cells and Promotes Protective Memory Responses to Infection

(2017) Seong-Ji Han et al.   IMMUNITY

Foundations of Immunometabolism and Implications for Metabolic Health and Disease

(2017) Gökhan S. Hotamisligil   IMMUNITY

Mathematical modeling of atopic dermatitis reveals “double-switch” mechanisms underlying 4 common disease phenotypes

(2017) Elisa Domínguez-Hüttinger et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis

(2017) Allyson L. Byrd et al.   Science Translational Medicine

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

A longitudinal study of the diabetic skin and wound microbiome

(2017) Melissa Gardiner et al.   PeerJ

An algorithm for designing minimal microbial communities with desired metabolic capacities

(2016) Alexander Eng et al.   BIOINFORMATICS

Role of Metabolism in the Immunobiology of Regulatory T Cells

(2016) Mario Galgani et al.   JOURNAL OF IMMUNOLOGY

Metabolomics enables precision medicine: “A White Paper, Community Perspective”

(2016) Richard D. Beger et al.   Metabolomics

Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design

(2016) Feifei Han et al.   Molecular BioSystems

Skin-bacteria communication: Involvement of the neurohormone Calcitonin Gene Related Peptide (CGRP) in the regulation of Staphylococcus epidermidis virulence

(2016) Awa R. N’Diaye et al.   Scientific Reports

Effect of Substance P in Staphylococcus aureus and Staphylococcus epidermidis Virulence: Implication for Skin Homeostasis

(2016) Awa N'Diaye et al.   Frontiers in Microbiology

The Skin Microbiome: Is It Affected by UV-induced Immune Suppression?

(2016) VijayKumar Patra et al.   Frontiers in Microbiology

Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species

(2016) Matthew M. Ramsey et al.   Frontiers in Microbiology

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

Malasseziaspecies and their associated skin diseases

(2015) Kazutoshi Harada et al.   JOURNAL OF DERMATOLOGY

Microbial endocrinology: host-bacteria communication within the gut microbiome

(2015) S. Sandrini et al.   JOURNAL OF ENDOCRINOLOGY

The Skin Immune Atlas: Three-Dimensional Analysis of Cutaneous Leukocyte Subsets by Multiphoton Microscopy

(2015) Philip L. Tong et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

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

(2015) Shruti Naik et al.   NATURE

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Propionibacterium acnes: from Commensal to Opportunistic Biofilm-Associated Implant Pathogen

(2014) Y. Achermann et al.   CLINICAL MICROBIOLOGY REVIEWS

Biophysical constraints on the evolution of tissue structure and function

(2014) P. J. Hunter et al.   JOURNAL OF PHYSIOLOGY-LONDON

Patient-specific modeling of the neuroendocrine HPA-axis and its relation to depression: Ultradian and circadian oscillations

(2014) Johanne Gudmand-Hoeyer et al.   MATHEMATICAL BIOSCIENCES

Perivascular leukocyte clusters are essential for efficient activation of effector T cells in the skin

(2014) Yohei Natsuaki et al.   NATURE IMMUNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Superficial Fungal Infections in Children

(2014) Danielle M. Hawkins et al.   PEDIATRIC CLINICS OF NORTH AMERICA

Staphylococcus aureus Osteomyelitis: Bad to the Bone

(2013) Michael E. Olson et al.   Cell Host & Microbe

Steroidogenesis in the skin: Implications for local immune functions

(2013) Andrzej Slominski et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

The Opportunistic Pathogen Propionibacterium acnes: Insights into Typing, Human Disease, Clonal Diversification and CAMP Factor Evolution

(2013) Andrew McDowell et al.   PLoS One

Effects of a Skin Neuropeptide (Substance P) on Cutaneous Microflora

(2013) Lily Mijouin et al.   PLoS One

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

The microbiome extends to subepidermal compartments of normal skin

(2013) Teruaki Nakatsuji et al.   Nature Communications

A systems biology approach to studying the role of microbes in human health

(2012) Ines Thiele et al.   CURRENT OPINION IN BIOTECHNOLOGY

Microbiological and biochemical origins of human axillary odour

(2012) A. Gordon James et al.   FEMS MICROBIOLOGY ECOLOGY

Increased Incidence of Cutaneous Nontuberculous Mycobacterial Infection, 1980 to 2009: A Population-Based Study

(2012) Ashley B. Wentworth et al.   MAYO CLINIC PROCEEDINGS

Pathogen espionage: multiple bacterial adrenergic sensors eavesdrop on host communication systems

(2012) Michail H. Karavolos et al.   MOLECULAR MICROBIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Histamine Derived from Probiotic Lactobacillus reuteri Suppresses TNF via Modulation of PKA and ERK Signaling

(2012) Carissa M. Thomas et al.   PLoS One

Modeling Cortisol Dynamics in the Neuro-endocrine Axis Distinguishes Normal, Depression, and Post-traumatic Stress Disorder (PTSD) in Humans

(2012) K. Sriram et al.   PLoS Computational Biology

Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc

(2012) Miles Trupp et al.   GENOME BIOLOGY

Microbiome dynamics of human epidermis following skin barrier disruption

(2012) Patrick LJM Zeeuwen et al.   GENOME BIOLOGY

Prediction of metabolic pathways from genome-scale metabolic networks

(2011) Karoline Faust et al.   BIOSYSTEMS

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

(2011) Lore Cloots et al.   CURRENT OPINION IN MICROBIOLOGY

Spatial mapping by imaging mass spectrometry offers advancements for rapid definition of human skin proteomic signatures

(2011) Domenico Taverna et al.   EXPERIMENTAL DERMATOLOGY

The scent of disease: volatile organic compounds of the human body related to disease and disorder

(2011) M. Shirasu et al.   JOURNAL OF BIOCHEMISTRY

The skin microbiome

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

A theory of biological relativity: no privileged level of causation

(2011) D. Noble   Interface Focus

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Parasitic, fungal and prion zoonoses: an expanding universe of candidates for human disease

(2010) N. Akritidis   CLINICAL MICROBIOLOGY AND INFECTION

Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization

(2010) Tadayuki Iwase et al.   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Ecology and Transmission of Buruli Ulcer Disease: A Systematic Review

(2010) Richard W. Merritt et al.   PLoS Neglected Tropical Diseases

The neuroendocrine hormone norepinephrine increases Pseudomonas aeruginosa PA14 virulence through the las quorum-sensing pathway

(2009) Manjunath Hegde et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Gender-Specific Differences between the Concentrations of Nonvolatile (R)/(S)-3-Methyl-3-Sulfanylhexan-1-Ol and (R)/(S)-3-Hydroxy-3-Methyl-Hexanoic Acid Odor Precursors in Axillary Secretions

(2009) M. Troccaz et al.   CHEMICAL SENSES

Staphylococcus aureusBacteremia: Epidemiology, Pathophysiology, and Management Strategies

(2009) Christoph K. Naber   CLINICAL INFECTIOUS DISEASES

The Hair Follicle as a Dynamic Miniorgan

(2009) Marlon R. Schneider et al.   CURRENT BIOLOGY

Topological Signatures of Species Interactions in Metabolic Networks

(2009) Elhanan Borenstein et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Gender-linked differences in human skin

(2009) Paolo U. Giacomoni et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Staphylococcus epidermidis — the 'accidental' pathogen

(2009) Michael Otto   NATURE REVIEWS MICROBIOLOGY

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

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

Analyses of volatile organic compounds from human skin

(2008) M. Gallagher et al.   BRITISH JOURNAL OF DERMATOLOGY

A diversity profile of the human skin microbiota

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

A Systems Biology Approach to Anatomic Diversity of Skin

(2008) John L. Rinn et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An exploratory comparative study of volatile compounds in exhaled breath and emitted by skin using selected ion flow tube mass spectrometry

(2008) Claire Turner et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY