Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

CODIFI (Concordance in Diabetic Foot Ulcer Infection): a cross-sectional study of wound swab versus tissue sampling in infected diabetic foot ulcers in England

(2018) Andrea Nelson et al.   BMJ Open

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Evaluation of the effectiveness and cost-effectiveness of lightweight fibreglass heel casts in the management of ulcers of the heel in diabetes: a randomised controlled trial

(2017) William Jeffcoate et al.   HEALTH TECHNOLOGY ASSESSMENT

Temporal Stability in Chronic Wound Microbiota Is Associated With Poor Healing

(2017) Michael Loesche et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers

(2016) Karen Smith et al.   BMC MICROBIOLOGY

α-ketoglutarate is associated with delayed wound healing in diabetes

(2016) Qin Tan et al.   CLINICAL ENDOCRINOLOGY

IWGDF guidance on the diagnosis and management of foot infections in persons with diabetes

(2016) Benjamin A. Lipsky et al.   DIABETES-METABOLISM RESEARCH AND REVIEWS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species

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

Microbiota is a primary cause of pathogenesis of chronic wounds

(2016) R. Wolcott et al.   Journal of Wound Care

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the chronic wound microbiota of 2,963 patients by 16S rDNA pyrosequencing

(2015) Randall D. Wolcott et al.   WOUND REPAIR AND REGENERATION

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

The oral microbiome and the immunobiology of periodontal disease and caries

(2014) Massimo Costalonga et al.   IMMUNOLOGY LETTERS

The dynamics of gut-associated microbial communities during inflammation

(2013) Sebastian E Winter et al.   EMBO REPORTS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

(2013) George R. Feehery et al.   PLoS One

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

(2012) R. Carr et al.   BIOINFORMATICS

The Neuropathic Diabetic Foot Ulcer Microbiome Is Associated With Clinical Factors

(2012) S. E. Gardner et al.   DIABETES

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

An unrestrained proinflammatory M1 macrophage population induced by iron impairs wound healing in humans and mice

(2011) Anca Sindrilaru et al.   JOURNAL OF CLINICAL INVESTIGATION

An In Vivo Polymicrobial Biofilm Wound Infection Model to Study Interspecies Interactions

(2011) Trevor Dalton et al.   PLoS One

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response

(2010) E. A. Grice et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use of the SINBAD Classification System and Score in Comparing Outcome of Foot Ulcer Management on Three Continents

(2008) P. Ince et al.   DIABETES CARE

Prediction of outcome in individuals with diabetic foot ulcers: focus on the differences between individuals with and without peripheral arterial disease. The EURODIALE Study

(2008) L. Prompers et al.   DIABETOLOGIA

Polymicrobial Nature of Chronic Diabetic Foot Ulcer Biofilm Infections Determined Using Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP)

(2008) Scot E. Dowd et al.   PLoS One

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