Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Bacterial chitinases and chitin-binding proteins as virulence factors

(2013) R. F. Frederiksen et al.   MICROBIOLOGY-SGM

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

The Dental Plaque Microbiome in Health and Disease

(2013) Scott N. Peterson et al.   PLoS One

The Listeria monocytogenes ChiA Chitinase Enhances Virulence through Suppression of Host Innate Immunity

(2013) S. Chaudhuri et al.   mBio

Porphyromonas gingivalisfimbriae

(2013) Morten Enersen et al.   Journal of Oral Microbiology

Autophagy in periodontitis patients and gingival fibroblasts: unraveling the link between chronic diseases and inflammation

(2012) Pedro Bullon et al.   BMC Medicine

Prevalence of Periodontitis in Adults in the United States: 2009 and 2010

(2012) P.I. Eke et al.   JOURNAL OF DENTAL RESEARCH

Prevalence of β-lactamase-producing bacteria in human periodontitis

(2012) T. E. Rams et al.   JOURNAL OF PERIODONTAL RESEARCH

Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis

(2012) R. C. V. Casarin et al.   JOURNAL OF PERIODONTAL RESEARCH

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

(2012) Bo Liu et al.   PLoS One

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing

(2012) Xuejian Xiong et al.   PLoS One

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

(2011) Ann L Griffen et al.   ISME Journal

The oral metagenome in health and disease

(2011) Pedro Belda-Ferre et al.   ISME Journal

Tannerella forsythia invasion in oral epithelial cells requires phosphoinositide 3-kinase activation and clathrin-mediated endocytosis

(2011) E. Mishima et al.   MICROBIOLOGY-SGM

Linear amplification for deep sequencing

(2011) Wieteke A M Hoeijmakers et al.   Nature Protocols

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes

(2011) Christopher T. Brown et al.   PLoS One

Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed

(2010) C. C. G. M. Booijink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Chitinolytic Activity of Listeria monocytogenes EGD Is Regulated by Carbohydrates but Also by the Virulence Regulator PrfA

(2010) M. H. Larsen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The struggle for iron - a metal at the host-pathogen interface

(2010) Manfred Nairz et al.   CELLULAR MICROBIOLOGY

Role ofTannerella forsythiaNanH Sialidase in Epithelial Cell Attachment

(2010) Kiyonobu Honma et al.   INFECTION AND IMMUNITY

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth

(2010) E. L. Gross et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Fusobacterium nucleatum regulation of neutrophil transcription

(2010) H. J. Wright et al.   JOURNAL OF PERIODONTAL RESEARCH

Human viruses in periodontitis

(2010) Jørgen Slots   PERIODONTOLOGY 2000

Contribution of Porphyromonas gingivalis lipopolysaccharide to periodontitis

(2010) Sumita Jain et al.   PERIODONTOLOGY 2000

Microbial shift and periodontitis

(2010) Alex B. Berezow et al.   PERIODONTOLOGY 2000

Gut Microbial Gene Expression in Mother-Fed and Formula-Fed Piglets

(2010) Valeriy Poroyko et al.   PLoS One

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

The role of beta-lactamase-producing-bacteria in mixed infections

(2009) Itzhak Brook   BMC INFECTIOUS DISEASES

Comparisons of Subgingival Microbial Profiles of Refractory Periodontitis, Severe Periodontitis, and Periodontal Health Using the Human Oral Microbe Identification Microarray

(2009) Ana Paula V. Colombo et al.   JOURNAL OF PERIODONTOLOGY

The Association of Virulence Factors with Genomic Islands

(2009) Shannan J. Ho Sui et al.   PLoS One

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial complexes in supragingival plaque

(2008) A. D. Haffajee et al.   Oral microbiology and immunology