Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis

Microbiota diversity and gene expression dynamics in human oral biofilms

(2014) Alfonso Benítez-Páez et al.   BMC GENOMICS

Cytokines and chemokines are differentially expressed in patients with periodontitis: Possible role for TGF-β1 as a marker for disease progression

(2014) Hazem Khalaf et al.   CYTOKINE

Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease

(2014) Akiko Endo et al.   ISME Journal

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

(2014) Ana E Duran-Pinedo et al.   ISME Journal

Global Burden of Severe Periodontitis in 1990-2010

(2014) N.J. Kassebaum et al.   JOURNAL OF DENTAL RESEARCH

Filifactor alocis: The Newly Discovered Kid on the Block with Special Talents

(2014) W. Aruni et al.   JOURNAL OF DENTAL RESEARCH

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

(2014) R. Louwen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The inflammophilic character of the periodontitis-associated microbiota

(2014) G. Hajishengallis   Molecular Oral Microbiology

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

(2014) P. Jorth et al.   mBio

Functional expression of dental plaque microbiota

(2014) Scott N. Peterson et al.   Frontiers in Cellular and Infection Microbiology

Salivary biomarker analysis complementing regular clinical examination

(2013) Eran Front et al.   Biomarkers in Medicine

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

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Respiratory bacterial infections in cystic fibrosis

(2013) Oana Ciofu et al.   CURRENT OPINION IN PULMONARY MEDICINE

Bacterial markers vs. clinical markers to predict progression of chronic periodontitis: a 2-yr prospective observational study

(2013) Georgios Charalampakis et al.   EUROPEAN JOURNAL OF ORAL SCIENCES

Environmental Stimuli Shape Biofilm Formation and the Virulence of Periodontal Pathogens

(2013) Marja Pöllänen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation

(2013) Loreto Abusleme et al.   ISME Journal

Calculating Sample Size Estimates for RNA Sequencing Data

(2013) Steven N. Hart et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Potassium transport of Salmonella is important for type III secretion and pathogenesis

(2013) Y. Liu et al.   MICROBIOLOGY-SGM

The Ktr potassium transport system inStaphylococcus aureusand its role in cell physiology, antimicrobial resistance and pathogenesis

(2013) Casey M. Gries et al.   MOLECULAR MICROBIOLOGY

PATRIC, the bacterial bioinformatics database and analysis resource

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

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

(2012) Benoit Liquet et al.   BMC BIOINFORMATICS

Filifactor alocis - involvement in periodontal biofilms

(2012) Sebastian Schlafer et al.   BMC MICROBIOLOGY

Pyrosequencing reveals unique microbial signatures associated with healthy and failing dental implants

(2012) Purnima S. Kumar et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Isoprenoid biosynthesis in bacterial pathogens

(2012) S. Heuston et al.   MICROBIOLOGY-SGM

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic abundance estimation and diagnostic testing on species level

(2012) Martin S. Lindner et al.   NUCLEIC ACIDS RESEARCH

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Visualising associations between paired ‘omics’ data sets

(2012) Ignacio González et al.   BioData Mining

Association between genetic risk score and periodontitis onset and progression: A pilot study

(2011) M. Ricci et al.   ARCHIVES OF ORAL BIOLOGY

Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement

(2011) George Hajishengallis et al.   Cell Host & Microbe

Clustering of subgingival microbial species in adolescents with’ periodontitis

(2011) Rodrigo López et al.   EUROPEAN JOURNAL OF ORAL SCIENCES

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

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

Characterization of the Porphyromonas gingivalis conjugative transposon CTnPg1: determination of the integration site and the genes essential for conjugal transfer

(2011) M. Naito et al.   MICROBIOLOGY-SGM

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

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Genetic analysis of mobile tetQ elements in oral Prevotella species

(2010) Gena D. Tribble et al.   ANAEROBE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Emergence of Pseudomonas aeruginosa Strains Producing High Levels of Persister Cells in Patients with Cystic Fibrosis

(2010) L. R. Mulcahy et al.   JOURNAL OF BACTERIOLOGY

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

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetics and environmental regulation of Shigella iron transport systems

(2009) Elizabeth E. Wyckoff et al.   BIOMETALS

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

(2009) Itzhak Brook   BMC INFECTIOUS DISEASES

Hydrogen Sulfide Production From Cysteine and Homocysteine by Periodontal and Oral Bacteria

(2009) Akihiro Yoshida et al.   JOURNAL OF PERIODONTOLOGY

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

Progression of chronic periodontitis can be predicted by the levels ofPorphyromonas gingivalisandTreponema denticolain subgingival plaque

(2009) S. J. Byrne et al.   Oral microbiology and immunology

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

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

Microbial complexes in supragingival plaque

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