Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Oral Health: The Silent Epidemic

(2017) Regina M. Benjamin   PUBLIC HEALTH REPORTS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Determining trace metal elements in the tooth enamel from Hui and Han Ethnic groups in China using microwave digestion and inductively coupled plasma mass spectrometry (ICP-MS)

(2016) Maoyong He et al.   MICROCHEMICAL JOURNAL

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

(2015) Anna Edlund et al.   ISME Journal

Solving the etiology of dental caries

(2015) Aurea Simón-Soro et al.   TRENDS IN MICROBIOLOGY

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”

(2014) Brian P. Hedlund et al.   EXTREMOPHILES

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

(2014) Chris L. Dupont et al.   PLoS One

Changes in Abundance of Oral Microbiota Associated with Oral Cancer

(2014) Brian L. Schmidt et al.   PLoS One

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

(2014) Anuj Camanocha et al.   Journal of Oral Microbiology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/β-Catenin Signaling via its FadA Adhesin

(2013) Mara Roxana Rubinstein et al.   Cell Host & Microbe

Global Burden of Oral Conditions in 1990-2010

(2013) W. Marcenes et al.   JOURNAL OF DENTAL RESEARCH

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Trace elements can influence the physical properties of tooth enamel

(2013) Elnaz Ghadimi et al.   SpringerPlus

Evaluation method for the potential functionome harbored in the genome and metagenome

(2012) Hideto Takami et al.   BMC GENOMICS

Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.

(2012) J. Downes et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A novel F420-dependent anti-oxidant mechanism protectsMycobacterium tuberculosisagainst oxidative stress and bactericidal agents

(2012) Meera Gurumurthy et al.   MOLECULAR MICROBIOLOGY

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis

(2012) Erin L. Gross et al.   PLoS One

The Peri/Postnatal Epigenetic Twins Study (PETS)

(2012) Yuk Jing Loke et al.   Twin Research and Human Genetics

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Cultivable Anaerobic Microbiota of Severe Early Childhood Caries

(2011) A. C. R. Tanner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Unexpected Abundance of Coenzyme F420-Dependent Enzymes in Mycobacterium tuberculosis and Other Actinobacteria

(2010) J. D. Selengut et al.   JOURNAL OF BACTERIOLOGY

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

The Role of Bacteria in the Caries Process

(2010) N. Takahashi et al.   JOURNAL OF DENTAL RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Characterization of Prochlorococcus clades from iron-depleted oceanic regions

(2010) D. B. Rusch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

The Isolation of Bifidobacteria from Occlusal Carious Lesions in Children and Adults

(2009) M. Mantzourani et al.   CARIES RESEARCH

Metals, minerals and microbes: geomicrobiology and bioremediation

(2009) G. M. Gadd   MICROBIOLOGY-SGM

Nitrate and nitrite in biology, nutrition and therapeutics

(2009) Jon O Lundberg et al.   Nature Chemical Biology

Conversion of NO2 to NO by reduced coenzyme F420 protects mycobacteria from nitrosative damage

(2009) E. Purwantini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Bacteria of Dental Caries in Primary and Permanent Teeth in Children and Young Adults

(2008) J. A. Aas et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Association betweenBifidobacteriaceaeand the clinical severity of root caries lesions

(2008) M. Mantzourani et al.   Oral microbiology and immunology