Probing the diversity of healthy oral microbiome with bioinformatics approaches

The bright side of microbial dark matter: lessons learned from the uncultivated majority

(2016) Lindsey Solden et al.   CURRENT OPINION IN MICROBIOLOGY

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Context and the human microbiome

(2015) Daniel McDonald et al.   Microbiome

Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa

(2014) Jing Li et al.   BMC MICROBIOLOGY

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

(2014) Afiahayati et al.   DNA RESEARCH

Oral cavity contains distinct niches with dynamic microbial communities

(2014) Xin Xu et al.   ENVIRONMENTAL MICROBIOLOGY

The oral microbiome diversity and its relation to human diseases

(2014) Jinzhi He et al.   FOLIA MICROBIOLOGICA

Effects of sample treatments on genome recovery via single-cell genomics

(2014) Scott Clingenpeel et al.   ISME Journal

Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients

(2014) J.-H. Moon et al.   Molecular Oral Microbiology

Characterization and in vitro properties of oral lactobacilli in breastfed infants

(2013) Nelly Romani Vestman et al.   BMC MICROBIOLOGY

MetaRef: a pan-genomic database for comparative and community microbial genomics

(2013) Katherine Huang et al.   NUCLEIC ACIDS RESEARCH

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz 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

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

(2013) Kelvin Li et al.   PLoS One

Deep Sequencing Identifies Ethnicity-Specific Bacterial Signatures in the Oral Microbiome

(2013) Matthew R. Mason et al.   PLoS One

Biogeography of the ecosystems of the healthy human body

(2013) Yanjiao Zhou et al.   GENOME BIOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

(2012) William L Trimble et al.   BMC BIOINFORMATICS

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

(2012) S. S. Stahringer et al.   GENOME RESEARCH

Oral Microbial Profile Discriminates Breast-fed From Formula-fed Infants

(2012) Pernilla L. Holgerson et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

(2012) Susan M. Huse et al.   PLoS One

Bioinformatics for the Human Microbiome Project

(2012) Dirk Gevers et al.   PLoS Computational Biology

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational 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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Combining gene prediction methods to improve metagenomic gene annotation

(2011) Non G Yok et al.   BMC BIOINFORMATICS

Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

(2011) Wim Crielaard et al.   BMC Medical Genomics

Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

(2011) O.-S. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Mode of Birth Delivery Affects Oral Microbiota in Infants

(2011) P. Lif Holgerson et al.   JOURNAL OF DENTAL RESEARCH

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

(2011) David R. Kelley et al.   NUCLEIC ACIDS RESEARCH

The oral microbiome in health and disease and the potential impact on personalized dental medicine

(2011) MF Zarco et al.   ORAL DISEASES

CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome

(2011) Ann L. Griffen et al.   PLoS One

Comparative Analysis of Salivary Bacterial Microbiome Diversity in Edentulous Infants and Their Mothers or Primary Care Givers Using Pyrosequencing

(2011) Kimberly D. Cephas et al.   PLoS One

High Diversity of the Saliva Microbiome in Batwa Pygmies

(2011) Ivan Nasidze et al.   PLoS One

Analyzing taxonomic classification using extensible Markov models

(2010) Rao M. Kotamarti et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Study of inter- and intra-individual variations in the salivary microbiota

(2010) Vladimir Lazarevic et al.   BMC GENOMICS

The Human Oral Microbiome

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

(2010) Carlos W Nossa   WORLD JOURNAL OF GASTROENTEROLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Diversity and site-specificity of the oral microflora in the elderly

(2009) D. Preza et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Global diversity in the human salivary microbiome

(2009) I. Nasidze et al.   GENOME RESEARCH

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Differences in subgingival microflora of Korean and German periodontal patients

(2008) T.S. Kim et al.   ARCHIVES OF ORAL BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics