4.6 Article

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus

Related references

Note: Only part of the references are listed.
Article Ecology

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

Felix M. Key et al.

NATURE ECOLOGY & EVOLUTION (2020)

Article Multidisciplinary Sciences

New insights from uncultivated genomes of the global human gut microbiome

Stephen Nayfach et al.

NATURE (2019)

Article Microbiology

Transmission of human-associated microbiota along family and social networks

Ilana L. Brito et al.

NATURE MICROBIOLOGY (2019)

Article Multidisciplinary Sciences

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750)

Marcel Keller et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

Maria A. Spyrou et al.

NATURE COMMUNICATIONS (2019)

Article Biotechnology & Applied Microbiology

Dimensionality reduction for visualizing single-cell data using UMAP

Etienne Becht et al.

NATURE BIOTECHNOLOGY (2019)

Article Veterinary Sciences

British Red Squirrels Remain the Only Known Wild Rodent Host for Leprosy Bacilli

Anna-Katarina Schilling et al.

FRONTIERS IN VETERINARY SCIENCE (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

137 ancient human genomes from across the Eurasian steppes

Peter de Barros Damgaard et al.

NATURE (2018)

Review Biochemistry & Molecular Biology

Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments

William H. Bowen et al.

TRENDS IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin

Allison E. Mann et al.

SCIENTIFIC REPORTS (2018)

Review Genetics & Heredity

A genomic overview of the population structure of Salmonella

Nabil-Fareed Alikhan et al.

PLOS GENETICS (2018)

Article Microbiology

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe

Verena J. Schuenemann et al.

PLOS PATHOGENS (2018)

Article Microbiology

Improving saliva shotgun metagenomics by chemical host DNA depletion

Clarisse A. Marotz et al.

MICROBIOME (2018)

Article Ecology

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico

Ashild J. Vagene et al.

NATURE ECOLOGY & EVOLUTION (2018)

Article Biochemistry & Molecular Biology

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Zhemin Zhou et al.

GENOME RESEARCH (2018)

Article Dentistry, Oral Surgery & Medicine

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries?

Jeffrey A. Banas et al.

BMC ORAL HEALTH (2018)

Review Microbiology

Repertoire of bacterial species cultured from the human oral cavity and respiratory tract

Maxime D. M. Fonkou et al.

FUTURE MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Laura S. Weyrich et al.

NATURE (2017)

Article Biochemical Research Methods

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

Alexander Sczyrba et al.

NATURE METHODS (2017)

Article Biotechnology & Applied Microbiology

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Alexa B. R. McIntyre et al.

GENOME BIOLOGY (2017)

Article Immunology

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status

Vincent P. Richards et al.

INFECTION AND IMMUNITY (2017)

Article Dentistry, Oral Surgery & Medicine

The Microbiome in Populations with a Low and High Prevalence of Caries

I. Johansson et al.

JOURNAL OF DENTAL RESEARCH (2016)

Article Biotechnology & Applied Microbiology

Mash: fast genome and metagenome distance estimation using MinHash

Brian D. Ondov et al.

GENOME BIOLOGY (2016)

Editorial Material Multidisciplinary Sciences

Plague is an ancient pathogen

[Anonymous]

NATURE (2015)

Article Biochemistry & Molecular Biology

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Vincent Lefort et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

Xuan Zhang et al.

NATURE MEDICINE (2015)

Review Biochemistry & Molecular Biology

Solving the etiology of dental caries

Aurea Simon-Soro et al.

TRENDS IN MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

Gemma L. Kay et al.

NATURE COMMUNICATIONS (2015)

Review Biology

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

Christina Warinner et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2015)

Article Biochemistry & Molecular Biology

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

Simon Rasmussen et al.

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Genetics & Heredity

Pathogens and host immunity in the ancient human oral cavity

Christina Warinner et al.

NATURE GENETICS (2014)

Article Multidisciplinary Sciences

Relating the metatranscriptome and metagenome of the human gut

Eric A. Franzosa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Francesc Coll et al.

NATURE COMMUNICATIONS (2014)

Article Biochemical Research Methods

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Hakon Jonsson et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans

Omar E. Cornejo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Multidisciplinary Sciences

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

Bo Liu et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

A draft genome of Yersinia pestis from victims of the Black Death

Kirsten I. Bos et al.

NATURE (2011)

Article Anthropology

Oral Health and Frailty in the Medieval English Cemetery of St Mary Graces

Sharon N. DeWitte et al.

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY (2010)

Article Dentistry, Oral Surgery & Medicine

Prevalence and distribution of principal periodontal pathogens worldwide

Mette Rylev et al.

JOURNAL OF CLINICAL PERIODONTOLOGY (2008)

Review Dentistry, Oral Surgery & Medicine

Periodontal microbial ecology

SS Socransky et al.

PERIODONTOLOGY 2000 (2005)

Article Multidisciplinary Sciences

Genomic insights that advance the species definition for prokaryotes

KT Konstantinidis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Computer Science, Artificial Intelligence

Gene selection for cancer classification using support vector machines

I Guyon et al.

MACHINE LEARNING (2002)