Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Ancient DNA analysis of dental calculus

(2015) Laura S. Weyrich et al.   JOURNAL OF HUMAN EVOLUTION

Ancient human microbiomes

(2015) Christina Warinner et al.   JOURNAL OF HUMAN EVOLUTION

Subsistence strategies in traditional societies distinguish gut microbiomes

(2015) Alexandra J. Obregon-Tito et al.   Nature Communications

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

The future of ancient DNA: Technical advances and conceptual shifts

(2014) Michael Hofreiter et al.   BIOESSAYS

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

(2014) Suleyman Yildirim et al.   ISME Journal

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

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

(2014) C. Warinner et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe

(2014) Annina Krüttli et al.   PLoS One

Rapid changes in the gut microbiome during human evolution

(2014) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans

(2013) Junhai Ou et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

The saliva microbiome of Pan and Homo

(2013) Jing Li et al.   BMC MICROBIOLOGY

Sequencing the human microbiome in health and disease

(2013) M. J. Cox et al.   HUMAN MOLECULAR GENETICS

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Osteological evidence of short-limbed dwarfism in a nineteenth century Dutch family: Achondroplasia or hypochondroplasia

(2013) Andrea L. Waters-Rist et al.   International Journal of Paleopathology

DNA FROM HUMAN ANCIENT BACTERIA: A NOVEL SOURCE OF GENETIC EVIDENCE FROM ARCHAEOLOGICAL DENTAL CALCULUS

(2012) C. DE LA FUENTE et al.   ARCHAEOMETRY

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

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

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Insights from Characterizing Extinct Human Gut Microbiomes

(2012) Raul Y. Tito et al.   PLoS One

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

(2012) M. E. Allentoft et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Average genome size: a potential source of bias in comparative metagenomics

(2010) Bánk Beszteri et al.   ISME Journal

The Human Oral Microbiome

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

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

(2010) Sophie Champlot et al.   PLoS One

Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities

(2010) Suleyman Yildirim et al.   PLoS One

Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System?

(2010) Y. K. Lee et al.   SCIENCE

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

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

A rapid column-based ancient DNA extraction method for increased sample throughput

(2009) NADIN ROHLAND et al.   Molecular Ecology Resources