Assessing alignment-based taxonomic classification of ancient microbial DNA

Proper Authentication of Ancient DNA Is Still Essential

(2018) Raphael Eisenhofer et al.   Genes

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

(2018) Åshild J. Vågene et al.   Nature Ecology & Evolution

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research

(2018) Irina M. Velsko et al.   mSystems

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

(2017) Isabelle Glocke et al.   GENOME RESEARCH

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

(2017) Laura S. Weyrich et al.   NATURE

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication

(2017) Felix M. Key et al.   TRENDS IN GENETICS

The influence of Antarctic subglacial volcanism on the global iron cycle during the Last Glacial Maximum

(2017) Silvia Frisia et al.   Nature Communications

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

gargammel: a sequence simulator for ancient DNA

(2016) Gabriel Renaud et al.   BIOINFORMATICS

Higher classification sensitivity of short metagenomic reads with CLARK- S

(2016) Rachid Ounit et al.   BIOINFORMATICS

The 5300-year-old Helicobacter pylori genome of the Iceman

(2016) F. Maixner et al.   SCIENCE

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

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

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

Ancient DNA analysis of dental calculus

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

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

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

(2015) Kirsten A. Ziesemer et al.   Scientific Reports

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Reply to Santiago-Rodriguezet al.: WasluxSreally isolated from 25- to 40-million-year-old bacteria?

(2014) Laura S. Weyrich et al.   FEMS MICROBIOLOGY LETTERS

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

(2014) Kirsten I. Bos et al.   NATURE

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

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

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

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

(2012) J Gregory Caporaso et al.   ISME Journal

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 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

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

(2011) Kirsten I. Bos et al.   NATURE

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS