Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

(2019) Erik L. Clarke et al.   Microbiome

Assessing alignment-based taxonomic classification of ancient microbial DNA

(2019) Raphael Eisenhofer et al.   PeerJ

The Integrative Human Microbiome Project

(2019)   NATURE

Virome and bacteriome: two sides of the same coin

(2019) Jonathan Stern et al.   Current Opinion in Virology

The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain)

(2018) Vicente Pérez-Brocal et al.   PLoS One

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

(2018) Barbara Mühlemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neolithic and medieval virus genomes reveal complex evolution of hepatitis B

(2018) Ben Krause-Kyora et al.   eLife

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

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

Ancient hepatitis B viruses from the Bronze Age to the Medieval period

(2018) Barbara Mühlemann et al.   NATURE

Systematic evaluation of error rates and causes in short samples in next-generation sequencing

(2018) Franziska Pfeiffer et al.   Scientific Reports

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research

(2018) Irina M. Velsko et al.   mSystems

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

(2018) Nicolás Rascovan et al.   CELL

Complex virome in feces from Amerindian children in isolated Amazonian villages

(2018) Juliana D. Siqueira et al.   Nature Communications

17 th Century Variola Virus Reveals the Recent History of Smallpox

(2016) Ana T. Duggan et al.   CURRENT BIOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

(2016) Michael Worobey et al.   NATURE

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

Population genomics of Bronze Age Eurasia

(2015) Morten E. Allentoft et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

(2014) Anna-Sapfo Malaspinas et al.   CURRENT BIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Ancient DNA Damage

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

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

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer 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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL