decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods

Microbial source tracking using metagenomics and other new technologies

(2021) Shahbaz Raza et al.   JOURNAL OF MICROBIOLOGY

Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

(2021) Andrew G. Farrer et al.   Scientific Reports

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community

(2021) Clio Der Sarkissian et al.   mSystems

Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics

(2020) Jordan J. McGhee et al.   PeerJ

Present‐Day DNA Contamination in Ancient DNA Datasets

(2020) Stéphane Peyrégne et al.   BIOESSAYS

Source tracking of antibiotic resistance genes in the environment — Challenges, progress, and prospects

(2020) Li-Guan Li et al.   WATER RESEARCH

Data structures based on k-mers for querying large collections of sequencing data sets

(2020) Camille Marchet et al.   GENOME RESEARCH

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes

(2020) Jonas Coelho Kasmanas et al.   NUCLEIC ACIDS RESEARCH

FEAST: fast expectation-maximization for microbial source tracking

(2019) Liat Shenhav et al.   NATURE METHODS

The efficacy of whole human genome capture on ancient dental calculus and dentin

(2018) Kirsten A. Ziesemer et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

The European Bioinformatics Institute in 2018: tools, infrastructure and training

(2018) Charles E Cook et al.   NUCLEIC ACIDS RESEARCH

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

(2016) Rebekah Henry et al.   WATER RESEARCH

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

(2016)   Microbiome

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

(2016) Nam-Phuong Nguyen et al.   npj Biofilms and Microbiomes

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

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

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

DSK: k-mer counting with very low memory usage

(2013) G. Rizk et al.   BIOINFORMATICS

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

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS