PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

Reconstruction of ancient microbial genomes from the human gut

(2021) Marsha C. Wibowo et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Dental calculus as a tool to study the evolution of the mammalian oral microbiome

(2020) Jaelle C Brealey et al.   MOLECULAR BIOLOGY AND EVOLUTION

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

(2020) Maxime Borry et al.   PeerJ

Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver

(2020) Hirak Ranjan Dash et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial succession from a subsequent secondary death event following mass mortality

(2020) Lindsay Harrison et al.   BMC MICROBIOLOGY

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa

(2019) Stephanie L. Schnorr et al.   BMC MICROBIOLOGY

A genetic analysis of the Gibraltar Neanderthals

(2019) Lukas Bokelmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe

(2019) Stéphane Peyrégne et al.   Science Advances

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

(2019) Adrian Tett et al.   Cell Host & Microbe

Antimicrobial Resistance in Bacteria: Mechanisms, Evolution, and Persistence

(2019) Eirini Christaki et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2018) Allison E. Mann et al.   Scientific Reports

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Influence of diet on the gut microbiome and implications for human health

(2017) Rasnik K. Singh et al.   Journal of Translational Medicine

Improving ancient DNA genome assembly

(2017) Alexander Seitz et al.   PeerJ

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

(2017) Henrik B. Hansen et al.   PLoS One

gargammel: a sequence simulator for ancient DNA

(2016) Gabriel Renaud et al.   BIOINFORMATICS

Insights into human evolution from ancient and contemporary microbiome studies

(2016) Stephanie L Schnorr et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Subsistence strategies in traditional societies distinguish gut microbiomes

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

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

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

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

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

(2014) Pontus Skoglund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Ancient DNA Damage

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS