Combining bleach and mild predigestion improves ancient DNA recovery from bones

metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data

(2016) Guillaume Louvel et al.   Molecular Ecology Resources

Reducing microbial and human contamination in DNA extractions from ancient bones and teeth

(2015) Petra Korlević et al.   BIOTECHNIQUES

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

(2015) Cristina Gamba et al.   Molecular Ecology Resources

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Improving access to endogenous DNA in ancient bones and teeth

(2015) Peter B. Damgaard et al.   Scientific Reports

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

(2015) Ron Pinhasi et al.   PLoS One

Ancient Whole Genome Enrichment Using Baits Built from Modern DNA

(2014) Jacob M. Enk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shotgun microbial profiling of fossil remains

(2014) C. Der Sarkissian et al.   MOLECULAR ECOLOGY

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

(2014) Mikkel Schubert et al.   Nature Protocols

Patterns of coding variation in the complete exomes of three Neandertals

(2014) S. Castellano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

(2013) Meredith L. Carpenter et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location

(2013) Bastiaan Star et al.   BMC MICROBIOLOGY

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

(2013) J. S. Pedersen et al.   GENOME RESEARCH

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

(2013) Ludovic Orlando et al.   NATURE

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

Improving the performance of True Single Molecule Sequencing for ancient DNA

(2012) Aurelien Ginolhac et al.   BMC GENOMICS

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

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

DNA in ancient bone – Where is it located and how should we extract it?

(2011) Paula F. Campos et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

True single-molecule DNA sequencing of a pleistocene horse bone

(2011) L. Orlando et al.   GENOME RESEARCH

A bone sample cleaning method using trypsin for the isolation of DNA

(2011) Richard Li et al.   Legal Medicine

Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics

(2011) Marc García-Garcerà et al.   PLoS One

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

(2011) V. J. Schuenemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE