Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Present‐Day DNA Contamination in Ancient DNA Datasets

(2020) Stéphane Peyrégne et al.   BIOESSAYS

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples

(2019) Gabriel Renaud et al.   GENETICS

A comprehensive genomic history of extinct and living elephants

(2018) Eleftheria Palkopoulou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

(2018) Cesare de Filippo et al.   BMC BIOLOGY

A new model for ancient DNA decay based on paleogenomic meta-analysis

(2017) Logan Kistler et al.   NUCLEIC ACIDS RESEARCH

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

(2016) Stephan Schiffels et al.   Nature Communications

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

(2015) Petra Korlević et al.   BIOTECHNIQUES

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

(2015) Simon Rasmussen et al.   CELL

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

(2015) Eleftheria Palkopoulou et al.   CURRENT BIOLOGY

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

(2015) Cristina Gamba et al.   Molecular Ecology Resources

Population genomics of Bronze Age Eurasia

(2015) Morten E. Allentoft et al.   NATURE

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

Ancient genomics

(2014) C. Der Sarkissian 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

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

(2013) Ludovic Orlando et al.   NATURE

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

Ancient DNA Damage

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

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score

(2012) Hayan Lee et al.   BIOINFORMATICS

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

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Computational challenges in the analysis of ancient DNA

(2010) Kay Prüfer et al.   GENOME BIOLOGY

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

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

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