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

Ancient Whole Genome Enrichment Using Baits Built from Modern DNA

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

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

(2014) Morten Rasmussen et al.   NATURE

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

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

(2014) B. Shapiro et al.   SCIENCE

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

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

DNA analysis of an early modern human from Tianyuan Cave, China

(2013) Q. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root

(2012) Doron M. Behar et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

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 High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Setting the stage – Building and working in an ancient DNA laboratory

(2011) Michael Knapp et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

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

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA

(2009) M. Stiller et al.   GENOME RESEARCH

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

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

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

Identification of genetic variants using bar-coded multiplexed sequencing

(2008) David W Craig et al.   NATURE METHODS