Quantitative PCR as a predictor of aligned ancient DNA read counts following targeted enrichment

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

Emulsion PCR-coupled target enrichment: An effective fishing method for high-throughput sequencing of poorly preserved ancient DNA

(2013) Makio Kihana et al.   GENE

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

(2013) A. Harrison et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Phylogenomics of Modern and Ancient Equids

(2013) Julia T. Vilstrup et al.   PLoS One

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

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Choosing the Best Plant for the Job: A Cost-Effective Assay to Prescreen Ancient Plant Remains Destined for Shotgun Sequencing

(2012) Nathan Wales et al.   PLoS One

Genotype of a historic strain of Mycobacterium tuberculosis

(2012) A. S. Bouwman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

(2011) V. C. Mason et al.   GENOME RESEARCH

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

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

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

(2011) Jacob Enk et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

(2010) Johannes Krause et al.   CURRENT BIOLOGY

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

(2010) Johannes Krause et al.   NATURE

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

(2010) David Reich et al.   NATURE

Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries

(2010) Michal Mokry et al.   NUCLEIC ACIDS RESEARCH

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Simultaneous assessment of average fragment size and amount in minute samples of degraded DNA

(2009) Marthe Colotte et al.   ANALYTICAL BIOCHEMISTRY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts

(2009) Christine E. King et al.   BIOTECHNIQUES

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains

(2009) Carsten Schwarz et al.   NUCLEIC ACIDS RESEARCH

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths

(2008) Regis Debruyne et al.   CURRENT BIOLOGY

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

(2008) M. T. P. Gilbert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA