AntCaller: an accurate variant caller incorporating ancient DNA damage

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

(2016) Matthias Meyer et al.   NATURE

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc

(2016) Choongwon Jeong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early farmers from across Europe directly descended from Neolithic Aegeans

(2016) Zuzana Hofmanová et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

MAFsnp: A Multi-Sample Accurate and Flexible SNP Caller Using Next-Generation Sequencing Data

(2015) Jiyuan Hu et al.   PLoS One

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia

(2015) Justin C. Tackney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Morten Rasmussen et al.   NATURE

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

(2014) Kirsten I. Bos et al.   NATURE

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

(2014) B. Shapiro et al.   SCIENCE

Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers

(2014) P. Skoglund et al.   SCIENCE

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

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

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

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Glacial Survival of Boreal Trees in Northern Scandinavia

(2012) L. Parducci et al.   SCIENCE

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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The RdgC protein employs a novel mechanism involving a finger domain to bind to circular DNA

(2010) G. S. Briggs et al.   NUCLEIC ACIDS RESEARCH

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing

(2008) Richard E. Green et al.   CELL

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH