Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

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

(2014) Iosif Lazaridis et al.   NATURE

The timing and spatiotemporal patterning of Neanderthal disappearance

(2014) Tom Higham et al.   NATURE

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

(2014) Qiaomei Fu et al.   NATURE

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

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

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

Genomic structure in Europeans dating back at least 36,200 years

(2014) A. Seguin-Orlando et al.   SCIENCE

Theory and applications of a deterministic approximation to the coalescent model

(2014) Ethan M. Jewett et al.   THEORETICAL POPULATION BIOLOGY

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers

(2013) Gabriel Renaud et al.   BIOINFORMATICS

Accurate sex identification of ancient human remains using DNA shotgun sequencing

(2013) Pontus Skoglund et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow

(2013) Mark Lipson et al.   MOLECULAR BIOLOGY AND EVOLUTION

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

(2011) M. Rasmussen et al.   SCIENCE

The joint allele frequency spectrum of multiple populations: A coalescent theory approach

(2011) Hua Chen   THEORETICAL POPULATION BIOLOGY

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

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

(2010) David Reich et al.   NATURE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Neandertal genome and ancient DNA authenticity

(2009) Richard E Green et al.   EMBO JOURNAL

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

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

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

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

(2008) Richard E. Green et al.   CELL