Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe

Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

(2018) Sharon R. Browning et al.   CELL

The genome of the offspring of a Neanderthal mother and a Denisovan father

(2018) Viviane Slon et al.   NATURE

Reconstructing the genetic history of late Neanderthals

(2018) Mateja Hajdinjak et al.   NATURE

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

(2018) Cesare de Filippo et al.   BMC BIOLOGY

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

(2017) Isabelle Glocke et al.   GENOME RESEARCH

Single-stranded DNA library preparation from highly degraded DNA usingT4DNA ligase

(2017) Marie-Theres Gansauge et al.   NUCLEIC ACIDS RESEARCH

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

(2017) Cosimo Posth et al.   Nature Communications

A fourth Denisovan individual

(2017) Viviane Slon et al.   Science Advances

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

(2016) Matthias Meyer et al.   NATURE

Ancient gene flow from early modern humans into Eastern Neanderthals

(2016) Martin Kuhlwilm et al.   NATURE

Mammalian mitochondrial capture, a tool for rapid screening of DNA preservation in faunal and undiagnostic remains, and its application to Middle Pleistocene specimens from Qesem Cave (Israel)

(2016) Viviane Slon et al.   QUATERNARY INTERNATIONAL

Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis

(2016) Samantha Brown et al.   Scientific Reports

Neandertal cannibalism and Neandertal bones used as tools in Northern Europe

(2016) Hélène Rougier et al.   Scientific Reports

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

(2015) Paul R. Staab et al.   BIOINFORMATICS

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

(2015) Petra Korlević et al.   BIOTECHNIQUES

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Nuclear and mitochondrial DNA sequences from two Denisovan individuals

(2015) Susanna Sawyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving access to endogenous DNA in ancient bones and teeth

(2015) Peter B. Damgaard et al.   Scientific Reports

jmodeltest.org: selection of nucleotide substitution models on the cloud

(2014) J. M. Santorum et al.   BIOINFORMATICS

Selective enrichment of damaged DNA molecules for ancient genome sequencing

(2014) Marie-Theres Gansauge et al.   GENOME RESEARCH

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

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud 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

Neandertal roots: Cranial and chronological evidence from Sima de los Huesos

(2014) J. L. Arsuaga et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A mitochondrial genome sequence of a hominin from Sima de los Huesos

(2013) Matthias Meyer et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

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

Ancient DNA Damage

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

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

A NEW DATE FOR THE NEANDERTHALS FROM EL SIDRÓN CAVE (ASTURIAS, NORTHERN SPAIN)*

(2012) R. E. WOOD et al.   ARCHAEOMETRY

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

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

Anterior tooth root morphology and size in Neanderthals: Taxonomic and functional implications

(2012) Adeline Le Cabec et al.   JOURNAL OF HUMAN EVOLUTION

The bonobo genome compared with the chimpanzee and human genomes

(2012) Kay Prüfer et al.   NATURE

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Revising the human mutation rate: implications for understanding human evolution

(2012) Aylwyn Scally et al.   NATURE REVIEWS GENETICS

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Hand to Mouth in a Neandertal: Right-Handedness in Regourdou 1

(2012) Virginie Volpato et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

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

(2011) H. Li   BIOINFORMATICS

True single-molecule DNA sequencing of a pleistocene horse bone

(2011) L. Orlando et al.   GENOME RESEARCH

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Hua Chen   THEORETICAL POPULATION BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) Johannes Krause et al.   CURRENT BIOLOGY

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Estimation of Population Divergence Times from Non-Overlapping Genomic Sequences: Examples from Dogs and Wolves

(2010) P. Skoglund et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Ebb and flow or regional extinctions? On the character of Neandertal occupation of northern environments

(2009) Jean-Jacques Hublin et al.   COMPTES RENDUS PALEVOL

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

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

(2008) Richard E. Green et al.   CELL

Complete Mitochondrial Genome Sequence of the Tyrolean Iceman

(2008) Luca Ermini et al.   CURRENT BIOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

(2008) M. T. P. Gilbert et al.   SCIENCE