Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments

Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia

(2020) Kseniya A. Kolobova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

(2020) Marie-Theres Gansauge et al.   Nature Protocols

A high-coverage Neandertal genome from Chagyrskaya Cave

(2020) Fabrizio Mafessoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

THE INTCAL20 NORTHERN HEMISPHERE RADIOCARBON AGE CALIBRATION CURVE (0–55 CAL kBP)

(2020) Paula J Reimer et al.   RADIOCARBON

Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave

(2019) Katerina Douka et al.   NATURE

Timing of archaic hominin occupation of Denisova Cave in southern Siberia

(2019) Zenobia Jacobs et al.   NATURE

A genetic analysis of the Gibraltar Neanderthals

(2019) Lukas Bokelmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

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

(2019) Stéphane Peyrégne et al.   Science Advances

snpAD: an ancient DNA genotype caller

(2018) Kay Prüfer   BIOINFORMATICS

Single-grain OSL dating of the Middle Palaeolithic site of Galería de las Estatuas, Atapuerca (Burgos, Spain)

(2018) Martina Demuro et al.   Quaternary Geochronology

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

A Neandertal foot phalanx from the Galería de las Estatuas site (Sierra de Atapuerca, Spain)

(2018) Adrián Pablos et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

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

(2018) Cesare de Filippo et al.   BMC BIOLOGY

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis

(2018) Gregory A. Taylor et al.   Genes

Evidence of paleoecological changes and Mousterian occupations at the Galería de las Estatuas site, Sierra de Atapuerca, northern Iberian plateau, Spain

(2017) Juan Luis Arsuaga et al.   QUATERNARY 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

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

(2016) Matthias Meyer et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

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

(2016) Fernando Racimo et al.   PLoS Genetics

Bayesian Analysis of Radiocarbon Dates

(2016) Christopher Bronk Ramsey   RADIOCARBON

An early modern human from Romania with a recent Neanderthal ancestor

(2015) Qiaomei Fu et al.   NATURE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary 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

Postcranial morphology of the middle Pleistocene humans from Sima de los Huesos, Spain

(2015) Juan Luis Arsuaga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

Neanderthal settlement patterns during MIS 4–3 in Sierra de Atapuerca (Burgos, Spain)

(2014) Marta Navazo et al.   QUATERNARY INTERNATIONAL

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

(2014) J. L. Arsuaga et al.   SCIENCE

Species Delimitation using Genome-Wide SNP Data

(2014) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

Improvements in 230Th dating, 230Th and 234U half-life values, and U–Th isotopic measurements by multi-collector inductively coupled plasma mass spectrometry

(2013) Hai Cheng et al.   EARTH AND PLANETARY SCIENCE LETTERS

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

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

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

(2013) Maanasa Raghavan et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

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

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

OSL dating of the Middle Palaeolithic Hotel California site, Sierra de Atapuerca, north-central Spain

(2012) Lee J. Arnold et al.   BOREAS

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012)   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

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS 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

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

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

(2008) Richard E. Green et al.   CELL

The first hominin of Europe

(2008) Eudald Carbonell et al.   NATURE