Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Mitochondrial Phylogenomics of Modern and Ancient Equids

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

RAxML-Light: a tool for computing terabyte phylogenies

(2012) A. Stamatakis et al.   BIOINFORMATICS

Improving the performance of True Single Molecule Sequencing for ancient DNA

(2012) Aurelien Ginolhac et al.   BMC GENOMICS

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing the origin and spread of horse domestication in the Eurasian steppe

(2012) V. Warmuth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication

(2012) A. Achilli 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

Site-specific deamidation of glutamine: a new marker of bone collagen deterioration

(2012) Nienke L. van Doorn et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

(2012) Molly E. McCue et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

(2011) Sebastian Lippold et al.   BMC EVOLUTIONARY BIOLOGY

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

(2011) Hiroki Goto et al.   Genome Biology and Evolution

True single-molecule DNA sequencing of a pleistocene horse bone

(2011) L. Orlando et al.   GENOME RESEARCH

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

(2011) Enrico Cappellini et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Species-specific responses of Late Quaternary megafauna to climate and humans

(2011) Eline D. Lorenzen et al.   NATURE

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) David Reich et al.   NATURE

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

Permafrost response to last interglacial warming: field evidence from non-glaciated Yukon and Alaska

(2010) Alberto V. Reyes et al.   QUATERNARY SCIENCE REVIEWS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Gold Run tephra: a Middle Pleistocene stratigraphic and paleoenvironmental marker across west-central Yukon Territory, Canada

(2009) J. A. Westgate et al.   CANADIAN JOURNAL OF EARTH SCIENCES

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Revising the recent evolutionary history of equids using ancient DNA

(2009) L. Orlando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Ancient Permafrost and a Future, Warmer Arctic

(2008) D. G. Froese et al.   SCIENCE