Improving ancient DNA read mapping against modern reference genomes

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

True single-molecule DNA sequencing of a pleistocene horse bone

(2011) L. Orlando et al.   GENOME RESEARCH

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

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

(2011) Eline D. Lorenzen et al.   NATURE

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

(2011) V. J. Schuenemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

(2011) M. Rasmussen et al.   SCIENCE

Withering Away--25,000 Years of Genetic Decline Preceded Cave Bear Extinction

(2010) M. Stiller 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

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen 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

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

Virtual terminator nucleotides for next-generation DNA sequencing

(2009) Jayson Bowers et al.   NATURE METHODS

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

(2009) C. M. Wade et al.   SCIENCE

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

Sequencing the nuclear genome of the extinct woolly mammoth

(2008) Webb Miller et al.   NATURE

Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

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