The source of the Black Death in fourteenth-century central Eurasia

Plague and the Fall of Baghdad (1258)

(2021) Nahyan Fancy et al.   MEDICAL HISTORY

A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis

(2021) Julian Susat et al.   Cell Reports

Ten millennia of hepatitis B virus evolution

(2021) Arthur Kocher et al.   SCIENCE

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

(2020) Felix M. Key et al.   Nature Ecology & Evolution

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

(2020) Sebastian Duchene et al.   MOLECULAR BIOLOGY AND EVOLUTION

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 treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe

(2020) Karen Giffin et al.   Scientific Reports

Plague reservoir species throughout the world

(2020) Ahmad MAHMOUDI et al.   Integrative Zoology

Ancient pathogen genomics as an emerging tool for infectious disease research

(2019) Maria A. Spyrou et al.   NATURE REVIEWS GENETICS

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

(2019) Marcel Keller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

(2019) Maria A. Spyrou et al.   Nature Communications

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

(2019) Zhemin Zhou et al.   GENOME RESEARCH

137 ancient human genomes from across the Eurasian steppes

(2018) Peter de Barros Damgaard et al.   NATURE

Human ectoparasites and the spread of plague in Europe during the Second Pandemic

(2018) Katharine R. Dean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague

(2018) Maria A. Spyrou et al.   Nature Communications

Phylogeny and Classification of Yersinia pestis Through the Lens of Strains From the Plague Foci of Commonwealth of Independent States

(2018) Vladimir V. Kutyrev et al.   Frontiers in Microbiology

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico

(2018) Åshild J. Vågene et al.   Nature Ecology & Evolution

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

(2018) Zhemin Zhou et al.   GENOME RESEARCH

Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period

(2018) Amine Namouchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan

(2017) Galina A. Eroshenko et al.   PLoS One

Network theory may explain the vulnerability of medieval human settlements to the Black Death pandemic

(2017) José M. Gómez et al.   Scientific Reports

A High-CoverageYersinia pestisGenome from a Sixth-Century Justinianic Plague Victim

(2016) Michal Feldman et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

(2016) Kirsten I Bos et al.   eLife

Genome-wide patterns of selection in 230 ancient Eurasians

(2015) Iain Mathieson et al.   NATURE

Massive migration from the steppe was a source for Indo-European languages in Europe

(2015) Wolfgang Haak et al.   NATURE

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

Climate-driven introduction of the Black Death and successive plague reintroductions into Europe

(2015) Boris V. Schmid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

(2014) Kirsten I. Bos et al.   NATURE

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

(2014) N. Rohland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

(2012) Y. Cui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Kirsten I. Bos et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

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

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Rodents for comparative aging studies: from mice to beavers

(2008) Vera Gorbunova et al.   AGE