Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic

INVESTIGATING DIETARY LIFE HISTORIES AND MOBILITY IN CHILDREN BURIED IN ST GERTRUDE CHURCH CEMETERY, RIGA, LATVIA (15 TH – 17 TH CENTURIES AD)

(2019) E. Petersone‐Gordina et al.   ARCHAEOMETRY

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

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

Dental disease and dietary isotopes of individuals from St Gertrude Church cemetery, Riga, Latvia

(2018) Elina Petersone-Gordina et al.   PLoS One

Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

(2018) Ben Krause-Kyora et al.   Nature Communications

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

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

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

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

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

(2018) Nicolás Rascovan et al.   CELL

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

Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

(2018) Thiseas C. Lamnidis et al.   Nature Communications

Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics

(2016) Maria A. Spyrou et al.   Cell Host & Microbe

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

(2016) Kirsten I Bos et al.   eLife

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

(2015) Simon Rasmussen et al.   CELL

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

Early emergence of Yersinia pestis as a severe respiratory pathogen

(2015) Daniel L. Zimbler et al.   Nature Communications

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Retracing the Evolutionary Path that Led to Flea-Borne Transmission of Yersinia pestis

(2014) Yi-Cheng Sun et al.   Cell Host & Microbe

Ancient human genomes suggest three ancestral populations for present-day Europeans

(2014) Iosif Lazaridis et al.   NATURE

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

(2014) Kirsten I. Bos et al.   NATURE

Posttranscriptional Regulation of the Yersinia pestis Cyclic AMP Receptor Protein Crp and Impact on Virulence

(2014) W. W. Lathem et al.   mBio

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

(2011) Kirsten I. Bos et al.   NATURE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The smpB-ssrA Mutant of Yersinia pestis Functions as a Live Attenuated Vaccine To Protect Mice against Pulmonary Plague Infection

(2010) N. A. Okan et al.   INFECTION AND IMMUNITY

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Molecular Darwinian Evolution of Virulence in Yersinia pestis

(2009) D. Zhou et al.   INFECTION AND IMMUNITY

Biology oftrans-Translation

(2008) Kenneth C. Keiler   Annual Review of Microbiology