Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis.

[1]  D. Raoult,et al.  Yersinia pestis Orientalis in Remains of Ancient Plague Patients , 2007, Emerging infectious diseases.

[2]  David J D Earn,et al.  Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death , 2011, Proceedings of the National Academy of Sciences.

[3]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[4]  Dawn N. Birdsell,et al.  Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague , 2013, PLoS pathogens.

[5]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[6]  Matthias Meyer,et al.  Illumina sequencing library preparation for highly multiplexed target capture and sequencing. , 2010, Cold Spring Harbor protocols.

[7]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[8]  B. J. Hinnebusch,et al.  Structural insights into Ail-mediated adhesion in Yersinia pestis. , 2011, Structure.

[9]  M. Simmonds,et al.  Genome sequence of Yersinia pestis, the causative agent of plague , 2001, Nature.

[10]  Ruifu Yang,et al.  Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis , 2012, Proceedings of the National Academy of Sciences.

[11]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[12]  G. Grupe,et al.  Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.). , 2005, American journal of physical anthropology.

[13]  Adam M. Phillippy,et al.  Efficient oligonucleotide probe selection for pan-genomic tiling arrays , 2009, BMC Bioinformatics.

[14]  R. Pollitzer.  Plague studies. 1. A summary of the history and survey of the present distribution of the disease. , 1951, Bulletin of the World Health Organization.

[15]  H. Wanner,et al.  2500 Years of European Climate Variability and Human Susceptibility , 2011, Science.

[16]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[17]  S. Scott,et al.  What caused the Black Death? , 2005, Postgraduate Medical Journal.

[18]  Briana M. Young,et al.  Identification of regions of Ail required for the invasion and serum resistance phenotypes , 2001, Molecular microbiology.

[19]  Matthias Meyer,et al.  A draft genome of Yersinia pestis from victims of the Black Death , 2011, Nature.

[20]  S. B. Pole,et al.  Plague dynamics are driven by climate variation , 2006, Proceedings of the National Academy of Sciences.

[21]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[22]  Giovanna Morelli,et al.  Phylogenetic diversity and historical patterns of pandemic spread of Yersinia pestis , 2010, Nature Genetics.

[23]  B. Zietz,et al.  The history of the plague and the research on the causative agent Yersinia pestis , 2004, International Journal of Hygiene and Environmental Health.

[24]  R. Villems,et al.  Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia. , 2012, American journal of human genetics.

[25]  P. Keim,et al.  Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases , 2009, Nature Reviews Microbiology.

[26]  R. Perry,et al.  Yersinia pestis--etiologic agent of plague , 1997, Clinical microbiology reviews.

[27]  Yue Zhang,et al.  A Yersinia Effector with Enhanced Inhibitory Activity on the NF-κB Pathway Activates the NLRP3/ASC/Caspase-1 Inflammasome in Macrophages , 2011, PLoS pathogens.

[28]  T. Burkot,et al.  Climate and vectorborne diseases. , 2008, American journal of preventive medicine.

[29]  G. Andersen,et al.  Genome plasticity in Yersinia pestis. , 2002, Microbiology.

[30]  J. C. Russell.  That earlier plague , 1968, Demography.

[31]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[32]  L. K. Little.  Plague and the end of Antiquity : the pandemic of 541-750 , 2006 .

[33]  Martin Kircher,et al.  Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform , 2011, Nucleic acids research.

[34]  G. D. Sussman.  Was the Black Death in India and China? , 2011, Bulletin of the history of medicine.

[35]  A. Aubrey,et al.  New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains , 2009, Nucleic acids research.

[36]  E. Altschuler,et al.  Was the Justinian Plague caused by the 1918 flu virus? , 2009, Medical hypotheses.

[37]  Kay Nieselt,et al.  Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae , 2013, Science.

[38]  C. Médigue,et al.  Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Steven Salzberg,et al.  BIOINFORMATICS ORIGINAL PAPER , 2004 .