Related references
Note: Only part of the references are listed.The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
Zhemin Zhou et al.
GENOME RESEARCH (2020)
Ancient pathogen genomics as an emerging tool for infectious disease research
Maria A. Spyrou et al.
NATURE REVIEWS GENETICS (2019)
Bioarchaeology of Neolithic Catalhoyuk reveals fundamental transitions in health, mobility, and lifestyle in early farmers
Clark Spencer Larsen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
HOPS: automated detection and authentication of pathogen DNA in archaeological remains
Ron Huebler et al.
GENOME BIOLOGY (2019)
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
Zhemin Zhou et al.
CURRENT BIOLOGY (2018)
A genomic overview of the population structure of Salmonella
Nabil-Fareed Alikhan et al.
PLOS GENETICS (2018)
Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico
Ashild J. Vagene et al.
NATURE ECOLOGY & EVOLUTION (2018)
LNCediting: a database for functional effects of RNA editing in lncRNAs
Jing Gong et al.
NUCLEIC ACIDS RESEARCH (2017)
Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication
Felix M. Key et al.
TRENDS IN GENETICS (2017)
Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes
James A. Fellows Yates et al.
SCIENTIFIC REPORTS (2017)
The Salmonella pathogenicity island 13 contributes to pathogenesis in streptomycin pre-treated mice but not in day-old chickens
Jacob R. Elder et al.
GUT PATHOGENS (2016)
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
Andrew Rambaut et al.
VIRUS EVOLUTION (2016)
EAGER: efficient ancient genome reconstruction
Alexander Peltzer et al.
GENOME BIOLOGY (2016)
The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data
Sebastian Duchene et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Massive migration from the steppe was a source for Indo-European languages in Europe
Wolfgang Haak et al.
NATURE (2015)
World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis
Martyn D. Kirk et al.
PLOS MEDICINE (2015)
PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands
Sung Ho Yoon et al.
NUCLEIC ACIDS RESEARCH (2015)
Partial uracil - DNA - glycosylase treatment for screening of ancient DNA
Nadin Rohland et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2015)
Patterns of genome evolution that have accompanied host adaptation in Salmonella
Gemma C. Langridge et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Gabriel Renaud et al.
GENOME BIOLOGY (2015)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
ANGSD: Analysis of Next Generation Sequencing Data
Thorfinn Sand Korneliussen et al.
BMC BIOINFORMATICS (2014)
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis et al.
NATURE (2014)
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
Kirsten I. Bos et al.
NATURE (2014)
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever
Zhemin Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Repeated isolation of Salmonella enterica Goverdhan, a very rare serovar, from Danish poultry surveillance samples
Karl Pedersen et al.
VETERINARY MICROBIOLOGY (2014)
Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not
Jessica Hedge et al.
MBIO (2014)
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Remco Bouckaert et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Hakon Jonsson et al.
BIOINFORMATICS (2013)
HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment
Dario Vianello et al.
HUMAN MUTATION (2013)
Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
Tanja Stadler et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
INTCAL13 AND MARINE13 RADIOCARBON AGE CALIBRATION CURVES 0-50,000 YEARS CAL BP
Paula J. Reimer et al.
RADIOCARBON (2013)
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments
Jesse Dabney et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Population Genetic Structure of 4,12:a:- Salmonella enterica Strains from Harbor Porpoises
Jana K. Haase et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
Keith A. Jolley et al.
MICROBIOLOGY-SGM (2012)
Identification of a common immune signature in murine and human systemic Salmonellosis
Seung-Joo Lee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Recombination and Population Structure in Salmonella enterica
Xavier Didelot et al.
PLOS GENETICS (2011)
The role of the spv genes in Salmonella pathogenesis
Donald G. Guiney et al.
FRONTIERS IN MICROBIOLOGY (2011)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
Adrian W. Briggs et al.
NUCLEIC ACIDS RESEARCH (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes
Carlos J. Blondel et al.
BMC GENOMICS (2009)
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
Robert A. Kingsley et al.
GENOME RESEARCH (2009)
Fast model-based estimation of ancestry in unrelated individuals
David H. Alexander et al.
GENOME RESEARCH (2009)
Salmonella paratyphi C: Genetic Divergence from Salmonella choleraesuis and Pathogenic Convergence with Salmonella typhi
Wei-Qiao Liu et al.
PLOS ONE (2009)
Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
Nicholas R. Thomson et al.
GENOME RESEARCH (2008)
High rates of molecular evolution in hantaviruses
Cadhla Ramsden et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
The Salmonella Typhi hlyE gene plays a role in invasion of cultured epithelial cells and its functional transfer to S. Typhimurium promotes deep organ infection in mice
Juan A. Fuentes et al.
RESEARCH IN MICROBIOLOGY (2008)
Patterns of damage in genomic DNA sequences from a Neandertal
Adrian W. Briggs et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Population structure and eigenanalysis
Nick Patterson et al.
PLOS GENETICS (2006)
Interpolated variable order motifs for identification of horizontally acquired DNA:: revisiting the Salmonella pathogenicity islands
Georgios S. Vernikos et al.
BIOINFORMATICS (2006)
Identification of Salmonella gallinarum virulence genes in a chicken infection model using PCR-based signature-tagged mutagenesis
DH Shah et al.
MICROBIOLOGY-SGM (2005)
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
J Parkhill et al.
NATURE (2001)
Host adapted serotypes of Salmonella enterica
S Uzzau et al.
EPIDEMIOLOGY AND INFECTION (2000)
Host adaptation and the emergence of infectious disease:: the Salmonella paradigm
RA Kingsley et al.
MOLECULAR MICROBIOLOGY (2000)