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

Ancient pathogen genomics as an emerging tool for infectious disease research

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

Bioarchaeology of Neolithic Çatalhöyük reveals fundamental transitions in health, mobility, and lifestyle in early farmers

(2019) Clark Spencer Larsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

(2018) Zhemin Zhou et al.   CURRENT BIOLOGY

A genomic overview of the population structure of Salmonella

(2018) Nabil-Fareed Alikhan et al.   PLoS Genetics

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

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

Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication

(2017) Felix M. Key et al.   TRENDS IN GENETICS

Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes

(2017) James A. Fellows Yates et al.   Scientific Reports

LNCediting: a database for functional effects of RNA editing in lncRNAs

(2016) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

The Salmonella pathogenicity island 13 contributes to pathogenesis in streptomycin pre-treated mice but not in day-old chickens

(2016) Jacob R. Elder et al.   Gut Pathogens

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Wolfgang Haak et al.   NATURE

World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis

(2015) Martyn D. Kirk et al.   PLOS MEDICINE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

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

PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands

(2014) Sung Ho Yoon et al.   NUCLEIC ACIDS RESEARCH

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

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

Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

(2014) Z. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of genome evolution that have accompanied host adaptation inSalmonella

(2014) Gemma C. Langridge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeated isolation of Salmonella enterica Goverdhan, a very rare serovar, from Danish poultry surveillance samples

(2014) Karl Pedersen et al.   VETERINARY MICROBIOLOGY

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

(2014) Jessica Hedge et al.   mBio

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment

(2013) Dario Vianello et al.   HUMAN MUTATION

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

IntCal13 and Marine13 Radiocarbon Age Calibration Curves 0–50,000 Years cal BP

(2013) Paula J Reimer et al.   RADIOCARBON

Population Genetic Structure of 4,12:a:− Salmonella enterica Strains from Harbor Porpoises

(2012) Jana K. Haase et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

(2012) K. A. Jolley et al.   MICROBIOLOGY-SGM

Identification of a common immune signature in murine and human systemic Salmonellosis

(2012) S.-J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

The Role of the spv Genes in Salmonella Pathogenesis

(2011) Donald G. Guiney et al.   Frontiers in Microbiology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Comparative genomic analysis uncovers 3 novel loci encoding type six secretion systems differentially distributed in Salmonella serotypes

(2009) Carlos J Blondel et al.   BMC GENOMICS

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

(2009) R. A. Kingsley et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

Salmonella paratyphi C: Genetic Divergence from Salmonella choleraesuis and Pathogenic Convergence with Salmonella typhi

(2009) Wei-Qiao Liu et al.   PLoS One

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

(2008) N. R. Thomson et al.   GENOME RESEARCH

High Rates of Molecular Evolution in Hantaviruses

(2008) C. Ramsden et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2008) Juan A. Fuentes et al.   RESEARCH IN MICROBIOLOGY