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

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

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

A molecular portrait of maternal sepsis from Byzantine Troy

(2017) Alison M Devault et al.   eLife

The 5300-year-old Helicobacter pylori genome of the Iceman

(2016) F. Maixner et al.   SCIENCE

What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B

(2016) Thomas R. Connor et al.   mBio

A time transect of exomes from a Native American population before and after European contact

(2016) John Lindo et al.   Nature Communications

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

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

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

(2016) B. Llamas et al.   Science Advances

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

Typhoid fever

(2015) John Wain et al.   LANCET

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

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Parallel detection of ancient pathogens via array-based DNA capture

(2014) K. I. Bos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ

(2014) Ohad Gal-Mor et al.   Frontiers in Microbiology

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

(2013) Hákon Jónsson et al.   BIOINFORMATICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

Salmonella Uses Energy Taxis to Benefit from Intestinal Inflammation

(2013) Fabian Rivera-Chávez et al.   PLoS Pathogens

Prospects for analyzing ancient RNA in preserved materials

(2013) Paul L. Guy   Wiley Interdisciplinary Reviews-RNA

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

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

(2011) Kirsten I. Bos et al.   NATURE

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The RdgC protein employs a novel mechanism involving a finger domain to bind to circular DNA

(2010) G. S. Briggs et al.   NUCLEIC ACIDS RESEARCH

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

Computational challenges in the analysis of ancient DNA

(2010) Kay Prüfer et al.   GENOME BIOLOGY

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

(2009) Emily Hodges et al.   Nature Protocols

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

(2009) Wei-Qiao Liu et al.   PLoS One

Molecular Characterization of the Salmonella enterica Serovar Typhi Vi-Typing Bacteriophage E1

(2008) D. Pickard et al.   JOURNAL OF BACTERIOLOGY