Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains

Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively

(2017) Lenka Mikalová et al.   PLoS Neglected Tropical Diseases

Novel Treponema pallidum Recombinant Antigens for Syphilis Diagnostics: Current Status and Future Prospects

(2017) Aleksey Kubanov et al.   Biomed Research International

Tools for opening new chapters in the book of Treponema pallidum evolutionary history

(2016) J.F. Gogarten et al.   CLINICAL MICROBIOLOGY AND INFECTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen

(2016) Justin D. Radolf et al.   NATURE REVIEWS MICROBIOLOGY

HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing

(2016) Hansi Weissensteiner et al.   NUCLEIC ACIDS RESEARCH

Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster

(2016) Natasha Arora et al.   Nature Microbiology

Challenges and key research questions for yaws eradication

(2015) Michael Marks et al.   LANCET INFECTIOUS DISEASES

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Endemic Treponematoses

(2014) L. Giacani et al.   CLINICAL MICROBIOLOGY REVIEWS

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Whole Genome Sequence of the Treponema pallidum subsp. endemicum Strain Bosnia A: The Genome Is Related to Yaws Treponemes but Contains Few Loci Similar to Syphilis Treponemes

(2014) Barbora Štaudová et al.   PLoS Neglected Tropical Diseases

Yaws

(2013) Oriol Mitjà et al.   LANCET

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

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

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

(2012) Pablo Cingolani et al.   FLY

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Neonate Human Remains: A Window of Opportunity to the Molecular Study of Ancient Syphilis

(2012) Rafael Montiel et al.   PLoS One

Whole Genome Sequence of Treponema pallidum ssp. pallidum, Strain Mexico A, Suggests Recombination between Yaws and Syphilis Strains

(2012) Helena Pětrošová et al.   PLoS Neglected Tropical Diseases

Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence

(2012) Darina Čejková et al.   PLoS Neglected Tropical Diseases

The origin and antiquity of syphilis revisited: An Appraisal of Old World pre-Columbian evidence for treponemal infection

(2011) Kristin N. Harper et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Genetic diversity in Treponema pallidum: Implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws

(2011) David Šmajs et al.   INFECTION GENETICS AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome Analysis of Treponema pallidum subsp. pallidum and subsp. pertenue Strains: Most of the Genetic Differences Are Localized in Six Regions

(2010) Lenka Mikalová et al.   PLoS One

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Emily Hodges et al.   Nature Protocols

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

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

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation

(2008) E. M. Hearn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Origin of the Treponematoses: A Phylogenetic Approach

(2008) Kristin N. Harper et al.   PLoS Neglected Tropical Diseases