Integrated view ofVibrio choleraein the Americas

Genomic history of the seventh pandemic of cholera in Africa

(2017) François-Xavier Weill et al.   SCIENCE

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand

(2017) Achiraya Siriphap et al.   PLoS One

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Origins of the current seventh cholera pandemic

(2016) Dalong Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Diversity of Vibrio cholerae Associated with Endemic Cholera in Mexico from 1991 to 2008

(2016) Seon Young Choi et al.   mBio

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Is El Niño a long-distance corridor for waterborne disease?

(2016) Jaime Martinez-Urtaza et al.   Nature Microbiology

Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola

(2016) Taj Azarian et al.   Scientific Reports

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The Dynamics of Genetic Interactions betweenVibrio metoecusandVibrio cholerae, Two Close Relatives Co-Occurring in the Environment

(2015) Fabini D. Orata et al.   Genome Biology and Evolution

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Fast Dating Using Least-Squares Criteria and Algorithms

(2015) Thu-Hien To et al.   SYSTEMATIC BIOLOGY

The Role of China in the Global Spread of the Current Cholera Pandemic

(2015) Xavier Didelot et al.   PLoS Genetics

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Genomic and Phenotypic Characterization of Vibrio cholerae Non-O1 Isolates from a US Gulf Coast Cholera Outbreak

(2014) Bradd J. Haley et al.   PLoS One

Occurrence in Mexico, 1998–2008, ofVibrio choleraeCTX+El Tor carrying an additional truncated CTX prophage

(2014) Munirul Alam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acquisition and Evolution of SXT-R391 Integrative Conjugative Elements in the Seventh-Pandemic Vibrio cholerae Lineage

(2014) M. Spagnoletti et al.   mBio

Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic

(2014) Mark Eppinger et al.   mBio

Epidemic cholera spreads like wildfire

(2014) Manojit Roy et al.   Scientific Reports

The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India

(2014) Moataz Abd El Ghany et al.   PLoS Neglected Tropical Diseases

Vibrio ecology, pathogenesis, and evolution

(2014) Daniela Ceccarelli et al.   Frontiers in Microbiology

Sequence polymorphisms of rfbT among the Vibrio cholerae O1 strains in the Ogawa and Inaba serotype shifts

(2013) Weili Liang et al.   BMC MICROBIOLOGY

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Study on the Geophylogeny of Clinical and Environmental Vibrio cholerae in Kenya

(2013) John Kiiru et al.   PLoS One

Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti

(2013) L. S. Katz et al.   mBio

Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic

(2013) A. Islam et al.   Open Biology

Vibrio cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico

(2012) M. Alam et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic diversity of 2010 Haitian cholera outbreak strains

(2012) N. A. Hasan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia

(2011) C. C. Thompson et al.   JOURNAL OF BACTERIOLOGY

Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads

(2011) Paula Juliana Pérez Chaparro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak

(2011) R. S. Hendriksen et al.   mBio

The Cholera Pandemic, Still with Us after Half a Century: Time to Rethink

(2011) Edward T. Ryan   PLoS Neglected Tropical Diseases

Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae

(2010) Bradd J Haley et al.   BMC MICROBIOLOGY

Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae

(2010) C. J. Grim et al.   JOURNAL OF BACTERIOLOGY

Cholera between 1991 and 1997 in Mexico Was Associated with Infection by Classical, El Tor, and El Tor Variants of Vibrio cholerae

(2010) M. Alam et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular Analyses of Vibrio cholerae O1 Clinical Strains, Including New Nontoxigenic Variants Isolated in Mexico during the Cholera Epidemic Years between 1991 and 2000

(2009) M. L. Lizarraga-Partida et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae

(2009) J. Chun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Recalibrated Molecular Clock and Independent Origins for the Cholera Pandemic Clones

(2008) Lu Feng et al.   PLoS One