Genomic insights into the ancient spread of Lyme disease across North America

Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States

(2016) Giovanna Carpi et al.   BMC GENOMICS

County-Scale Distribution ofIxodes scapularisandIxodes pacificus(Acari: Ixodidae) in the Continental United States

(2016) Rebecca J. Eisen et al.   JOURNAL OF MEDICAL ENTOMOLOGY

Invasion of two tick-borne diseases across New England: harnessing human surveillance data to capture underlying ecological invasion processes

(2016) Katharine S. Walter et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

(2016) Monika Gulia-Nuss et al.   Nature Communications

Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity

(2016) Katharine S. Walter et al.   PLoS Pathogens

Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

(2015) Giovanna Carpi et al.   BMC GENOMICS

Recent and rapid population growth and range expansion of the Lyme disease tick vector,Ixodes scapularis, in North America

(2015) Camilo E. Khatchikian et al.   EVOLUTION

Measurably evolving pathogens in the genomic era

(2015) Roman Biek et al.   TRENDS IN ECOLOGY & EVOLUTION

Complex Population Structure of Borrelia burgdorferi in Southeastern and South Central Canada as Revealed by Phylogeographic Analysis

(2014) S. Mechai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Detection of Heterogeneity of Borrelia burgdorferi in Ixodes Ticks by Culture-Dependent and Culture-Independent Methods

(2012) G. Xu et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

(2012) Sherwood R. Casjens et al.   PLoS One

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

(2012) Roman Biek et al.   PLoS Pathogens

Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection inBorrelia burgdorferi, the Lyme Disease Bacterium

(2011) James Haven et al.   GENETICS

Whole Genome Sequence of an Unusual Borrelia burgdorferi Sensu Lato Isolate

(2011) S. R. Casjens et al.   JOURNAL OF BACTERIOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

UNCOORDINATED PHYLOGEOGRAPHY OF BORRELIA BURGDORFERI AND ITS TICK VECTOR, IXODES SCAPULARIS

(2010) Parris T. Humphrey et al.   EVOLUTION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Whole-Genome Sequences of Thirteen Isolates of Borrelia burgdorferi

(2010) S. E. Schutzer et al.   JOURNAL OF BACTERIOLOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing Spatiotemporal Hypothesis of Bacterial Evolution Using Methicillin-Resistant Staphylococcus aureus ST239 Genome-wide Data within a Bayesian Framework

(2010) R. R. Gray et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Characterization of the Highly Regulated Antigen BBA05 in the Enzootic Cycle of Borrelia burgdorferi

(2009) H. Xu et al.   INFECTION AND IMMUNITY

GuaA and GuaB Are Essential for Borrelia burgdorferi Survival in the Tick-Mouse Infection Cycle

(2009) M. W. Jewett et al.   JOURNAL OF BACTERIOLOGY

Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events

(2009) A. G. Hoen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Both Decorin-Binding Proteins A and B Are Critical for the Overall Virulence of Borrelia burgdorferi

(2008) Y. Shi et al.   INFECTION AND IMMUNITY

Borrelia burgdorferiGenotype Predicts the Capacity for Hematogenous Dissemination during Early Lyme Disease

(2008) Gary P. Wormser et al.   JOURNAL OF INFECTIOUS DISEASES

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE

MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi

(2008) G. Margos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA