Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

(2016) Hannah Trewby et al.   Epidemics

State-space modeling to support management of brucellosis in the Yellowstone bison population

(2015) N. Thompson Hobbs et al.   ECOLOGICAL MONOGRAPHS

Effects of elk density on elk aggregation patterns and exposure to brucellosis

(2015) Kelly M. Proffitt et al.   JOURNAL OF WILDLIFE MANAGEMENT

Changing migratory patterns in the Jackson elk herd

(2015) Eric K. Cole et al.   JOURNAL OF WILDLIFE MANAGEMENT

A single natural nucleotide mutation alters bacterial pathogen host tropism

(2015) David Viana et al.   NATURE GENETICS

Measurably evolving pathogens in the genomic era

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

Limitations to estimating bacterial cross-species transmission using genetic and genomic markers: inferences from simulation modeling

(2014) Julio A. Benavides et al.   Evolutionary Applications

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Assembling evidence for identifying reservoirs of infection

(2014) Mafalda Viana et al.   TRENDS IN ECOLOGY & EVOLUTION

Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal

(2014) D. M. Engelthaler et al.   mBio

A multi-scale assessment of animal aggregation patterns to understand increasing pathogen seroprevalence

(2014) Angela Brennan et al.   Ecosphere

DNA Genotyping Suggests that Recent Brucellosis Outbreaks in the Greater Yellowstone Area Originated from Elk

(2013) Albano Beja-Pereira et al.   JOURNAL OF WILDLIFE DISEASES

STATUS OF BRUCELLOSIS IN FREE-RANGING ELK AND BISON IN WYOMING

(2013) Brandon M. Scurlock et al.   JOURNAL OF WILDLIFE DISEASES

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

(2013) N. R. Faria et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts

(2013) A. E. Mather et al.   SCIENCE

Inferring the Source of Transmission with Phylogenetic Data

(2013) Erik M. Volz et al.   PLoS Computational Biology

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

Molecular Epidemiology of Brucella abortus Isolates from Cattle, Elk, and Bison in the United States, 1998 to 2011

(2012) James Higgins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Roman Biek et al.   PLoS Pathogens

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

(2011) F. Bielejec et al.   BIOINFORMATICS

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Bayesian analysis of elapsed times in continuous-time Markov chains

(2010) Marco A. R. Ferreira et al.   CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE

Probable causes of increasing brucellosis in free-ranging elk of the Greater Yellowstone Ecosystem

(2010) P. C. Cross et al.   ECOLOGICAL APPLICATIONS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Migration of northern Yellowstone elk: implications of spatial structuring

(2010) P. J. White et al.   JOURNAL OF MAMMALOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

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

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Viral phylodynamics and the search for an 'effective number of infections'

(2010) S. D. W. Frost et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mapping Brucellosis Increases Relative to Elk Density Using Hierarchical Bayesian Models

(2010) Paul C. Cross et al.   PLoS One

Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats

(2010) D. G. Streicker et al.   SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Many-core algorithms for statistical phylogenetics

(2009) M. A. Suchard et al.   BIOINFORMATICS

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

(2009) P. Librado et al.   BIOINFORMATICS

Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella

(2009) J. T. Foster et al.   JOURNAL OF BACTERIOLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION