Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Antifungal Drug Susceptibility and Phylogenetic Diversity among Cryptococcus Isolates from Dogs and Cats in North America

(2014) L. M. Singer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Microevolution During Serial Mouse Passage Demonstrates FRE3 as a Virulence Adaptation Gene in Cryptococcus neoformans

(2014) G. Hu et al.   mBio

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

(2014) Guilhem Janbon et al.   PLoS Genetics

Congenic Strains for Genetic Analysis of Virulence Traits in Cryptococcus gattii

(2013) Pinkuan Zhu et al.   INFECTION AND IMMUNITY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Cryptococcus gattii in the United States: Genotypic Diversity of Human and Veterinary Isolates

(2013) Shawn R. Lockhart et al.   PLoS One

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

(2013) Ferry Hagen et al.   PLoS One

Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data

(2013) Erica Bree Rosenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unisexual and Heterosexual Meiotic Reproduction Generate Aneuploidy and Phenotypic Diversity De Novo in the Yeast Cryptococcus neoformans

(2013) Min Ni et al.   PLOS BIOLOGY

Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen Cryptococcus gattii

(2013) Kerstin Voelz et al.   PLoS Genetics

Emerging Infectious Diseases: Threats to Human Health and Global Stability

(2013) David M. Morens et al.   PLoS Pathogens

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Gene Conversion Occurs within the Mating-Type Locus of Cryptococcus neoformans during Sexual Reproduction

(2012) Sheng Sun et al.   PLoS Genetics

DNA Mutations Mediate Microevolution between Host-Adapted Forms of the Pathogenic Fungus Cryptococcus neoformans

(2012) Denise A. Magditch et al.   PLoS Pathogens

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole Genome Sequence Analysis of Cryptococcus gattii from the Pacific Northwest Reveals Unexpected Diversity

(2011) John D. Gillece et al.   PLoS One

Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts

(2011) C. A. D'Souza et al.   mBio

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

(2010) A. McKenna et al.   GENOME RESEARCH

Self-Mating in the Definitive Host Potentiates Clonal Outbreaks of the Apicomplexan Parasites Sarcocystis neurona and Toxoplasma gondii

(2010) Jered M. Wendte et al.   PLoS Genetics

Cryptococcus neoformans Overcomes Stress of Azole Drugs by Formation of Disomy in Specific Multiple Chromosomes

(2010) Edward Sionov et al.   PLoS Pathogens

Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States

(2010) Edmond J. Byrnes et al.   PLoS Pathogens

Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS

(2009) Benjamin J Park et al.   AIDS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Spores as Infectious Propagules of Cryptococcus neoformans

(2009) R. Velagapudi et al.   INFECTION AND IMMUNITY

Molecular Evidence That the Range of the Vancouver Island Outbreak ofCryptococcus gattiiInfection Has Expanded into the Pacific Northwest in the United States

(2009) Edmond J. Byrnes III et al.   JOURNAL OF INFECTIOUS DISEASES

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

Dating the emergence of pandemic influenza viruses

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

Systematic Genetic Analysis of Virulence in the Human Fungal Pathogen Cryptococcus neoformans

(2008) Oliver W. Liu et al.   CELL