Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum

Species boundaries in the human pathogen Paracoccidioides

(2017) David A. Turissini et al.   FUNGAL GENETICS AND BIOLOGY

Multispecies coalescent delimits structure, not species

(2017) Jeet Sukumaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest

(2016) Jacob L. Steenwyk et al.   BMC GENOMICS

Histoplasmosis

(2016) Lawrence J. Wheat et al.   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma

(2016) Marcus de M. Teixeira et al.   PLoS Neglected Tropical Diseases

Quantitative Microplate-Based Growth Assay for Determination of Antifungal Susceptibility of Histoplasma capsulatum Yeasts

(2015) Kristie D. Goughenour et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Histoplasmosis: Up-to-Date Evidence-Based Approach to Diagnosis and Management

(2015) Marwan Azar et al.   SEMINARS IN RESPIRATORY AND CRITICAL CARE MEDICINE

The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia

(2015) José F. Muñoz et al.   PLoS Genetics

Implementing a Class of Permutation Tests: ThecoinPackage

(2015) Torsten Hothorn et al.   Journal of Statistical Software

Perspective on Coccidioidomycosis and Histoplasmosis

(2014) Kenneth S. Knox   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparison of Phylogenetically Distinct Histoplasma Strains Reveals Evolutionarily Divergent Virulence Strategies

(2014) V. E. Sepulveda et al.   mBio

Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion

(2013) Stefano F.F. Torriani et al.   FUNGAL GENETICS AND BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Multilocus sequence typing ofHistoplasma capsulatumin formalin-fixed paraffin-embedded tissues from cats living in non-endemic regions reveals a new phylogenetic clade

(2012) S. Arunmozhi Balajee et al.   MEDICAL MYCOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma

(2012) Yu Sun et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

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

(2011) Mark A DePristo et al.   NATURE GENETICS

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Comparative Morphology and Immunology of Members of the Genus Histoplasma

(2010) Libero Ajello   MYCOSES

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species’ delimitation across basidiomycete fungi

(2009) Karen W. Hughes et al.   NEW PHYTOLOGIST

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS