An Indian lineage of Histoplasma with strong signatures of differentiation and selection

pixy : Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

(2021) Katharine L Korunes et al.   Molecular Ecology Resources

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global epidemiology of emerging Histoplasma species in recent years

(2020) Anderson Messias Rodrigues et al.   STUDIES IN MYCOLOGY

Fungal species concepts in the genomics era

(2020) Jianping Xu   GENOME

Biodiverse Histoplasma Species Elicit Distinct Patterns of Pulmonary Inflammation following Sublethal Infection

(2020) Grant S. Jones et al.   mSphere

Paracoccidioides Genomes Reflect High Levels of Species Divergence and Little Interspecific Gene Flow

(2020) Heidi Mavengere et al.   mBio

Differential Thermotolerance Adaptation between Species of Coccidioides

(2020) Heather L. Mead et al.   Journal of Fungi

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata

(2019) Tuomas Hämälä et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fungal species boundaries in the genomics era

(2019) Daniel R. Matute et al.   FUNGAL GENETICS AND BIOLOGY

Molecular regulation of Histoplasma dimorphism

(2019) Anita Sil   CURRENT OPINION IN MICROBIOLOGY

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

(2018) James B. Pease et al.   AMERICAN JOURNAL OF BOTANY

Fungal species and their boundaries matter – Definitions, mechanisms and practical implications

(2018) Emma T. Steenkamp et al.   Fungal Biology Reviews

Environmental and Wilderness-Related Risk Factors for Histoplasmosis: More Than Bats in Caves

(2018) James H. Diaz   WILDERNESS & ENVIRONMENTAL MEDICINE

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

Macrophage activation by IFN-γ triggers restriction of phagosomal copper from intracellular pathogens

(2018) Qian Shen et al.   PLoS Pathogens

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

(2018) Milan Malinsky et al.   Nature Ecology & Evolution

Species boundaries in the human pathogen Paracoccidioides

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

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Admixture and Ancestry Inference from Ancient and Modern Samples through Measures of Population Genetic Drift

(2017) Alexandre M. Harris et al.   HUMAN BIOLOGY

Eng1 and Exg8 Are the Major β-Glucanases Secreted by the Fungal PathogenHistoplasma capsulatum

(2017) Andrew L. Garfoot et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Using multi-locus sequence data for addressing species boundaries in commonly accepted lichen-forming fungal species

(2017) Xin Zhao et al.   ORGANISMS DIVERSITY & EVOLUTION

Why Concatenation Fails Near the Anomaly Zone

(2017) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum

(2017) Victoria E. Sepúlveda et al.   mBio

Powerful methods for detecting introgressed regions from population genomic data

(2016) Benjamin K. Rosenzweig et al.   MOLECULAR ECOLOGY

Recurrent specialization on a toxic fruit in an islandDrosophilapopulation

(2016) Amir Yassin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eng1 β-Glucanase Enhances Histoplasma Virulence by Reducing β-Glucan Exposure

(2016) Andrew L. Garfoot et al.   mBio

Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma

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

Histoplasmosis-Associated Hospitalizations in the United States, 2001–2012

(2016) Kaitlin Benedict et al.   Open Forum Infectious Diseases

Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 duringH.capsulatuminfection

(2015) Dervla T. Isaac et al.   MOLECULAR MICROBIOLOGY

Tuberculosis and Histoplasmosis among Human Immunodeficiency Virus–Infected Patients: A Comparative Study

(2014) Antoine Adenis et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

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

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

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Comparison of Phylogenetically Distinct Histoplasma Strains Reveals Evolutionarily Divergent Virulence Strategies

(2014) V. E. Sepulveda et al.   mBio

MFS multidrug transporters in pathogenic fungi: do they have real clinical impact?

(2014) Catarina Costa et al.   Frontiers in Physiology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles

(2013) Jessica A Edwards et al.   BMC GENOMICS

Species Detection and Identification in Sexual Organisms Using Population Genetic Theory and DNA Sequences

(2013) C. William Birky   PLoS One

Inhibition of PbGP43 Expression May Suggest that gp43 is a Virulence Factor in Paracoccidioides brasiliensis

(2013) Isaura Torres et al.   PLoS One

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Influence of Different Media, Incubation Times, and Temperatures for Determining the MICs of Seven Antifungal Agents against Paracoccidioides brasiliensis by Microdilution

(2012) R. C. Cruz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Functionality of the Paracoccidioides Mating α-Pheromone-Receptor System

(2012) Jéssica A. Gomes-Rezende et al.   PLoS One

Hidden Killers: Human Fungal Infections

(2012) G. D. Brown et al.   Science Translational Medicine

Extracellular Superoxide Dismutase Protects Histoplasma Yeast Cells from Host-Derived Oxidative Stress

(2012) Brian H. Youseff et al.   PLoS Pathogens

The Ubiquitin-Proteasome System and F-box Proteins in Pathogenic Fungi

(2012) Tong-Bao Liu et al.   MYCOBIOLOGY

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Isolation of Histoplasma capsulatum from bats in the urban area of São Paulo State, Brazil

(2011) M. A. GALVÃO DIAS et al.   EPIDEMIOLOGY AND INFECTION

SRE1 Regulates Iron-Dependent and -Independent Pathways in the Fungal Pathogen Histoplasma capsulatum

(2011) Lena H. Hwang et al.   EUKARYOTIC CELL

Definition of the Extracellular Proteome of Pathogenic-PhaseHistoplasma capsulatum

(2011) Eric D. Holbrook et al.   JOURNAL OF PROTEOME RESEARCH

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

(2011) Mark A DePristo et al.   NATURE GENETICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Insertional mutagenesis enables cleistothecial formation in a non-mating strain of Histoplasma capsulatum

(2010) Meggan C Laskowski et al.   BMC MICROBIOLOGY

The Yeast-Phase Virulence Requirement for α-Glucan Synthase Differs among Histoplasma capsulatum Chemotypes

(2010) Jessica A. Edwards et al.   EUKARYOTIC CELL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Computing the Distribution of a Tree Metric

(2009) D. Bryant et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

Vesicular transport inHistoplasma capsulatum: an effective mechanism for trans-cell wall transfer of proteins and lipids in ascomycetes

(2008) Priscila Costa Albuquerque et al.   CELLULAR MICROBIOLOGY

The Histoplasma capsulatum vacuolar ATPase is required for iron homeostasis, intracellular replication in macrophages and virulence in a murine model of histoplasmosis

(2008) Jeremy Hilty et al.   MOLECULAR MICROBIOLOGY

Metabolic adaptation inCryptococcus neoformansduring early murine pulmonary infection

(2008) Guanggan Hu et al.   MOLECULAR MICROBIOLOGY

Temperature-induced switch to the pathogenic yeast form of Histoplasma capsulatum requires Ryp1, a conserved transcriptional regulator

(2008) V. Q. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum

(2008) R. H. Webster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for Positive Selection in Putative Virulence Factors within the Paracoccidioides brasiliensis Species Complex

(2008) Daniel R. Matute et al.   PLoS Neglected Tropical Diseases

Histoplasma Requires SID1, a Member of an Iron-Regulated Siderophore Gene Cluster, for Host Colonization

(2008) Lena H. Hwang et al.   PLoS Pathogens