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

Intracellular Growth Is Dependent on Tyrosine Catabolism in the Dimorphic Fungal Pathogen Penicillium marneffei

(2015) Kylie J. Boyce et al.   PLoS Pathogens

Indoleamine 2,3-Dioxygenase Controls Fungal Loads and Immunity in Paracoccidioidomicosis but is More Important to Susceptible than Resistant Hosts

(2014) Eliseu F. Araújo et al.   PLoS Neglected Tropical Diseases

Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily

(2013) Jonathan M. Goldberg et al.   BIOINFORMATICS

Factors Supporting Cysteine Tolerance and Sulfite Production in Candida albicans

(2013) Florian Hennicke et al.   EUKARYOTIC CELL

Redundant Catalases Detoxify Phagocyte Reactive Oxygen and Facilitate Histoplasma capsulatum Pathogenesis

(2013) Eric D. Holbrook et al.   INFECTION AND IMMUNITY

Keratin Degradation by Dermatophytes Relies on Cysteine Dioxygenase and a Sulfite Efflux Pump

(2013) Maria Grumbt et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A Dimorphic Fungus Causing Disseminated Infection in South Africa

(2013) Chris Kenyon et al.   NEW ENGLAND JOURNAL OF MEDICINE

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Analysis Reveals a Cryptic Species Blastomyces gilchristii, sp. nov. within the Human Pathogenic Fungus Blastomyces dermatitidis

(2013) Elizabeth M. Brown et al.   PLoS One

Factors Required for Activation of Urease as a Virulence Determinant in Cryptococcus neoformans

(2013) A. Singh et al.   mBio

A Temperature-Responsive Network Links Cell Shape and Virulence Traits in a Primary Fungal Pathogen

(2013) Sinem Beyhan et al.   PLOS BIOLOGY

IL-22 and IDO1 Affect Immunity and Tolerance to Murine and Human Vaginal Candidiasis

(2013) Antonella De Luca et al.   PLoS Pathogens

Structure and Function of a Fungal Adhesin that Binds Heparin and Mimics Thrombospondin-1 by Blocking T Cell Activation and Effector Function

(2013) T. Tristan Brandhorst et al.   PLoS Pathogens

Identification of the Mating-Type ( MAT ) Locus That Controls Sexual Reproduction of Blastomyces dermatitidis

(2012) Wenjun Li et al.   EUKARYOTIC CELL

The 3-Hydroxy-Methylglutaryl Coenzyme A LyaseHCL1Is Required for Macrophage Colonization by Human Fungal Pathogen Histoplasma capsulatum

(2012) Dervla T. Isaac et al.   INFECTION AND IMMUNITY

Adiaspiromycosis Causing Respiratory Failure and a Review of Human Infections Due to Emmonsia and Chrysosporium spp.

(2012) G. M. Anstead et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Histoplasma capsulatumpreferentially induces IDO in the lung

(2012) Chadi A. Hage et al.   MEDICAL MYCOLOGY

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

(2012) D. A. Martinez et al.   mBio

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

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

Candida albicans Scavenges Host Zinc via Pra1 during Endothelial Invasion

(2012) Francesco Citiulo et al.   PLoS Pathogens

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Population Genetic Structure of Clinical and Environmental Isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

(2011) Jennifer K. Meece et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The two-component histidine kinases DrkA and SlnA are required for in vivo growth in the human pathogen Penicillium marneffei

(2011) Kylie J. Boyce et al.   MOLECULAR MICROBIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

LTR Retrotransposons in Fungi

(2011) Anna Muszewska et al.   PLoS One

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

(2011) Christopher A. Desjardins et al.   PLoS Genetics

Epidemiology of Invasive Mycoses in North America

(2010) Michael A. Pfaller et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Discordant Influence of Blastomyces dermatitidis Yeast-Phase-Specific Gene BYS1 on Morphogenesis and Virulence

(2010) T. Krajaejun et al.   INFECTION AND IMMUNITY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis and Siderophore Biosynthesis

(2010) Gregory M. Gauthier 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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Production of Pyomelanin, a Second Type of Melanin, via the Tyrosine Degradation Pathway in Aspergillus fumigatus

(2008) J. Schmaler-Ripcke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

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

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY