Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)

Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes

(2013) Alexandra N. Marshall et al.   PLoS Genetics

Surviving the Heat of the Moment: A Fungal Pathogens Perspective

(2013) Michelle D. Leach et al.   PLoS Pathogens

Global Expression Profiling of Transcription Factor Genes Provides New Insights into Pathogenicity and Stress Responses in the Rice Blast Fungus

(2013) Sook-Young Park et al.   PLoS Pathogens

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi

(2012) Salvador Capella-Gutiérrez et al.   BMC BIOLOGY

A Global Analysis of Mucormycosis in France: The RetroZygo Study (2005-2007)

(2012) F. Lanternier et al.   CLINICAL INFECTIOUS DISEASES

Pathogenesis of Mucormycosis

(2012) Ashraf S. Ibrahim et al.   CLINICAL INFECTIOUS DISEASES

Evidence Implicating Thamnostylum lucknowense as an Etiological Agent of Rhino-Orbital Mucormycosis

(2012) I. Xess et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Zygomycota associated with traditional meju, a fermented soybean starting material for soy sauce and soybean paste

(2012) Seung-Beom Hong et al.   JOURNAL OF MICROBIOLOGY

Lichtheimia Species Exhibit Differences in Virulence Potential

(2012) Volker U. Schwartze et al.   PLoS One

Iron – A Key Nexus in the Virulence of Aspergillus fumigatus

(2012) Hubertus Haas   Frontiers in Microbiology

Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007

(2011) A. Skiada et al.   CLINICAL MICROBIOLOGY AND INFECTION

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

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

Mycobiota of cocoa: From farm to chocolate

(2011) Marina V. Copetti et al.   FOOD MICROBIOLOGY

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

Antifungal Susceptibility and Phylogeny of Opportunistic Members of the Order Mucorales

(2011) Roxana G. Vitale et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences

(2011) Katharina Jahn   JOURNAL OF COMPUTATIONAL BIOLOGY

Functional characterization of the ferroxidase, permease high-affinity iron transport complex from Candida albicans

(2011) Lynn Ziegler et al.   MOLECULAR MICROBIOLOGY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Fungi isolated from olive ecosystems and screening of their potential biotechnological use

(2011) Milla Alves Baffi et al.   New Biotechnology

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genome Characterization of the Oleaginous Fungus Mortierella alpina

(2011) Lei Wang et al.   PLoS One

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

(2011) D. C. Eastwood et al.   SCIENCE

Genomic Transition to Pathogenicity in Chytrid Fungi

(2011) Suzanne Joneson et al.   PLoS Pathogens

The Homeostasis of Iron, Copper, and Zinc in Paracoccidioides Brasiliensis, Cryptococcus Neoformans Var. Grubii, and Cryptococcus Gattii: A Comparative Analysis

(2011) Mirelle Garcia Silva et al.   Frontiers in Microbiology

Antifungal Susceptibility Profile of Human-Pathogenic Species of Lichtheimia

(2010) A. Alastruey-Izquierdo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Species Recognition and Clinical Relevance of the Zygomycetous Genus Lichtheimia (syn. Absidia Pro Parte, Mycocladus)

(2010) A. Alastruey-Izquierdo et al.   JOURNAL OF CLINICAL MICROBIOLOGY

New evidence of the involvement ofLichtheimia corymbiferain farmer's lung disease

(2010) Anne-Pauline Bellanger et al.   MEDICAL MYCOLOGY

The Evolution of Sex: a Perspective from the Fungal Kingdom

(2010) S. C. Lee et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The high affinity iron permease is a key virulence factor required for Rhizopus oryzae pathogenesis

(2010) Ashraf S. Ibrahim et al.   MOLECULAR MICROBIOLOGY

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

(2010) J. E. Stajich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Pulmonary Zygomycosis in Solid Organ Transplant Recipients in the Current Era

(2009) H.-Y. Sun et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

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

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

(2009) Marina Marcet-Houben et al.   BMC EVOLUTIONARY BIOLOGY

Current experience in treating invasive zygomycosis with posaconazole

(2009) O.A. Cornely et al.   CLINICAL MICROBIOLOGY AND INFECTION

The role of iron and iron chelators in zygomycosis

(2009) A.S. Symeonidis   CLINICAL MICROBIOLOGY AND INFECTION

Spectrum of Zygomycete Species Identified in Clinically Significant Specimens in the United States

(2009) E. Alvarez et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Computation of Median Gene Clusters

(2009) Sebastian Böcker et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

(2009) Li-Jun Ma et al.   PLoS Genetics

Rapid Global Expansion of the Fungal Disease Chytridiomycosis into Declining and Healthy Amphibian Populations

(2009) Timothy Y. James et al.   PLoS Pathogens

Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees

(2009) R. Scott Cornman et al.   PLoS Pathogens

Siderophores in Fungal Physiology and Virulence

(2008) Hubertus Haas et al.   Annual Review of Phytopathology

EPoS: a modular software framework for phylogenetic analysis

(2008) T. Griebel et al.   BIOINFORMATICS

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

(2008) A. Wehe et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Transcription factors in fungi

(2008) Ekaterina Shelest   FEMS MICROBIOLOGY LETTERS

Evolution of host resistance in a toxin-producing bacterial–fungal alliance

(2008) Imke Schmitt et al.   ISME Journal

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY