Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance

Molecular characterization, mycelial compatibility grouping, and aggressiveness of a newly emerging phytopathogen, Sclerotinia sclerotiorum, causing white mold disease in new host crops in Bangladesh

(2020) M. M. E. Rahman et al.   JOURNAL OF PLANT PATHOLOGY

Immunoproteomic Approach of Extracellular Antigens From Paracoccidioides Species Reveals Exclusive B-Cell Epitopes

(2020) André Luís Elias Moreira et al.   Frontiers in Microbiology

Transcriptional responses of Candida glabrata biofilm cells to fluconazole are modulated by the carbon source

(2020) Rosana Alves et al.   npj Biofilms and Microbiomes

Unique Cell Surface Mannan of Yeast Pathogen Candida auris with Selective Binding to IgG

(2020) Lufeng Yan et al.   ACS Infectious Diseases

Pseudohyphal Growth of the Emerging Pathogen Candida auris Is Triggered by Genotoxic Stress through the S Phase Checkpoint

(2020) Gustavo Bravo Ruiz et al.   mSphere

Combatting the evolution of antifungal resistance in Cryptococcus neoformans

(2020) Arianne Bermas et al.   MOLECULAR MICROBIOLOGY

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting

(2020) Mohammad Rubayet Hasan et al.   Scientific Reports

The Role of Single-Cell Technology in the Study and Control of Infectious Diseases

(2020) Weikang Nicholas Lin et al.   Cells

Characteristics of Extracellular Vesicles Released by the Pathogenic Yeast-Like Fungi Candida glabrata, Candida parapsilosis and Candida tropicalis

(2020) Justyna Karkowska-Kuleta et al.   Cells

Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris

(2020) Mariolina Bruno et al.   Nature Microbiology

Immunometabolism in fungal infections: the need to eat to compete

(2020) Harshini Weerasinghe et al.   CURRENT OPINION IN MICROBIOLOGY

OMeta: an ontology-based, data-driven metadata tracking system

(2019) Indresh Singh et al.   BMC BIOINFORMATICS

Twenty Years of the SENTRY Antifungal Surveillance Program: Results for Candida Species From 1997–2016

(2019) Michael A Pfaller et al.   Open Forum Infectious Diseases

The Yin and Yang of Current Antifungal Therapeutic Strategies: How Can We Harness Our Natural Defenses?

(2019) Tomas Di Mambro et al.   Frontiers in Pharmacology

Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis

(2019) Lisa R. McTaggart et al.   Frontiers in Microbiology

The Still Underestimated Problem of Fungal Diseases Worldwide

(2019) Fausto Almeida et al.   Frontiers in Microbiology

Intercellular cooperation in a fungal plant pathogen facilitates host colonization

(2019) Rémi Peyraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Profiling of Candida auris, a Newly-Emerging Multi-Drug Resistant Candida Species, by GC-MS

(2019) Mohammad H. Semreen et al.   MOLECULES

Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus

(2019) Thomas R. Sewell et al.   mBio

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin

(2019) Verónica Mixão et al.   Frontiers in Genetics

Moonlighting proteins are variably exposed at the cell surfaces of Candida glabrata, Candida parapsilosis and Candida tropicalis under certain growth conditions

(2019) Justyna Karkowska-Kuleta et al.   BMC MICROBIOLOGY

Attack, Defend and Persist: How the Fungal Pathogen Candida auris was Able to Emerge Globally in Healthcare Environments

(2019) Auke W. de Jong et al.   MYCOPATHOLOGIA

On the Emergence of Candida auris: Climate Change, Azoles, Swamps, and Birds

(2019) Arturo Casadevall et al.   mBio

Multi-omics Signature of Candida auris, an Emerging and Multidrug-Resistant Pathogen

(2019) Daniel Zamith-Miranda et al.   mSystems

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

(2019) Farhana R. Pinu et al.   Metabolites

Proteomics of Rat Lungs Infected by Cryptococcus gattii Reveals a Potential Warburg-like Effect

(2019) Rafael L. Rosa et al.   JOURNAL OF PROTEOME RESEARCH

Variation in isolates of Sclerotinia sclerotiorum (Lib.) de Bary causing white mold disease in Bangladesh crops

(2019) M.S. Nahar et al.   CROP PROTECTION

Fusarium Head Blight in Durum Wheat: Recent Status, Breeding Directions, and Future Research Prospects

(2019) Jemanesh K. Haile et al.   PHYTOPATHOLOGY

A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes

(2019) Carina Félix et al.   Scientific Reports

Making multi-omics data accessible to researchers

(2019) Ana Conesa et al.   Scientific Data

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses

(2019) Chen-Hsin Yu et al.   Microbial Genomics

New pathogens, new tricks: emerging, drug-resistant fungal pathogens and future prospects for antifungal therapeutics

(2018) Jennifer Geddes-McAlister et al.   Annals of the New York Academy of Sciences

Glucose Homeostasis Is Important for Immune Cell Viability during Candida Challenge and Host Survival of Systemic Fungal Infection

(2018) Timothy M. Tucey et al.   Cell Metabolism

OUP accepted manuscript

(2018)   MEDICAL MYCOLOGY

Metabolomic profiling for the identification of potential biomarkers involved in a laboratory azole resistance in Candida albicans

(2018) Ling Li et al.   PLoS One

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

(2018) R. P. Vivek-Ananth et al.   Scientific Reports

Metabolomics: Eavesdropping on silent conversations between hosts and their unwelcome guests

(2018) Sydney N. Newsom et al.   PLoS Pathogens

Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators

(2018) Benjamin Hommel et al.   PLoS Pathogens

Genomic Organization and Expression of Iron Metabolism Genes in the Emerging Pathogenic Mold Scedosporium apiospermum

(2018) Yohann Le Govic et al.   Frontiers in Microbiology

The first isolate of Candida auris in China: clinical and biological aspects

(2018) Xiaojuan Wang et al.   Emerging Microbes & Infections

Mechanisms of Cryptococcus neoformans-Mediated Host Damage

(2018) Arturo Casadevall et al.   Frontiers in Immunology

Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance

(2018) Ryan Kean et al.   mSphere

Limited ERG11 Mutations Identified in Isolates of Candida auris Directly Contribute to Reduced Azole Susceptibility

(2018) Kelley R. Healey et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

(2018) Natacha Couto et al.   Scientific Reports

Fungal secondary metabolism: regulation, function and drug discovery

(2018) Nancy P. Keller   NATURE REVIEWS MICROBIOLOGY

Current status of Fusarium oxysporum formae speciales and races

(2018) Véronique Edel-Hermann et al.   PHYTOPATHOLOGY

Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species

(2018) José F. Muñoz et al.   Nature Communications

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

(2017) Peralam Yegneswaran Prakash et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Direct detection of Exophiala and Scedosporium species in sputa of patients with cystic fibrosis

(2017) Min Chen et al.   MEDICAL MYCOLOGY

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

(2017) Pierre-Yves Dupont et al.   G3-Genes Genomes Genetics

Azole Resistance in Aspergillus fumigatus: A Consequence of Antifungal Use in Agriculture?

(2017) Sarah Berger et al.   Frontiers in Microbiology

Progress in Top-Down Proteomics and the Analysis of Proteoforms

(2016) Timothy K. Toby et al.   Annual Review of Analytical Chemistry

Methods for the integration of multi-omics data: mathematical aspects

(2016) Matteo Bersanelli et al.   BMC BIOINFORMATICS

The present and future ofde novowhole-genome assembly

(2016) Jang-il Sohn et al.   BRIEFINGS IN BIOINFORMATICS

Simultaneous Emergence of Multidrug-ResistantCandida aurison 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses

(2016) Shawn R. Lockhart et al.   CLINICAL INFECTIOUS DISEASES

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH

(2016) Ruedi Aebersold et al.   PROTEOMICS

Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation

(2016) J. M. H. Geddes et al.   mBio

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi

(2016) Marcus C. Chibucos et al.   Nature Communications

In Vitro Analysis of Metabolites Secreted during Infection of Lung Epithelial Cells by Cryptococcus neoformans

(2016) Kah Leong Liew et al.   PLoS One

Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A

(2015) Jennifer M. H. Geddes et al.   BMC MICROBIOLOGY

Immunotherapy of Fungal Infections

(2015) Kausik Datta et al.   IMMUNOLOGICAL INVESTIGATIONS

Multidrug-Resistant Candida auris Misidentified as Candida haemulonii: Characterization by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and DNA Sequencing and Its Antifungal Susceptibility Profile Variability by Vitek 2, CLSI Broth Microdilution, and Etest Method

(2015) Shallu Kathuria et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Candida albicans Shaving to Profile Human Serum Proteins on Hyphal Surface

(2015) Elvira Marín et al.   Frontiers in Microbiology

Transcriptome Profiles of Human Lung Epithelial Cells A549 Interacting with Aspergillus fumigatus by RNA-Seq

(2015) Fangyan Chen et al.   PLoS One

Serum Antibody Signature Directed against Candida albicans Hsp90 and Enolase Detects Invasive Candidiasis in Non-Neutropenic Patients

(2014) Aida Pitarch et al.   JOURNAL OF PROTEOME RESEARCH

Quorum Sensing-Mediated, Cell Density-Dependent Regulation of Growth and Virulence in Cryptococcus neoformans

(2014) P. Albuquerque et al.   mBio

The Spectrum of Fungi That Infects Humans

(2014) J. R. Kohler et al.   Cold Spring Harbor Perspectives in Medicine

The Mannoprotein Cig1 Supports Iron Acquisition From Heme and Virulence in the Pathogenic Fungus Cryptococcus neoformans

(2013) Brigitte Cadieux et al.   JOURNAL OF INFECTIOUS DISEASES

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

Crop pests and pathogens move polewards in a warming world

(2013) Daniel P. Bebber et al.   Nature Climate Change

Emergence of Azole-Resistant Aspergillus fumigatus Strains due to Agricultural Azole Use Creates an Increasing Threat to Human Health

(2013) Anuradha Chowdhary et al.   PLoS Pathogens

Host genetics and invasive fungal diseases: towards improved diagnosis and therapy?

(2012) Cristina Cunha et al.   Expert Review of Anti-Infective Therapy

The Top 10 fungal pathogens in molecular plant pathology

(2012) RALPH DEAN et al.   MOLECULAR PLANT PATHOLOGY

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Triazole Fungicides Can Induce Cross-Resistance to Medical Triazoles in Aspergillus fumigatus

(2012) Eveline Snelders et al.   PLoS One

Whole Genome Sequence Typing to Investigate the Apophysomyces Outbreak following a Tornado in Joplin, Missouri, 2011

(2012) Kizee A. Etienne et al.   PLoS One

Hidden Killers: Human Fungal Infections

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

Colletotrichum – current status and future directions

(2012) P.F. Cannon et al.   STUDIES IN MYCOLOGY

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Sequencing the fungal tree of life

(2011) F. Martin et al.   NEW PHYTOLOGIST

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

(2011) D. O. Inglis et al.   NUCLEIC ACIDS RESEARCH

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2007: a 10.5-Year Analysis of Susceptibilities of Candida Species to Fluconazole and Voriconazole as Determined by CLSI Standardized Disk Diffusion

(2010) M. A. Pfaller et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Global Warming Will Bring New Fungal Diseases for Mammals

(2010) M. A. Garcia-Solache et al.   mBio

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

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

A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex

(2009) Kerry O’Donnell et al.   FUNGAL GENETICS AND BIOLOGY

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

Aspergillus fumigatus germ tube growth and not conidia ingestion induces expression of inflammatory mediator genes in the human lung epithelial cell line A549

(2009) A.-P. Bellanger et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Candida aurissp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital

(2009) Kazuo Satoh et al.   MICROBIOLOGY AND IMMUNOLOGY

Epidemiological trends in skin mycoses worldwide

(2008) Blanka Havlickova et al.   MYCOSES

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Recent developments in the molecular discrimination offormae specialesofFusarium oxysporum

(2008) Bart Lievens et al.   PEST MANAGEMENT SCIENCE

The biosecurity threat to the UK and global environment from international trade in plants

(2008) C. M. Brasier   PLANT PATHOLOGY