Fungal Pathogen Genomics workshop

For the past three years, a week-long Fungal Pathogen Genomics workshop has run at the Sanger Inst in Hinxton UK, generously supported by the Wellcome Trust Advanced Courses program.  This workshop provides exposure to many publicly-available informatics resources (EnsemblGenomes, FungiDB, MycoCosm, SGD/CGD), and is primarily intended for lab-based fungal biologists (i.e. not just computational biologists).  Recent participants have found the workshop extremely valuable.

The 2020 Fungal Pathogen Genomics Workshop will be held May 11-16, with an application deadline of Feb 27.  If you are interested, further information and application materials are available here:

Applications are accepted from anywhere in the world; the Trust covers all local expenses, and limited bursary support for travel is available for selected applicants who would not otherwise be able to attend


Fungal Biodiversity 2020

This yearly course has now been transformed into a 1-week course. The course provides a concise overview of the biodiversity of organisms representing the Kingdom Fungi. The course focuses on systematics and general ecology of fungi, as well as related topics such as soil mycology and diagnostics of plant pathogens. Both visual and molecular recognition methods will be discussed and practical hands-on experience will be gained in the morphological recognition and cultivation of fungi. The course is intended for (micro)biology students, PhD students, technicians and scientists/students who would like to obtain a fundamental understanding of fungi

Outline of the topics treated in this course:

  •  General Introduction 
  •  General methods: Aseptic working, media and incubation, microscopic examination of Fungi
  •  Introduction to the Fungal Kingdom with examples: Zygomycota, Ascomycota, Basidiomycota, deuteromycetes, yeasts
  •  Zygomycota (Mucoromycotina)
  •  Asexual morphs and conidiogenesis
  •  Ascomycota:
  • Eurotiomycetes: Aspergillus, Penicillium, Paecilomyces and sexual morphs with examples;
  • Sordariomycetes I: Chaetomium, Bartalinia, Pestalotiopsis, Colletotrichum, Gliomastix, Microascus/Scopulariopsis, Sordaria, Thielaviopsis;
  • Sordariomycetes  II: Neocosmospora/Fusarium, Cylindrocarpon, Cylindrocladium, Trichoderma.
  • Dothidiomycetes and selected genera of Leotiomycetes: Cladosporium, Septoria, Alternaria, Curvularia, Didymella, Epicoccum, Paraphaeosphaeria, Ascodesmis, Botrytis, Pezicula.
  •  Basidiomycota – an introduction with examples of species in culture
  •  Molecular methods for identification
  •  Yeasts: biology, phylogenies and polyphasic identification
  •  Polyphasic identification and other aspects of bioinformatics
  •  Clinical fungi diagnostics
  •  Fungi in our daily life 
  •  Tour through the CBS collection

Course leaders:
Prof Dr Pedro Crous and Dr Gerard Verkley.
Topical lectures will be presented by specialists from the Westerdijk Institute and invited speakers.

Language of instruction:
The course is given in the English language, but several other languages are spoken (Dutch, German).

Lunches and the Course book Laboratory Manual Series I: Fungal Biodiversity by Crous et al. are included in course fee. Accomodation and other meals are excluded.

Price: € 1700

Venue: Westerdijk Fungal Biodiversity Institute, Utrecht, Uppsalalaan 8, The Netherlands.

Public evening “Fungal Catastrophies”

At the 50th International Earth Day on Wednesday, April 22, 2020, the Westerdijk Fungal Biodiversity Institute is organizing a public evening about the emergence of novel and resistant fungi and its consequences for people and the environment. The public evening is the opening of the international scientific symposium “Rise of the Fungi”. Three renowned scientists will talk about the emergence of new pathogenic fungi and resistance to antifungal agents. How should infections be fought in humans if fungi are resistant to the usual drugs? What are the prospects for developing new antifungal agents? Is there a solution to the global problem of the dying banana trees caused by mold? What impact does the introduction of fungi in new living environments have on the biodiversity of the amphibians present there? The lectures will be in English.

18.30 – 19.00: Registration & Coffee/Tea

19.00 – 19.10: Opening

19.10 – 19.40: Costing the Earth: Catastrophic losses of amphibian biodiversity caused by chytrid fungi (Prof. Dr. Matthew Fisher, Imperial College, London, United Kingdom)

19.40 – 20.10: Going bananas: the global fungal attack on bananas (Prof. dr. ir. Gert Kema, Wageningen University & Research, Wageningen, The Netherlands)

20.10 – 20.40: Unsolved: Public health challenges in fungal infections (Prof. dr. Cornelia Lass-Flörl, Medical University of Innsbrück, Innsbrück, Austria)

20.40 – 21.30: Drinks and bites

Molecular Mycology (MOMY): Current Approaches to Fungal Pathogenesis

2019 registration is closing soon!

Please register at: ).  The “Molecular Mycology (MOMY): Current Approaches to Fungal Pathogenesis” course was established at Marine Biological Laboratory (MBL, in 1997.  The 2019 MOMY course will be held from July 17 to August 2, 2019 at MBL, MA, USA. Applications are due by March 29, 2019. Please apply online from the course website.  Need-based financial assistance is available for participants, including non-U.S. citizens. 


This course is designed to train advanced graduate students, postdocs, and independent investigators in different molecular approaches and models at the forefront of research to study human fungal pathogens and the diseases they cause. Course training includes laboratory exercises, visiting seminar speakers (~20 prominent medical mycologists), demonstration exercises, and informal panel discussions. Since its creation, this course has contributed significantly to the use of genetic techniques in analysis of pathogenic fungi and provided a community support for new investigators. Global participation helps strengthen the medical mycology field. 

Azole resistance in Aspergillus fumigatus: the next step

Azole resistance is a concern for the management of diseases caused by Aspergillus fumigatus in humans. Azole fungicide use in the environment has been identified as possible cause for resistance development, and thus increases the complexity and number of stakeholders involved in this emerging problem. We aim to bring together relevant stakeholders including medical and agricultural researchers, representatives from the government, fungicide producers and users, and public health to review the current evidence supporting environmental resistance selection and to discuss which research and measures are needed to retain the azole class for environmental and medical applications.

prof. P. Verweij
prof J. Lucas
dr B. Fraaije
prof B. Zwaan

Medical Mycology

This four-week course is intended for microbiologists (MDs, PharmDs, PhDs & veterinarians) willing to catch up with the most recent advances in diagnosis and identification procedures and principles of therapy for fungal infections.

Lectures, bench sessions & informal panel discussions will cover numerous technical and medical aspects related to fungal cultures, antifungal drugs, diagnosis and monitoring of patients, polyphasic identification of strains, epidemiology, diagnostic criteria and principles of therapeutic management of the most important yeast and filamentous fungal infections.

Expected lecturers:

A. Alanio (France), M. Arendrup, (Denmark), T. Boekhout (The Netherlands), S. Bretagne (France), T. Calandra (Switzerland), A. Carvalho (Portugal), M. Cuenca-Estrella (Spain), C. d’Enfert (France), J. Dupont (France), F. Dromer (France), J.-P. Gangneux (France), D. Garcia-Hermoso (France), J. Guillot (France), R. Hay (UK), V. Jullien (France), G. Jouvion (France), F. Lanternier (France), C. Lass-Flörl (Austria), F. Lamoth (Switzerland), O. Lortholary (France), J. Maertens (Belgium), P. Munoz (Spain), R. Piarroux (France), M. Richardson (UK), V. Robert (The Netherlands), D. Sanglard (Switzerland), M. Sanguinetti (Italy), A. Stchigel (Spain), P. Verweij (The Netherlands), J. Quintin (France).

Online registration:


Dea Garcia Hermoso 
Olivier Lortholary

Head of practical sessions:

Dea Garcia Hermoso

Practical information:

Deadline for application: December 20, 2018

Attendees: 20 students


Fungal Pathogen Genomics

Application deadline – 7 Feb 2019

The kingdom of Fungi includes a biologically diverse group of organisms adapted to diverse environmental niches, playing important roles in ecosystems and human/animal/plant health. Fusarium, Magnaporthe, Ustilago, Puccinia, and Zymoseptoria species threaten agricultural ecosystems and food security worldwide, while Aspergillus, Candida, Coccidioides, Cryptococcus, Histoplasma, Pneumocystis, Batrachochytrium and other human and animal fungal pathogens cause allergies, serious illnesses, and sometimes life-threatening infections that are of great concern for veterinary and medical professionals arounds the world. Furthermore, fungi are also important model systems for basic and applied research and workhorses in biotechnology, food, pharmaceutical, and biofuel industries.

Advancements in high throughput ‘omics’ data generation technologies enable researchers to carry out large-scale analyses to investigate genomes, transcriptomes, proteomes, and metabolomes of numerous fungal organisms to address questions about pathogenicity, host-pathogen interactions, and identify new drug targets. To facilitate accessibility and analysis, a number of online fungal bioinformatic resources have been developed.
This week-long course is a collaborative teaching effort between the web-based fungal data mining resources:

The Fungal Pathogen Genomics course provides hands-on training on how to take advantage of unique tools offered by each database; develop testable hypotheses, and investigate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces.

Daily activities at the workshop will include individual and group hands-on training exercises, supplementary lectures on bioinformatic techniques and tools used by various databases, and presentations by distinguished guest speakers. For example, you will learn how to:

  • Perform RNA-seq and SNP analysis and visualization via EuPathDB Galaxy workspace in FungiDB
  • Identify secondary metabolite clusters in MycoCosm
  • Find virulence genes and annotation in Ensembl
  • Access genetic interactions in CGD/SGD
  • Discover taxonomic conservation or phenotypes in PomBase

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