Transcriptomics and Multi-Omics of Fungi
RNA-seq analysis and integration with proteomic and metabolomic data to understand fungal responses, development and metabolism.
Program identification
- 1.1Program name
- Transcriptomics and Multi-Omics of Fungi
- 1.2Type of qualification
- Course
- 1.3Provider / endorsing institution
- Fungaris – International Institute of Mycology, School of Digital Mycology: AI, Genomics & Data. A Fungaris program of its own, not endorsed by a university.
- 1.4Mode of study
- Online, with live sessions in a small group, recordings and a virtual campus.
- 1.5Duration (hours / ECTS credits)
- 3 months (12 weeks) · 72 hours in total · 6 modules of 12 hours · 12 live sessions of 2 hours. ECTS credits: not applicable (Fungaris own program, not an official university degree).
- 1.6Language
- English
- 1.7Start and end dates / intake
- Next intake: January 11, 2027 to April 2, 2027. Enrollment closes on January 4, 2027. Following intake: March 8, 2027. How intakes work →
Overview
2.1Program description
Transcriptomics and Multi-Omics of Fungi takes you through RNA-seq from experimental design to biological interpretation, then shows how to combine it with proteomic and metabolomic data. You plan experiments with adequate replication, map and quantify reads, run differential expression analyses and test for enriched functions and pathways. Introductory modules on proteomics and metabolomics prepare you to integrate several data layers in a coherent analysis.
Transcriptomics is the most common way to study how fungi respond to hosts, substrates, stress and development, and multi-omics integration is increasingly expected in high-quality studies. Poor design and over-interpreted gene lists, however, remain frequent problems. The course suits molecular biologists and bioinformaticians with some R or command-line experience. In the final project you analyze a public fungal RNA-seq dataset, add at least one other omics layer if available and write a concise results section with figures and a critical discussion.
2.2Why it matters / what need it meets
It meets a practical need: applied, up-to-date knowledge in digital mycology, useful in areas such as academic research, industrial biotechnology, plant health research, pharmaceutical and natural products research.
Mycology is moving fast and good practical training is still scarce. This program gives you a structured path, taught live by people who work in the field, so you can apply what you learn with judgment and safety.
Objectives and competences
3.1General objective
To finish the program able to apply its content professionally and with judgment. In short:
RNA-seq analysis and integration with proteomic and metabolomic data to understand fungal responses, development and metabolism.
3.2Specific objectives
- Build the foundations: RNA-seq experimental design; Read mapping and quantification.
- Put them into practice: Differential expression analysis; Functional enrichment and pathways.
- Apply everything to a real case: Proteomics and metabolomics basics; Integrating multi-omics datasets.
- Complete a final project reviewed by your instructor.
3.3Competences you will gain
- Design RNA-seq experiments with suitable replication and controls.
- Map, quantify and quality-check fungal RNA-seq data.
- Perform differential expression analysis with DESeq2 or edgeR.
- Run functional enrichment using fungal-relevant annotations.
- Integrate transcriptomic, proteomic and metabolomic datasets coherently.
Student profile
4.1Who it is for (entry profile)
Molecular biologists and bioinformaticians.
4.2Entry requirements
Basic molecular biology and some experience with R or the command line are expected.
4.3Career paths (exit profile)
- Bioinformatician in a fungal molecular biology lab
- Research scientist studying host-fungus interactions
- Omics data analyst in biotechnology
- Core facility analyst for transcriptomics
- Postdoctoral researcher in fungal physiology
Outcomes depend on your experience and on your local market.
Study plan
5.1Overall structure (modules and workload)
| Module | Title | Phase | Topics | Hours |
|---|---|---|---|---|
| 01 | RNA-seq experimental design | Foundations | 3 | 12 |
| 02 | Read mapping and quantification | Foundations | 3 | 12 |
| 03 | Differential expression analysis | Practice | 3 | 12 |
| 04 | Functional enrichment and pathways | Practice | 3 | 12 |
| 05 | Proteomics and metabolomics basics | Application & project | 3 | 12 |
| 06 | Integrating multi-omics datasets | Application & project | 3 | 12 |
| Total | 72 |
6 modules × 12 hours = 72 hours: 24 hours of live sessions, and the rest for campus study, exercises and the final project.
5.2Content by module
Hover or tap a module to follow the path from the first session to the final project. Open a module to see the topics it covers.
- Questions RNA-seq can answer
- Replication and batch effects
- Library types and sequencing depth
- Aligners and pseudo-aligners
- Counting reads per gene
- Quality checks after mapping
- Normalization methods
- DESeq2 and edgeR
- Visualizing expression results
- Gene Ontology enrichment
- KEGG and pathway analysis
- CAZymes and fungal-specific annotations
- Mass spectrometry basics
- Proteomics data processing
- Untargeted metabolomics
- Correlation and network approaches
- Multi-omics factor analysis
- Interpreting integrated results
5.3Company placement
This program does not include a company placement. Practice is built into every module through exercises, case studies and the final project.
5.4Final project
A complete analysis of a public fungal RNA-seq dataset, integrated with another omics layer where available.
Methodology
6.1How it is taught
- Live online sessions, usually weekly, with a working professional and a small group.
- Recordings of every session, so you can catch up if work or time zones get in the way.
- Exercises and real case studies in every module.
- Tutoring: your instructor answers questions and gives feedback on your exercises and project.
6.2Platform and resources
A Moodle virtual campus with session recordings, readings, exercises and forums for each module. You need a computer, an up-to-date browser and a stable connection; a webcam and microphone are recommended.
Technical requirements →6.3Estimated weekly workload
About 6 hours a week for 12 weeks: one 2-hour live session on a weekday evening, plus study and exercises on the campus at your own pace.
Assessment
7.1Assessment system and weighting
Progress is assessed through participation in live sessions, analysis exercises in each module and a final project reviewed by the instructor.
7.2Requirements to pass
- Complete every module, by attending the live sessions or watching the recordings.
- Hand in the module exercises.
- Have your final project approved by your instructor.
Teaching team
8.1Academic direction
At Fungaris, the Digital Mycology school coordinates the content and quality of this program. The academic director of each intake is named in the intake guide.
8.2Faculty
Taught by professionals who work in the field. The instructor for each intake is confirmed before the start.
Meet our faculty →Certificate
9.1Certificate awarded
Course Certificate
On completing the program and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognizes them depends on that organization and on local rules in each country.
9.2Issuing body / recognition
Issued by Fungaris (operated by Nexora Generation, S.L.) as a digital certificate. It is a Fungaris certificate of its own: it is not an official university degree and does not award ECTS credits.
About our certificates →Admission and enrollment
10.1Admission process (steps)
- Send your request through the form or write to admissions.
- Admissions reviews your profile and confirms the start date, the session schedule and the fee.
- You secure your place with full payment or a 40% reservation.
- You receive your campus access and welcome guide before the first session.
10.2Documents required
- A valid identity document.
- Contact and billing details (personal or company).
10.3Deadlines
Enrollment for the intake starting on January 11, 2027 is open until January 4, 2027, or until the group is full (maximum 20 students).
10.4Fee and payment options
Fee: $450
- Full payment before the start: $360 (20% reduction).
- 40% reservation ($180) and 3 monthly installments of $90.
10.5Grants, discounts and funding
Discounts: 10% for Fungaris alumni and 15% for groups of three or more people from the same organization. Discounts cannot be combined with each other or with the full-payment reduction.
Your employer can pay for the program and receive the invoice in the company name. Whether a public or employer training budget can cover the fee depends on your country, so check with them.
10.6Cancellation policy
The conditions for canceling, withdrawing or moving to a later intake are explained in our cancellation policy and in your enrollment confirmation. Nothing there limits your rights under the consumer law that applies to you.
Cancellation and refunds →Additional information
11.1Frequently asked questions
Do I need experience to study Transcriptomics and Multi-Omics of Fungi?
Basic molecular biology and some experience with R or the command line are expected.
How is Transcriptomics and Multi-Omics of Fungi taught?
Live online, in 6 modules with a working professional, a small group and a final project.
How am I assessed?
Progress is assessed through participation in live sessions, analysis exercises in each module and a final project reviewed by the instructor.
What is the final project?
A complete analysis of a public fungal RNA-seq dataset, integrated with another omics layer where available.
What certificate do I get?
On completing the program and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognizes them depends on that organization and on local rules in each country.
What can I study after Transcriptomics and Multi-Omics of Fungi?
The natural next step is Diploma in Fungal Bioinformatics.
11.2Alumni testimonials
We only publish verified testimonials from real students. This program does not have any published yet; they will appear here once its first intakes finish.
11.3Admissions contact
Write to info@fungaris.institute or use the contact form. Admissions answers in your language.
Keep branching.
Join the next intake.
Pay in full with a 20% reduction, or reserve your place with 40% and pay the rest in monthly installments. All prices are stated in US dollars (USD).