HoloGen training materials
Open online resource for training materials from the HoloGen MSCA Doctoral Network. Each retreat below lists its full programme of lectures and workshops. Slides are linked where the presenter has agreed to share them openly; sessions without a link have no slides published.
Retreat dates are listed on the events page.
Note
Every retreat also includes project presentations by the doctoral candidates. These cover ongoing internal work, so the material is not yet shared publicly.
Retreat 1 — Introduction to Hologenomics
Copenhagen, May 2025. Programme
- Torgeir Hvidsten — Introduction to HoloGen & MSCA green charter guidelines
- Ostaizka Aizpurua — Theoretical and practical introduction to hologenomics
- Marc Marti-Renom — Workshop: Individual PhD project presentations
- Torgeir Hvidsten — About HoloGen training network (symposium)
- Lindsay Hall — Shaping the infant hologenome (symposium)
- Karoline Faust — Interactions between human gut microbes (symposium)
- Ostaizka Aizpurua — Seizing causality (symposium)
- Gareth Difford — Quantifying host genetic and microbial contributions to trait variance (symposium)
- Leo Lahti — Statistical programming framework for multi-source data integration (symposium)
- Aki Havulinna — Bayesian disease mapping for hologenomics in Finland (symposium)
- Kati Hanhineva — Metabolomics analytics (symposium)
- Simen Rød Sandve — Atlantic salmon (symposium)
- Marc Marti-Renom — The discovery of fossil chromosomes (symposium)
- Antton Alberdi — A PhD student’s voyage: purpose, strategy, task management
- Ostaizka Aizpurua — Research ethics
- Antton Alberdi — Task and conflict management (video)
- Leo Lahti — Introduction to code and data management I & II
- Leo Lahti — Introduction to statistical concepts and methods
- Antton Alberdi — A PhD student’s voyage II
- Torgeir Hvidsten — HoloGen going forward
Retreat 2 — High-Throughput Profiling
Barcelona, November 2025. Programme
- Torgeir Hvidsten — Introduction to HoloGen
- Pranvera Hiseni — Industry: Genetic Analysis
- Kati Hanhineva — Industry: Afekta
- Nicole Reisinger — Industry: DSM-Firmenich
- Ostaizka Aizpurua — Industry: Ziba
- Ostaizka Aizpurua — Sequencing technologies for hologenomics
- Ostaizka Aizpurua — Workshop: Metagenomics — data generation and design considerations
- Leo Lahti — Workshop: Metagenomics — downstream data analysis
- Nikolai (CNAG) — Workshop: Modelling the intestinal environment with Gorgona
- Workshop: Communicating Across Cultures
- Torgeir Hvidsten — HoloGen going forward
Retreat 3 — Data analysis and Open Science
Turku, May 2026. Programme
- Leo Lahti — Welcome & introduction
- Lindsay Hall — Communication activities & storyboarding
- Susanna Repo (ELIXIR) — Data management, database resources in life sciences
- Karoline Faust — Methods for studying host–microbiota interactions
Retreat 4 — Dissemination, Exploitation and Communication
Leuven, October 2026. Preliminary programme
- Torgeir Hvidsten — Announcements
- Lindsay Hall — Science communication and outreach
- Lindsay Hall / Jennifer — Workshop: Scientific writing exercise
- Tina — DCs meet the PhD coordinator: career development
- Karoline Faust — Welcome and introduction to community modelling
- Ksenia Guseva — Metacommunities of soil microbiomes: patterns, processes and implications for inference
- Julien Tap — Multiscale associations between diet and the gut microbiome in a nationwide French cohort
- Lulla Opatowski — Application of meta-community modelling to pathogens spreading in hospitals
- Ksenia Guseva / Karoline Faust — Workshop: Tutorial on community modelling
- Leo Lahti — Methods and strategies of scientific data visualisation
- Simen Rød Sandve — Best practices for not failing with PowerPoint presentations
- Aki Havulinna — Application case: species distribution modelling and visualisation
- Jan Aerts (KU Leuven) — Introduction to data visualisation techniques
- Ivo De Baere (KU Leuven) — Presentation on patents, with notes on copyright and trademarks
- Torgeir Hvidsten — Wrap-up
This project has received funding from the European Union’s Horizon 2023 programme under grant agreement No 101169005.