Project P01 is the central coordination hub of the SFB.
P01 will have two main tasks:
- Administration of the consortium
- Overseeing data integration
Iris Gratz – Speaker of EpiFlaMe heads the coordination project P01
Iris Gratz
University of Salzburg
Hellbrunner Straße 34
5020 Salzburg
Tel.: +43 662 8044-5764
Email:
Web: www.plus.ac.at/gratz
ORCID: 0000-0001-7470-7277
The coordination project’s administrative role in the consortium.
Iris Gratz together with an administrative assistant (50%) will manage the following tasks
- General administration of the SFB
- Joint recruitment and personnel development
- Interaction with the (international) community and dissemination
- Critical evaluation of SFB research program and progress
- Coordinate the SFB platforms (including the work of two wet lab technicians)
Two wet lab technicians (located in Salzburg) will work across projects to perform key tasks required for the generation of standardized and integratable biological data. Among other tasks they will run the “Organoid and composite organotypic (co-)culture systems platform” where they will offer standardized in-house production of organoid factors (e.g., Wnt3a, R-Spondin, Noggin), validation of additional factors, Matrigel batches and ECM components (e.g., fibrinogen, laminin), and the isolation and routine cultivation of mouse and patient organoids, which will be available as well-characterized samples stored in a patient biobank in collaboration with our clinical partners.
Who are we looking for? Biologists or lab technicians or individuals with equivalent education are invited to apply for this position (see open positions).
Keywords: cell culture, organoids, protein expression, standardization
Nikolaus Fortelny will oversee data integration and mentor the bioinformaticians:
Nikolaus Fortelny
University of Salzburg
Hellbrunner Straße 34
5020 Salzburg
Tel.: +43 662 8044-5797
Email:
Web: www.plus.ac.at/fortelny
ORCID: 0000-0003-4025-9968
Two bioinformaticians (one postdoc and one technician) will form the bioinformatic data integration platform, which will perform integrative bioinformatic processing and analysis of multi-omics profiles (focused on sorted bulk RNA-seq and ATAC-seq but also including single-cell and spatial datasets) obtained from epithelial cells across organs after inducing inflammatory memory in order to compare these processes across cell types, and upon oncogene induction.
The platform will (i) ensure consistent sample collection and annotation, (ii) perform bioinformatic pre-processing and quality control to ensure rapid feedback to wet-lab groups, and (iii) perform statistical comparisons to identify molecular signatures of inflammatory memory. It will further analyze single-cell and spatial omics data and compare EpiFlaMe data to relevant publicly available datasets. The platform will further help interpret these data, in particular by inferring regulatory proteins that mediate inflammatory memory (target identification). These data will directly support the target prioritization and validation strategy across the EpiFlaMe consortium. Finally, the platform will develop approaches to share data and analyses within the EpiFlaMe consortium and with the public. The platform will also train PhD students and Postdocs in basic bioinformatics.
Keywords: bioinformatics, statistics, AI/ML, transcriptional and epigenetic regulation
