Integrative meta-analysis of public and novel vertebrate BBB omics data and establishment of the BBBhub platform

ESR 4 vision / project

David Francisco - University of Bern

ESR 4: 07/09/2021

Integrative meta-analysis of public and novel vertebrate BBB omics data and establishment of the BBBhub platform

Project Results

ESR4 established the BBBHub with core functionalities and implemented the corresponding server infrastructure. As a framework for the BBBHub, we used openBIS1 – a flexible framework for managing and analyzing complex data in biology research – and developed several add-ons and modifications. They include modifications to the user authentication user spaces to account for privacy and security, the implementation of a data upload system and the establishment of metadata fields. These are required for organization, analysis, searchability and communication between the user side, the openBIS system and the compute cluster. ESR4 implemented a Snakemake2 based RNA-Seq analytical pipeline. This pipeline ensures consistency in the analysis of the uploaded raw data allowing comparisons across datasets. The result files can be downloaded and visualized natively.

Currently, ESR4 is optimizing the BBBHub for public launch by improving the search systems, changing the graphical user interface to become more user-friendly and adding publicly available datasets. The public launch is scheduled to Q1 of 2020.

ESR4 also worked closely with other ESRs, particularly in experimental design, in-depth data analysis and results interpretation of the projects of ESR8 and ESR12. ESR4 also wrote a RNA-Seq in Brain Barriers guidelines paper together with ESRs 6, 7, 8 and 12. The objective is to provide best practices for experimental design and publication in the field.

1 Bauch, Angela et al. “openBIS: a flexible framework for managing and analyzing complex data in biology research.” BMC bioinformatics vol. 12 468. 8 Dec. 2011, doi:10.1186/1471-2105-12-468

2 Köster, Johannes et al. ”Snakemake—a scalable bioinformatics workflow engine” Bioinformatics vol. 28 19. 1 Oct. 2012,

Title of PhD thesis

Next Generation Transcriptomics of the Brain Barriers: Generating novel experiments, establishing guidelines, and creating the BBBHub

Current position

Post-Doc Researcher at Interfaculty Bioinformatics Unit, University of Bern

BtRAIN publications

Marchetti L, Francisco D, Soldati S, Haghayegh Jahromi N, Barcos S, Gruber I, Pareja JR, Thiriot A, von Andrian U, Deutsch U, Lyck R, Bruggmann R, Engelhardt B. ACKR1 favors transcellular over paracellular T-cell diapedesis across the blood-brain barrier in neuroinflammation in vitro. Eur J Immunol. 2021 Sep 15. doi: 10.1002/eji.202149238. Epub ahead of print. PMID: 34524684.

Francisco DMF, Marchetti L, Rodríguez-Lorenzo S, Frías-Anaya E, Figueiredo RM; BtRAIN Network, Winter P, Romero IA, de Vries HE, Engelhardt B, Bruggmann R. Advancing brain barriers RNA sequencing: guidelines from experimental design to publication. Fluids Barriers CNS. 2020 Aug 18;17(1):51. doi: 10.1186/s12987-020- 00207-2. PMID: 32811511; PMCID: PMC7433166.

Heymans M, Figueiredo R, Dehouck L, Francisco D, Sano Y, Shimizu F, Kanda T, Bruggmann R, Engelhardt B, Winter P, Gosselet F, Culot M. Contribution of brain pericytes in blood-brain barrier formation and maintenance: a transcriptomic study of cocultured human endothelial cells derived from hematopoietic stem cells. Fluids Barriers CNS. 2020 Jul 28;17(1):48. doi: 10.1186/s12987-020-00208-1. PMID: 32723387; PMCID: PMC7385894.

Rodríguez-Lorenzo S, Ferreira Francisco DM, Vos R, van Het Hof B, Rijnsburger M, Schroten H, Ishikawa H, Beaino W, Bruggmann R, Kooij G, de Vries HE. Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis. Acta Neuropathol Commun. 2020 Mar 19;8(1):35. doi: 10.1186/s40478-020-00903-y. PMID: 32192527; PMCID: PMC7083003

Hosting institution

University of Bern, Interfaculty Bioinformatics Unit, Switzerland


Rémy Bruggmann

Early Stage Researcher

David Francisco