Genome Data Science
// BIST / Institute for Research in Biomedicine (IRB Barcelona) / Cancer Science programme / @GenomeDataLab
In the GenomeDataLab, we use statistical genomics and machine learning to study quality control (QC) mechanisms that protect the integrity of information stored in the cell: its genome and the transcriptome, as well as gene functional links.
We perform large-scale bioinformatic studies of multi-omic data from human tumors (somatic mutations, and transcriptomes), human populations (germline variation) and metagenomes (incl. human microbiomes).
We study mechanisms of maintaining genome stability in human cells via statistical analyses of mutation patterns in cancer, which often result from deficient DNA repair [ 1 ]. Next, we are interested in how mRNA synthesis and turnover pathways shape genomes and transcriptomes in health and disease [ 2 ]. Finally, we combine experimental work and genomics to scan cancer genomes for genetic interactions to predict tumor evolution and identify novel synthetic lethalities [ 3 ]. More generally, we study novel approaches using machine learning to infer gene function from massive genomic data [ 4 ].
Some recent research from the GenomeDataLab:
read more about our work on:  genomic signatures of DNA repair failures;  transcriptome quality control via NMD;  predicting driver genes and cancer evolution; and  automated gene function prediction methods.
Meet the GenomeDataLab team:
We gratefully acknowledge our funders:
European Research Council ERC Starting Grant #757700 HYPER-INSIGHT "Insight into genome maintenance and cancer vulnerabilities provided by an extreme burden of somatic mutations "
CaixaResearch foundation "POTENT-IMMUNO" -Boosting immunotherapy by genomic prediction and NMD inhibitors.
EU H2020 "DECIDER" Clinical Decision via Integrating Multiple Data Levels to Overcome Chemotherapy Resistance in High-Grade Serous Ovarian Cancer
We are further funded by the "Severo Ochoa" centres of excellence program (to IRB), the Spanish Ministry of Science, Innovation and Universities ("REPAIRSCAPE"), the Catalan Science Agency (AGAUR) SGR support and FI fellowships. More information on projects >>>
Some collaborations of the GenomeDataLab:
Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.
J Biayna, I Garcia-Cao, [...]
F Supek*, T Stracker* (2021)
(w/ Travis Stracker lab, currently at NIH)
Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours.
A Avgustinova*, A Symeonidi, [...],
F Supek*, S Aznar-Benitah* (2018)
Nature Cell Biology.
(w/ Salvador Aznar lab at IRB)
Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers.
S Park*, F Supek*, B Lehner* (2021) Nature Communications.
(w/ Ben Lehner lab, at CRG)
Proton and alpha radiation-induced mutational profiles in human cells
TM Delhomme, M Munteanu, M Buonanno, V Grilj, J Biayna, F Supek (2022) bioRxiv
(w/ RARAF facility at Columbia university)
We are a part of the Institute for Research in Biomedicine (IRB Barcelona), a member of the Barcelona Institute of Science and Technology:
"Prediction is very difficult, especially about the future." -- Niels Bohr.