Simple yet very interesting challenge! Keep them coming #bioinfo #R #datascience

By selecting keywords that should be either in the gene set name or description, and using the R package 'msigdbr' (igordot.github.io/msigdbr/), voilá!

github.com/andrebolerba...

This folder contains a .qmd file and respective html report, with an excel file containing the final info dataset.

The first challenge came up in a conversation about a project: how can I check gene sets across different databases (e.g., GO terms, KEGG Pathways, ...) involved in specific processes, like iron processing or lipid metabolism?

Congratulations Maria! Really interested to see you defend and to watch your future career in science!!

A special thank you to the PhD community, the facilities, and the community at IGC, now @gimmfoundation.bsky.social , for providing the right context for this thesis to see the light of day.

Thank you to everyone who supported me through this journey, from my supervisor @lferreiramoita.bsky.social , to my lab members - especially Henrique Colaço, @katiajesus.bsky.social and Elsa Seixas and, to the jury members - Vitor Cabral, Sarela García Santamarina, Nelson Frazao and Vera Martins.

5/n

The following paper provides an excellent overview of sequence-to-graph mapping algorithms—covering their principles, trade-offs, and performance benchmarks. It’s a great starting point if you’re interested on the topic

genomebiology.biomedcentral.com/articles/10....

#bioinformatics #bioinfo

4/n

From equitable precision medicine to large-scale population studies and evolutionary research, pangenomics graphs and graph mapping excel in capturing diversity—especially in highly variable or repetitive genome regions where linear mapping fails.

3/n

Unlike linear references, which favour the “reference” allele (known as reference bias), the integration of multiple haplotypes in pangenomic graphs and respective mapping reduces bias, improves alignment quality, and makes analyses fairer across diverse populations.

2/n
Pangenome graphs represent variants as alternative paths, so reads can follow the path matching their true sequence.
These graphs can represent SNPs, indels, structural variants, and complex rearrangements, all in one model—boosting variant calling accuracy for common and rare alleles.

12/12

"It is an ethical imperative that research be designed and analysed to avoid wasting investment of animals, research dollars and effort".

#biostatistics #stats

11/n

Ultimately, understanding the C&N concepts, design experiments, and analytical approaches accounting for that are fundamental for rigorous and reproducible preclinical research.

10/n

In a collaborative setting, another key element is a good and clear communication between the experimentalists and the data analysts. Only then can we have sound and robust experiments, with efficient analysis, that can really provide insight into the questions being asked.