Quarterly updates from the Lab!

This June, the focus is on Alexandre Areias Castro, who is working on metabolic modeling of the microbiome with the aim of giving us a new view on microbial composition, focused of "functional roles" instead of taxonomy

bigdatabiology.substack.com/p/bdb-lab-up...

"A global survey of eco-evolutionary pressures acting on horizontal gene transfer" by
Marija Dmitrijeva et al.
https://buff.ly/3DDBBgj

Review paper with Celio Dias Junior and De La Fuente Upenn

How mining small peptides from (meta)genomes is different from mining full-sized enzymes and how we need new methods and approaches (AI/ML instead of sequence alignment)

https://buff.ly/3ONEr4w

Revisiting when argNorm became part of nf-core/funcscan!

Great work from Vedanth to get this integrated

Back in August, A/P @luispedrocoelho.bsky.social , presented at
ISME's conference in South Africa. Luis spoke about microbes and the microbiome to local school children of Cape Town. To find out more about CMR's exciting research, reach out.

To promote the use of the catalog, we also provide a tool called GMSC-mapper, which can annotate smORFs from microbial genomes with taxonomy, habitat, quality, and conserved domain annotations

We also found that archaea harbor more smORFs proportionally than bacteria, and the ratio of archaeal small proteins predicted to be transmembrane or secreted is higher than bacterial small proteins

(or our tools behave differently between the two domains! A lot of unknowns!)

We found that even conserved small protein families from multiple habitats and phyla still lack functional domain annotation

The small fraction of small proteins that we can annotate are mainly related to ribosomal proteins and DNA binding

Latest Big Data Biology Lab Updates
t.co/akVYnWAuka