Genomics of Gene Expression

The last month of spring began as May went, with Ana traveling through Europe. The first week of June, both Ana and Fabian attended the Elixir meeting that was held in Thesaloniki. Fabian came back so exited from the event that he was talking about it for a week straight. Being there, with so many colleagues sharing the same enthusiasm that he has for Bioinformatics was just magical.

 

However, just before Ana and Fabian left for Greece, another extraordinary event happened at I2SysBio. We were visited by the nobel prize winner Randy Shenkman and Peter Walker. We had the chance to have a converstaion with them and PhDs from our institute, and their insight left none of us indiferent. Not everyday a Nobel Laureate joins us for coffee in the office!

In the meantime, the SQANTI-team was busy working on a new minor release, 5.5, introducing a big change in the Open Reading Frame prediction. After many months thinking about it, they found the time to replace the good ol’ GeneMarkS-T for TransDecoder2. TD2 offers a newer and more reliable approach towards ORFs prediction, and has better integration with SQANTI3, thanks to being coded in python. So far, the team is happy with the new results, and more changes are being cooked. To spread part of the new developments of the SQANTI-verse through SQANTI-Tusco, Tian gave the a super seminar as part of the program of Theoretical and Computational Systems Biology of the I2SysBio.

We shouldn’t forget our first step back into the wet-lab… In June we received the first sequencer of the lab! After Carolina obtained a grant from the “Oxford Nanopore Grant Programme” to purchase a PromethION P2 Solo, we received the sequencer on the 24th of June. We are now looking forward to setting it up and start our own sequencing experiments. Through this program, Carol also attended the PromethION Users Club Meeting from Oxford Nanopore in Barcelona on the 30th of June, where I not only learned about tips and tricks to set up the technology, but also had the chance to catch up with our collaborator Silvia Carbonell, she is a star in all things Nanopore and also gave us a lot of feedback to set up the technology. 

Just when the month was about to finish, Lucia stayed with us for three days. She is part of the Master on Integrative Synthetic Biology, where they do every month a stay in different CSIC centers. She was under the guide of Pablo and Tian, who tried to fry her brain with the SQANTI-verse, but she was able to take it in and even enjoy it. She even got to do some hands on with the new TD2 results and look for transcripts that were outliers. In the end, we were all super happy with her time with us.

We survived the hotter-than-usual June, and added our grain of salt in the celebrations of Pride 2025, showing our support to the community, to wrap up the month!