It’s beginning to look a lot like Christmas… Which means finally getting some holidays and turning off the computer! In the ConesaLab, we are excited to take a well-deserved small break until next year. These last two months have been a blast, full of activities and exciting discoveries.
To start with, Ana, Fabián, and Julen kickstarted the month of November by attending the BioHackathon Europe in Berlin (well, in a hotel near a lake, near a forest, near Berlin…). A whole week full of coding and fun! Ana led a hacking project focused on analyzing the latest methods for transcriptome reconstruction using long reads—a much-needed analysis after the success of the original LRGASP initiative. In Julen’s own words: “It was a fantastic opportunity to contribute to a critical area of bioinformatics and advance our understanding of long-read sequencing technologies.” Fabián, on the other hand, fell in love with the surroundings. Julen had to literally stop him from buying a nice property with lake and forest views. Overall, everyone came back to the lab super happy with the experience.
It's VEGA
Ana became the happiest of the PIs in the whole city because finally her beloved Vega has arrived. For those of you who don’t know, Vega is the latest sequencing machine from PacBio. This resulted in overexcitement, and you could read the fear in Virtu’s face thinking about all the sequencing that is coming her way. These machines will be shared by the UV and CSIC, one of the best things that can be done within science: collaboration. As well, the TELLME initiative has been approved by ELIXIR, and funding is coming to our lab so we can get to work on developing an AI service that can generate clear and unbiased explanations on complex systems biology and multi-omics models. Now, we are closer to the day where scrolling through thousands of papers to make sense of your un-understandable metabolic map will be over.
Another important remark from November was our step up the sustainability ladder for the lab: we achieved the Bronze certification of the GreenDiSC initiative! Fabián, as always, did amazing work in forcing us to keep our directories clean and tidy, and optimizing the resources we use while working. This is one of those opportunities to remind us how we can contribute to saving our planet with the small things we do in our everyday lives. Small steps make for a big impact.
More steps were taken in November, this time towards cooler science. We officially announced the seminar we are organizing with the LongTrec Network. Next summer, the city of Valencia will host the first-ever symposium solely dedicated to long-read transcriptomics. A whole 4 days full of incredible speakers and posters to showcase the growing community of this vital field in the genomics world. If you think that you know nothing about the topic but would still like to participate, don’t worry, we got you covered! The week before, we are also hosting a course on long-read transcriptomics—the perfect kickstart. Just think about it: three days of learning about the topic, a weekend of sun, beach, and paella, and then, to finish, a super-duper cool symposium. Now you know what to ask Santa for (an early inscription to everything!).
November ended with Pablo making his way to the lively city of Sevilla. He spent the whole of December doing a stay at the Andalusian Center for Developmental Biology (CABD) with Ana Rojas’s group. There, he learned almost everything there is to know about Protein language models, and he will now try to apply them to the SQANTI-verse. Who knows, perhaps in the future you will see a SQANTI-flamenco around. This has been a great experience, where he expanded his network of peers and learned many useful techniques and ways of analyzing data.
Meanwhile, things have not been idle in Valencia. The main highlight has been Virtu’s adventure… She went full mission impossible mode into Italy to rescue Tian’s cells. Carol, on the other hand, published the beta-release of her latest tool: SQANTI-browser. Tired of having to work with IGV and not being able to put the super-duper-cool-and-cute Conesa Colors on the isoforms, she decided to take matters into her own hands and start working on a plugin for the UCSC Genome Browser. With this new commodity, you can visualize your transcripts and the orthogonal data of SQANTI3 in real-time, as well as dynamically filter your tools. Go on and give it some love, and do not hesitate to report any issue you find or feature you would like! Let’s build together.
To finish off, Fabián has published his preprint on “To join-and-call or to call-and-join”. I know y’all have always asked yourselves this question, and I won’t spoil the answer for you, so please, go and give it a read to find out—the perfect Christmas cozy reading! 🙂
From the ConesaLab we want to wish you a Merry Christmas, Happy Holidays, and a Happy New Year 2026. We will be celebrating our famous Christmas Party after the vacation time this year, once we are all together. Enjoy this time with your loved ones and regain energy to push science even further in 2026!