@mariottilab
Comparative genomics of gene expression lab at Universitat de Barcelona @geneticsub.bsky.social, led by Marco Mariotti. Interests: Translational recoding, bioinformatics, evolution, biotech, rare diseases. https://www.mariottigenomicslab.com/
🔬 Recerca UB | IV Jornada sobre Recerca en Malalties Rares. Una iniciativa de la Càtedra @ub.edu en Malalties Rares per compartir avenços en recerca.
📅 05/03
⏰ 09:00
📍 Aula Magna Ramon Parés, Facultat de Biologia
Acte obert a tot el públic
🔗 Més informació a https://f.mtr.cool/onjapobfyu
We will continue to advocate with public bioinformatics institutions to correct the annotation of selenoproteins, and eventually other cases of translational recoding, in public databases
To fix this issue, we present an upgraded version of our pipeline Selenoprofiles to automatically and accurately annotate selenoproteins at scale, matching manual curation quality. This may help to uncover overlooked biology tied to redox homeostasis and protein function.
We show that the great majority of vertebrate selenoprotein genes are misannotated in major public databases, meaning that they appear often missing or incorrect. Since annotations are a foundational resource upon which much of bioinformatics is built, these flaws impact many downstream analysis.
Selenoproteins are special proteins incorporating the amino acid selenocysteine, which play many essential biological roles, most notably for antioxidant defense. Selenocysteine is encoded by the UGA stop codon via translational recoding, making selenoproteins notoriously hard to annotate.
We're happy to share that our article "Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases" has been published:
journals.plos.org/ploscompbiol... #bioinformatics #recoding #selenoproteins #geneannotation Collab with @rodericguigo.bsky.social
🧬 Avui hem pogut gaudir del Simposi organitzat per @geneticsub.bsky.social sobre l’actualitat i les aplicacions de la tecnologia #CRISPR.
🗣️ L’acte ha comptat amb la participació dels ponents Anna Cereseto, @lluismontoliu.bsky.social, @vtoulis.bsky.social i Jean-Luc Gallois
Mañana estaré en Barcelona @biologiaub.bsky.social @unibarcelonathe.bsky.social participando en este simposio sobre actualidad y aplicaciones #CRISPR que organizan desde el departamento de @geneticsub.bsky.social junto a Anna Cereseto @vtoulis.bsky.social y Jean-Luc Gallois
ub.edu/portal/web/bio…
🧬 Year after year, @geneticsub.bsky.social remains firmly committed to continuous improvement.
🥇 This year has been highly rewarding and we look forward to the opportunities that 2026 will bring.
🎉 Thanks to all our members for your hard work and dedication! Together, we make a strong team.
📢 Our beloved symposium on #CRISPR is scheduled earlier than usual this year.
‼️ It's open without registration.
🗓 Mark your calendars: 9th January
📍 @biologiaub.bsky.social
👥 Organizers: Marco Mariotti, Marc Valls, Jesús Lozano, Mercedes Rocafort, from @geneticsub.bsky.social
We welcome feedback and contributions! Use GitHub to report issues or request features, and to follow our Continuous-Integration-compliant development: github.com/pyranges/pyr...
Wannabe contributors can find guidelines here: pyranges1.readthedocs.io/en/latest/de...
Pyranges works best as python library, but if you are a die-hard bash enthusiast that despises Python for some reason, you may access its functionalities from the command line, thanks to pyranger, a Pyranges wrapper based on Google Python Fire library.
pyranges1.readthedocs.io/en/latest/py...
Developed for max speed, Pyranges is also suitable for interactive data exploration, supported by convenient data access functions and intuitive Jupyter-compatible representations, including an early prototype of the companion graphics library Pyrangeyes 🐍👀(pyrangeyes.readthedocs.io).
Pyranges is ready for AI-assisted coding. It provides utilities to turn chatbots (e.g. ChatGPT, Gemini) into specialized coding assistants that can build readable Pyranges-based workflows from simple user requests. Guide: pyranges1.readthedocs.io/en/latest/tu...
Examples of AI-generated workflows:
Our library is designed to be user-friendly. The PyRanges object (representing a table of genomic interval-based data) is a subclass of pandas.DataFrame, allowing users to seamlessly leverage the familiar pandas API while combining it with Pyranges-specific methods. See how in our linked tutorial!
With big data, Pyranges is ~5× faster than BEDTools and ~3× faster than GenomicRanges, largely due to its Rust-based core engine, ruranges. In addition, Pyranges uses about half the memory required by these alternative tools. See the preprint for details.
This library allows you to read lots of diverse omics data (e.g. gene annotations, mapped NGS reads, chromosome and protein domains, in many file formats) and readily build complex pipelines by combining efficient methods for overlapping, counting, slicing intervals, and much more. Cheatsheet below.
Bioinformaticians, spread the word! Pyranges v1 is here: a Python framework for ultrafast sequence interval operations (aka genome arithmetic). Documentation (installation, tutorial, API, how-to-pages): pyranges1.readthedocs.io
Preprint: doi.org/10.64898/202... #bioinformatics #genomics #python 🧬💻🐍
I'm happy to announce that I obtained a tenured position at @geneticsub.bsky.social @biologiaub.bsky.social ! 🧬🎉
calling "Acetylysine" the 21st amino acid is a declaration of war
The iGEM UB team has come back from the competition with amazing results!🥇🤩
The team worked in developing a first prototype of an inducible stop codon readthrough riboswitch in Marco Mariotti's lab, here at @geneticsub.bsky.social 🧬1/2
Learn more on the wiki: 2025.igem.wiki/barcelona-ub/
Video presentation (15 min): video.igem.org/w/c6034b4e-8...
Skippit fuses a SECIS element (readthrough driver) with a theophylline-binding aptamer, yielding the first readthrough-based riboswitch.
By changing ligand concentration, you can flip between producing the canonical protein isoform or the readthrough isoform:
video.igem.org/w/rDM2PWQi8Y...
The project Skippit uses stop codon readthrough as a synthetic biology control knob. In readthrough, the ribosome occasionally ignores a stop codon and keeps translating — extending the protein instead of terminating it:
video.igem.org/w/9U3qG3tzMA...
Ecstatic about the success of our iGEM Barcelona-UB team at the 2025 Jamboree!
Gold medal 🥇 + 5 Special Prize nominations 🏆 + TOP TEN overall 🔝🤯
#iGEM2025 #iGEM
@geneticsub.bsky.social @biologiaub.bsky.social @ub.edu
Short explanation below 👇
The @geneticsub.bsky.social section, was well represented at #EDRC2025 @edrc2025.bsky.social by Nadia and Marco @mariottilab.bsky.social Sofia @sofiajaraujo.bsky.social and Núria @nuriacorbella.bsky.social @araujolabub.bsky.social and Ivan from the Serras’ lab who presented their results
Loving the #EDRC2025 @edrc2025.bsky.social conference so far! Great science and a terrific community. Tomorrow it's our turn to present: Marco will give a talk at the RNA biology session, while Nadya will present a poster shortly after! ❤️🧬🪰 Come and learn why stop makes sense in Drosophila!
3, 2, 1 and we are on!!! #EDRC2025 is starting! Welcome to our more than 740 participants from more than 40 countries! Thank you to all our sponsors!
Only a few hours left before our meeting starts! Are you travelling to #EDRC2025 now? Let us know by using the oficial #EDRC2025 hashtag!
The FlyBase situation has made the national news www.nbcnews.com/science/scie...