iiinova — where your digital self keeps evolving

Mariotti Genomics Lab @mariottilab.bsky.social · 16/07/2026

Congratulations to Nadya, the first PhD in our lab, for defending her thesis yesterday!!!

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Mariotti Genomics Lab @mariottilab.bsky.social · 01/07/2026

Looking forward to Martina Yordanova's talk in our department! If you're around, don't miss it!

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

We started this project thinking that stop codon readthrough was mainly about generating diverse C-terminal extensions to modulate protein functions. Our results suggest that SCR also boosts the amount of protein produced from an mRNA, pointing to a potential new and broad regulatory role.

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

Our biggest surprise: we expected abundant insect SCR to reflect overall inefficient translation termination. It doesn't: termination rate is very similar in insect and mammalian cells. The key difference is the response to SCR-promoting sequence elements,underscoring enhanced regulatory mechanisms.

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

Using a high-throughput reporter screen in Drosophila S2 cells, we identify stop proximal cis-acting sequence elements in these genes that are sufficient to trigger constitutive SCR for any stop codon. Surprisingly, the majority remain active in mammalian cells, yet at lower efficiency.

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

We map the regulatory landscape of SCR and find that it is far from uniform. Some genes undergo SCR constitutively across tissues and developmental stages, whereas others appear restricted to neurons. We also find evidence for distinct transcriptional and translational modes of regulation.

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

We identify ~1,400 genes with experimental evidence of SCR and bearing hallmarks of evolutionarily conserved, programmed SCR. They reveal characteristic sequence signatures, including specific stop contexts, GC-rich codon-optimized coding sequence, and conserved RNA structures near the stop.

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

How do you study a phenomenon of this scale? We combine ribosome profiling, comparative genomics, proteomics, and cell-based functional screening to characterize SCR genome-wide in Drosophila. Check if your gene does readthrough in our Atlas: mariottigenomicslab.bio.ub.edu/dmel_scr_atl...

mariottigenomicslab.bio.ub.edu

Drosophila Stop Codon Readthrough Atlas

Click on the grey cells in tables and you will get distribution plots. So you can compare selected value either with background (non SCR genes) or with genes predicted to have SCR based on evoultionary conservation (Jungreis detected)

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Mariotti Genomics Lab @mariottilab.bsky.social · 16/06/2026

🧬 Excited to share our preprint: Regulatory landscape of widespread stop codon readthrough (SCR) in Drosophila 🪰 Stop codons supposedly mark the end of protein synthesis. Sometimes they don’t: >1,000 Drosophila genes undergo SCR, a process wherein translation continues past the stop.

doi.org

Regulatory landscape of widespread stop codon readthrough in Drosophila

In stop codon readthrough (SCR), ribosomes continue to translate past the stop. While programmed SCR is rare in mammals, it appears remarkably widespread in insects, yet its regulation and biological ...

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Facultat de Biologia UB @biologiaub.bsky.social · 28/02/2026

🔬 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 f.mtr.cool/onjapobfyu

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Mariotti Genomics Lab @mariottilab.bsky.social · 14/01/2026

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

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Mariotti Genomics Lab @mariottilab.bsky.social · 14/01/2026

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.

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Mariotti Genomics Lab @mariottilab.bsky.social · 14/01/2026

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.

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Mariotti Genomics Lab @mariottilab.bsky.social · 14/01/2026

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.

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Genetics UB @geneticsub.bsky.social · 09/01/2026

🧬 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

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Lluis Montoliu @lluismontoliu.bsky.social · 08/01/2026

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…

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Genetics UB @geneticsub.bsky.social · 29/12/2025

🧬 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.

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Genetics UB @geneticsub.bsky.social · 19/12/2025

📢 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

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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...

github.com

GitHub - pyranges/pyranges_1.x: Pyranges: a Python framework for ultrafast sequence interval operations

Pyranges: a Python framework for ultrafast sequence interval operations - pyranges/pyranges_1.x

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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...

pyranges1.readthedocs.io

Command-line interface: pyranger — pyranges documentation

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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).

pyrangeyes.readthedocs.io

Pyrangeyes documentation — pyrangeyes documentation

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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:

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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!

pyranges1.readthedocs.io

Tutorial — pyranges documentation

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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.

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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.

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Mariotti Genomics Lab @mariottilab.bsky.social · 15/12/2025

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 🧬💻🐍

doi.org

Pyranges v1: a Python framework for ultrafast sequence interval operations

Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice interva...

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Mariotti Genomics Lab @mariottilab.bsky.social · 19/11/2025

I'm happy to announce that I obtained a tenured position at @geneticsub.bsky.social @biologiaub.bsky.social ! 🧬🎉

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Pedro Friedmann Angeli @angelifriedmann.bsky.social · 24/10/2025

calling "Acetylysine" the 21st amino acid is a declaration of war

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Genetics UB @geneticsub.bsky.social · 05/11/2025

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

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Mariotti Genomics Lab @mariottilab.bsky.social · 05/11/2025

Learn more on the wiki: 2025.igem.wiki/barcelona-ub/ Video presentation (15 min): video.igem.org/w/c6034b4e-8...

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Mariotti Genomics Lab @mariottilab.bsky.social · 05/11/2025

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...

video.igem.org

Barcelona-UB: switch scr (2025) [English]

Accessory Video for explanations https://2025.igem.wiki/barcelona-ub/index.html

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Mariotti Genomics Lab @mariottilab.bsky.social · 05/11/2025

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...

video.igem.org

Barcelona-UB: SCR Translational influence (2025)

SCR Translational influence https://2025.igem.wiki/barcelona-ub

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Mariotti Genomics Lab @mariottilab.bsky.social · 05/11/2025

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 👇

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Genetics UB @geneticsub.bsky.social · 28/09/2025

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

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Mariotti Genomics Lab @mariottilab.bsky.social · 26/09/2025

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!

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EDRC2025 @edrc2025.bsky.social · 25/09/2025

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!

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EDRC2025 @edrc2025.bsky.social · 24/09/2025

Only a few hours left before our meeting starts! Are you travelling to #EDRC2025 now? Let us know by using the oficial #EDRC2025 hashtag!

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Mariotti Genomics Lab @mariottilab.bsky.social · 02/09/2025

Here's an interesting paper @natmethods.nature.com introducing the term "Translon", filling a terminology gap in the field of gene expression. Kudos to Pasha Baranov for leading this initiative and gathering many contributors (including myself) for an healthy discussion on fundamental principles 👏

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Mariotti Genomics Lab @mariottilab.bsky.social · 01/06/2025

We had lots of fun at the #FestaCiènciaUB with our workshop on gene expression! It seems participants loved it too ❤️🧬! Thanks to the lab members, including the iGem UB team, and all the organizers of the event 👏

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Genetics UB @geneticsub.bsky.social · 30/05/2025

🧬 Un any més, la secció de @geneticsub.bsky.social es suma a la #FestaCiènciaUB amb un munt de tallers que podeu visitar fins demà a la @ub.edu 🎉 No us ho perdeu!

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Universitat de Barcelona @ub.edu · 30/05/2025

#LaUBDivulga | 🧪 Més de 1.800 infants han visitat l’XI #FestaCiènciaUB i han descobert, de la mà dels investigadors #UB, la recerca que fem a la Universitat. 🤩 I dissabte, 31 de maig, vine amb la família! T’hi esperem de 10:00 a 14:00! 👉 web.ub.edu/ca/web/actua... @ubdivulga.bsky.social

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Mariotti Genomics Lab @mariottilab.bsky.social · 30/05/2025

Today and tomorrow you will find us at the Science Fest of UB #FestaCiènciaUB ! Come and play to our workshop and learn to decipher the code of life 🧬. Free entrance!

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Mariotti Genomics Lab @mariottilab.bsky.social · 03/04/2025

On my way to Sevilla! Looking forward to visiting the @cabd-upo-csic.bsky.social

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Reposted by Mariotti Genomics Lab

Alfonso Valencia @alfonsovalencia.bsky.social · 22/01/2025

Interesting large scale study on the thrust on scientist and their role in society around the world. Note: Spain is by far the European country scoring higher - why this is not translated into better conditions and funding ? - a mistery. www.nature.com/articles/s41...

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Genetics UB @geneticsub.bsky.social · 13/01/2025

🧬 Our mini-symposium on "New advances in CRISPR-Cas" returns on January 24th at @geneticsub.bsky.social ! It's open for attendance without registration. Talks by Anna Cereseto, @robertasu.bsky.social, Annarita Miccio, and Josep Mª Casacuberta!

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