Lorenzo Calviello

Happy too see this peer reviewed! A project stemming from work with @stephenfloor and @TheSilverLab, we focus on mRNAs who seem upregulated while translation is down or unchanged. If you're into RBPs, mRNA stability, the almighty GC content and much more, this one's for you!

Exciting times - two more positions in my lab to work on poly(A) tail length regulation in mammalian (and not only!) cells. More details on the science and links to the positions (1 technician + 1 postdoc) below

🧬 What controls how long an #mRNA molecule survives inside a cell? 🔬 Our @ILegnini Group leads POLARIS, a new €1.35M FIS3 project exploring how poly(A) tails regulate mRNA stability and gene expression. Read more 👉 humantechnopole.it/en/news/polari…

Looking for bioinformatician for exciting projects across the Centre of Genomics at the Human Technople. We also work with the FANTOM6 Consortium and other international consortia/projects. Details in the call. careers.humantechnopole.it/job/Bioinforma…

🧬 What if hidden proteins could become new immunotherapy targets? 💻 🔬 Our @translatomics Group secures a @AIRC_it My First Grant to uncover cancer-specific proteins in colorectal cancer with computational & organoid models humantechnopole.it/en/news/from-r…

@emi_aeruginosa Perfect for our next journal club, congrats!

Our latest work describing how viral infections drive functional remodeling of ribosome-associated factors is out as a preprint! biorxiv.org/content/10.648…

🔬 Inside the cell’s #RNA control system: can cells sense and fine-tune their own mRNA levels? 🧬 Our @Fabio_Marcuccio has been awarded a #MSCA Postdoctoral Fellowship to explore how RNA stability is regulated, with long-term implications for therapies. humantechnopole.it/en/news/inside…

📣Following my PhD experience with @SENTINEL_ITN, I’m very happy to announce that I’ve been awarded a Marie Skłodowska-Curie Postdoctoral Fellowship for my project RNAhome🧬 Excited to continue my journey with @REA_research and @HorizonEU at @humantechnopole in beautiful Milan!🏔️

“Show me the mechanism of action.” “Uh. from the p-p-perturb seq? right here. Knocks down Gene X, and the cells shift into Cluster 7." “You used fkn UMAP again. FUCK. Zoom in.” “Sorry?” “Zoom. The fuck. In.” “…Okay.” “Do you see it?” “…See what?” “He doesn’t see it. The cell biology postdoc from Stanford does not know how to see a cell. He stares at a two-million-cell embedding and doesn’t see the conflations he just planted in my S3 bucket. WHERE is the temporal resolution?” “The… what?” “Where is the time? You hit the cell with a perturbation and you measured it once. Once. That’s not a mechanism. That’s a fucking POSTCARD!” “We sequenced at 72 hours. That’s standard.” “Standard is not the same as correct. You are aliasing causality. You compressed a dynamic process into a static endpoint and you’re think you will cure metastatic cancer.” “But the differential expression is significant.” “WOW! DIFFEWENTIAL EXPRESSION IS SIGNIFICANT! WOW! WHEN THE FUCK IS IT NOT. Yes, because statistics is Mario Kart. A fantasy land where causality is optional and variance disappears if you collect enough cells. Real biology has inertia. Feedback. Competing pathways. Do you understand the difference between correlation and mechanism? Or did you flunk out of STAT 101?” “…I mean, we saw Gene X regulate Pathway Y.” “No. You saw Pathway Y exist in the same cell after you kicked it down the stairs and waited three days. That’s not even a crime scene, you dimwit. That is a post-mortem autopsy.” “The model inferred a trajectory--” “STOP the buffoonery. Do not blame the model. The model is a mirror. In this particular case, you can see it mirrors the clusterfuck you just created in my biosafety cabinet. If the reflection is warped, it’s because your measurement is warped.” “Pull up the raw counts.” “…Okay.” “Scroll. Cell 14,982. Read it to me. What does it say?” “Uh… mitochondrial genes up, ribosomal genes down-” “And?” “…And stress response markers?” “Yes. Because you poisoned the cell and waited long enough for it to panic. Where is the early signaling? Where is the metabolic inflection? Where is the first irreversible decision?” “We don’t capture that.” “Exactly. You built a platform that cannot see the mechanism. YOUR PLATFORM IS FUCKING BLIND.” “The virtual cell...showed the perturbation effect cleanly.” “Yes. because your VIRTUAL CELL IS VIRTUAL. it assumes the cell is a bag of transcripts. Do you think metabolites show up? OR AN ISOFORM? AN ISOFORM, THAT WILL DEGRADE IN THE CELL BEFORE YOU EVER REACH YOUR SENSOR? THAT ONE? YOU THINK THAT'S HOW CELLS WORK?” “So what do you want me to do?” “Delete the atlas.” “What?” “Delete it. The whole thing.” “But that’s the core result.” “It’s three weeks of garbage narrative built on a blind instrument. Delete it.” “…Now what?” “Now you rebuild the measurement. You observe the cell while the perturbation propagates. You track chemistry, not just transcripts. You capture the first divergence, not the final corpse.” “That’s… not perturb-seq anymore.” “Exactly.” door slams

@OdedRechavi @cshperspectives @openrxiv @biorxivpreprint @qedScience So now we get better reviews from bioRxiv than fancy journals? What a time to be alive

Let's go! Super excited to partner with @cshperspectives and the fantastic @openrxiv @biorxivpreprint team - Preprints have been the best thing that happened to science publishing during my lifetime, and we're happy @qedScience can make preprints do more 👊

@AndrewHulshult Whatever conceived this will never be broken, take care man! open.spotify.com/track/0hC8wXTF…

Was recently diagnosed with ADHD/anxiety and other fun expansion packs that come with it. Started on some light meds until I feel like I can get a grip on things without them. I'm not bummed out or anything. I'm relieved that there is a way to at least push back on the "noise".

Online Now: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome dlvr.it/TN0GcP

When you want to fry an egg but also have to do data-driven integrative research

@betulland Movements - Solar Field open.spotify.com/album/26sqA3Kt… Light Years - Stellardrone open.spotify.com/album/6uQHo7fe… Hydroponic Garden - Carbon Based Lifeforms open.spotify.com/album/4cxA3mCC…

Looking for spacey/cosmic techno tracks to run to, any suggestions? Or is this too niche?

@mitchguttman @CellCellPress @jimmykguo Amazing method and paper! Would it be possible to obtain bigwigs of binding profiles for each RBP?

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @CellCellPress, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. sciencedirect.com/science/articl…

The EU initiative has crossed 1.25 million signatures! I think 250k is the current record for invalid signatures thrown out on other initiatives, so we MIGHT be safe, but I could see us breaking that record also. The more margin we get, the better! eci.ec.europa.eu/045/public/#/s…

Neural Cellular Automata (NCA) are a new approach combining AI with mechanistic modelling. We designed a novel NCA architecture to handle the stochasticity of biological tissues. These can be trained on spatial 'omics data to *learn the rules* of normal and cancer growth.

📄 In this work, we try to bridge two parallel research areas: the well-established literature on agent-based modeling in biological systems and recent advances in learning update rules in CA from data with autodifferentiation. arxiv.org/abs/2506.20486

@IwasakiLabRIKEN Wonderful work as always! Any plans to make the GEO open soon? ncbi.nlm.nih.gov/geo/query/acc.…

Our latest preprint is online! Local translation atlas across organelles is revealed!

@metalsucks Amazing!

Igorrr Serve Up Some “Blastbeat Falafel” with a Little Help From Trey Spruance and Timba Harris metalsucks.net/2025/05/21/igo…

Americans: Soccer is boring Soccer: