Luca Pinello
Computational methods for epigenetic, CRISPR genome editing and single-cell genomics. Associate Professor at MGH / Harvard Medical School. http://pinellolab.org
- 1/ Thrilled to share our DNA-Diffusion paper, co-led by Lucas Ferreira and @ssenan.bsky.social is now out in @NatureGenet! New experimental results: STARR-Seq validation across 3 cell types (episomal) and EXTRA-Seq for endogenous activation of AXIN2, a leukemia protective gene! x.com/lucapinello/...
- 2/ Previously, we showed DNA-Diffusion generates sequences that recapitulate endogenous grammar and have greater in silico activation potential than training sequences. Now, using STARR-Seq, we've experimentally validated these predictions.
- 3/ Despite not being trained on expression data, our top DNA-Diffusion sequences consistently outperformed the strongest validated genomic enhancers experimentally.
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View full thread10/ We're continuing to explore generative AI to decode gene regulation through regulatory element modeling and experimental validation, building the next generation of precision gene therapies. If this work excites you or you want to collaborate, send us a message!
- Reposted by Luca PinelloWe are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n
- Reposted by Luca PinelloVery proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!
- We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)
- 🚨 Exciting opportunity! The Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard is recruiting exceptional postdocs for 2026 at the intersection of ML/math and biomedicine. Shape the future of computational biology 🧵👇
- The mission: Create the theoretical & algorithmic foundations to understand the programs of life across scales. You'll choose mentors from faculty across @broadinstitute.org, @mit.edu and @harvard.edu and collaborate across these amazing institutions.
- What they're looking for: ✅ Strong background in ML, statistics, or applied math ✅ Drive to push biomedical research frontiers ✅ Computational/theoretical method development skills Biology experience? Helpful but NOT required! They value diverse perspectives.
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View full threadApplications are open NOW! Review starts December 22, so don't wait. Apply here: academicjobsonline.org/ajo/jobs/30714 Questions? → ewsc-postdocs@broadinstitute.org Know someone perfect for this? Please RT and tag them! Let's help spread the word about this opportunity 🚀
- Reposted by Luca PinelloI'm happy to share that our gReLU package is now published in Nature Methods! www.nature.com/articles/s41...
- 🧬Excited to be at #ASHG2025! My lab is presenting 5 studies this week. Join us for talks and posters on #SingleCell #CRISPR, #DeepLearning & more! Thread below with all presentation details 👇
- @zainmunirpatel.bsky.social will also present this afternoon 2.30 to 4.30 Poster 4022W. Systematic benchmarking of computational methods for SVG detection. #spatial #ASHG2025
- Reposted by Luca Pinello15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
- Reposted by Luca PinelloI wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:
- Reposted by Luca Pinello🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: www.nature.com/articles/s42... 📖 News & Views: www.nature.com/articles/s42... 💻 Code: corneto.org 🧵 Thread 👇
- Reposted by Luca PinelloInterested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU
- Excited to be at #ISMBECCB2025! I'll be presenting at RegSys on "Learning the Regulatory Genome by Destruction and Creation" (Thursday 3:15PM in Room 11BC). I'm looking forward to connecting with both new and old friends throughout the conference! 🧬 #CRISPR #Genomics #Diffusion
- 🧵 It's raining outside, perfect for some vibe coding... ☔ So I built something cool with @anthropic.com's Claude Desktop! Introducing Claude Text Editor - edit ANY text, ANYWHERE on macOS with Claude's help. No more copy-paste gymnastics! 🚀
- The magic? Select text → Hit ⌥⌘. → Claude edits it → Auto-copies to clipboard! 📋 Works in Gmail, Slack, VS Code, Terminal - literally ANY app. It's like having Claude as your co-pilot, always ready. Built with @anthropic.com's MCP protocol 🔧
- Quick setup: git clone github.com/lucapinello/... cd claude-text-editor ./install.sh Import shortcut → Assign ⌥⌘. in System Settings → Done! 🎯
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View full threadThis changed how I write. No context switching, no copying - just select, shortcut, done! 👉 github.com/lucapinello/claude-text-editor Feedback welcome! Thanks @anthropic.com for MCP, Claude Code and Claude Desktop! What will you build on your next rainy afternoon? 🌧️✨
- Great to see it finally out —such a fantastic collaboration with @bkleinstiver.bsky.social , @rachelsilverstein9.bsky.social and team!
- In @nature.com we describe the use of scalable #proteinengineering & #machinelearning to predict millions of bespoke CRISPR enzymes, offering safer & more efficient genome editing tools 🧬🖥️ @rachelsilverstein9.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social www.nature.com/articles/s41...
- Reposted by Luca PinelloExcited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...
- Reposted by Luca PinelloOut today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n www.nature.com/articles/s41...
- 1/ 🎄 What’s the best gift under the tree for a computational biologist? 🎁 A new experimental assay that refines our view of gene regulation: ACCESS-ATAC! This creative idea from Richard Sherwood was developed collaboratively between his lab and mine. #Genomics www.biorxiv.org/content/10.1...
- 2/ Led by @timtimy.bsky.social @zhijianli.bsky.social and Ellie Gibbs, in this collaborative effort we harness the genome editing abilities of double-stranded DNA cytosine deaminase (Ddd) enzymes to overcome the resolution limitations of ATAC-seq.
- 3/ ACCESS-ATAC is simple to employ—we add a motif-agnostic Ddd enzyme (DddSs) to the standard Tn5 (ATAC) treatment of bulk or single-cell nuclei and use nextgen sequencing to read out chromatin accessibility. It adds no additional cost or effort to the conventional workflow.
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View full thread8/ We’d love your feedback and are excited to see ACCESS-ATAC adopted widely, inspiring new computational methods to harness the potential of this groundbreaking assay. Happy holidays! 🎄✨#ACCESSATAC #GeneRegulation
- Excited to be visiting Duke University to share insights on computational methods for single-cell genomics and CRISPR genome editing! Thank you for hosting me @yi-zhang-compbio.bsky.social 🙏
- Happening this week with special guest @lucapinello.bsky.social! Check out dmpi.duke.edu/duke-single-... for more information. We hope to see you all there 🧬
- Amazing new assay that allows testing of multiple DNA sequences, similar to MPRA, but in an endogenous setting. Incredible potential! Congrats @jk-swietek.bsky.social , @bartdeplancke.bsky.social and the entire team – grateful and lucky to be an early adopter. Check it out!
- Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale! www.biorxiv.org/content/10.1... A 🧵about what it can do: #SynBio #DeepLearning #GeneRegulation
- Attending #NeurIPS2024 this week and excited to connect with anyone exploring the intersection of #GenerativeAI, #DeepLearning, and #Genomics! I’m presenting our DNA-diffusion work at the LatinX in AI workshop today at 2:30—drop by if you’re around. Looking forward to meeting and learning from you!
- Excited to visit the @humantechnopole.bsky.social 🇮🇹today to share our work on computational approaches in functional genomics! Looking forward to discussions with amazing scientists about #singlecell, #CRISPR, and #syntheticbiology. 🧬Special thanks to @nicolesoranzo for the invitation 🙏
- Hello World! Very glad to be here and see the scientific community growing 🌱. It’s so refreshing to scroll through a feed full of exciting science! Looking forward to reconnecting with old friends and collaborators and meeting new ones. Let’s keep the science flowing! 🌟
