Group Leader, PI. Interested in developmental genetics, chromatin architecture, genome regulation, and computational biology

Joined November 2009
When I created Twitter account, I promised myself not to post anything unrelated to science. However, the current situation goes beyond all conceivable limits. Unfortunately, I can't change anything, but at least I can say it here: THE WAR MUST BE STOPPED.
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1/12 CTCF has updated its LinkedIn again! Our preprint tracks CTCF's “career” across Bilateria. From DNA-binding to transcription regulation & genome architecture. Read it: biorxiv.org/content/10.64898… And back-to-back work from Darío Lupiáñez's group: biorxiv.org/content/10.64898… vvv
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11/12 So CTCF was always associated with transcription regulation in bilateria; during evolution, it didn't quit its old job; it took on more responsibilities.
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The next AlphaFold won’t design drugs. It will find the right biology to target. Evolution has already run billions of years of experiments and genomes are the compressed record. The big question: How much phenotype is already latent in the language of evolution? genomicintelligence.substack… #Genomics #AIforBiology #DrugDiscovery #FoundationModels
🤖 Made with AI
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This Monday (Aug 10) I’ll give a webinar with @PhysaliaCourses on applying @GenomeLayer models to biology. From gene finding to genomic function prediction and regulatory DNA design for gene therapy, including workflows driven with Codex prompts. physalia-courses.org/courses…
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Scientific agents can now call Genomic Intelligence models @GenomeLayer directly from Biomni Lab and ClawBio to Claude, Cursor, and any MCP client. One genomic execution layer for promoters, expression, splicing, and genetic variants. Try it yourself: genomicintelligence.ai/blog/…
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One GLP-1 response variant became 229 new hypotheses worth testing We analyzed 2,734 DNA changes around GLP1R and found hundreds predicted to have larger effects, including rare variants that population studies may miss This is the opportunity for genomic AI: turning overlooked DNA into testable biology across drugs and diseases genomicintelligence.ai/blog/… #GLP1 #GenomicAI #DrugDiscovery
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Why does Ozempic work better for some people than others? A Nature study linked a GLP1R variant to greater weight loss. Our genomic models suggest a second mechanism: the variant may affect not only how the receptor works, but also how much of it the body produces. We then screened rare variants that GWAS can miss—collectively carried by an estimated 527M people worldwide. This is what genomic AI makes possible: moving from population-level association to individual, testable biological hypotheses. Read the study and try the workflow on your own genome: genomicintelligence.ai/blog/… #Genomics #GLP1 #PrecisionMedicine #AIforScience
🤖 Made with AI
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Genomic Intelligence models are now available in Biomni @phylo_bio ! They cover expression prediction from seq, promoters, splice sites & more To try them, head to Settings->External Integrations and enable Genomic Intelligence. API key: gi_ujbfpL9-RNRHk9HvKcANCZCylMzsjlsb
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The genome is becoming programmable through natural language We partnered with @PhyloBio to bring @GenomeLayer models into Biomni Lab so researchers can move from a biological question to regulatory DNA analysis, expression prediction, variant interpretation, and sequence optimization inside one agentic workflow Try it yourself ↓ genomicintelligence.ai/blog/… #AIForScience #Genomics #Biotech
One step closer to making genomic analysis directly accessible through scientific agents. @GenomeLayer partnered with @PhyloBio to bring genomic models into Biomni Lab. You can now use natural language to analyze regulatory DNA, predict gene expression, interpret genetic variants, and optimize biological sequences in reproducible workflows. Try it yourself: genomicintelligence.ai/blog/… #AIForScience #Genomics #Biotech #AgenticAI #Bioinformatics
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1/n We introduce new open benchmarks for ab initio gene annotation from DNA sequence alone: Gene segmentation only benchmark: huggingface.co/spaces/AIRI-I… Complete annotation benchmark: huggingface.co/spaces/AIRI-I… Paper: biorxiv.org/content/10.64898…
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I hope these benchmarks will be useful for groups developing DNA language models, gene prediction tools, and genome annotation pipelines. Especially communities around @ensembl, @GencodeGenes, @darwintreelife, @EBPgenome @genomeark, @SangerVGP, @VGP_GenomeArk, & @EarthBioGenome
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Would be very happy to see new models from the Tiberius/BRAKER, Helixer, SegmentNT/NTv3, Evo2 (@arcinstitute), AlphaGenome, Caduceus, HyenaDNA (@HazyResearch), DNABERT/GUE, and BEND (@WouterBoomsmaDK) communities on the leaderboard.
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