iiinova — where your digital self keeps evolving

Timothy P. Jenkins @tpjenkins.bsky.social · 31/07/2025

🧪🐍 AI vs venom! Our Nature paper with David Baker shows AI-designed proteins can block deadly snake toxins. Now featured by Reuters! 🎥 ✅ 80–100% survival in mice 💸 Cheap, fast, scalable 🌍 A step toward better antivenoms 📄 www.nature.com/articles/s41... 🎬 youtu.be/gnvEDMEr2mc

youtu.be

AI-designed antivenom could offer new hope for snakebite victims | REUTERS

YouTube video by Reuters

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Timothy P. Jenkins @tpjenkins.bsky.social · 24/07/2025

We believe this approach can accelerate the development of safer, more effective immunotherapies for patients. And a special thank you to the talented @mfernandezquintero.bsky.social & Johannes Loeffler for the stunning graphic! 🎨 #CancerResearch #Immunotherapy #AI

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Timothy P. Jenkins @tpjenkins.bsky.social · 24/07/2025

This was a monumental team effort bringing together immunology, computational biology, and structural biology. A huge congratulations to the incredible teams at DTU HealthTech, DTU Bioengineering, & @scripps.edu and to all my brilliant co-authors, especially @Kristoffer Haurum Johansen.

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Timothy P. Jenkins @tpjenkins.bsky.social · 24/07/2025

Our platform's key achievements include: ⚡️ Speed: A rapid 4-6 week pipeline from computer design to validated lab result.  🎯 Precision: An AI-driven process to screen for specificity & reduce off-target risks.  🤝 Personalization: It works even for a patient's unique tumor mutation.

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Timothy P. Jenkins @tpjenkins.bsky.social · 24/07/2025

In this work, we designed completely novel proteins, or ‘minibinders,’ from scratch. 🤖 These act as a high-precision guidance system, leading a patient's own T-cells (black) to recognize and destroy cancer cells (red) with remarkable accuracy. #ProteinDesign #GenerativeAI

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Timothy P. Jenkins @tpjenkins.bsky.social · 24/07/2025

Thrilled to announce our paper, "De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells," is officially out in @science.org! We used generative AI to build a 'GPS' for immune cells to hunt cancer. Read it here: doi.org/10.1126/scie...

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Timothy P. Jenkins @tpjenkins.bsky.social · 16/07/2025

While I’m bouncing between emails and desperately waiting for my holiday, it’s good to know at least something in the lab is holding it together. Thermal stability might not be glamorous, but it’s underrated. Designerbodies: even when things get heated, still doing their job ;)

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Timothy P. Jenkins @tpjenkins.bsky.social · 11/06/2025

Designing binders instead of screening for months? Can’t wait to disappoint reviewers in new and innovative ways.

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Timothy P. Jenkins @tpjenkins.bsky.social · 11/06/2025

At AffinityAI we’re moving from “finders keepers” to “designers binders”, one generative model at a time. If you could have a binder to anything, what would it be? (Proteins, obscure signalling pathways, that one reviewer who never gets back to you…;)

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Reposted by Timothy P. Jenkins

AffinityAI @affinityaibio.bsky.social · 02/06/2025

Ægget redefined the lounge. We're redefining what it means to design a protein. At AffinityAI, we combine Danish design sensibilities with precision molecular engineering. Elegant. Efficient. Engineered to bind. 🧬 Discover how we’re reshaping molecular function: www.affinityai.bio

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Timothy P. Jenkins @tpjenkins.bsky.social · 30/05/2025

💡 Curious about: – How generative AI is transforming protein research? – Why mass spec is such a rich (but messy) playground for AI? – What it takes to go from spectrum to sequence to structure? Give it a listen 🎧

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Timothy P. Jenkins @tpjenkins.bsky.social · 30/05/2025

🎧 Had the pleasure of joining Anders Høeg Nissen on the AI Denmark Podcast to talk about how we’re using AI to crack the protein code 🧬 Catch my segment from 9:30 (and yes — it’s in English 😉) 🎙️ open.spotify.com/episode/4g3R...

open.spotify.com

AI giver proteinforskningen turboboost

AI Denmark · Episode

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Timothy P. Jenkins @tpjenkins.bsky.social · 16/05/2025

Great to see #AffinityAI represented by Esperanza and Oliver at the DTU Startup Day 💪 Lots of interest in what we’re building, especially the fact that we deliver #real #reagents rather than just #AI predictions. Excited for what's to come!

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Timothy P. Jenkins @tpjenkins.bsky.social · 14/05/2025

🚨 We’re hiring a PhD student! 🚨 Join us at DTU Bioengineering + collaborators Messoud & Håkan Ashina + Esperanza Rivera de Torre to bring preventative migraine therapeutics from 💻 to 🧠 🔗 Apply: lnkd.in/dCRU_EN3 🔍 Project: lnkd.in/dbpi8MwX

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Timothy P. Jenkins @tpjenkins.bsky.social · 12/05/2025

🚨 Big news! We’ve received a NovoNordisk Foundation Tandem Grant for #MIGRAINE — designing #AI-powered #GPCR-targeting biologics for chronic migraine. From computer to human in 4 years. Proud to team up with Messoud and Hakan Ashina, as well as Esperanza Rivera de Torre! 🧠 + 💊 + 🧬 = new hope.

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Timothy P. Jenkins @tpjenkins.bsky.social · 08/05/2025

We’re already supporting: – Proteins that are hard to purify – Assays that demand specificity – Targets that need quantitative detection Please reach out if you want to hear more. #StartupLaunch #Founder #AffinityAI

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Timothy P. Jenkins @tpjenkins.bsky.social · 08/05/2025

What we offer: – Designerbodies™ with pM–nM affinity – ARCANE™ designs for affinity, stability, and expression – RAVEN™ screens candidates at scale Built for diagnostics, therapeutics, and biotech pipelines. #AIinBiotech #SyntheticBiology

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Timothy P. Jenkins @tpjenkins.bsky.social · 08/05/2025

🚀 Big news: AffinityAI is live We’ve built a platform for custom protein binders, AI-designed, in vitro validated, and entirely animal-free. I'm proud to lead this as CEO. 🔗 affinityai.org #AffinityAI #Biotech #ProteinEngineering

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Timothy P. Jenkins @tpjenkins.bsky.social · 09/04/2025

3/ v1.1 generalises well: In a GluC-treated HeLa dataset, we reached 81.3% peptide recall—higher depth, same model. Improved confidence metrics = better precision, fewer false positives, more IDs. Code: bit.ly/43ExRGI

bit.ly

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Timothy P. Jenkins @tpjenkins.bsky.social · 09/04/2025

2/ What’s new in InstaNovo v1.1? 🧬 +13.5% recall 🎯 +42.6% more exact PSMs 🔍 145% more peptides & 35% more proteins @ 5% FDR 🧪 Support for 7 PTMs: phosphorylation, deamidation, carbamylation, ammonia loss, oxidation, acetylation, carbamidomethylation Paper: bit.ly/3XBeJFh

bit.ly

InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments - Nature Machine Intelligence

InstaNovo, a transformer-based model, and InstaNovo+, a multinomial diffusion model, enhance de novo peptide sequencing, enabling discovery of novel peptides, improved therapeutics sequencing coverage...

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Timothy P. Jenkins @tpjenkins.bsky.social · 09/04/2025

1/ 🚀 InstaNovo just got a major upgrade. Our Nature Machine Intelligence paper with @instadeepai presents v0.1—but while the paper was under review, we kept building. Now releasing InstaNovo v1.1, with major gains. Blog: bit.ly/4lircYB 🧵

bit.ly

Introducing the next generation of InstaNovo models

Since our InstaNovo paper is now published, we’d like to share an update on what we’ve been working on while our manuscript was under review. With the release of our preprint over a year ago, we were ...

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Reposted by Timothy P. Jenkins

Andreas H. Laustsen-Kiel @andreaslaustsen.bsky.social · 20/03/2025

I am very excited to announce the publication of this new research article on "Orally delivered toxin–binding protein protects against diarrhoea in a murine cholera model", which is a topic I sincerely care about: nature.com/articles/s41... Thanks to all co-authors and funders!

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Reposted by Timothy P. Jenkins

Andreas H. Laustsen-Kiel @andreaslaustsen.bsky.social · 31/03/2025

Excited to share a new paper in Nature Machine Intelligence that I had the pleasure of contributing to, alongside great collaborators from Europe! InstaNovo is a deep learning model for de novo peptide sequencing — pushing proteomics beyond databases. 📄 www.nature.com/articles/s42...

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Timothy P. Jenkins @tpjenkins.bsky.social · 01/04/2025

Thanks for sharing our work!🎉

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Reposted by Timothy P. Jenkins

Jorge Bravo Abad @bravo-abad.bsky.social · 31/03/2025

Eloff et al.’s InstaNovo uses transformers plus a diffusion refinement to perform high-throughput de novo peptide sequencing. It recovers more novel peptides at low FDR, outperforms current tools, and extends proteomics beyond database limits. www.nature.com/articles/s42...

nature.com

InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments - Nature Machine Intelligence

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Reposted by Timothy P. Jenkins

Scott McGrath @smcgrath.phd · 31/03/2025

New AI tools InstaNovo and InstaNovo+ can now detect proteins previously beyond reach, opening doors in cancer research and disease biology. Early results are promising, though 5% may be false positives. 🧬💻

sciencenews.org

AI is helping scientists decode previously inscrutable proteins

A new set of artificial intelligence models could make protein sequencing even more powerful for better understanding cell biology and diseases.

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Timothy P. Jenkins @tpjenkins.bsky.social · 01/04/2025

Thanks for sharing our work!🎉

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Timothy P. Jenkins @tpjenkins.bsky.social · 01/04/2025

Thanks to our funders: 💙 Novo Nordisk Foundation 💡 ERC 🔬 Wellcome Trust 🧪 PRO-MS 🏛️ Villum Fonden #AI #Proteomics #DeNovoSequencing #MassSpec #InstaNovo #NatureMachineIntelligence

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Timothy P. Jenkins @tpjenkins.bsky.social · 01/04/2025

These models boost peptide discovery by 50%+ 📈 over prior tools. Applications include: 🧬 Personalised cancer immunotherapy ⚗️ Direct protein sequencing 🦠 Pathogen discovery in complex samples

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Timothy P. Jenkins @tpjenkins.bsky.social · 01/04/2025

We developed InstaNovo & InstaNovo+, combining transformers 🧠 with diffusion models 🔁 to solve one of proteomics' hardest problems: 🚫 No genome? No problem. ✅ De novo sequencing from raw spectra — fast & accurate.

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Timothy P. Jenkins @tpjenkins.bsky.social · 18/02/2025

This is an interdisciplinary project bringing together DTU Bioengineering, Compute, Electro, Health Tech, and Novo Nordisk. Let’s shape the future! Apply now & join us! 🚀 #AI #Biologics #DTU #NovoNordisk

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Timothy P. Jenkins @tpjenkins.bsky.social · 18/02/2025

🔬 Postdoc in AI-Driven Binder Design (DTU Compute) 🔗 efzu.fa.em2.oraclecloud.com/hcmUI/Candid... 🛠️ Postdoc in Closed-Loop Protein Design (DTU Bioengineering) 🔗 efzu.fa.em2.oraclecloud.com/hcmUI/Candid... (4/5)

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Timothy P. Jenkins @tpjenkins.bsky.social · 18/02/2025

🧫 PhD in AI-Driven Protein Design (DTU Bioengineering) 🔗 efzu.fa.em2.oraclecloud.com/hcmUI/Candid... 🤖 Postdoc in Robotics for Protein Design (DTU Electro) 🔗 efzu.fa.em2.oraclecloud.com/hcmUI/Candid... (3/5)

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Timothy P. Jenkins @tpjenkins.bsky.social · 18/02/2025

🔬 PhD positions: 🧪 PhD in Knowledge Systems & Robotics (DTU Electro) 🔗 efzu.fa.em2.oraclecloud.com/hcmUI/Candid... 🧬 PhD in AI Oracles for Binder Optimization (DTU Health Tech) 🔗 efzu.fa.em2.oraclecloud.com/hcmUI/Candid... (2/5)

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Timothy P. Jenkins @tpjenkins.bsky.social · 18/02/2025

🚀 Tackling one of life science’s biggest challenges: AI-driven biologics design! Excited to lead #DTU’s collaboration with #NovoNordisk to build a closed-loop #AI platform for binder design & optimization. Even better? We’re hiring! 📢 6 open positions! 🎉 (1/5)

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Timothy P. Jenkins @tpjenkins.bsky.social · 21/01/2025

Thanks for sharing our research!

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Timothy P. Jenkins @tpjenkins.bsky.social · 21/01/2025

Thanks for sharing our work! Might have something more qantum for you soon ;)

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Timothy P. Jenkins @tpjenkins.bsky.social · 21/01/2025

Thanks for sharing our research!

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Timothy P. Jenkins @tpjenkins.bsky.social · 19/01/2025

Thanks for sharing our research 🎉

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