Timothy P. Jenkins
@tpjenkins.bsky.social
I am an Associate Professor at DTU and leading the Digital Biotechnology Lab. I am passionate about harnessing the power of modern technology such as AI Protein Design to innovate the biotechnological landscape and develop real world solutions.
🧪🐍 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
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
AI-designed antivenom could offer new hope for snakebite victims | REUTERS
YouTube video by Reuters
youtu.be
July 31, 2025 at 9:34 AM
🧪🐍 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
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
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...
We used generative AI to build a 'GPS' for immune cells to hunt cancer.
Read it here: doi.org/10.1126/scie...
July 24, 2025 at 6:27 PM
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...
We used generative AI to build a 'GPS' for immune cells to hunt cancer.
Read it here: doi.org/10.1126/scie...
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 ;)
Thermal stability might not be glamorous, but it’s underrated.
Designerbodies: even when things get heated, still doing their job ;)
Whether you're on holiday 🏖️ or still in the lab 🧪 trying to keep cool, at least one thing isn't melting: our DesignerBodies.
Generatively designed. Thermally stable ❄️ Reliable reagents that don’t need a break 💪
#ProteinDesign #AI #Biotech
Generatively designed. Thermally stable ❄️ Reliable reagents that don’t need a break 💪
#ProteinDesign #AI #Biotech
July 16, 2025 at 8:53 AM
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 ;)
Thermal stability might not be glamorous, but it’s underrated.
Designerbodies: even when things get heated, still doing their job ;)
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…;)
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…;)
We’re rethinking what a binding reagent can be.
Most antibodies weren’t designed, they were discovered. At AffinityAI, we’re flipping that logic: we build binders from first principles, guided by generative AI.
What targets would you be interested in having a binder to?
Most antibodies weren’t designed, they were discovered. At AffinityAI, we’re flipping that logic: we build binders from first principles, guided by generative AI.
What targets would you be interested in having a binder to?
June 11, 2025 at 7:35 AM
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…;)
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…;)
Reposted by Timothy P. Jenkins
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
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
June 2, 2025 at 1:49 PM
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
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
🎧 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...
Catch my segment from 9:30 (and yes — it’s in English 😉)
🎙️ open.spotify.com/episode/4g3R...
AI giver proteinforskningen turboboost
AI Denmark · Episode
open.spotify.com
May 30, 2025 at 8:35 AM
🎧 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...
Catch my segment from 9:30 (and yes — it’s in English 😉)
🎙️ open.spotify.com/episode/4g3R...
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!
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!
Great energy at DTU Startup Day 🎉
Big thanks to @DTUSkylab for bringing together researchers, investors, and innovators.
We had a blast sharing what we're building at AffinityAI.
#AffinityAI #DTUSkylab #StartupLife
Big thanks to @DTUSkylab for bringing together researchers, investors, and innovators.
We had a blast sharing what we're building at AffinityAI.
#AffinityAI #DTUSkylab #StartupLife
May 16, 2025 at 11:42 AM
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!
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!
🚨 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
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
May 14, 2025 at 9:33 PM
🚨 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
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
🚨 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.
🧠 + 💊 + 🧬 = new hope.
May 12, 2025 at 11:39 AM
🚨 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.
🧠 + 💊 + 🧬 = new hope.
🚀 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
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
May 8, 2025 at 12:44 PM
🚀 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
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
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
🧵
🚀 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
🧵
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 ...
bit.ly
April 9, 2025 at 3:58 PM
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
🧵
🚀 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
🧵
Reposted by Timothy P. Jenkins
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!
Thanks to all co-authors and funders!
March 20, 2025 at 1:24 PM
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!
Thanks to all co-authors and funders!
Reposted by Timothy P. Jenkins
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...
InstaNovo is a deep learning model for de novo peptide sequencing — pushing proteomics beyond databases.
📄 www.nature.com/articles/s42...
March 31, 2025 at 9:15 AM
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...
InstaNovo is a deep learning model for de novo peptide sequencing — pushing proteomics beyond databases.
📄 www.nature.com/articles/s42...
Reposted by Timothy P. Jenkins
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...
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...
www.nature.com
March 31, 2025 at 2:06 PM
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...
Reposted by Timothy P. Jenkins
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. 🧬💻
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.
www.sciencenews.org
March 31, 2025 at 3:27 PM
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. 🧬💻
🎉 Big news! Our paper is out in Nature Machine Intelligence!
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵
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...
www.nature.com
April 1, 2025 at 7:30 AM
🎉 Big news! Our paper is out in Nature Machine Intelligence!
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵
🚀 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)
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)
February 18, 2025 at 12:05 PM
🚀 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)
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)
Reposted by Timothy P. Jenkins
Nature research paper: De novo designed proteins neutralize lethal snake venom toxins
https://go.nature.com/4fZU9EI
https://go.nature.com/4fZU9EI
De novo designed proteins neutralize lethal snake venom toxins - Nature
Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible antivenom treatments.
go.nature.com
January 16, 2025 at 1:15 PM
Nature research paper: De novo designed proteins neutralize lethal snake venom toxins
https://go.nature.com/4fZU9EI
https://go.nature.com/4fZU9EI
Reposted by Timothy P. Jenkins
Deep learning methods aid in de novo design of proteins to neutralize lethal snake venom toxins in vitro and protect mice from a lethal neurotoxin challenge. www.nature.com/articles/s41... #NBThighlight
De novo designed proteins neutralize lethal snake venom toxins - Nature
Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...
www.nature.com
January 16, 2025 at 9:46 AM
Deep learning methods aid in de novo design of proteins to neutralize lethal snake venom toxins in vitro and protect mice from a lethal neurotoxin challenge. www.nature.com/articles/s41... #NBThighlight
Reposted by Timothy P. Jenkins
This pretty much settles it: we're entering the era of low-cost, on-demand binders for everything
Excited to see what people build now that "inject a llama with some junk and bleed it a month later" is no longer the cutting-edge tech
www.nature.com/articles/s41...
Excited to see what people build now that "inject a llama with some junk and bleed it a month later" is no longer the cutting-edge tech
www.nature.com/articles/s41...
De novo designed proteins neutralize lethal snake venom toxins - Nature
Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...
www.nature.com
January 15, 2025 at 9:04 PM
This pretty much settles it: we're entering the era of low-cost, on-demand binders for everything
Excited to see what people build now that "inject a llama with some junk and bleed it a month later" is no longer the cutting-edge tech
www.nature.com/articles/s41...
Excited to see what people build now that "inject a llama with some junk and bleed it a month later" is no longer the cutting-edge tech
www.nature.com/articles/s41...
Reposted by Timothy P. Jenkins
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
De novo designed proteins neutralize lethal snake venom toxins - Nature
Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...
www.nature.com
January 15, 2025 at 8:25 PM
EXTREMELY cool and demonstrates clearly the promise of deep learning + bio.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Timothy P. Jenkins
Loved talking to @tpjenkins.bsky.social about this work 🐍
🚨AI designs ‘breakthrough’ snakebite treatment that could turbocharge antivenom development 🐍
Mice were protected against lethal snake toxins for the first time, in a ‘breakthrough’ moment thanks to artificial intelligence
@sneweyy.bsky.social has the latest 👇
www.telegraph.co.uk/global-healt...
Mice were protected against lethal snake toxins for the first time, in a ‘breakthrough’ moment thanks to artificial intelligence
@sneweyy.bsky.social has the latest 👇
www.telegraph.co.uk/global-healt...
AI designs ‘breakthrough’ snakebite treatment that could turbocharge antivenom development
Mice were protected against lethal snake toxins for the first time, in a ‘breakthrough’ moment thanks to artificial intelligence
www.telegraph.co.uk
January 16, 2025 at 2:27 AM
Loved talking to @tpjenkins.bsky.social about this work 🐍
🚨 Revolutionising Snakebite Treatments with AI-Designed Proteins 🐍
I'm proud to share our latest study published in hashtag#Nature, driven by Susana Vazquez Torres, and co-led by David Baker (Institute for Protein Design, University of Washington) and myself.
I'm proud to share our latest study published in hashtag#Nature, driven by Susana Vazquez Torres, and co-led by David Baker (Institute for Protein Design, University of Washington) and myself.
January 15, 2025 at 8:16 PM
🚨 Revolutionising Snakebite Treatments with AI-Designed Proteins 🐍
I'm proud to share our latest study published in hashtag#Nature, driven by Susana Vazquez Torres, and co-led by David Baker (Institute for Protein Design, University of Washington) and myself.
I'm proud to share our latest study published in hashtag#Nature, driven by Susana Vazquez Torres, and co-led by David Baker (Institute for Protein Design, University of Washington) and myself.
🎉Looking for an exciting opportunity in proteomics and data science?🎉
Join DTU Bioengineering as a #Data #Science Specialist in #Proteomics! Based at our state-of-the-art DTU Proteomics Core.
You'll also collaborate with me and the DTU Bioengineering Data Science Hub.
lnkd.in/d2zHaMys
Join DTU Bioengineering as a #Data #Science Specialist in #Proteomics! Based at our state-of-the-art DTU Proteomics Core.
You'll also collaborate with me and the DTU Bioengineering Data Science Hub.
lnkd.in/d2zHaMys
January 13, 2025 at 7:43 PM
🎉Looking for an exciting opportunity in proteomics and data science?🎉
Join DTU Bioengineering as a #Data #Science Specialist in #Proteomics! Based at our state-of-the-art DTU Proteomics Core.
You'll also collaborate with me and the DTU Bioengineering Data Science Hub.
lnkd.in/d2zHaMys
Join DTU Bioengineering as a #Data #Science Specialist in #Proteomics! Based at our state-of-the-art DTU Proteomics Core.
You'll also collaborate with me and the DTU Bioengineering Data Science Hub.
lnkd.in/d2zHaMys
🌟 Thrilled to announce that our project, Deep Immune Receptor Modeling (#DIRM), has been awarded funding under the (@novo-nordisk.bsky.social) Nordisk Foundation Data Science Collaborative Research Programme! 🎉
December 19, 2024 at 4:04 PM
🌟 Thrilled to announce that our project, Deep Immune Receptor Modeling (#DIRM), has been awarded funding under the (@novo-nordisk.bsky.social) Nordisk Foundation Data Science Collaborative Research Programme! 🎉