Daniel Ukaegbu
@darniee.bsky.social
PhD student in computational toxicology @johnshopkins.bsky.social
Reposted by Daniel Ukaegbu
For solving a 50-year mystery by uncovering the machinery behind BMP, a molecule with protective effects against various disorders, Uche Medoh is the winner of the 2025 Science & SciLifeLab Prize for Young Scientists.
🎉 Learn more about the work: https://scim.ag/4qVpK1a
🎉 Learn more about the work: https://scim.ag/4qVpK1a
November 13, 2025 at 8:34 PM
For solving a 50-year mystery by uncovering the machinery behind BMP, a molecule with protective effects against various disorders, Uche Medoh is the winner of the 2025 Science & SciLifeLab Prize for Young Scientists.
🎉 Learn more about the work: https://scim.ag/4qVpK1a
🎉 Learn more about the work: https://scim.ag/4qVpK1a
Reposted by Daniel Ukaegbu
50 % Cloud Restaurant, Yunnan, China
Cheng Chung Design transformed artist Luo Xu’s red-brick installation into a restaurant and art lounge. Its organic arches, skylights and flowing brick forms merge architecture, nature and art into a unique multi-sensory dining experience.
Cheng Chung Design transformed artist Luo Xu’s red-brick installation into a restaurant and art lounge. Its organic arches, skylights and flowing brick forms merge architecture, nature and art into a unique multi-sensory dining experience.
November 3, 2025 at 8:02 PM
50 % Cloud Restaurant, Yunnan, China
Cheng Chung Design transformed artist Luo Xu’s red-brick installation into a restaurant and art lounge. Its organic arches, skylights and flowing brick forms merge architecture, nature and art into a unique multi-sensory dining experience.
Cheng Chung Design transformed artist Luo Xu’s red-brick installation into a restaurant and art lounge. Its organic arches, skylights and flowing brick forms merge architecture, nature and art into a unique multi-sensory dining experience.
Reposted by Daniel Ukaegbu
We have progressed from data collection to data analysis.
November 1, 2025 at 12:31 AM
We have progressed from data collection to data analysis.
Reposted by Daniel Ukaegbu
Nice to see he’s bringing a new album out.
October 29, 2025 at 7:12 PM
Nice to see he’s bringing a new album out.
Reposted by Daniel Ukaegbu
Achira is growing! We’re looking for talented software engineers, ML research engineers, and AI/ML scientists to join our team in building foundation simulation models to power the future of drug discovery.
Apply at achira.ai
Apply at achira.ai
Achira
Building foundation simulation models for drug discovery
achira.ai
October 24, 2025 at 12:20 PM
Achira is growing! We’re looking for talented software engineers, ML research engineers, and AI/ML scientists to join our team in building foundation simulation models to power the future of drug discovery.
Apply at achira.ai
Apply at achira.ai
Reposted by Daniel Ukaegbu
I see that @kelbadry.bsky.social has won a MacArthur Foundation fellowship (Genius award)! Congratulations 🧪🔭
www.nytimes.com/2025/10/08/a...
www.nytimes.com/2025/10/08/a...
MacArthur Foundation Announces 2025 ‘Genius Grant’ Winners
www.nytimes.com
October 14, 2025 at 1:55 PM
I see that @kelbadry.bsky.social has won a MacArthur Foundation fellowship (Genius award)! Congratulations 🧪🔭
www.nytimes.com/2025/10/08/a...
www.nytimes.com/2025/10/08/a...
Reposted by Daniel Ukaegbu
"The Internet has Google. Now biology has MetaGraph. Detailed today in Nature1, the search engine can quickly sift through the staggering volumes of biological data housed in public repositories." 🧪 www.nature.com/articles/d41... anyone try this? What's it like?
‘Google for DNA’ brings order to biology’s big data
MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.
www.nature.com
October 9, 2025 at 10:25 PM
"The Internet has Google. Now biology has MetaGraph. Detailed today in Nature1, the search engine can quickly sift through the staggering volumes of biological data housed in public repositories." 🧪 www.nature.com/articles/d41... anyone try this? What's it like?
Reposted by Daniel Ukaegbu
Immunity researchers win the 2025 #NobelPrize in Physiology or Medicine
Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi receive the prize for understanding how the immune system is kept in check. Read more: cen.acs.org/people/nobel...
#chemsky #immunosky 🧪
Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi receive the prize for understanding how the immune system is kept in check. Read more: cen.acs.org/people/nobel...
#chemsky #immunosky 🧪
October 6, 2025 at 1:19 PM
Immunity researchers win the 2025 #NobelPrize in Physiology or Medicine
Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi receive the prize for understanding how the immune system is kept in check. Read more: cen.acs.org/people/nobel...
#chemsky #immunosky 🧪
Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi receive the prize for understanding how the immune system is kept in check. Read more: cen.acs.org/people/nobel...
#chemsky #immunosky 🧪
Reposted by Daniel Ukaegbu
💸 🐦 🧪
🪶 If you are able, you donate here: birdpop.org/pages/do...
We lost roughly $1 million in funding without warning. Projects cancelled included all of our bird monitoring work for the National Park Service & projects w/ the Bureau of Land Management on Gunnison's Sage-Grouse, Pinyon Jays & more. 1/4
We lost roughly $1 million in funding without warning. Projects cancelled included all of our bird monitoring work for the National Park Service & projects w/ the Bureau of Land Management on Gunnison's Sage-Grouse, Pinyon Jays & more. 1/4
October 5, 2025 at 1:41 PM
💸 🐦 🧪
Reposted by Daniel Ukaegbu
Very happy this paper got accepted to NeurIPS 2025 as a Spotlight! 😁
Main takeaway: In mechanistic interpretability, we need assumptions about how DNNs encode concepts in their representations (eg, the linear representation hypothesis). Without them, we can claim any DNN implements any algorithm!
Main takeaway: In mechanistic interpretability, we need assumptions about how DNNs encode concepts in their representations (eg, the linear representation hypothesis). Without them, we can claim any DNN implements any algorithm!
Mechanistic interpretability often relies on *interventions* to study how DNNs work. Are these interventions enough to guarantee the features we find are not spurious? No!⚠️ In our new paper, we show many mech int methods implicitly rely on the linear representation hypothesis🧵
October 1, 2025 at 3:00 PM
Very happy this paper got accepted to NeurIPS 2025 as a Spotlight! 😁
Main takeaway: In mechanistic interpretability, we need assumptions about how DNNs encode concepts in their representations (eg, the linear representation hypothesis). Without them, we can claim any DNN implements any algorithm!
Main takeaway: In mechanistic interpretability, we need assumptions about how DNNs encode concepts in their representations (eg, the linear representation hypothesis). Without them, we can claim any DNN implements any algorithm!
Reposted by Daniel Ukaegbu
I’m not sure the linked in crowd is getting my snark about Virtual Cells 😄🫣
www.linkedin.com/posts/anneca...
www.linkedin.com/posts/anneca...
I’d like to take this opportunity to rebrand our lab's prior research as creating AI Virtual Cells! | Anne Carpenter
I’d like to take this opportunity to rebrand our lab's prior research as creating AI Virtual Cells! 🎉 😅
Like many others released lately, ours are mostly one-trick ponies, but we have a stable ...
www.linkedin.com
July 13, 2025 at 1:31 PM
I’m not sure the linked in crowd is getting my snark about Virtual Cells 😄🫣
www.linkedin.com/posts/anneca...
www.linkedin.com/posts/anneca...
Reposted by Daniel Ukaegbu
This week's #RDKit blog post shows how to create simple protein--ligand interaction diagrams.
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
Drawing simple protein–ligand interaction diagrams with the RDKit – RDKit blog
Quick, but useful
greglandrum.github.io
September 26, 2025 at 3:58 PM
This week's #RDKit blog post shows how to create simple protein--ligand interaction diagrams.
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
I think there's potential to take this a bit further...
greglandrum.github.io/rdkit-blog/p...
Reposted by Daniel Ukaegbu
Jerusalem is an amazing city!
September 23, 2025 at 6:35 PM
Jerusalem is an amazing city!
Reposted by Daniel Ukaegbu
Our new workflow maps whole human fallopian tubes at single-cell resolution. In healthy FTs, we detected (many) STIC precancerous lesions.
We can also simulate virtual sectioning as done in the clinic and show how current protocols undersample FTs.
More here:
www.biorxiv.org/content/10.1...
We can also simulate virtual sectioning as done in the clinic and show how current protocols undersample FTs.
More here:
www.biorxiv.org/content/10.1...
September 23, 2025 at 4:30 PM
Our new workflow maps whole human fallopian tubes at single-cell resolution. In healthy FTs, we detected (many) STIC precancerous lesions.
We can also simulate virtual sectioning as done in the clinic and show how current protocols undersample FTs.
More here:
www.biorxiv.org/content/10.1...
We can also simulate virtual sectioning as done in the clinic and show how current protocols undersample FTs.
More here:
www.biorxiv.org/content/10.1...
Reposted by Daniel Ukaegbu
🧬 PFAS change gene activity
A new study of US firefighters shows some PFAS chemicals alter how genes work, linking them to cancers, autoimmune disease, and neurological disorders.
🔗 www.theguardian.com/environment/...
#SciComm #PFAS #Health 🧪
A new study of US firefighters shows some PFAS chemicals alter how genes work, linking them to cancers, autoimmune disease, and neurological disorders.
🔗 www.theguardian.com/environment/...
#SciComm #PFAS #Health 🧪
Exposure to some common Pfas changes gene activity, new study finds
Findings help decipher mechanisms through which ‘forever chemicals’ cause disease, aiding in treating health problems
www.theguardian.com
August 17, 2025 at 4:50 AM
🧬 PFAS change gene activity
A new study of US firefighters shows some PFAS chemicals alter how genes work, linking them to cancers, autoimmune disease, and neurological disorders.
🔗 www.theguardian.com/environment/...
#SciComm #PFAS #Health 🧪
A new study of US firefighters shows some PFAS chemicals alter how genes work, linking them to cancers, autoimmune disease, and neurological disorders.
🔗 www.theguardian.com/environment/...
#SciComm #PFAS #Health 🧪
Reposted by Daniel Ukaegbu
My talk at Accelerating Bio-Innovation gives a flavor for how cell-based images are propelling new treatments:
www.youtube.com/watch?v=kP-G...
www.youtube.com/watch?v=kP-G...
Anne Carpenter at 2025 ABI at MIT: How Imaging Propels Medicine in the Age of AI
YouTube video by Anne Carpenter
www.youtube.com
August 4, 2025 at 8:35 PM
My talk at Accelerating Bio-Innovation gives a flavor for how cell-based images are propelling new treatments:
www.youtube.com/watch?v=kP-G...
www.youtube.com/watch?v=kP-G...
Reposted by Daniel Ukaegbu
My first post and I would like to plug my project - pharmacophore-toolkit. I thought others in the #cheminformatics, #molecularmodeling, #drugdiscovery, or the #chemsky #compchem community would find it helpful. github.com/tlint101/pha...
GitHub - tlint101/pharmacophore-toolkit: Generate simple pharmacophore models from RDKit
Generate simple pharmacophore models from RDKit. Contribute to tlint101/pharmacophore-toolkit development by creating an account on GitHub.
github.com
July 23, 2025 at 10:35 AM
My first post and I would like to plug my project - pharmacophore-toolkit. I thought others in the #cheminformatics, #molecularmodeling, #drugdiscovery, or the #chemsky #compchem community would find it helpful. github.com/tlint101/pha...
Reposted by Daniel Ukaegbu
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
patwalters.github.io/Three-Papers...
July 22, 2025 at 1:40 PM
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
patwalters.github.io/Three-Papers...
Reposted by Daniel Ukaegbu
Barack Obama encourages young men to have more diverse friend groups:
“I had a gay professor in college […] who became one of my favorite professors and was a great guy and would call me out when I started saying stuff that was ignorant. You need that to show empathy and kindness.”
“I had a gay professor in college […] who became one of my favorite professors and was a great guy and would call me out when I started saying stuff that was ignorant. You need that to show empathy and kindness.”
July 21, 2025 at 7:56 PM
Barack Obama encourages young men to have more diverse friend groups:
“I had a gay professor in college […] who became one of my favorite professors and was a great guy and would call me out when I started saying stuff that was ignorant. You need that to show empathy and kindness.”
“I had a gay professor in college […] who became one of my favorite professors and was a great guy and would call me out when I started saying stuff that was ignorant. You need that to show empathy and kindness.”
Reposted by Daniel Ukaegbu
🧪 Inflammation has a pH switch
This study shows that as inflammation lowers cell pH, it switches off certain inflammatory genes.
A key protein, BRD4, senses the acidity, helping tune the immune response and limit damage.
🔗 www.cell.com/cell/fulltex...
#SciComm #Immunology #CellBiology
This study shows that as inflammation lowers cell pH, it switches off certain inflammatory genes.
A key protein, BRD4, senses the acidity, helping tune the immune response and limit damage.
🔗 www.cell.com/cell/fulltex...
#SciComm #Immunology #CellBiology
Regulation of inflammatory responses by pH-dependent transcriptional condensates
BRD4 functions as an intracellular pH sensor through a conserved histidine-rich intrinsically
disordered region. Inflammation-associated acidification triggers a pH-dependent switch
in transcriptional...
www.cell.com
July 20, 2025 at 2:43 PM
🧪 Inflammation has a pH switch
This study shows that as inflammation lowers cell pH, it switches off certain inflammatory genes.
A key protein, BRD4, senses the acidity, helping tune the immune response and limit damage.
🔗 www.cell.com/cell/fulltex...
#SciComm #Immunology #CellBiology
This study shows that as inflammation lowers cell pH, it switches off certain inflammatory genes.
A key protein, BRD4, senses the acidity, helping tune the immune response and limit damage.
🔗 www.cell.com/cell/fulltex...
#SciComm #Immunology #CellBiology
Reposted by Daniel Ukaegbu
Are we hitting a wall with scaling molecular foundation models?
Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...
Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...
Towards transfer learning in molecular foundation models
Are multi-modal molecular foundation models learning transferable representations across biology and chemistry?
chaitjo.substack.com
July 16, 2025 at 10:25 AM
Are we hitting a wall with scaling molecular foundation models?
Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...
Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...
Reposted by Daniel Ukaegbu
As always, a very nice talk from Francois Lanusse: Generative Al for Inverse Problems and Forecasting
Slides: eiffl.github.io/talks/Paris2...
Slides: eiffl.github.io/talks/Paris2...
July 3, 2025 at 4:23 PM
As always, a very nice talk from Francois Lanusse: Generative Al for Inverse Problems and Forecasting
Slides: eiffl.github.io/talks/Paris2...
Slides: eiffl.github.io/talks/Paris2...
Reposted by Daniel Ukaegbu
Can using synthetic approaches to build biology help teach us the design principles of how embryos build themselves? 👷♀️🔧
If this is a question that interests you, come and share your thoughts at this Royal Society Workshop on Generative Biology
royalsociety.org/science-even...
If this is a question that interests you, come and share your thoughts at this Royal Society Workshop on Generative Biology
royalsociety.org/science-even...
July 3, 2025 at 4:26 PM
Can using synthetic approaches to build biology help teach us the design principles of how embryos build themselves? 👷♀️🔧
If this is a question that interests you, come and share your thoughts at this Royal Society Workshop on Generative Biology
royalsociety.org/science-even...
If this is a question that interests you, come and share your thoughts at this Royal Society Workshop on Generative Biology
royalsociety.org/science-even...
Reposted by Daniel Ukaegbu
🧪 New preprint: "Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings"
We generate complete, all-atom protein conformational ensembles, capturing both backbone and side-chain dynamics of, e.g., the Dopamine D2 receptor.
arxiv.org/abs/2506.17064
We generate complete, all-atom protein conformational ensembles, capturing both backbone and side-chain dynamics of, e.g., the Dopamine D2 receptor.
arxiv.org/abs/2506.17064
June 26, 2025 at 9:53 AM
🧪 New preprint: "Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings"
We generate complete, all-atom protein conformational ensembles, capturing both backbone and side-chain dynamics of, e.g., the Dopamine D2 receptor.
arxiv.org/abs/2506.17064
We generate complete, all-atom protein conformational ensembles, capturing both backbone and side-chain dynamics of, e.g., the Dopamine D2 receptor.
arxiv.org/abs/2506.17064