Daniel Ukaegbu

YouTube video by Anne Carpenter Anne Carpenter at 2025 ABI at MIT: How Imaging Propels Medicine in the Age of AI

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...

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.

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...

New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...

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.”

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...

🧪 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

Towards transfer learning in molecular foundation models Are multi-modal molecular foundation models learning transferable representations across biology and chemistry?

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...

As always, a very nice talk from Francois Lanusse: Generative Al for Inverse Problems and Forecasting
Slides: eiffl.github.io/talks/Paris2...

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...

🧪 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

Apply molecular filter more easily #RDKit #Datamol #Cheminformatics

Molecular filter is important for removing unwanted molecules from huge amout of comound dataset. And there are lots of filters are available in these days. For example, PAINS, Role of 5, Role of CNS etc... These filters are…

Happy birthday 🎉

Read more about our MLIP distillation preprint in John’s thread! 🙂 #compchem #chemsky

People With Severe Diabetes Are Cured in Small Trial of New Drug

Some exciting news for friends w/diabetes.
Zimislecel treatment restored pancreatic islet cell function in a small group of 12 patients. Ten of the 12 patients no longer needed insulin. This #research is a culmination of 20 yrs of hard work & $50 M in funding.

🎁🔗🧪 www.nytimes.com/2025/06/20/h...

Distillation of atomistic foundation models across architectures and chemical domains Machine-learned interatomic potentials have transformed computational research in the physical sciences. Recent atomistic `foundation' models have changed the field yet again: trained on many differen...

Distilling atomistic foundation models! ⚗️🧪🤖 In this #compchem preprint, we describe a general (“architecture-agnostic”) approach to creating fast, application-specific MLIP models via synthetic data – led jointly by @jla-gardner.bsky.social & @dft-dutoit.bsky.social arxiv.org/abs/2506.10956

Movie poster for Treasure Planet with the tagline “Robert Louis Stevenson’s greatest adventure Treadure Island as it has never been seen before”

Tonight, the kid and I are watching TREASURE PLANET
#filmsky

😂😂😂😂

Importance of sample size on the quality and utility of AI-based prediction models for healthcare Rigorous study design and analytical standards are required to generate reliable findings in healthcare from artificial intelligence (AI) research. On…

**New Lancet DH paper**

"Importance of sample size on the quality & utility of AI-based prediction models for healthcare"

- for broad audience
- explains why inadequate SS harms #AI model training, evaluation & performance
- pushback to claims SS irrelevant to AI research

👇
tinyurl.com/yrje52fn

Text reads "Congratulations to the 2025 Leading Edge Fellows" followed by the Leading Edge logo and www.leadingedgesymposium.org. Below are the headshots and names of the 40 new Leading Edge Fellows. They are Cel Welch Lianna Wat Maria Toro Moreno Sarah Talley Xulu Sun Ines Sturmlechner Virginia Savy Amelie Raz Kali Pruss Caterina Profaci Sarah Pierce Melissa Pamula Kehinde Odufowora Patricia Nano Ariana Musa de Aquino Nour El Houda Mimouni Kathleen Martin Brea Manuel Mable Lam Miri Krupkin Elaine Kouame Megan Kirchgessner Sumin Kim Shubhangini Kataruka Geraldine Jowett Andrea Jones Leanne Iannucci Emily Heckman Allison Girasole Florencia Fernandez Chiappe Tonie Farris Hannah Elam Erin Doherty Xiaoyun Ding Maria Bustillo Julia Brunner Debadrita Bhattacharya Lorena Benedetti Ashley Anderson Krisha Aghi

We are thrilled to announce the 2025 Leading Edge Fellows! 40 outstanding postdoctoral fellows doing pioneering research in a wide range of biological and biomedical disciplines.

Learn more about these exceptional scientists:

www.leadingedgesymposium.org/fellows

Warm congrats to our PhD graduates.

🤣

This #RDKit blog post builds on the earlier one about chemical words; this time I'm using Morgan fingerprint bits as the "words".

greglandrum.github.io/rdkit-blog/p...

ChatGPT can now handle SMILES strings 🧪⚛️

This has been a long journey, but it's now out in final form. @kjamali.bsky.social

academic.oup.com/bioinformati...

Increased ERC funding for top global researchers moving to Europe now confirmed The European Research Council (ERC) decision to increase its support for leading researchers moving to Europe has today been formally adopted. On top of its standard grants, the ERC offers additional ...

The European Research Council (ERC) decision to increase its support for leading researchers moving to Europe has today been formally adopted 🧪
erc.europa.eu/news-events/...

Came close to tears while making my summer writing plan.

From awe at @mirya.bsky.social writing 3 books in one year, but also because I am *losing it* over the idea of finishing my book ms. this summer.

Objectively I'm close, but how can I get to DONE with a 4 wk field trip and 3 wks vaca*?

Expertitis I will never call myself an expert for to do so would be to take the first step down a very slippery slope.  It is important to remember th...

With Nobel Prize laureates occasionally straying outside their applicability domains, I thought it might be helpful to re-post Expertitis #DrugDiscovery 🧪
fbdd-lit.blogspot.com/2015/04/expe...

The layout of the mobile surgery unit in New Zealand 🚑

#MedSky #BlueSly #DocSky

The best sign was “It’s transGENIC mice, Idiot!”