Yu Zhang

This is figure 1, which shows the exploration of global venoms for antimicrobial discovery.

A study in Nature Communications used AI to mine global venom proteomes and discovered novel peptides with antimicrobial activity. Several candidates showed efficacy against drug-resistant bacteria in laboratory and animal tests. go.nature.com/4f0zYb4 #medsky 🧪

The Open Molecules 2025 dataset is out! With >100M gold-standard ωB97M-V/def2-TZVPD calcs of biomolecules, electrolytes, metal complexes, and small molecules, OMol is by far the largest, most diverse, and highest quality molecular DFT dataset for training MLIPs ever made 1/N

Automated orthogonal tRNA generation - Nature Chemical Biology Genetic code expansion and reprogramming require orthogonal tRNAs. Methods have now been developed for the automated generation of chimeric orthogonal tRNAs and discovery of their cognate synthetases....

Interesting work on a computational approach to develop orthogonal aminoacyl-tRNA synthetase/tRNA pairs in E. coli www.nature.com/articles/s41...

Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer Anti-tumor immunity is crucial for high-grade serous ovarian cancer (HGSC) prognosis, yet its adaptation upon standard chemotherapy remains poorly und…

1/n New paper alert 🚨 We're thrilled to share our just published paper in #CancerCell
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch

Ordinal Confidence Level Assignments for Regression Model Predictions We present a simple method for assigning accurate confidence levels to molecular property predictions from regression models. These confidence levels are easy to interpret and useful for making decisi...

Excellent new paper (with code) by my former colleagues Steven Kearnes and Patrick Riley describing a procedure for associating confidence levels with regression model predictions in drug discovery. pubs.acs.org/doi/10.1021/...

Cell Painting: a decade of discovery and innovation in cellular imaging - Nature Methods This Review synthesizes the literature from over 10 years of Cell Painting for image-based profiling and highlights how advances in this technology enable new biological discovery of cellular phenotyp...

Cell Painting: a decade of discovery and innovation in cellular imaging

"Cell Painting has been used in various applications, alone or with other -omics data, to decipher the mechanism of action of a compound, its toxicity profile, and other biological effects."

www.nature.com/articles/s41...

GitHub - EBjerrum/rdeditor: Simple RDKit molecule editor GUI using PySide Simple RDKit molecule editor GUI using PySide. Contribute to EBjerrum/rdeditor development by creating an account on GitHub.

Thanks! It's rdEditor, the Python and RDKit based molecular editor, that's inside to deliver selection and editing capabilities: github.com/EBjerrum/rde...

E coli are red
S aureus are blue
Hans Christian Gram
Stained them for you

Scaling Down for Efficiency: Medium-Sized Transformer Models for Protein Sequence Transfer Learning Protein language models such as the transformer-based Evolutionary Scale Modeling 2 (ESM2) can offer deep insights into evolutionary and structural properties of proteins. While larger models, such as...

The complete guide for transfer learning with the protein language model ESM-2.

(In brief: Use ESM-2 650M and calculate mean embeddings across sites.)
www.biorxiv.org/content/10.1...

"Productive stupidity" is such a useful concept! The best thing I learned in my (literary) PhD is to say "I don't know." That's the moment you can listen, explore, find out something new.

I often say my PhD has gone unused because I'm not a professor, but in truth I use it every day. It's a gift.

would love to be added if there is still spot left. thank you!

Review: The lives of cells, recorded https://www.nature.com/articles/s41576-024-00788-w (read free: https://rdcu.be/d1s8d) 🧬🖥️🧪

A project 10 years in the making w/ Terry Sejnowski, led by @philosophaki.bsky.social

Insights into ryanodine receptor activation & calcium-induced Ca2+ release from a stochastic explicit-particle 3D simulation of cardiac dyad w/ realistic geometry (from TEM)

www.sciencedirect.com/science/arti...

Covers of Science and Nature journals in the past 2 weeks denoting remarkable progress of life science with A.I. tools

A vertical takeoff of life science with #AI LLLMs.
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...

MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics Abstract. Spatially Resolved Transcriptomics (SRT) serves as a cornerstone in biomedical research, revealing the heterogeneity of tissue microenvironments.

MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics #SingleCell 🧬🖥️ academic.oup.com/bib/article/...

The Broken Lens: Antimicrobial Resistance in Humanitarian Settings MSF report on treating AMR in people caught in challenging humanitarian settings

Our recent report on #AntimicrobialResistance & the need for improved surveillance, testing, infection control, #antibiotic stewardship, funding & global commitments for #AMR solutions in humanitarian settings. #WAAW2024 #MedSky

msfaccess.org/broken-lens-...

Would love to be added, thanks !

Over 100 postdocs are registered for tomorrow's Postdoc Night Science Boston session! I can't wait to help other places get their own club started.

Learning on compressed molecular representations Last year, a preprint gained notoriety, proposing that a k-nearest neighbour classifier is able to outperform large-language models using compressed text as input and normalised compression distance (...

Fresh off the presses:
In "Learning on compressed molecular representations" Jan Weinreich and I looked into whether GZIP performed better than Neural Networks in chemical machine learning tasks. Yes, you've read that right.

TL;DR: Yes, GZIP can perform better than baseline GNNs and MLPs. It can ..

Hi! 👋🏻 I'd love to join!

Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging 5.7k words, 26 minutes reading time

Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging

www.owlposting.com/p/why-recurs...

After over a decade,Recursion Pharmaceuticals changed its primary assay. Why is that? I answer that question over 5.6k words (26 minutes to read)

first journalism-y piece!

A cartoon robot using a chainsaw on a log

There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... .

GitHub - NVIDIA/bionemo-framework: BioNeMo Framework: For building and adapting AI models in drug discovery at scale BioNeMo Framework: For building and adapting AI models in drug discovery at scale - NVIDIA/bionemo-framework

If you're building AI models for drug discovery, you should check out the newly open-source #BioNeMo Framework:

code: github.com/NVIDIA/bione...
paper: arxiv.org/abs/2411.10548
docs: docs.nvidia.com/bionemo-fram...
explainer: t.co/7MOamSChGN