Kejia Li

One of the main stories of my postdoc is finally out! It builds on an intuition from my early days in omics data analysis: our signaling pathways are simply too small, underrepresenting cellular complexity after stimulation. Something obvious, yet surprisingly hard to quantify.

Simple but smart idea💡

A very intriguing press release👍

‘An AlphaFold 4’ – scientists marvel at DeepMind drug spin-off’s exclusive new AI Isomorphic Lab’s proprietary drug-discovery model is a major advance, but scientists developing open-source tools are left guessing how to achieve similar results.

“It’s a major advance, on the scale of an AlphaFold4. The problem, of course, is that we know nothing of the details.”

Isomorphic Lab’s proprietary drug-discovery model is a major advance
go.nature.com/3Mm2ZnQ

When I first learned about omics at university, I confidently stopped caring about single proteins. Fast-forward 4 years of a system’s biology PhD, I now have the most amazing favorite single protein which I can’t stop thinking about. Here is the story of how that happened 👀

Rewiring of oncogenic signaling in #DrugResistance is a moving target. In our new study, we used biophysical phosphoproteomics to investigate #BRAF mutant cancer, linking phosphorylation changes to protein function and #MolecularMechanisms through #Multi-Omics integration.
tinyurl.com/funsignaling

The Escherichia coli PeptideAtlas Build: Characterizing the Observed Escherichia coli Pan-Proteome and Its Post-Translational Modifications pubs.acs.org/doi/10....

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#proteomics #prot-paper

Deep contrastive learning enables genome-wide virtual screening Recent breakthroughs in protein structure prediction have opened new avenues for genome-wide drug discovery, yet existing virtual screening methods remain computationally prohibitive. We present DrugC...

In a new Science study, researchers introduce DrugCLIP, a contrastive learning framework that virtually screens small molecules and protein pockets, analyzing protein-ligand interactions 10 million times faster than most standard molecular docking approaches. https://scim.ag/45FfSj2

In this month's Editorial, we highlight some of the Nature Methods editorial team members' favorite papers we published in 2025!

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

After working on proteomics for eight years, first time to present a poster but at an AI symposium😅 Happy to know, always happy to learn #AI in drug discovery & development

A Very comprehensive study! Some previous studies have used drug-induced changes in target abundance to identify targets; although it’s not always the case.

Proteome-wide model for human disease genetics Nature Genetics - popEVE is a proteome-wide deep generative model to identify and predict pathogenicity of missense mutations causing genetic disorders.

popEVE is out in Nature Genetics! 🎉
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K

Joined a conference talk a week ago
in EMBL, which introduced how mammal cells detoxify m6A and how the accumulation influences metabolism. Was wondering how about bacteria. What’s the function of m6A or m6dA in Ecoli. Very in-time preprint 👋

Thanks, Shuyao😘

Thanks a lot, Pablo! 😄

Finally out! 🤩 Check out our HT- PELSA for high throughput screening！

HT-PELSA, a new proteomics tool by EMBL researchers, processes samples 100x faster and works directly with complex crude cell, tissue, and bacterial lysates – developments which could accelerate drug discovery and basic biological research 💊

🔗 www.embl.org/news/science...

NAD+ is a central molecule in bacterial immunity. An excellent and timely review by Hugo Vausset and Aude Bernheim

Cool!

Congrats!

The emerging roles of long non-coding RNAs in the nervous system - Nature Reviews Neuroscience Long non-coding RNAs are abundant in the brain, where they are proposed to regulate numerous processes. In this Review, Mattick and colleagues describe our current understanding of their mechanisms of...

The emerging roles of long non-coding RNAs in the nervous system

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

In situ proximity labeling of proteins associated with circRNA and RNA G-quadruplexes - Nature Chemical Biology Mo, Chen, Cui and colleagues report a proximity-labeling-based method termed TAPRIP for profiling RNA–protein interactions in living cells, enabling the identification of circular RNA regulators and r...

A new paper reports a proximity labeling-based method termed TAPRIP for profiling RNA-protein interactions in living cells, enabling the identification of circular RNA regulators and RNA G-quadruplex-specific binding proteins

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

Wow!

‘Wildest thing’: solar-powered slug steals chloroplasts and stores them for emergencies Nature - Marine creatures house contraband structures in special organelles, which the animal raids for food in times of need.

‘Solar-powered’ sea slugs have specialized depots in their cells that store photosynthetic equipment looted from algae

https://go.nature.com/4l27lMN

Chemical biology approaches to resolve the subcellular GPCR signaling landscape - Nature Chemical Biology This Review highlights recent advances in understanding compartmentalized GPCR signaling using chemical biology approaches with a focus on tools for real-time monitoring, site-selective tuning of sign...

A new Review highlights recent advances in understanding compartmentalized GPCR signaling using chemical biology approaches with a focus on tools for real-time monitoring, site-selective tuning of signaling protein networks and mechanistic screening

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

Not directly relevant to the paper: pick up your chemistry as it will definitely help you to better understand many cellular biological processes.

Good to know which metrics should be evaluated from a quantitative perspective

Good to learn how metabolites influence the protein complex formation and the multifaceted functions of metabolites in different processes!

EndoMAP.v1 charts the structural landscape of human early endosome complexes - Nature A study presents EndoMAP.v1, a resource that combines information on protein interactions and crosslink-supported structural predictions to map the interaction landscape of early endosomes.

New work @harvard by Miguel Gonzalez-Lozano @harperlabhms.bsky.social & @ernstschmid.bsky.social in Johannes Walter lab charts structural interactome of endosomes. #XL-MS #Alphafold Funded by @asapresearch.parkinsonsroadmap.org & NIH. Science continues-despite attacks www.nature.com/articles/s41...

The human proteome with direct physical access to DNA Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes with single-amino-aci...

🚨Our new paper is online🚨
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...