Kejia Li
@kejiali.bsky.social
Postdoc in Savitski lab, EMBL, Heidelberg. Interested in functional proteomics, microbiology, metabolism, and drug target discovery.
Super cool work!!!🎉
Tara Bartolec@tarabartolec.bsky.social · 2mo agoSo happy to share that this work is finally out, now in @nature.com! Lots of new goodies since preprint so plz check it out (old thread below). Giant thank you to everybody involved + all @savitski-lab.bsky.social and @typaslab.bsky.social lab members 🙏🙏🙏 @embl.org nature.com/articles/s41...
Cool!
Harvard Med Cell Biology@harvardcellbio.bsky.social · 2mo agoNew work from the Gygi and Cantley labs @harvardcellbio.bsky.social provides a unique structure-based protein kinase specificity atlas across the human proteome. An exciting resource for biological discovery! www.nature.com/articles/s41...
It is interesting that the different specificities of sponge proteins to signaling molecules may explain different mechanisms in the phage-bacteria arms race.
Romi Hadary@romihadary.bsky.social · 4mo agoExcited to see our work out in @natmicrobiol.nature.com! We uncovered broad functional diversity within phage sponge families🧽. Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social ! www.nature.com/articles/s41...
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com 🌐 https://search.foldseek.com/folddisco
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
nature.com
Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco
Oh interesting! ubiquitination not only regulates protein stability but also glycogen? 🧐
Nature@nature.com · 4mo agoResearch Briefing: The results of a new Nature paper indicate that the breakdown of liver glycogen molecules into glucose might be regulated by ubiquitination. go.nature.com/4e2m2gK
Very happy to share our new paper. Together with our wonderful collaborators, we found that L-2-HG, a metabolite often viewed as “toxic,” also has an essential physiological function in mice. www.nature.com/articles/s41...
Mitochondrial l-2-hydroxyglutarate is a physiological signalling metabolite - Nature
l-2-Hydroxyglutarate is identified as a legitimate physiological signalling metabolite, and control of its levels is essential for postnatal growth and survival and correct renal development and funct...
nature.com
A deep redox proteomics study identifies redox-regulated and druggable cysteines in immune proteins www.nature.com/articles/s41...
A druggable redox switch on SHP1 controls macrophage inflammation - Nature Chemical Biology
Post-translational redox modification of protein cysteine residues has emerged as a mode of immune cell regulation. Now, a deep redox proteomics study identifies redox-regulated and druggable cysteine...
nature.com
Interesting, but how does it know which gene is the mutated one when the two alleles are different? Dose this happen for only deleterious mutations, or also happen for beneficial ones
Nature@nature.com · 7mo agoThese are the first asexual vertebrate species known to science go.nature.com/4s2N0dM
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.
Saez-Rodriguez Group@saezlab.bsky.social · 7mo agoInterested in kinase-driven signaling interactions? Check out our (now peer-reviewed) paper together with @savitski-lab.bsky.social on reconstructing signaling networks from phosphoproteomics data and prior knowledge: ➡️ doi.org/10.1038/s414...
A very intriguing press release👍
EMBL@embl.org · 8mo agoOur cells are experts at navigating inherently noisy and complicated environments. EMBL researchers are using theoretical physics approaches to uncover fundamental principles behind how cells use complex information to self-organise. www.embl.org/news/science...
“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
‘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.
go.nature.com
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 👀
Savitski Lab@savitski-lab.bsky.social · 8mo agoRewiring 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
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.... --- #proteomics #prot-paper
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
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...
scim.ag
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...
Client Challenge
nature.com
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.
@nataliescholes.bsky.social · 10mo agoExcited to share our work on inhibitors turning degraders now out: doi.org/10.1038/s415...
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
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.
rdcu.be
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 👋
Sorek Lab@soreklab.bsky.social · 11mo agoPreprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides tinyurl.com/ch3damp We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity Revealed by the amazing Ilya Osterman. See his thread below👇
Finally out! 🤩 Check out our HT- PELSA for high throughput screening！
Savitski Lab@savitski-lab.bsky.social · 11mo agoHappy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
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
Aude Bernheim@audeber.bsky.social · 12mo agoMany antiphage systems use NAD+, in many ways. @hugovaysset.bsky.social reviewed them all! Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity! www.cell.com/molecular-ce...
Congrats!
Kusterlab@kusterlab.bsky.social · last yr.New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...
The emerging roles of long non-coding RNAs in the nervous system www.nature.com/articles/s41...
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...
nature.com
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...
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...
nature.com
Wow!
Chris Parker@chrisgparker.bsky.social · last yr.Excited to share a new preprint from the lab. We show that PTMs like phosphorylation & glycosylation dynamically reshape proteome-wide ligandability in cells, including proteins like KRAS. Great collaboration with the Huang Lab, @forlilab.bsky.social and BMS. www.biorxiv.org/content/10.1...
‘Solar-powered’ sea slugs have specialized depots in their cells that store photosynthetic equipment looted from algae https://go.nature.com/4l27lMN
‘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.
go.nature.com
