Great collaboration with Miki Ebisuyas lab!

Miki Ebisuya@ebisuyamiki.bsky.social · 24h ago

New paper from the lab! authors.elsevier.com/sd/article/S... We find that protein degradation is broadly slower in human segmentation clock cells than in mouse cells, regardless of the degradation pathway or protein category! 1/

Bolor's paper is now out! Read the final story here: www.nature.com/articles/s41... See below 👇 for the main highlights

Systematic profiling of growth interactions in human gut microbiome species - Nature Communications

Here, Buyanbadrakh et al. systematically map growth interactions among gut bacteria, revealing predominantly inhibitory effects, and identifying extracellular vesicles and pH modulation as mechanisms ...

nature.com

Mateus lab@mateuslab.com · 8mo ago

New preprint from the lab is out! 🥳 We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions. www.biorxiv.org/content/10.6... 👇

Phosphorylation-driven signaling plays a central role in how cells communicate. In this study, together with @saezlab.bsky.social , we revisit the EGF signaling pathway and ask: How well does our traditional understanding hold up in the era of modern phosphoproteomics? www.nature.com/articles/s41...

Saez-Rodriguez Group@saezlab.bsky.social · 6mo ago

Interested 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...

10 years and still standing strong @EMBL 🍾💪 Huge thanks to all members, alumni, supporters & colleagues who made it possible. Here’s to the next decade! 🙏

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

ICYMI during the holidays. I am really proud of Bolor's efforts and the first work coming out of the lab! Read it here: www.biorxiv.org/content/10.6...

Systematic profiling of growth interactions in human gut microbiome species

Microbial interactions shape the composition and stability of the human gut microbiome. Yet, the molecular mechanisms underlying these relationships remain poorly understood. Here, we systematically p...

biorxiv.org

Mateus lab@mateuslab.com · 8mo ago

New preprint from the lab is out! 🥳 We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions. www.biorxiv.org/content/10.6... 👇

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...

Happy 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 ⬇️

High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria - Nature Structural & Molecular Biology

Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...

nature.com

Savitski Lab@savitski-lab.bsky.social · last yr.

Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...

So grateful and honored to receive the MCP Lectureship Award at the #ASBMBProteomics meeting at the Broad Institute! Huge thanks to the wonderful organizers and to everyone—past and present—who’s been part of our lab.

The final version of our multi-omics study on kidney fibrosis is out now (tinyurl.com/kidneyfibMSB). Together w/ Pepperkok + Savitski labs @embl.org, we present a time-resolved #multiomics + computational network modeling approach in combination w/ phenotypic assays to study #kidneyfibrosis

integrated temporally resolved transcriptomic, proteomic, and secretomic profiling of human kidney mesenchymal cells from @savitski-lab.bsky.social @saezlab.bsky.social @miraburtscher.bsky.social identify dynamic changes upon TGF-beta stimulation ➡️ www.embopress.org/doi/full/10....

Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...

nature.com

Some small molecules modulate protein condensation in cells, but how? Our latest work shows a possible mechanism of action of the small molecule lipoamide. This molecule prevents condensation of stress granules whose components are found as protein aggregates in ALS. www.nature.com/articles/s41...

Small-molecule dissolution of stress granules by redox modulation benefits ALS models - Nature Chemical Biology

Uechi et al. found that a small-molecule lipoamide dissolves stress granules (SGs) by targeting SFPQ, a redox-sensitive disordered SG protein, alleviating pathological phenotypes caused by amyotrophic...

nature.com

Hiro's paper is out! @hiro-cg5445.bsky.social Collaboration and Tour de Force with Richard Wheeler @zephyris-science.bsky.social and many other coauthors. Big congratulations and thank you to anyone involved! www.nature.com/articles/s41...

Small-molecule dissolution of stress granules by redox modulation benefits ALS models - Nature Chemical Biology

Uechi et al. found that a small-molecule lipoamide dissolves stress granules (SGs) by targeting SFPQ, a redox-sensitive disordered SG protein, alleviating pathological phenotypes caused by amyotrophic...

nature.com

Thank you for this great perspective on our #glycoproteomics study @timveth.bsky.social and @nmriley.bsky.social!

Trends in Biochemical Sciences@cp-trendsbiochem.bsky.social · last yr.

Online now - the Spotlight "Accelerating the stride toward functional #glycoproteomics" from @timveth.bsky.social and @nmriley.bsky.social. #Glycoproteins #Glycoforms #Glycoprofiling #DQGlyco #Glycotime authors.elsevier.com/a/1l3k53S6Gf...

Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...

High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria

Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detectin...

biorxiv.org

Bacteria can influence how sugars modify proteins in the brain – shown for the first time by EMBL researchers. In their study, the scientists describe a new method to study glycosylation systematically & quantitatively, leading to new biological insights. 🧪🧠📈 www.embl.org/news/science...

We are very happy to present our work on N-glycoproteomics!🍬 Our method enables the selective enrichment and precise quantification of intact N-glycopeptides to explore the dynamics of glycosylation microheterogeneity. www.nature.com/articles/s41...