We seek principles in the coordination among protein synthesis, metabolism, cell growth and differentiation PI: @slavov_n Videos: youtube.slavovlab.net

Boston, MA
We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability. biorxiv.org/content/10.1101/…
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Beyond heterogeneity, single-cell analysis can reveal functional coherence. Coherence, regularity and principles advance science. Full recording: piped.video/watch?v=z0dIhG4C…
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Millions of PBMCs have been analyzed by scRNA-seq. Have we seen it all ? We profiled thousands of single PBMCs — proteomes and transcriptomes side by side — and uncovered functional coordination undetectable in the deepest scRNA-seq we could perform. biorxiv.org/content/10.64898… 1/
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A very thoughtful and insightful discussion with @JShendure. Most of it focuses on the development of DNA sequencing by synthesis, but the ideas and lessons from that experience are general and applicable to other technologies. piped.video/watch?v=tXrVFmch…
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Among the numerous metrics evaluating academics, one stands out for me: Our intellectual heritage reflected in our students and colleagues, and their intellectual growth. That amplifies the initial sparks and bears more fruit than any one of us could have produced.
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Some of the most important scientific results were initially rejected before they became important milestones of scientific progress. 🔷 If you have great results, this is one of the most effective ways to help them succeed: blog.slavovlab.net/2024/02/1… 1/
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Nature just published a tech feature on single-cell proteomics. It highlights our journey from skepticism to robust technology and biological discoveries. I love that the feature starts with a biological discovery enabled by the technology: cell.com/cell/fulltext/S0092… 1/
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Replying to @ItaiYanai
My personal experience is different. I always felt motivated to take risks, and my most recognized success is based upon taking risks. I recently talked about this experience: piped.video/z0dIhG4C3qI?si=9JDF…
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High-throughput omics are powerful, but they don’t substitute for thinking. Discovering new biology often starts with intellectual input: frame sharp questions first, then choose the methods that can answer them, not the one that’s most convenient or currently fashionable. 1/
Agree. But this is not a specific issue with omics. Comes down to a lack of serious consideration of expt. designs that can enable answering well defined questions. Vague problem definitions/formulations, arbitrary designs, scaling modalities just cuz u can. Huge waste.
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My personal experience is different. I always felt motivated to take risks, and my most recognized success is based upon taking risks. I recently talked about this experience: piped.video/z0dIhG4C3qI?si=9JDF…
🔥Does academia stifle creativity? This new perspective argues that academia is currently structured to select against creativity, intellectual risk-taking and bold ideas. Young scientists – who may be best positioned for new ideas – are particularly incentivized to play it safe.
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What sets protein gradients in the liver ? The latest single-cell analysis from @ParallelSqTech shows it's often spatially regulated rates of protein synthesis and degradation. Liver cells (hepatocytes) form a gradient from the portal to the central vein, with variable protein abundance along this axis. Based on in vivo metabolic pulses with isotope labeled amino acids, we found zonated proteins whose mRNA levels don't track their protein levels: Their degradation rates do. A clear example is Mttp, a lipid-transfer protein that rises from portal to central cells. Its RNA doesn't explain that gradient. Its degradation rate does: Mttp is broken down faster in portal cells and more slowly in central cells. 🔷 The spatial pattern is set by protein stability. Zooming out, this wasn't a one-off. Across functional categories, zonated protein half-lives lined up with zonated protein abundance — a systematic signature of degradation shaping spatial identity. Interestingly, portal cells showed globally longer protein half-lives than central cells, especially for long-lived proteins. ⬛ A takeaway: Spatial identity in tissues isn't just about which genes get turned on — it's also about spatially regulated rates of protein degradation. Post-translational regulation is a driver of tissue architecture. 📄 Article: biorxiv.org/content/10.1101/…
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These numbers are key to understanding RNA and protein analysis. The different counting statistics fundamentally shape technological challenges and opportunities. nature.com/articles/s41592-0… 1/
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These results bode well for the feasibility of massively scaling up single-cell proteomics while preserving and increasing the depth of coverage and quantitative accuracy. 1/
Accurately quantifying over 700K precursors in a single 9-plexDIA set of 20ng proteomes is a new milestone. JMod achieves high quantitative accuracy over a 32-fold dynamic range of proteome spiked-in ratios across single-cell and bulk sample sizes. 1/ doi.org/10.1101/2025.05.22.6…
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Accurately quantifying over 700K precursors in a single 9-plexDIA set of 20ng proteomes is a new milestone. JMod achieves high quantitative accuracy over a 32-fold dynamic range of proteome spiked-in ratios across single-cell and bulk sample sizes. 1/ doi.org/10.1101/2025.05.22.6…
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Understanding protein biology at the molecular level can unlock entirely new ways to engineer protein interactions, and with them, a new generation of powerful therapies.
A new pharmacological strategy -- based on engineering protein surfaces -- just achieved major success against pancreatic cancer. It points toward a much broader class of cancer therapies. Yesterday, the FDA approved daraxonrasib (Rasonque), a drug that targets the RAS proteins driving most pancreatic cancers. What makes it especially fascinating is how it works. Rather than simply finding a conventional pocket on RAS, daraxonrasib binds the chaperone protein cyclophilin A and uses it to create a new protein surface. This drug–cyclophilin complex then engages active RAS, forming a three-part complex that blocks RAS interactions with downstream effectors. Remarkably, the complex can also stimulate GTP hydrolysis, further suppressing RAS signaling. This is chemical biology at its most powerful: a small molecule is not merely inhibiting a protein: It is engineering a new protein–protein interaction inside the cell to pharmacologically control a previously “undruggable” protein. The clinical impact is already impressive: in a randomized phase III trial, median survival in metastatic pancreatic cancer increased from 6.7 to 13.2 months compared with standard chemotherapy. 🔷 Perhaps the most exciting aspect is what comes next. If we can pharmacologically engineer new protein surfaces and interactions, rather than being restricted to naturally occurring binding pockets, the universe of druggable proteins—and potentially the range of cancers we can treat—could expand dramatically. A beautiful example of how understanding and engineering proteins can open entirely new therapeutic possibilities.
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Exactly 5 years ago, I presented projections for single-cell proteomics. It's fun and instructive to reflect on the projections, progress over the last 5 years, and on their correlation. The agreement is excellent 🚀 piped.video/HEA9Ua_mx8s?si=Zrjn…
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A major update -- prompted by constructive peer feedback -- shows remarkable gradients within basal cells: 🔷 Strong within-cell-type variation of protein abundance synthesis and degradation due to simple biophysical principles. > RNA doesn't reflect it. biorxiv.org/content/10.1101/…
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Save the date: Our 10th meeting will be on July 12 - 14, 2027 single-cell.net/proteomics/s…
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Our article is in today's issue of Nature. It shows that our proteome is more diverse than we thought, remarkably so ! This has been a long and exhilarating journey, beginning in 2019. It has opened perspectives that we are very eager to explore.
Our article is in today's issue of Nature. It shows that our proteome is more diverse than we thought, remarkably so ! This has been a long and exhilarating journey beginning in 2019. It has opened perspectives that we are very eager to explore.
Article

RNA Decoding Beyond the Genetic Code

Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA. Most proteomics follows this framework: predict protein sequences, then use mass spectrometry to measure

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A highlight of our recent Nature article reporting numerous stable proteins with amino acid sequences not predicted by the genetic code. Cells have more ways to diversify their proteomes. 📰 news.northeastern.edu/2026/0…
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