These numbers are key to understanding RNA and protein analysis. The different counting statistics fundamentally shape technological challenges and opportunities. nature.com/articles/s41... 1/

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/

Nikolai Slavov@slavov-n.bsky.social · 5d ago

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...

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...

Many things are beyond our control, but we control how we treat other people. We can choose to act with integrity. We can choose to be authentic & empathetic. We can choose to pay attention, help, support and encourage our colleagues. 𝐂𝐡𝐨𝐨𝐬𝐞 𝐭𝐨 𝐛𝐞𝐡𝐚𝐯𝐞 𝐚𝐬 𝐭𝐡𝐞 𝐩𝐞𝐫𝐬𝐨𝐧 𝐲𝐨𝐮 𝐰𝐚𝐧𝐭 𝐭𝐨 𝐛𝐞.

If the deal goes through, it would be breaking with 150 years of American precedent at the birthplace of the national park system.

Adam Keiper@adamkeiper.com · last wk.

"For more than a year, the National Park Service has been quietly working to fulfill an unprecedented directive from Trump officials: Parcel off a corner of Yosemite National Park to give to a private developer." www.notus.org/agencies/tru...

I came to the U.S. 25 years ago to study at @mit.edu. I found a welcoming and generous country that attracted a disproportionate number of my friends from the International Science Olympiads. We found an open and rigorous academic environment that encouraged and respected independent thought. 1/

Is single nucleus RNA-seq representative of single-cell transcriptomes and proteomes ? This comparison shows that: 1⃣ Both scRNA-seq and snRNA-seq correlate weakly to single-cell proteomes. 2⃣ The correlation is much lower for snRNA-seq 1/

Single-cell RNA-seq is often characterized as providing comprehensive quantification of cellular transcriptomes. It doesn't. The number of distinct gene products (transcript fragments) detected by RNA sequencing in individual cells, is substantially below 20,000.

How is the rise of LLMs reshaping the public funding landscape ? NSF and NIH proposals tell a story. 1/

Two new companion articles emphasize the fundamental importance of protein degradation rates in shaping physiology, focussing on early mammalian development. They show that human cells degrade proteins ~1.5x slower than mouse cells across the proteome (segmentation clock + neural progenitors). 1/

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 🚀 youtu.be/HEA9Ua_mx8s?...

Strategies for driving single-cell proteomics forward | Nikolai Slavov | SCP2021

YouTube video by Nikolai Slavov

youtu.be

Let's start by resolving political and ethical problems supported by broad consensus: - Anyone using public office for self-enrichment should be forced to resign.

Nikolai Slavov@slavov-n.bsky.social · 6mo ago

Our world is beset by deep crises. What are well-reasoned, constructive visions for overcoming them ? Please share comments or references to forward-looking perspectives focused on overcoming our political and societal problems.

High spending and low taxes is good short-term politics, but it's bad for the country. A prosperous nation is not piling debt. It is building brighter future for its children.

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 data doesn't reflect it. www.biorxiv.org/content/10.1...

AI has excelled at some narrow verifiable tasks. Can it excel at open-ended research? The authors tested agents on the central, open-ended research questions from two unpublished NeurIPS submissions. 1/

Over the past week, I’ve been addressing peer reviews comments for multiple articles. I’m struck by how many of the reviews are deeply insightful, reflecting a careful reading of the research and asking thoughtful, constructive questions. 1/ blog.slavovlab.net/2023/04/15/p...

Peer review works

I cannot read it and agree with claims that peer review “is broken” and does not work. Such claims are at best oversimplifying the problems and selectively excluding evidence.

blog.slavovlab.net

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. nikolaislavov.substack.com/p/rna-decodi...

RNA Decoding Beyond the Genetic Code

What Have We Been Missing in the Proteome?

nikolaislavov.substack.com

Save the date: The 10th Single Cell Proteomics Conference (SCP2027) will be on July 12 - 14, 2027 single-cell.net/proteomics/s...

AI is extremely powerful in many ways. Perhaps its most impressive power is the ability to completely evade the critical thinking of many, including smart people. 🧠

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/2026/08/10/p...

A new study suggests that our bodies produce more proteins than we thought

Protein sequence determination depends on more than DNA, Northeastern research finds, with new clues into cancer and Alzheimer's.

news.northeastern.edu

Information is more accessible than ever. AI models excel at information retrieval. And yet, the quality of popular & influential information sources is declining. How do we reverse this dangerous trend ? ℹ️

Developing treatments for Alzheimer’s and Parkinson’s diseases is limited by the incomplete understanding of the molecular processes underlying them. Single-cell proteomics is opening a new window into these diseases: - It allows for a different type of analysis, different in kind. 1/

A revision in response to very constructive suggestions by the peer reviewers. The results became even more compelling. Thanks for the feedback!

Slavov Laboratory@slavovlab.bsky.social · last mo.

In this revision, we expanded our analysis across more tissue types & more model systems. The conclusions held. Proteomes are strongly shaped by tissue type-specific protein degradation rates ▶️ This effect strongly depends on the cell growth rates. 🔗 www.biorxiv.org/content/10.1...

In this revision, we expanded our analysis across more tissue types & more model systems. The conclusions held. Proteomes are strongly shaped by tissue type-specific protein degradation rates ▶️ This effect strongly depends on the cell growth rates. 🔗 www.biorxiv.org/content/10.1...

We're looking for mass spectrometry enthusiasts who thrive on quantitative rigor, innovation and enjoy challenges: - Colleagues eager to propel biological discoveries by inventing the technologies of the future.

Organizing our ideas in thoughtful, coherent written form is among the best mechanisms to train our thinking and become better communicators. However we use AI, we should not miss on practicing thinking so that we can sharpen & elevate our intellect.

A pioneer of AI-in-biology rebuts the "AI will cure cancer" narrative. Not smarter models. Measurements. 90%+ of clinical trials fail — usually the molecule was fine, the mechanism was wrong. Scalable mass spec proteomics = a real path to the functional data we're missing. 🧵

I enjoyed this conference ! Many presentations combined relatively simple, intuitive biophysical models with clear predictions that were experimentally tested. I especially appreciated when speakers were explicit about their study assumptions and limitations, facilitating critical discussions.

Nikolai Slavov@slavov-n.bsky.social · last mo.

I recently attended two Gordon Research Conferences on very different topics. The most memorable talks had one thing in common: They focused deeply on a single project, taught something new with rigor, made their assumptions and caveats clear, and invited critical thinking. 1/

I recently attended two Gordon Research Conferences on very different topics. The most memorable talks had one thing in common: They focused deeply on a single project, taught something new with rigor, made their assumptions and caveats clear, and invited critical thinking. 1/

One fold. Many different jobs. Antibodies, T-cell receptors, MHC molecules, cell adhesion proteins, even a giant muscle protein like titin — all of them use the same ancient structural building block: a small β-sandwich domain called the immunoglobulin fold. 1/