Slavov Laboratory
@slavovlab.bsky.social
We seek principles in the coordination among protein synthesis, metabolism, cell growth and differentiation. PI: @slavov-n.bsky.social
Web: https://slavovlab.net
Videos: http://youtube.slavovlab.net
Web: https://slavovlab.net
Videos: http://youtube.slavovlab.net
Mass spectrometry enables omics scale quantification of the rates of macromolecule synthesis and degradation in the single cells of a living mammalian tissue.
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Single-cell omics methods are mighty but bound to static snapshot when analyzing 𝑖𝑛 𝑣𝑖𝑣𝑜 tissues.
Mass spec offers a solution.
⬛️ It enables omics scale quantification of the rates of macromolecule synthesis and degradation in a living organism.
blog.slavovlab.net/2025/11/19/i...
Mass spec offers a solution.
⬛️ It enables omics scale quantification of the rates of macromolecule synthesis and degradation in a living organism.
blog.slavovlab.net/2025/11/19/i...
November 20, 2025 at 2:59 PM
Mass spectrometry enables omics scale quantification of the rates of macromolecule synthesis and degradation in the single cells of a living mammalian tissue.
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The majority of isoform pairs (of alternatively spliced transcripts) share less than 50% of their interactions.
In the context of interactome networks, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other.
In the context of interactome networks, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other.
Proteoforms encoded by the same gene have different interactomes.
This challenges:
1⃣ The interpretation of data from affinity reagents directed towards shared epitopes.
2⃣ The assignment of functions to genes.
When will biological research focus on such functional differences?
This challenges:
1⃣ The interpretation of data from affinity reagents directed towards shared epitopes.
2⃣ The assignment of functions to genes.
When will biological research focus on such functional differences?
November 6, 2025 at 1:41 PM
The majority of isoform pairs (of alternatively spliced transcripts) share less than 50% of their interactions.
In the context of interactome networks, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other.
In the context of interactome networks, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other.
Protein degradation plays major roles in aging physiology & pathology.
We can start analyzing it quantitatively at higher resolution & scale.
A promising new direction for aging research 🚀
We can start analyzing it quantitatively at higher resolution & scale.
A promising new direction for aging research 🚀
Aging is associated with changes in protein abundance in many organs and tissues.
We find that the protein changes are cell-type specific, and thus muted in previous bulk analysis.
Protein clearance rates change with age and drive the ...
www.biorxiv.org/content/10.1...
We find that the protein changes are cell-type specific, and thus muted in previous bulk analysis.
Protein clearance rates change with age and drive the ...
www.biorxiv.org/content/10.1...
October 30, 2025 at 2:52 PM
Protein degradation plays major roles in aging physiology & pathology.
We can start analyzing it quantitatively at higher resolution & scale.
A promising new direction for aging research 🚀
We can start analyzing it quantitatively at higher resolution & scale.
A promising new direction for aging research 🚀
Mechanotransduction in the nucleus
Multiple TFs transmit mechanical forces into transcriptional regulation.
Nuclear shape, size, and chromatin abnormalities are common features of many diseases.
Multiple TFs transmit mechanical forces into transcriptional regulation.
Nuclear shape, size, and chromatin abnormalities are common features of many diseases.
October 27, 2025 at 9:48 AM
Mechanotransduction in the nucleus
Multiple TFs transmit mechanical forces into transcriptional regulation.
Nuclear shape, size, and chromatin abnormalities are common features of many diseases.
Multiple TFs transmit mechanical forces into transcriptional regulation.
Nuclear shape, size, and chromatin abnormalities are common features of many diseases.
October 25, 2025 at 12:38 PM
Reposted by Slavov Laboratory
The big picture:
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
Proteomics: The arc of progress in life sciences | Research Fest by PTI
YouTube video by Nikolai Slavov
youtu.be
October 24, 2025 at 7:38 PM
The big picture:
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
A highlight of our results on alternate RNA decoding.
When the weirdo variant protein versions outnumber the “real” ones:
When Variant Proteins Aren't Actually the Variant Ones
www.science.org
October 25, 2025 at 12:30 PM
A highlight of our results on alternate RNA decoding.
Reposted by Slavov Laboratory
This article is a homecoming for me.
As a PhD student, I focused on the growth-rate transcriptional regulation in yeast.
Now, ~ 20 years later, we report protein regulation scaling with the growth rates of single cells in mammalian tissues.
www.biorxiv.org/content/10.1...
As a PhD student, I focused on the growth-rate transcriptional regulation in yeast.
Now, ~ 20 years later, we report protein regulation scaling with the growth rates of single cells in mammalian tissues.
www.biorxiv.org/content/10.1...
Principles of protein abundance regulation across single cells in a mammalian tissue
Protein synthesis and clearance are major regulatory steps of gene expression, but their in vivo regulatory roles across the cells comprising complex tissues remains unexplored. Here, we systematicall...
www.biorxiv.org
October 18, 2025 at 11:56 AM
This article is a homecoming for me.
As a PhD student, I focused on the growth-rate transcriptional regulation in yeast.
Now, ~ 20 years later, we report protein regulation scaling with the growth rates of single cells in mammalian tissues.
www.biorxiv.org/content/10.1...
As a PhD student, I focused on the growth-rate transcriptional regulation in yeast.
Now, ~ 20 years later, we report protein regulation scaling with the growth rates of single cells in mammalian tissues.
www.biorxiv.org/content/10.1...
Is your research important ?
If important, make it count.
Make it easy to reproduce.
Share the data.
Share the code.
Share the metadata.
Use community guidelines to facilitate reanalysis & reuse of your results.
nature.com/articles/s41...
If important, make it count.
Make it easy to reproduce.
Share the data.
Share the code.
Share the metadata.
Use community guidelines to facilitate reanalysis & reuse of your results.
nature.com/articles/s41...
October 18, 2025 at 11:53 AM
Is your research important ?
If important, make it count.
Make it easy to reproduce.
Share the data.
Share the code.
Share the metadata.
Use community guidelines to facilitate reanalysis & reuse of your results.
nature.com/articles/s41...
If important, make it count.
Make it easy to reproduce.
Share the data.
Share the code.
Share the metadata.
Use community guidelines to facilitate reanalysis & reuse of your results.
nature.com/articles/s41...
What is the relationship between the transcriptional induction of a gene and the fitness effect of its deletion ?
This study reported remarkably low correlations in the context of heat shock response and survival.
This study reported remarkably low correlations in the context of heat shock response and survival.
October 13, 2025 at 1:31 PM
What is the relationship between the transcriptional induction of a gene and the fitness effect of its deletion ?
This study reported remarkably low correlations in the context of heat shock response and survival.
This study reported remarkably low correlations in the context of heat shock response and survival.
Reposted by Slavov Laboratory
An amazing feat of regulation.
Two very different regulatory mechanisms converge to shape the mitochondrial proteome and keep us alive!
Two very different regulatory mechanisms converge to shape the mitochondrial proteome and keep us alive!
September 27, 2025 at 10:50 AM
An amazing feat of regulation.
Two very different regulatory mechanisms converge to shape the mitochondrial proteome and keep us alive!
Two very different regulatory mechanisms converge to shape the mitochondrial proteome and keep us alive!
Reposted by Slavov Laboratory
mRNA-mRNA correlations across the single cells from a tissue are rarely interpreted.
They differ from the corresponding protein-protein correlations?
𝐖𝐡𝐲 ❓
www.biorxiv.org/content/10.1...
🧵
They differ from the corresponding protein-protein correlations?
𝐖𝐡𝐲 ❓
www.biorxiv.org/content/10.1...
🧵
September 29, 2025 at 10:46 AM
mRNA-mRNA correlations across the single cells from a tissue are rarely interpreted.
They differ from the corresponding protein-protein correlations?
𝐖𝐡𝐲 ❓
www.biorxiv.org/content/10.1...
🧵
They differ from the corresponding protein-protein correlations?
𝐖𝐡𝐲 ❓
www.biorxiv.org/content/10.1...
🧵
The regulation of nuclear-encoded mitochondrial proteins is fascinating.
They are synthesized in a fully eukaryotic manner, with introns, splicing, and cytosolic ribosomes.
Yet, they are degraded by proteases that look and act bacterial.
blog.slavovlab.net/2025/09/23/m...
They are synthesized in a fully eukaryotic manner, with introns, splicing, and cytosolic ribosomes.
Yet, they are degraded by proteases that look and act bacterial.
blog.slavovlab.net/2025/09/23/m...
Mixing eukaryotic synthesis with prokaryotic degradation
The Evolutionary Balancing Act Coordinating gene regulation across two fundamentally different systems is one of the great balancing acts of life. Mitochondria embody this challenge: most of their …
blog.slavovlab.net
September 24, 2025 at 12:10 AM
The regulation of nuclear-encoded mitochondrial proteins is fascinating.
They are synthesized in a fully eukaryotic manner, with introns, splicing, and cytosolic ribosomes.
Yet, they are degraded by proteases that look and act bacterial.
blog.slavovlab.net/2025/09/23/m...
They are synthesized in a fully eukaryotic manner, with introns, splicing, and cytosolic ribosomes.
Yet, they are degraded by proteases that look and act bacterial.
blog.slavovlab.net/2025/09/23/m...
Reposted by Slavov Laboratory
Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
September 22, 2025 at 10:54 AM
Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
September 21, 2025 at 11:07 AM
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
A key mechanism controlling mitosis is the precise timing of over 32,000 phosphorylation events.
Below are some of the key regulators of mitosis.
Below are some of the key regulators of mitosis.
September 11, 2025 at 11:19 AM
A key mechanism controlling mitosis is the precise timing of over 32,000 phosphorylation events.
Below are some of the key regulators of mitosis.
Below are some of the key regulators of mitosis.
Proteins self-organize to build large structures, 100,000-fold larger then the proteins.
It's elegantly dynamic !
Proteins constantly self-assemble and disassemble to build skeletal structures in our cells, shaping and orchestrating life.
It's elegantly dynamic !
Proteins constantly self-assemble and disassemble to build skeletal structures in our cells, shaping and orchestrating life.
September 6, 2025 at 10:43 AM
Proteins self-organize to build large structures, 100,000-fold larger then the proteins.
It's elegantly dynamic !
Proteins constantly self-assemble and disassemble to build skeletal structures in our cells, shaping and orchestrating life.
It's elegantly dynamic !
Proteins constantly self-assemble and disassemble to build skeletal structures in our cells, shaping and orchestrating life.
𝐓𝐨𝐝𝐚𝐲 𝐦𝐚𝐫𝐤𝐬 𝐨𝐮𝐫 𝟏𝟎𝐭𝐡 𝐚𝐧𝐧𝐢𝐯𝐞𝐫𝐬𝐚𝐫𝐲 🎉
A decade of pushing the boundaries in proteomics, systems biology, and data-driven discovery.
🔬 Thank you to our collaborators, alumni & supporters!
A decade of pushing the boundaries in proteomics, systems biology, and data-driven discovery.
🔬 Thank you to our collaborators, alumni & supporters!
September 1, 2025 at 10:32 AM
𝐓𝐨𝐝𝐚𝐲 𝐦𝐚𝐫𝐤𝐬 𝐨𝐮𝐫 𝟏𝟎𝐭𝐡 𝐚𝐧𝐧𝐢𝐯𝐞𝐫𝐬𝐚𝐫𝐲 🎉
A decade of pushing the boundaries in proteomics, systems biology, and data-driven discovery.
🔬 Thank you to our collaborators, alumni & supporters!
A decade of pushing the boundaries in proteomics, systems biology, and data-driven discovery.
🔬 Thank you to our collaborators, alumni & supporters!
Reposted by Slavov Laboratory
Our findings (now published in @narjournal.bsky.social) identify the first metazoan RNase MRP-specific protein subunits.
We also define the RNA-targeting repertoire of this essential enzyme in mammalian cells.
academic.oup.com/nar/article/...
We also define the RNA-targeting repertoire of this essential enzyme in mammalian cells.
academic.oup.com/nar/article/...
August 29, 2025 at 10:56 AM
Our findings (now published in @narjournal.bsky.social) identify the first metazoan RNase MRP-specific protein subunits.
We also define the RNA-targeting repertoire of this essential enzyme in mammalian cells.
academic.oup.com/nar/article/...
We also define the RNA-targeting repertoire of this essential enzyme in mammalian cells.
academic.oup.com/nar/article/...
Reposted by Slavov Laboratory
The registration for SCP2026 is open !
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
August 25, 2025 at 11:13 AM
The registration for SCP2026 is open !
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
Neighboring gene effects account for much of the observed phenotypes of gene deletions.
This is a crucial factor to consider in knockout experiments.
Phenotypic similarity is exponentially related to chromosomal proximity in both yeast & human genomes.
Human Data 🔽
This is a crucial factor to consider in knockout experiments.
Phenotypic similarity is exponentially related to chromosomal proximity in both yeast & human genomes.
Human Data 🔽
August 20, 2025 at 12:28 PM
Neighboring gene effects account for much of the observed phenotypes of gene deletions.
This is a crucial factor to consider in knockout experiments.
Phenotypic similarity is exponentially related to chromosomal proximity in both yeast & human genomes.
Human Data 🔽
This is a crucial factor to consider in knockout experiments.
Phenotypic similarity is exponentially related to chromosomal proximity in both yeast & human genomes.
Human Data 🔽
The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts.
August 20, 2025 at 12:26 PM
The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts.
Protein synthesis is among the most energy demanding processes in a cell.
𝐖𝐡𝐲 𝐚𝐫𝐞 𝐭𝐡𝐞𝐧 𝐬𝐨𝐦𝐞 𝐩𝐫𝐨𝐭𝐞𝐢𝐧𝐬 𝐜𝐨𝐧𝐭𝐢𝐧𝐮𝐨𝐮𝐬𝐥𝐲 𝐬𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐳𝐞𝐝 𝐚𝐧𝐝 𝐢𝐦𝐦𝐞𝐝𝐢𝐚𝐭𝐞𝐥𝐲 𝐝𝐞𝐠𝐫𝐚𝐝𝐞𝐝 ?
blog.slavovlab.net/2025/08/16/p...
𝐖𝐡𝐲 𝐚𝐫𝐞 𝐭𝐡𝐞𝐧 𝐬𝐨𝐦𝐞 𝐩𝐫𝐨𝐭𝐞𝐢𝐧𝐬 𝐜𝐨𝐧𝐭𝐢𝐧𝐮𝐨𝐮𝐬𝐥𝐲 𝐬𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐳𝐞𝐝 𝐚𝐧𝐝 𝐢𝐦𝐦𝐞𝐝𝐢𝐚𝐭𝐞𝐥𝐲 𝐝𝐞𝐠𝐫𝐚𝐝𝐞𝐝 ?
blog.slavovlab.net/2025/08/16/p...
Proteins made to die
Protein synthesis is among the most energy-demanding processes in a cell. Yet, some proteins are synthesized and immediately degraded. This may seem like a futile cycle, but it’s a remarkable…
blog.slavovlab.net
August 18, 2025 at 12:46 PM
Protein synthesis is among the most energy demanding processes in a cell.
𝐖𝐡𝐲 𝐚𝐫𝐞 𝐭𝐡𝐞𝐧 𝐬𝐨𝐦𝐞 𝐩𝐫𝐨𝐭𝐞𝐢𝐧𝐬 𝐜𝐨𝐧𝐭𝐢𝐧𝐮𝐨𝐮𝐬𝐥𝐲 𝐬𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐳𝐞𝐝 𝐚𝐧𝐝 𝐢𝐦𝐦𝐞𝐝𝐢𝐚𝐭𝐞𝐥𝐲 𝐝𝐞𝐠𝐫𝐚𝐝𝐞𝐝 ?
blog.slavovlab.net/2025/08/16/p...
𝐖𝐡𝐲 𝐚𝐫𝐞 𝐭𝐡𝐞𝐧 𝐬𝐨𝐦𝐞 𝐩𝐫𝐨𝐭𝐞𝐢𝐧𝐬 𝐜𝐨𝐧𝐭𝐢𝐧𝐮𝐨𝐮𝐬𝐥𝐲 𝐬𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐳𝐞𝐝 𝐚𝐧𝐝 𝐢𝐦𝐦𝐞𝐝𝐢𝐚𝐭𝐞𝐥𝐲 𝐝𝐞𝐠𝐫𝐚𝐝𝐞𝐝 ?
blog.slavovlab.net/2025/08/16/p...
Spliceosome Dynamics
During splicing, stepwise assembly is one principle by which spliceosomes on the one hand ensure the faithful recognition of splice sites and on the other hand become susceptible to regulatory inputs to implement alternative splicing.
During splicing, stepwise assembly is one principle by which spliceosomes on the one hand ensure the faithful recognition of splice sites and on the other hand become susceptible to regulatory inputs to implement alternative splicing.
August 12, 2025 at 11:26 AM
Spliceosome Dynamics
During splicing, stepwise assembly is one principle by which spliceosomes on the one hand ensure the faithful recognition of splice sites and on the other hand become susceptible to regulatory inputs to implement alternative splicing.
During splicing, stepwise assembly is one principle by which spliceosomes on the one hand ensure the faithful recognition of splice sites and on the other hand become susceptible to regulatory inputs to implement alternative splicing.
Quantitative protein assays on Illumina chips.
A creative use of the impressive imaging capabilities developed for DNA sequencing by synthesis.
◼️ It allowed quantifying binding and enzyme catalysis
🧵
A creative use of the impressive imaging capabilities developed for DNA sequencing by synthesis.
◼️ It allowed quantifying binding and enzyme catalysis
🧵
August 11, 2025 at 11:16 AM
Quantitative protein assays on Illumina chips.
A creative use of the impressive imaging capabilities developed for DNA sequencing by synthesis.
◼️ It allowed quantifying binding and enzyme catalysis
🧵
A creative use of the impressive imaging capabilities developed for DNA sequencing by synthesis.
◼️ It allowed quantifying binding and enzyme catalysis
🧵