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
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
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.
Protein clearance rates vary across proteins in inverse proportion to the average cell-type doubling rate.
This explains the degree to which protein clearance (degradation) sets protein abundance.
biorxiv.org/content/10.1...
This explains the degree to which protein clearance (degradation) sets protein abundance.
biorxiv.org/content/10.1...
September 21, 2025 at 11:55 AM
Protein clearance rates vary across proteins in inverse proportion to the average cell-type doubling rate.
This explains the degree to which protein clearance (degradation) sets protein abundance.
biorxiv.org/content/10.1...
This explains the degree to which protein clearance (degradation) sets protein abundance.
biorxiv.org/content/10.1...
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
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules
September 21, 2025 at 11:54 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
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules
Our experimental design aimed for:
- Direct measurements
- Quantitative accuracy supporting confident modeling
- Scalable multiplexing & generalizable approach approach
- Direct measurements
- Quantitative accuracy supporting confident modeling
- Scalable multiplexing & generalizable approach approach
September 21, 2025 at 11:11 AM
Our experimental design aimed for:
- Direct measurements
- Quantitative accuracy supporting confident modeling
- Scalable multiplexing & generalizable approach approach
- Direct measurements
- Quantitative accuracy supporting confident modeling
- Scalable multiplexing & generalizable approach approach
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!
The neighboring gene knockout effects in yeast are even stronger.
In close range (below 1kb), the knockout affects the abundance of mRNA transcribed from nearby genes.
Yeast Data 🔽
In close range (below 1kb), the knockout affects the abundance of mRNA transcribed from nearby genes.
Yeast Data 🔽
August 20, 2025 at 12:29 PM
The neighboring gene knockout effects in yeast are even stronger.
In close range (below 1kb), the knockout affects the abundance of mRNA transcribed from nearby genes.
Yeast Data 🔽
In close range (below 1kb), the knockout affects the abundance of mRNA transcribed from nearby genes.
Yeast Data 🔽
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.
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.
Characterization of activity across the mutational landscape of an enzyme
August 11, 2025 at 11:16 AM
Characterization of activity across the mutational landscape of an enzyme
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
🧵
Cell size varies by many orders of magnitude.
The mechanisms that generate and maintain this extraordinary diversity of sizes remain incompletely understood.
The mechanisms that generate and maintain this extraordinary diversity of sizes remain incompletely understood.
July 16, 2025 at 2:33 PM
Cell size varies by many orders of magnitude.
The mechanisms that generate and maintain this extraordinary diversity of sizes remain incompletely understood.
The mechanisms that generate and maintain this extraordinary diversity of sizes remain incompletely understood.
Single-cell proteomics is gaining momentum.
It can analyze the proteomes of ~ 1,000 single cells / day, and we need to ensure high quality cell isolation and sample preparation:
⬛️ These approaches can help:
nature.com/articles/s41...
It can analyze the proteomes of ~ 1,000 single cells / day, and we need to ensure high quality cell isolation and sample preparation:
⬛️ These approaches can help:
nature.com/articles/s41...
May 9, 2025 at 11:09 AM
Single-cell proteomics is gaining momentum.
It can analyze the proteomes of ~ 1,000 single cells / day, and we need to ensure high quality cell isolation and sample preparation:
⬛️ These approaches can help:
nature.com/articles/s41...
It can analyze the proteomes of ~ 1,000 single cells / day, and we need to ensure high quality cell isolation and sample preparation:
⬛️ These approaches can help:
nature.com/articles/s41...
An alternative to tSNE & UMAP for more accurate data visualization:
Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data.
The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.
Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data.
The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.
May 9, 2025 at 11:07 AM
An alternative to tSNE & UMAP for more accurate data visualization:
Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data.
The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.
Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data.
The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.
May 4, 2025 at 10:57 AM
March 14, 2025 at 1:15 PM
pre-rRNA is cleaved into rRNA by a 500 kDa ribonucleoprotein, RNase MRP.
Why is such a large complex needed for a simple cleavage ?
We show how specific protein subunits distinguish RNase MRP from related enzymes and define its catalytic repertoar.
www.biorxiv.org/content/10.1...
Why is such a large complex needed for a simple cleavage ?
We show how specific protein subunits distinguish RNase MRP from related enzymes and define its catalytic repertoar.
www.biorxiv.org/content/10.1...
February 24, 2025 at 1:55 PM
pre-rRNA is cleaved into rRNA by a 500 kDa ribonucleoprotein, RNase MRP.
Why is such a large complex needed for a simple cleavage ?
We show how specific protein subunits distinguish RNase MRP from related enzymes and define its catalytic repertoar.
www.biorxiv.org/content/10.1...
Why is such a large complex needed for a simple cleavage ?
We show how specific protein subunits distinguish RNase MRP from related enzymes and define its catalytic repertoar.
www.biorxiv.org/content/10.1...
Our model & data unify previous observations with our new results and highlights a context-dependent and larger than previously appreciated contribution of protein degradation in shaping protein variation both across the proteome and across cell states.
February 13, 2025 at 1:04 PM
Our model & data unify previous observations with our new results and highlights a context-dependent and larger than previously appreciated contribution of protein degradation in shaping protein variation both across the proteome and across cell states.
What explains the divergence between RNA and protein levels ?
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
February 13, 2025 at 1:03 PM
What explains the divergence between RNA and protein levels ?
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵
Protein degradation is a HUGE factor.
It accounts for up to 50 % of protein variation across proteins & tissue types.
www.biorxiv.org/content/10.1...
🧵