Nikolai Slavov
@slavov-n.bsky.social
Mentor, scientist & engineer. Having fun in @slavovlab.bsky.social and Parallel Squared Technology Institute @parallelsq.bsky.social with biology & single-cell proteomics.
https://nikolai.slavovlab.net
https://nikolai.slavovlab.net
Pinned
Introduction to dimensionality reduction | Statistics for proteomics
YouTube video by Nikolai Slavov
youtu.be
A basic intro with some strategies how to avoid mistakes when using dimensionality reduction.
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youtu.be/nIB-WjWzDSc?...
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youtu.be/nIB-WjWzDSc?...
When the most fervent supporters of a politician have to say that he still has his mojo, he is losing it.
November 26, 2025 at 2:38 PM
When the most fervent supporters of a politician have to say that he still has his mojo, he is losing it.
A question relevant to mRNA-based virtual models:
Are protein and phosphorylation levels predictable from genomic and transcriptomic data ?
This study concluded:
"The performance of even the best-performing model was modest, ..."
Are protein and phosphorylation levels predictable from genomic and transcriptomic data ?
This study concluded:
"The performance of even the best-performing model was modest, ..."
November 26, 2025 at 2:09 PM
A question relevant to mRNA-based virtual models:
Are protein and phosphorylation levels predictable from genomic and transcriptomic data ?
This study concluded:
"The performance of even the best-performing model was modest, ..."
Are protein and phosphorylation levels predictable from genomic and transcriptomic data ?
This study concluded:
"The performance of even the best-performing model was modest, ..."
miRNA have multiple functions beyond their role in modulating translation.
November 23, 2025 at 3:18 PM
miRNA have multiple functions beyond their role in modulating translation.
Which is the most misguided editorial in a high-profile journal ?
I will nominate the first suggestion.
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I will nominate the first suggestion.
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November 23, 2025 at 2:59 PM
Which is the most misguided editorial in a high-profile journal ?
I will nominate the first suggestion.
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I will nominate the first suggestion.
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The time is ripe to advance our understanding of the complex world of translation.
We can profile the diverse pool of modified tRNAs and a wider spectrum of amino acid incorporation into proteins: www.biorxiv.org/content/10.1...
The synergy of these developments will exciting ❗️
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We can profile the diverse pool of modified tRNAs and a wider spectrum of amino acid incorporation into proteins: www.biorxiv.org/content/10.1...
The synergy of these developments will exciting ❗️
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November 21, 2025 at 3:29 PM
The time is ripe to advance our understanding of the complex world of translation.
We can profile the diverse pool of modified tRNAs and a wider spectrum of amino acid incorporation into proteins: www.biorxiv.org/content/10.1...
The synergy of these developments will exciting ❗️
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We can profile the diverse pool of modified tRNAs and a wider spectrum of amino acid incorporation into proteins: www.biorxiv.org/content/10.1...
The synergy of these developments will exciting ❗️
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Missing data are common in all omics data.
But they are not one thing.
They can have very different generative mechanisms.
Successful analysis starts with understanding their origin and continues with missing aware analysis.
youtu.be/KwprNYv5Pp0?...
But they are not one thing.
They can have very different generative mechanisms.
Successful analysis starts with understanding their origin and continues with missing aware analysis.
youtu.be/KwprNYv5Pp0?...
Types of missing data in proteomics | Statistics for proteomics
YouTube video by Nikolai Slavov
youtu.be
November 21, 2025 at 1:00 PM
Missing data are common in all omics data.
But they are not one thing.
They can have very different generative mechanisms.
Successful analysis starts with understanding their origin and continues with missing aware analysis.
youtu.be/KwprNYv5Pp0?...
But they are not one thing.
They can have very different generative mechanisms.
Successful analysis starts with understanding their origin and continues with missing aware analysis.
youtu.be/KwprNYv5Pp0?...
A wonderful visualization of the importance of perspective.
Keep it in mind the next time you do dimensionality reduction.
Keep it in mind the next time you do dimensionality reduction.
November 20, 2025 at 3:18 PM
A wonderful visualization of the importance of perspective.
Keep it in mind the next time you do dimensionality reduction.
Keep it in mind the next time you do dimensionality reduction.
Reposted by Nikolai Slavov
The multiplexing approaches that we are developing allow scaling up such rate measurements.
timePlex, PSMtags, and JMod can all support increased throughput for 𝑖𝑛 𝑣𝑖𝑣𝑜 metabolic pulse experiments, and thus make dynamic protein analysis more scalable.
Quote
timePlex, PSMtags, and JMod can all support increased throughput for 𝑖𝑛 𝑣𝑖𝑣𝑜 metabolic pulse experiments, and thus make dynamic protein analysis more scalable.
Quote
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 2:44 PM
The multiplexing approaches that we are developing allow scaling up such rate measurements.
timePlex, PSMtags, and JMod can all support increased throughput for 𝑖𝑛 𝑣𝑖𝑣𝑜 metabolic pulse experiments, and thus make dynamic protein analysis more scalable.
Quote
timePlex, PSMtags, and JMod can all support increased throughput for 𝑖𝑛 𝑣𝑖𝑣𝑜 metabolic pulse experiments, and thus make dynamic protein analysis more scalable.
Quote
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 2:43 PM
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...
I added "𝑇ℎ𝑒 𝑠𝑡𝑟𝑒𝑛𝑔𝑡ℎ 𝑜𝑓 𝑤𝑒𝑎𝑘 𝑡𝑖𝑒𝑠".
It was rejected.
The rejection so dispirited its author, that he did not resubmit it for years.
Now, it's a cornerstone having shaped a field.
It's been cited 78,352 times.
blog.slavovlab.net/2014/08/15/p...
It was rejected.
The rejection so dispirited its author, that he did not resubmit it for years.
Now, it's a cornerstone having shaped a field.
It's been cited 78,352 times.
blog.slavovlab.net/2014/08/15/p...
Papers that triumphed over their rejections
Kary Mullis: I knew PCR would spread across the world like wild fire. This time there was no doubt in my mind: Nature would publish it. They rejected it. So did Science … Fuck them, I said
blog.slavovlab.net
November 20, 2025 at 12:57 PM
I added "𝑇ℎ𝑒 𝑠𝑡𝑟𝑒𝑛𝑔𝑡ℎ 𝑜𝑓 𝑤𝑒𝑎𝑘 𝑡𝑖𝑒𝑠".
It was rejected.
The rejection so dispirited its author, that he did not resubmit it for years.
Now, it's a cornerstone having shaped a field.
It's been cited 78,352 times.
blog.slavovlab.net/2014/08/15/p...
It was rejected.
The rejection so dispirited its author, that he did not resubmit it for years.
Now, it's a cornerstone having shaped a field.
It's been cited 78,352 times.
blog.slavovlab.net/2014/08/15/p...
Among all proteome changes in Alzheimer’s disease (AD), 20S proteasomes stand out.
⬛️ Their abundance strongly declines in AD patients.
=> This decline parallels a reduction in 20S substrate proteins and leads to abnormal protein accumulation in AD.
www.biorxiv.org/content/10.1...
⬛️ Their abundance strongly declines in AD patients.
=> This decline parallels a reduction in 20S substrate proteins and leads to abnormal protein accumulation in AD.
www.biorxiv.org/content/10.1...
November 19, 2025 at 1:38 PM
Among all proteome changes in Alzheimer’s disease (AD), 20S proteasomes stand out.
⬛️ Their abundance strongly declines in AD patients.
=> This decline parallels a reduction in 20S substrate proteins and leads to abnormal protein accumulation in AD.
www.biorxiv.org/content/10.1...
⬛️ Their abundance strongly declines in AD patients.
=> This decline parallels a reduction in 20S substrate proteins and leads to abnormal protein accumulation in AD.
www.biorxiv.org/content/10.1...
Protein regulation varies across single cells, cell types, tissues, and organs.
The brain proteome is highly sculpted by protein degradation.
Why ?
This is our model: biorxiv.org/content/10.1...
The brain proteome is highly sculpted by protein degradation.
Why ?
This is our model: biorxiv.org/content/10.1...
November 17, 2025 at 1:14 PM
Protein regulation varies across single cells, cell types, tissues, and organs.
The brain proteome is highly sculpted by protein degradation.
Why ?
This is our model: biorxiv.org/content/10.1...
The brain proteome is highly sculpted by protein degradation.
Why ?
This is our model: biorxiv.org/content/10.1...
How do plants orient towards light ?
In the absence of obvious physical sensing organs like lenses, how do plants work out the precise direction from which light is coming ?
In the absence of obvious physical sensing organs like lenses, how do plants work out the precise direction from which light is coming ?
November 16, 2025 at 12:34 PM
How do plants orient towards light ?
In the absence of obvious physical sensing organs like lenses, how do plants work out the precise direction from which light is coming ?
In the absence of obvious physical sensing organs like lenses, how do plants work out the precise direction from which light is coming ?
Fitness influencers promote super-high-protein diets, and protein-fortified foods and protein supplements form a market worth tens of billions of USD.
Yet, studies show there’s only so much protein the body can use.
Yet, studies show there’s only so much protein the body can use.
November 15, 2025 at 4:17 PM
Fitness influencers promote super-high-protein diets, and protein-fortified foods and protein supplements form a market worth tens of billions of USD.
Yet, studies show there’s only so much protein the body can use.
Yet, studies show there’s only so much protein the body can use.
Dimensionality reduction can see structures that do not exist and miss structures that exist.
𝐓𝐡𝐞 𝐬𝐢𝐦𝐩𝐥𝐞𝐬𝐭 𝐞𝐱𝐩𝐥𝐚𝐧𝐚𝐭𝐢𝐨𝐧 𝐢𝐬𝐧’𝐭 𝐚𝐥𝐰𝐚𝐲𝐬 𝐭𝐡𝐞 𝐛𝐞𝐬𝐭 𝐨𝐧𝐞.
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𝐓𝐡𝐞 𝐬𝐢𝐦𝐩𝐥𝐞𝐬𝐭 𝐞𝐱𝐩𝐥𝐚𝐧𝐚𝐭𝐢𝐨𝐧 𝐢𝐬𝐧’𝐭 𝐚𝐥𝐰𝐚𝐲𝐬 𝐭𝐡𝐞 𝐛𝐞𝐬𝐭 𝐨𝐧𝐞.
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November 14, 2025 at 12:45 PM
Dimensionality reduction can see structures that do not exist and miss structures that exist.
𝐓𝐡𝐞 𝐬𝐢𝐦𝐩𝐥𝐞𝐬𝐭 𝐞𝐱𝐩𝐥𝐚𝐧𝐚𝐭𝐢𝐨𝐧 𝐢𝐬𝐧’𝐭 𝐚𝐥𝐰𝐚𝐲𝐬 𝐭𝐡𝐞 𝐛𝐞𝐬𝐭 𝐨𝐧𝐞.
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𝐓𝐡𝐞 𝐬𝐢𝐦𝐩𝐥𝐞𝐬𝐭 𝐞𝐱𝐩𝐥𝐚𝐧𝐚𝐭𝐢𝐨𝐧 𝐢𝐬𝐧’𝐭 𝐚𝐥𝐰𝐚𝐲𝐬 𝐭𝐡𝐞 𝐛𝐞𝐬𝐭 𝐨𝐧𝐞.
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Current efforts focus on predicting transcriptional responses to gene silencing.
Even if spectacularly successful, they leave open key questions:
◾️Functions of genetic mutations & polymorphisms
◾️Proteoform functions
◾️Protein abundance regulation
Biology is complex.
Even if spectacularly successful, they leave open key questions:
◾️Functions of genetic mutations & polymorphisms
◾️Proteoform functions
◾️Protein abundance regulation
Biology is complex.
November 13, 2025 at 3:39 PM
Current efforts focus on predicting transcriptional responses to gene silencing.
Even if spectacularly successful, they leave open key questions:
◾️Functions of genetic mutations & polymorphisms
◾️Proteoform functions
◾️Protein abundance regulation
Biology is complex.
Even if spectacularly successful, they leave open key questions:
◾️Functions of genetic mutations & polymorphisms
◾️Proteoform functions
◾️Protein abundance regulation
Biology is complex.
The protein and mRNA abundance voronoi diagrams offer remarkably different perspectives.
Each tile in the maps represents a gene product; its size is proportional to the fraction of the gene product in hepatocytes.
Each tile in the maps represents a gene product; its size is proportional to the fraction of the gene product in hepatocytes.
November 12, 2025 at 12:53 PM
The protein and mRNA abundance voronoi diagrams offer remarkably different perspectives.
Each tile in the maps represents a gene product; its size is proportional to the fraction of the gene product in hepatocytes.
Each tile in the maps represents a gene product; its size is proportional to the fraction of the gene product in hepatocytes.
A reminder that the abundance of 'housekeeping' proteins varies significantly across cells and tissues.
GAPDH is often slandered as a 'housekeeping' protein, and its abundance varies significantly across human tissues.
How do you define a 'housekeeping' protein ?
GAPDH is often slandered as a 'housekeeping' protein, and its abundance varies significantly across human tissues.
How do you define a 'housekeeping' protein ?
November 11, 2025 at 11:56 AM
A reminder that the abundance of 'housekeeping' proteins varies significantly across cells and tissues.
GAPDH is often slandered as a 'housekeeping' protein, and its abundance varies significantly across human tissues.
How do you define a 'housekeeping' protein ?
GAPDH is often slandered as a 'housekeeping' protein, and its abundance varies significantly across human tissues.
How do you define a 'housekeeping' protein ?
The protein concentration in the cytoplasm is so high that the average protein has a water hydration shell with a thickness of only ≈ 10 water molecules separating it from the adjacent protein hydration shell.
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November 10, 2025 at 12:57 PM
The protein concentration in the cytoplasm is so high that the average protein has a water hydration shell with a thickness of only ≈ 10 water molecules separating it from the adjacent protein hydration shell.
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"Some participants have already found a way to hack the score, exposing fundamental flaws in how bio-foundation models are evaluated."
𝐄𝐯𝐚𝐥𝐮𝐚𝐭𝐢𝐧𝐠 𝐦𝐨𝐝𝐞𝐥𝐬 𝐢𝐬 𝐡𝐚𝐫𝐝. 𝐈𝐭 𝐧𝐞𝐞𝐝𝐬 𝐦𝐨𝐫𝐞 𝐚𝐭𝐭𝐞𝐧𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐫𝐞𝐬𝐨𝐮𝐫𝐜𝐞𝐬.
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𝐄𝐯𝐚𝐥𝐮𝐚𝐭𝐢𝐧𝐠 𝐦𝐨𝐝𝐞𝐥𝐬 𝐢𝐬 𝐡𝐚𝐫𝐝. 𝐈𝐭 𝐧𝐞𝐞𝐝𝐬 𝐦𝐨𝐫𝐞 𝐚𝐭𝐭𝐞𝐧𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐫𝐞𝐬𝐨𝐮𝐫𝐜𝐞𝐬.
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November 9, 2025 at 4:08 PM
"Some participants have already found a way to hack the score, exposing fundamental flaws in how bio-foundation models are evaluated."
𝐄𝐯𝐚𝐥𝐮𝐚𝐭𝐢𝐧𝐠 𝐦𝐨𝐝𝐞𝐥𝐬 𝐢𝐬 𝐡𝐚𝐫𝐝. 𝐈𝐭 𝐧𝐞𝐞𝐝𝐬 𝐦𝐨𝐫𝐞 𝐚𝐭𝐭𝐞𝐧𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐫𝐞𝐬𝐨𝐮𝐫𝐜𝐞𝐬.
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𝐄𝐯𝐚𝐥𝐮𝐚𝐭𝐢𝐧𝐠 𝐦𝐨𝐝𝐞𝐥𝐬 𝐢𝐬 𝐡𝐚𝐫𝐝. 𝐈𝐭 𝐧𝐞𝐞𝐝𝐬 𝐦𝐨𝐫𝐞 𝐚𝐭𝐭𝐞𝐧𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐫𝐞𝐬𝐨𝐮𝐫𝐜𝐞𝐬.
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Reposted by Nikolai Slavov
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 🚀
Reposted by Nikolai Slavov
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Fantastic Proteins and Where to Find Them - PTI - Parallel Squared Technology Institute
Here, we will offer a tutorial for how to build instrument-specific spectral library predictions for PSMtag modified peptides using DIA-NN 2.3.0. This will allow users to do more accurate proteome-wid...
www.parallelsq.org
November 4, 2025 at 4:47 PM
#Proteomics Tutorial drop!
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
Had fun writing this, ping me if interested in other search engines. #TeamMassSpec
www.parallelsq.org/blog/fantast...
A beautiful example illustrating a difference between plasma protein analysis by different technologies.
Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others.
The measurements differ because they reflect different proteoforms !
Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others.
The measurements differ because they reflect different proteoforms !
November 8, 2025 at 2:03 PM
A beautiful example illustrating a difference between plasma protein analysis by different technologies.
Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others.
The measurements differ because they reflect different proteoforms !
Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others.
The measurements differ because they reflect different proteoforms !
Reposted by Nikolai Slavov
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.
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 12:52 PM
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?