Andrew Leduc
@andrewleduc.bsky.social
Post-doc Slavov Lab
https://andrew-leduc.github.io/
Studying how variation in protein half-life
leads to variation in protein levels
https://andrew-leduc.github.io/
Studying how variation in protein half-life
leads to variation in protein levels
Reposted by Andrew Leduc
These 3-L bottles contain one million tiny colored spheres each.
One sphere is black (1 ppm).
Finding the black sphere is comparable to detecting a protein present at ~ 6,000 copies in the proteome of a human cell.
Quantifying the protein requires analyzing multiple jars.
One sphere is black (1 ppm).
Finding the black sphere is comparable to detecting a protein present at ~ 6,000 copies in the proteome of a human cell.
Quantifying the protein requires analyzing multiple jars.
September 27, 2025 at 11:52 AM
These 3-L bottles contain one million tiny colored spheres each.
One sphere is black (1 ppm).
Finding the black sphere is comparable to detecting a protein present at ~ 6,000 copies in the proteome of a human cell.
Quantifying the protein requires analyzing multiple jars.
One sphere is black (1 ppm).
Finding the black sphere is comparable to detecting a protein present at ~ 6,000 copies in the proteome of a human cell.
Quantifying the protein requires analyzing multiple jars.
When designing antibodies for cell surface proteins, how much do the PTMs (glycosilation specifically) affect how well proteins can bind. Presumably these things are not possible to model with current approaches so I am surprised they apparently work so well
In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
September 24, 2025 at 3:34 PM
When designing antibodies for cell surface proteins, how much do the PTMs (glycosilation specifically) affect how well proteins can bind. Presumably these things are not possible to model with current approaches so I am surprised they apparently work so well
Check out our recent work interpreting the contribution of transcription, translation, and protein clearance on regulating protein abundance across cell types and single cells from a mammalian tissue!
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 23, 2025 at 7:47 PM
Check out our recent work interpreting the contribution of transcription, translation, and protein clearance on regulating protein abundance across cell types and single cells from a mammalian tissue!
Reposted by Andrew Leduc
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...
Reposted by Andrew Leduc
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...
🧵
What is the best way to compute the correlation of two transcripts across single cells?
June 27, 2025 at 3:45 PM
What is the best way to compute the correlation of two transcripts across single cells?
Help me build a virtual version of my apartment by training a hugeee (like so huge) neural network on temperature data from my stove.
Call to action from the community to achive this ambitious goal!
Call to action from the community to achive this ambitious goal!
June 26, 2025 at 7:14 PM
Help me build a virtual version of my apartment by training a hugeee (like so huge) neural network on temperature data from my stove.
Call to action from the community to achive this ambitious goal!
Call to action from the community to achive this ambitious goal!
* Transcript abundance predictor model
Register today for the Virtual Cell Challenge and use AI to solve one of biology’s most complex problems.
Announced in @cellcellpress.bsky.social, the competition is hosted by Arc Institute and sponsored by NVIDIA, @10xgenomics.bsky.social and Ultima Genomics.
Announced in @cellcellpress.bsky.social, the competition is hosted by Arc Institute and sponsored by NVIDIA, @10xgenomics.bsky.social and Ultima Genomics.
June 26, 2025 at 7:12 PM
* Transcript abundance predictor model
Is it well appreciated that droplet mRNA seq methods massively under-captures nuclear encoded mitochondrial transcripts?
They are essentially entirely unquantified by 10x sample preparation, probably because cell lysis is not sufficiently strong.
They are essentially entirely unquantified by 10x sample preparation, probably because cell lysis is not sufficiently strong.
June 20, 2025 at 12:30 PM
Is it well appreciated that droplet mRNA seq methods massively under-captures nuclear encoded mitochondrial transcripts?
They are essentially entirely unquantified by 10x sample preparation, probably because cell lysis is not sufficiently strong.
They are essentially entirely unquantified by 10x sample preparation, probably because cell lysis is not sufficiently strong.
Anyone out there working on single cell ribo seq, this is potentially an interesting alternative/complementary approach.
There are some differences in the information they give and would be interesting to explore.
There are some differences in the information they give and would be interesting to explore.
The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube:
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025
YouTube video by Nikolai Slavov
youtu.be
June 11, 2025 at 9:17 PM
Anyone out there working on single cell ribo seq, this is potentially an interesting alternative/complementary approach.
There are some differences in the information they give and would be interesting to explore.
There are some differences in the information they give and would be interesting to explore.
Reposted by Andrew Leduc
The aspiration to directly measure the 𝐫𝐚𝐭𝐞𝐬 of protein synthesis and degradation and control mechanisms of gene expression in the individual cells comprising mammalian tissues has always been a significant motivating factor for me to develop single-cell proteomic technologies.
1/n
1/n
The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube:
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025
YouTube video by Nikolai Slavov
youtu.be
June 11, 2025 at 1:12 PM
The aspiration to directly measure the 𝐫𝐚𝐭𝐞𝐬 of protein synthesis and degradation and control mechanisms of gene expression in the individual cells comprising mammalian tissues has always been a significant motivating factor for me to develop single-cell proteomic technologies.
1/n
1/n
How do different cell types regulate protein concentrations? Transcription is only part of the story!
Our project focuses on better understanding the regulation of protein abundance by measuring transcription, translation, and protein clearance in single cells.
Our project focuses on better understanding the regulation of protein abundance by measuring transcription, translation, and protein clearance in single cells.
The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube:
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025
YouTube video by Nikolai Slavov
youtu.be
June 11, 2025 at 8:18 PM
How do different cell types regulate protein concentrations? Transcription is only part of the story!
Our project focuses on better understanding the regulation of protein abundance by measuring transcription, translation, and protein clearance in single cells.
Our project focuses on better understanding the regulation of protein abundance by measuring transcription, translation, and protein clearance in single cells.
Reposted by Andrew Leduc
The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube:
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025
YouTube video by Nikolai Slavov
youtu.be
June 11, 2025 at 12:30 PM
The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube:
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧
youtu.be/adkY6txDyqs?...
You ever just flip through genes for a while reading the functions on uniprot and just think,
Wow cells do so much stuff
Wow cells do so much stuff
June 9, 2025 at 2:30 AM
You ever just flip through genes for a while reading the functions on uniprot and just think,
Wow cells do so much stuff
Wow cells do so much stuff
Reposted by Andrew Leduc
Yes, testis are special but not the only tissues in which we see substantial discrepancies.
We have seen them in all tissues that we have analyzed, and @andrewleduc.bsky.social has even more compelling examples from mouse trachea ... soon to be published!
We have seen them in all tissues that we have analyzed, and @andrewleduc.bsky.social has even more compelling examples from mouse trachea ... soon to be published!
June 7, 2025 at 5:11 PM
Yes, testis are special but not the only tissues in which we see substantial discrepancies.
We have seen them in all tissues that we have analyzed, and @andrewleduc.bsky.social has even more compelling examples from mouse trachea ... soon to be published!
We have seen them in all tissues that we have analyzed, and @andrewleduc.bsky.social has even more compelling examples from mouse trachea ... soon to be published!
Reposted by Andrew Leduc
must be incredibly frustrating and disheartening to have federal funding that was promised to you for important work suddenly and arbitrarily ripped away
“In light of the President's statement about cancellation of my government contracts, @SpaceX will begin decommissioning its Dragon spacecraft immediately”
June 5, 2025 at 8:15 PM
must be incredibly frustrating and disheartening to have federal funding that was promised to you for important work suddenly and arbitrarily ripped away
Reposted by Andrew Leduc
You can't comply your way out of fascism
June 4, 2025 at 7:09 PM
You can't comply your way out of fascism
Reposted by Andrew Leduc
mitochondrial function, stress response, apoptosis, and autophagy experts, is this right
June 3, 2025 at 5:05 AM
mitochondrial function, stress response, apoptosis, and autophagy experts, is this right
Congratulations Dr. Rahul Ragunathan on a successful defense @fanglab.org 🎉🎉
May 30, 2025 at 3:05 PM
Congratulations Dr. Rahul Ragunathan on a successful defense @fanglab.org 🎉🎉
More evidence for the role of protein degradation in significantly shaping the proteome of brain tissue!
Alzheimer's disease (AD) is associated with numerous proteome changes.
We find large & consistent decrease in the abundance and stoichiometry of 20S proteasome subunits.
⬛️ It leads to abnormal accumulation of 20S substrate proteins.
🧵
biorxiv.org/content/10.1...
We find large & consistent decrease in the abundance and stoichiometry of 20S proteasome subunits.
⬛️ It leads to abnormal accumulation of 20S substrate proteins.
🧵
biorxiv.org/content/10.1...
May 30, 2025 at 2:51 PM
More evidence for the role of protein degradation in significantly shaping the proteome of brain tissue!
Reposted by Andrew Leduc
Julia presented remarkably simple and interpretable models from sophisticated measurements.
May 28, 2025 at 6:36 PM
Julia presented remarkably simple and interpretable models from sophisticated measurements.
Multiplexed single cell proteomics to the moon 🚀 🚀
📊 Using stable isotopes of C/N/O, PSMtags increased protein datapoints from 4,340 (label-free) to 28,359 in the same time. We demonstrate 240 samples per day, but over 1,000 are possible with shorter runs.
That’s millions of protein data points per day.
That’s millions of protein data points per day.
May 28, 2025 at 5:52 PM
Multiplexed single cell proteomics to the moon 🚀 🚀
Reposted by Andrew Leduc
📊 Using stable isotopes of C/N/O, PSMtags increased protein datapoints from 4,340 (label-free) to 28,359 in the same time. We demonstrate 240 samples per day, but over 1,000 are possible with shorter runs.
That’s millions of protein data points per day.
That’s millions of protein data points per day.
May 28, 2025 at 12:24 PM
📊 Using stable isotopes of C/N/O, PSMtags increased protein datapoints from 4,340 (label-free) to 28,359 in the same time. We demonstrate 240 samples per day, but over 1,000 are possible with shorter runs.
That’s millions of protein data points per day.
That’s millions of protein data points per day.
Amazing amount of progress made advancing high throughput proteomics in such a short time from the team at @parallelsq.bsky.social 🚀
Links to our preprints:
timePlex (multiplexing with time-offsets): www.biorxiv.org/content/10.1...
JMod (search software for joint-modeling): www.biorxiv.org/content/10.1...
PSMtag (novel mass tag for 9-plexDIA): www.biorxiv.org/content/10.1...
timePlex (multiplexing with time-offsets): www.biorxiv.org/content/10.1...
JMod (search software for joint-modeling): www.biorxiv.org/content/10.1...
PSMtag (novel mass tag for 9-plexDIA): www.biorxiv.org/content/10.1...
May 28, 2025 at 11:16 AM
Amazing amount of progress made advancing high throughput proteomics in such a short time from the team at @parallelsq.bsky.social 🚀
Reposted by Andrew Leduc
We are excited to introduce ‘time’ as a new domain for proteomics multiplexing!
It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA
Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀
It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA
Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀
May 28, 2025 at 10:05 AM
We are excited to introduce ‘time’ as a new domain for proteomics multiplexing!
It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA
Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀
It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA
Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀