iiinova — where your digital self keeps evolving

Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 06/03/2026

Next week, @andrewleduc.bsky.social will present at the CSHL Systems Biology: Global Regulation of Gene Expression meeting. His talk will focus on in vivo protein regulation in single cells, including results from this preprint: www.biorxiv.org/content/10.1...

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Andrew Leduc @andrewleduc.bsky.social · 24/11/2025

Yeah, I really agree, it doesnt fully make sense to me. Maybe its not detrimental to the cell but ends up being a problem for the organ or something like that Also I dont get why not just base edit the mutation causing the early stop

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Andrew Leduc @andrewleduc.bsky.social · 22/11/2025

I think upon reading it more closely, the thing that i misunderstood was that even a very small rate of fixing the early stop proteins recovered function, maybe in this context it makes sense

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Andrew Leduc @andrewleduc.bsky.social · 20/11/2025

We are doing similar experiments right now and our results are so different from all the things you would need to be true for any of this to make sense.

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Andrew Leduc @andrewleduc.bsky.social · 20/11/2025

Yeah I mean or the ribosomes some how have other ways of filtering... but this is inconsistent, it really doesnt make sense in so many ways. Also, if you point edit change some of the natural tRNA, it must be bad to lose those copies for normal case, and how can the dosing be even close to correct

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Andrew Leduc @andrewleduc.bsky.social · 19/11/2025

I really dont understand how this sup-tRNA works, how can this possibly work as a therapy without extending natural proteins everywhere

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Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 27/09/2025

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.

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Andrew Leduc @andrewleduc.bsky.social · 24/09/2025

Also the cells are sorted by growth rate so idk some meaning to the ordering

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Andrew Leduc @andrewleduc.bsky.social · 24/09/2025

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

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Andrew Leduc @andrewleduc.bsky.social · 24/09/2025

Yeah its not great, it just made comparisons of the different modalities a bit easier to visualize than when we plotted a scatter but will revisit. Thanks for feedback!

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Andrew Leduc @andrewleduc.bsky.social · 23/09/2025

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!

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Andrew Leduc @andrewleduc.bsky.social · 23/09/2025

I have admittedly been on the non-PI side of this only to realize how true this must be after receiving a blank stare 😅

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Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 22/09/2025

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...

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Reposted by Andrew Leduc

Slavov Laboratory @slavovlab.bsky.social · 21/09/2025

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... 🧵

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Andrew Leduc @andrewleduc.bsky.social · 21/08/2025

Trust me, its better than whatever harm "doing their jobs" will cause...

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Andrew Leduc @andrewleduc.bsky.social · 05/07/2025

What about predictions that involve many proteins interacting together?

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Andrew Leduc @andrewleduc.bsky.social · 03/07/2025

Yeah, for sure not true but also probably looking under the lamp post effect as well!

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Andrew Leduc @andrewleduc.bsky.social · 27/06/2025

What is the best way to compute the correlation of two transcripts across single cells?

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Andrew Leduc @andrewleduc.bsky.social · 26/06/2025

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!

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Andrew Leduc @andrewleduc.bsky.social · 26/06/2025

* Transcript abundance predictor model

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Andrew Leduc @andrewleduc.bsky.social · 22/06/2025

Once you have a certain level of aggregation, it does become hard to imagine removing it easily. What if the aggregate is too large to fit in a lysosome? I dont know I guess what the size scales are

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Andrew Leduc @andrewleduc.bsky.social · 20/06/2025

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.

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Andrew Leduc @andrewleduc.bsky.social · 17/06/2025

What do you use to measure blood sugar?

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Andrew Leduc @andrewleduc.bsky.social · 11/06/2025

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.

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Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 11/06/2025

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

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Andrew Leduc @andrewleduc.bsky.social · 11/06/2025

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.

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Reposted by Andrew Leduc

Slavov Laboratory @slavovlab.bsky.social · 11/06/2025

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?...

youtu.be

Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025

YouTube video by Nikolai Slavov

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Andrew Leduc @andrewleduc.bsky.social · 10/06/2025

All ideas != create equal 😅

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Andrew Leduc @andrewleduc.bsky.social · 09/06/2025

You ever just flip through genes for a while reading the functions on uniprot and just think, Wow cells do so much stuff

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Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 07/06/2025

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!

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Reposted by Andrew Leduc

Adam Sternbergh @sternbergh.bsky.social · 05/06/2025

must be incredibly frustrating and disheartening to have federal funding that was promised to you for important work suddenly and arbitrarily ripped away

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Reposted by Andrew Leduc

Moosedog66 @moosedog66.bsky.social · 04/06/2025

You can't comply your way out of fascism

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Andrew Leduc @andrewleduc.bsky.social · 04/06/2025

Congrats! You should check out transfer learning workflows applied to RT calibration in alphaDIA from Wallmann et al. Worth a citation I think.

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Andrew Leduc @andrewleduc.bsky.social · 04/06/2025

If the idea has obvious significance utility over existing tools, its much more likely to be implemented well at some point in some form

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Reposted by Andrew Leduc

Gennady Gorin @goringennady.bsky.social · 03/06/2025

mitochondrial function, stress response, apoptosis, and autophagy experts, is this right

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Andrew Leduc @andrewleduc.bsky.social · 30/05/2025

Congratulations Dr. Rahul Ragunathan on a successful defense @fanglab.org 🎉🎉

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Andrew Leduc @andrewleduc.bsky.social · 30/05/2025

More evidence for the role of protein degradation in significantly shaping the proteome of brain tissue!

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Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 28/05/2025

Julia presented remarkably simple and interpretable models from sophisticated measurements.

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Andrew Leduc @andrewleduc.bsky.social · 28/05/2025

Multiplexed single cell proteomics to the moon 🚀 🚀

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Reposted by Andrew Leduc

Harrison Specht @harrisons.bsky.social · 28/05/2025

📊 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.

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Andrew Leduc @andrewleduc.bsky.social · 28/05/2025

Amazing amount of progress made advancing high throughput proteomics in such a short time from the team at @parallelsq.bsky.social 🚀

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Reposted by Andrew Leduc

Jason Derks @jasonderks.bsky.social · 28/05/2025

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 🚀

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Reposted by Andrew Leduc

Selbach Lab @selbachlab.bsky.social · 27/05/2025

Read our new paper in Nature Comms: SPIED-DIA = spike-in enhanced DIA phosphoproteomics -> Boosts detection of key phosphosites -> Reveals JNK activation upon MEK inhibition in CRC cells -> Dual MEK/JNK targeting impairs growth 🔗 rdcu.be/enPF2 #proteomics #DIA #cancer

rdcu.be

Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells

Nature Communications - Kinase inhibitors are key in cancer therapy, but resistance limits their efficacy. Here, the authors develop SPIED-DIA, a phosphoproteomics method enhancing detection of key...

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Reposted by Andrew Leduc

Emmottlab @emmottlab.bsky.social · 25/05/2025

We have projects available on single-cell proteomics, including methods development, and applications to antiviral development and resistance. If you have a strong background in proteomics and are considering an MSCA, get in touch! marie-sklodowska-curie-actions.ec.europa.eu/news/msca-op...

marie-sklodowska-curie-actions.ec.europa.eu

MSCA opens €404.3 million call for Postdoctoral Fellowships

Postdoctoral Fellowships offer researchers holding a PhD the opportunity to acquire new skills through advanced training and international, interdisciplinary, and inter-sectoral mobility.

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Reposted by Andrew Leduc

The Tennessee Holler @thetnholler.bsky.social · 21/05/2025

So you’re telling us the radical transparency people are against… transparency? www.politico.com/news/2025/05...

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Reposted by Andrew Leduc

Nikolai Slavov @slavov-n.bsky.social · 22/05/2025

The scientific literature is at risk of becoming flooded with papers that make misleading health claims. www.nature.com/articles/d41...

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Andrew Leduc @andrewleduc.bsky.social · 22/05/2025

Can you make a site that keeps this updating in real time as a running sum over time in office?

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Aatish Bhatia @aatishb.com · 22/05/2025

NEW: Under Trump, the National Science Foundation is awarding grants at the slowest pace in decades. We took a detailed look at every area of science affected by the funding lag. Here's a gift link: www.nytimes.com/interactive/...

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Andrew Leduc @andrewleduc.bsky.social · 22/05/2025

When I was starting out modeling data, I always assumed that I needed to learn lots of fancy techniques and read different statistics text books to do useful analysis. However, intuition has gotten me much farther than time spent reading about complicated techniques.

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Andrew Leduc @andrewleduc.bsky.social · 20/05/2025

Tune in to hear me give a talk on our work quantifying mechanisms protein abundance regulation in single cells from primary tissues!

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