Andrew Leduc

What about predictions that involve many proteins interacting together?

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

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!

* Transcript abundance predictor model

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

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.

What do you use to measure blood sugar?

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.

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

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.

YouTube video by Nikolai Slavov Quantification of gene expression control in a mammalian tissue at single cell resolution | SCP2025

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?...

All ideas != create equal 😅

You ever just flip through genes for a while reading the functions on uniprot and just think,

Wow cells do so much stuff

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!

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

You can't comply your way out of fascism

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

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

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

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!

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.

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

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 🚀

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...

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

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.

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...

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