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...

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.

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

Arc Institute@arcinstitute.org · 11mo ago

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.

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!

Nikolai Slavov@slavov-n.bsky.social · 11mo ago

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...

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...

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... 🧵

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

Arc Institute@arcinstitute.org · last yr.

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.

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.

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.

Slavov Laboratory@slavovlab.bsky.social · last yr.

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?...

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

Slavov Laboratory@slavovlab.bsky.social · last yr.

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?...

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.

Slavov Laboratory@slavovlab.bsky.social · last yr.

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?...

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 | SCP2025

YouTube video by Nikolai Slavov

youtu.be

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

Best of Dying Twitter@bestofdyingtwit.bsky.social · last yr.

“In light of the President's statement about cancellation of my government contracts, @SpaceX will begin decommissioning its Dragon spacecraft immediately”

You can't comply your way out of fascism

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

Christoph Bock Lab @ CeMM & MedUni Vienna@bocklab.bsky.social · 2y ago

🔍 We investigate one of the identified cell clusters, selecting its cells and prompting CellWhisperer with ‘Describe these cells in detail’. This interactive workflow is enabled by seamless integration of the CellWhisperer AI chat box into a version of @CELLxGENE Explorer (3/9)

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!

Nikolai Slavov@slavov-n.bsky.social · last yr.

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...

Julia presented remarkably simple and interpretable models from sophisticated measurements.

Nikolai Slavov@slavov-n.bsky.social · last yr.

We are streaming #SCP2025 www.youtube.com/live/UZCsU9s...

Multiplexed single cell proteomics to the moon 🚀 🚀

Harrison Specht@harrisons.bsky.social · last yr.

📊 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.

📊 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 🚀

Jason Derks@jasonderks.bsky.social · last yr.

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...

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 🚀

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

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...

rdcu.be

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...

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.

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

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

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