ESGI: Efficient splitting of generic indices in single-cellsequencing data https://www.biorxiv.org/content/10.64898/2026.03.04.709594v1
07.03.2026 01:48
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ESGI: Efficient splitting of generic indices in single-cellsequencing data https://www.biorxiv.org/content/10.64898/2026.03.04.709594v1
We;re hiring Junior Group Leaders! 🔬✨
We’re looking for researchers in immunology, chemical biology, AI in biology, or protein design to launch their own independent groups in our collaborative, international environment.
www.nki.nl/news-events/...
Postdoc alert in spatial biology!
Building upon our previous work with MSI cancers (e.g. de Vries et al, Nature, 2023), the Voest Group at the NKI is hiring a (fully funded) postdoctoral fellow with strong expertise in spatial cancer biology.
Learn more / apply here: www.nki.nl/careers-stud...
New paper! We reconstruct signaling networks from single-cell protein data by treating natural protein variation as "perturbation experiments." Enables comparison between cell states.
Led by Tim Stohn with Lodewyk Wessels @nkinl.bsky.social
and @klaasmulder.bsky.social .
doi.org/10.1093/bioi...
Aangrijpend verhaal over post-covidpatiënten die soms al 1000 dagen in het donker liggen. Hulp is er nauwelijks. www.volkskrant.nl/kijkverder/v...
There was never any point to having reference letters. That's why we've all started using AI to do this nonesense task.
References should only be used for short-listed candidates for important positions/awards, and ideally, be done via a call to get the most honest opinion possible.
Beyond excited to share my first work with Omer's group at Sanger!
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
We're going to see a lot of bullshit in the coming days and weeks about "causes of autism", and most will be based on flawed, over-interpreted observational studies (1/n)
Dear universities,
I am begging you to stop requiring letters of recommendation for master's programmes. You and I both know you don't read them, so stop asking for them.
Instead, have applicants list a name and get in touch if it's a borderline case.
Signed,
Everyone.
This Nakba Remembrance Day, instead of silencing voices in support of Palestinian human rights, the EU and all states must act and stop the genocide.
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
Wow! What an elegant/simple growth optimizing mechanism.
Heard from a former (undergrad) student who just defended her PhD. Students: tell your old profs about your successes and achievements. It's not bragging, and we love to hear about it. It's one of the best parts of being an educator.
#academicsky
A large study in Sweden found levels of autism *symptoms* were constant over time, even as autism *diagnoses* increased (implying broadening diagnostic criteria rather than real underlying increase) www.bmj.com/content/350/...
"Your job is to have ideas and spread them so that they impact other people’s work. Writing is your job. Nothing else. Therefore, everything else that you do is subservient to the activity of writing. Let this revolution take place in your mind."
www.nature.com/articles/s41...
How do embryos ensure precise tissue patterning? It’s all about timing cell divisions! Our new preprint reveals how cell proliferation syncs with signaling oscillations to regulate precision of somite formation and growth. Check the full story: www.biorxiv.org/content/10.1...
Europe as “a haven” for US researcher - The EU’s research funding bodies are thinking of ways to welcome US scientists and European ex-patriots who might be looking for a more sympathetic place to work now that Donald Trump is in the White House
#AcademicSky 🧪
sciencebusiness.net/internationa...
Decoupling.
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
Sad to know about the passing of Béla Novák. This review from Tyson, Chen and Novak was such a revelation for me as an introduction to control theory in biological systems. A classic that will remain relevant for many years to come. www.sciencedirect.com/science/arti...
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
Happy to share this concise review and outlook for single-cell sequencing methods to unravel cell biology of the nucleus! Big shoutout to my friend and former colleague Peter Zeller for sharing the work!
www.sciencedirect.com/science/arti...
Our paper on Stopless-ORF Circular RNAs (socRNAs) is now out in Cell. By high-res tracking and comparing translation by either single or multiple ribosomes, we find that ribosomes cooperate to overcome pausing to ensure fast and efficient translation
www.cell.com/cell/fulltex...
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
The FT reports OpenAI suspects DeepSeek of "a potential breach of intellectual property." As a columnist for NYT, which is suing OpenAI for copyright infringement, and the author of nine books OpenAI apparently used to train its model, I couldn't possibly comment. www.ft.com/content/a0df...
Cell-state specific drug-responses are associated with differences in signaling network wiring. https://www.biorxiv.org/content/10.1101/2025.01.27.635060v1
Graphical abstract of the paper.
How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...
Thanks for creating! Would love to be included!
Interesting thread from Carl on reproducibility strategies. His point that the issues in oncology =/ those in psychology etc echo my own conclusions from talking to people in the field
