We're looking for people with a solid computational background (Math, Physics, Computer science, Computational Biology, etcetera) to dive into biology! Come study the physical principles of cell-fate decisions using Bayesian data analysis and biophysical modeling!
One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!
7/ Code: github.com/tstohn/ESGI | Docs: tstohn.github.io/ESGI.documentation ESGI was developed by Tim Stohn at @vuamsterdam.bsky.social and @nkinl.bsky.social
6/ ESGI also outputs per-position QC metrics: where mapping fails, what edit operations occur at each barcode, and UMI amplification distributions. Useful for debugging novel protocols during development.
5/ We benchmarked ESGI on six datasets across four technologies: SIGNAL-seq, SPLiT-seq, Phospho-seq, and xDBiT spatial data. Count matrices are highly concordant with established pipelines
4/ ESGI allows for indels by using Levenshtein distance for barcode matching. This matters because deletions are the dominant error type in barcode synthesis. In our SIGNAL-seq and SPLiT-seq benchmarks we found that allowing for indels increased successfully demultiplexed reads by >10%
3/ ESGI maps barcodes sequentially, so each barcode's start position is determined by where the previous one ended. This naturally handles frameshifts caused by indels and variable-length barcodes (e.g. staggers).
2/ Most tools extract barcodes at fixed positions and use Hamming distance (substitutions only). If an indel occurs early in the read, it shifts all downstream barcode positions, causing misassignment even when the barcodes themselves are error-free.
🧵 1/ We just released ESGI, a flexible demultiplexing tool for barcoding based single-cell sequencing data. ESGI allows for demultiplexing and processing single-cell sequencing data with arbitrary barcode designs and uses Indel-aware barcode correction
www.biorxiv.org/content/10.6...
ESGI: Efficient splitting of generic indices in single-cellsequencing data www.biorxiv.org/content/10.64898/2026.03...
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.
