The empty drops you threw out in your single-cell RNA sequencing analysis might be hiding mysterious things 👀 check out our bioRxiv preprint!
The empty drops do not contain cells. Yet we can still use them to learn interesting things about biology and technology. 1/
Data is necessary but not sufficient for understanding!
(Thread is about a review that looks nice but I have not looked at yet)
New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations"
Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations?
rdcu.be/e7zx7
Immunotherapies for risk reduction in age-associated neurodegenerative diseases: impact of sex and treatment duration #NeuroDegeneration 🧪🧠
https://www.medrxiv.org/content/10.64898/2026.03.06.26347446v1
Massive-scale single-nucleus multi-omics identifies novel rare noncoding drivers of Parkinson's disease #NeuroDegeneration 🧪🧠
https://www.biorxiv.org/content/10.64898/2026.03.05.709922v1
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
an image promoting a substack article titled ‘25 medieva manuscripts you can look at online right now’
i made a starter back of beautiful and unique manuscripts you can browse online! (with links) for anyone that wants a good way to spend an afternoon :)
open.substack.com/pub/weirdmed...
Sparse autoencoders reveal organized biological knowledge but minimal regulatory logic in single-cell foundation models: a comparative atlas of Geneformer and scGPT #SingleCell 🧪🧬🖥️
https://arxiv.org/abs/2603.02952
GPU-accelerated single-cell analysis at scale with rapids-singlecell #SingleCell 🧪🧬🖥️
https://arxiv.org/abs/2603.02402
Three pictures of cats. Left: A domestic cat with leg over head, tongue out, washing itself, label is "GLM" Middle: A tiger in same pose, label is "GLMM" RIght: many cats together in same pose, label is "FIXED EFFECTS"
No matter the size or number, cats are always cats
Figure 1 in this paper is both informative and hillarious. The collider on self-perceived causal inference skill is too real
Scientists: for a new story, I have one big question—>
What is a “good day” in the lab?
I’m looking for epic examples of the best day ever to general criteria for what constitutes a “good day” compared to a nothing-burger day.
Ping me if you have examples to share!
Re-posts appreciated!
I'm constantly trying (/failing) to get this point across.
If you're a trained expert in a field, then it may be worthwhile to question the scientific consensus of your peers.
If you're not, the scientific consensus is absolutely the best you can do and it's arbitrary foolishness to disregard it.
Enhanced EBNA2-dependent activity in EBV-transformed B cells from patients with multiple sclerosis #NeuroDegeneration 🧪🧠
https://www.medrxiv.org/content/10.64898/2026.02.18.26346386v1
OpenSAFELY is open from today! Huge thanks to all who supported this vast collaboration: whole population GP data; in a productive platform; innovative privacy protections; unprecedented support from professions, privacy campaigners; &c
Now it's over to users!
www.bennett.ox.ac.uk/blog/2026/02...
This afternoon I took my mom to the ballet. She was as a dancer and choreographer for decades & has been in memory care for 8 years. She can’t recall many details of her past but dance—and her identity as a dancer—lives in her soul 1/
#alzheimers
Human CSF proteogenomics links genetic variation to neurodegenerative disease proteins #NeuroDegeneration 🧪🧠
https://www.medrxiv.org/content/10.64898/2026.02.12.26345733v1
Predicting when symptoms of Alzheimer's disease will occur with a single elevated p-tau217 blood test and a person's age, even 20+ years in advance
@naturemedicine.bsky.social
nature.com/articles/s41...
Three postdoctoral fellowships in quantitative biology are available as part of a new Quantitative Biology Initiative in the Department of Biology at the University of Maryland.
Best consideration date: 3/14
Job Ad:
umd.wd1.myworkdayjobs.com/en-US/UMCP/j...
Department:
biology.umd.edu/people
The Zampieri Lab at the University of Basel is recruiting a highly motivated PhD candidate to investigate how metabolic programs drive cancer metastasis.
📩 Only applications submitted through the official recruiting system of the University of Basel will be considered.
jobs.unibas.ch/offene-stell...
Very excited to get to share culmination of this large-scale project to understand spatial gene expression in schizophrenia. Really proud of the amazing team work here working out lots of roadblocks to deploy these spatial strategies and analysis methods at scale!
how to draw an owl meme. Step 1: Draw some circles. Step 2: Draw the rest of the owl
Everything is awful but there's a chance we will get this image on the cover of a special issue about statistical workflow. Really the best advertising decision the journal could make. I hope they go for it
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
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...
Parameter-free representations outperform single-cell foundation models on downstream benchmarks #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.02.11.705358v1
Latest from the lab, led by @ara-donia.bsky.social and @juliavdkorput.bsky.social
Huge team effort, with immense contributions by friends from nearby and around the globe.
www.science.org/doi/10.1126/...
Bluesky is the new science Twitter, new study by @whysharksmatter.bsky.social and Julia Wester concludes!
"Results show that for every reported professional benefit that scientists once gained from Twitter, scientists can now gain that benefit more effectively on Bluesky than on Twitter."
"Moderna's CEO announced the company will no longer invest in new Phase 3 vaccine trials for infectious diseases: 'You cannot make a return on investment if you don't have access to the U.S. market. Vaccines for Epstein-Barr virus, herpes, and shingles have been shelved.” 9:12 AM Feb 12, 2026 604.8K Views
In terms of what cures are being lost:
- Epstein-Barr virus is perhaps the major trigger for multiple sclerosis
- herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis
- shingles virus causes an intensely painful disease
Omnibenchmark (omnibenchmark.org): transparent, reproducible, extensible and standardized orchestration of solo and collaborative benchmarks arxiv.org/abs/2409.17038 🧬💻🧪
Happy birthday to one of my favourite haters, Charles Darwin
