We are so excited to see our work out in @nature.com! We present a multi-omic single-cell atlas of 12 organs in human fetal development, explore the enhancer landscape, use deep learning to infer rules of transcription factor activity, and interpret non-coding variants in complex traits: #GeneReg 🧬🖥️
orthogene
bioconductor.org/packages/rel...
Map your genes of interest across >700 species
Can do many:many
bioRxiv 2026
www.biorxiv.org/content/10.6...
(Data) research parasites nowadays have tons of exciting opportunities. I love this piece by @skinnider.bsky.social: academic.oup.com/gigascience/...
(Software) research parasites do as well!
The ρPCA method is implemented in an easy to use Python package github.com/pachterlab/r... Quick to install. Fast. We now use it routinely whenever engaging in exploratory data analysis. 8/
Everything is open: interactive preprint, count matrices, models, all 7,712 prediction tracks, code & reproducible figures → doi.org/10.62329/hxkk6249. Raw data: GEO GSE325776. Code: github.com/ChengxiangQiu/jax-atac-code
A more detailed thread on the paper below from @cxqiu.bsky.social.
bsky.app/profile/cxqi...
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
I have reviewed scRNA-seq datasets where half the interesting signal was dissociation artifact.
Your analysis pipeline cannot fix what went wrong at the bench.
pmc.ncbi.nlm.nih.gov/articles/PM...
New preprint with Garnett lab 🚀: from descriptive → causal single-cell atlases in CRC.We build the largest CRC atlas (>300 pts, 1.5M cells) using continual learning, and link cell states to causal drivers via Tahoe-100M, validated in organoids! www.biorxiv.org/content/10.6...
A powerful example of protein abundance regulation.
The degradation rate of p53 determines its abundance.
p53 is special, but regulation by protein degradation is not a special case. It's common:
doi.org/10.1101/2025...
In the spirit 👻 of Freaky Friday 🎃, here is a beautiful yet eery video of zebrafish retina development showing horizontal cells (🔵) finding their way out of the crowded amacrine (🟠) layer to settle beneath the photoreceptors. Happy #Halloween!
🎥: PhD student Rae Wong from the @nordenlab.bsky.social
Using EMS mutagenesis, authors generated & sequenced 12,069 viable C. elegans strains, identifying 541,102 missense mutations. They developed TaoChongBao, an open-access database integrating mutation data, greatly expanding functional variant resources. www.life-science-alliance.org/content/9/6/...
Some MYRF variants result in isolated ocular disease while others produce syndromic phenotypes
Lev Prasov & team find dominant variants that partially alter gene function or dosage may lead to ocular disease, while total LOF may lead to syndromic disease: doi.org/10.1172/jci....
Hao's Preprint Reading List
March 25 2026
Pericyte loss in🧠small vessel disease
Single-cell atlas of postnatal👤🫁development
Substrate microtrench confers Endothelial cell resilience to >200 dyn/cm2 shear
SuperFocus Single-cell spatial multi-omics
Zebrafish ZMAP
docs.google.com/document/d/e...
Pay attention to weight, hydraulic (I dislike mech) brakes, geometry, drivetrain (Microshift generally considered worse than Shimano/Sram), mount points. Test ride before buying to confirm fit is always helpful.
Excited to share this work with an amazing team:
@brunetlab.bsky.social, @deisseroth.bsky.social, @ravi-nath.bsky.social, Scott Linderman, Libby Zhang
Paper in Science:
www.science.org/doi/10.1126/...
New preprint! Our workflow for processing single cell and nuclei data, called 🎉 scprocess 🎉 We have been working on it for ~18 months now, over which time we have processed at least 2k samples with it, so it has had a decent amount of testing.
Ambient RNA & barcode swapping is a serious issue in single-cell genomics. Tools such as CellBender, scAR, DecontX & SoupX. We have developed CellSweep which is faster (in some cases by a lot) and much more accurate. Extensively tested and benchmarked. www.biorxiv.org/content/10.6... 1/
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/
Gene regulatory networks: from correlative models to causal explanations www.nature.com/articles/s41... 🧬💻🧪 rdcu.be/e7DIE
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
After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data!
But first, I would like to talk a bit about RNA velocity and normalization. 1/
Range extender mediates long-distance enhancer activity www.nature.com/articles/s4...
@ternbicycles.com One spring on my gen1 GSD atlas kickstand spring broke. Where can I get a replacement?
