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.
🧬 How do immune disease-relevant variants affect gene regulatory networks in CD4+ T cells?
🧪🖥️ We coupled two large-scale CRISPRi screens (>4M cells) to map the downstream cascades of thousands of SNPs
More details in the thread below 👇 or in the article 📖 on biorxiv tinyurl.com/CD4screens
The 2025 Best of #ExpHem roundup is here! Explore the top articles and special issues from this past year showcasing the latest advances in experimental hematology ➡️ conta.cc/4rhX9lJ
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/
Using semantic search to find publicly available gene-expression datasets academic.oup.com/bioinformati... 🧬💻🧪 github.com/srp33/GEO_NLP
Here’s a full draft of the upcoming second edition of my “Data Visualization: A Practical Introduction”: socviz.co
Proud of @juruehle.bsky.social for getting her PhD paper on biorxiv! In it, we take synthetic enhancer screens to the single cell level, offering new insight into how transcription factors and enhancers interact 👀
Single-cell atlas of AML reveals age-related gene regulatory networks in t(8;21) AML
Improving SCVI for low-count cells through self-supervised augmentation - www.nxn.se/p/improving-...
I’ve really been enjoying this podcast since it started a few months ago: The Rest is Science. tiny.cc/restsci
Professor Hannah Fry and VSauce's Michael Stevens are amazing at #sciencecommunication Highly recommend! Even better: partners with a good cause @cancerresearchuk.org
Did you read our paper applying SUM-seq in macrophages, T-cells and iPSCs (www.nature.com/articles/s41...) and think: I want to try this cost-effective single cell RNA & ATAC-seq method myself? 🧬
Find the complete protocol including tips, troubleshooting and timing now in Nature Protocols
New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu!
www.science.org/doi/10.1126/...
🚨 NEW
@FraticelliLab
PREPRINT JUST WENT LIVE
biorxiv.org/content/10.6...
Here, we describe PLSTCs, Soluplus-based expansion cultures of primary mouse *Acute Myeloid Leukemia* Stem Cells. And then we use LARRY barcoding to identify drivers of leukemogenicity and drug resistance!
🧵 That V-plot showing transcription factor binding? It might be an artifact.
New research shows chromatin fragmentation methods create patterns even on naked DNA. Here's what went wrong.
The 3 hardest things to learn as a scientist:
1. Trust the data.. especially when it’s not what you expected,
2. Trust the data.. allowing it to change your direction,
3. Trust the data.. but not too much: test with new data at every turn.
ggannotate: interactively add annotations to your {ggplot2} plots by pointing and clicking github.com/MattCowgill/... #Rstats
#Medsky🧪 A comprehensive single-cell atlas of endothelial cell (EC) development during mouse embryonic stages, covering 8 major organs and 26 time points.
The atlas reveals that
@cellpress.bsky.social
www.cell.com/cell/fulltex...
anndataR: converting single-cell data, from R to python and back tomsing1.github.io/blog/posts/a... #Rstats
Want to understand complex intrinsic and extrinsic metabolic regulation of HSCs? Our latest @natcellbio.nature.com review, led by @aysegulerdemm.bsky.social, synthesize insights into cell fate decisions and highlight implications for leukemogenesis. @nickvangastel.bsky.social
rdcu.be/e3smG
For anyone who asked "Do you have genome-wide trans-eQTLs?" when we published the first eQTLGen paper: we do now! 💫
See Robert's thread for details on eQTLGen phase 2, including finemapped cis-eQTLs, cis-trans gene pairs and integration of GWAS to identify trait-relevant pathways 🧬🖥
Congrats team!
Our new paper: Entropy Sorting Feature Selection (ESFS)
A computational framework for gene selection from single cell data that extracts biological signals in noisy data while avoiding artefacts from conventional dimensionality reduction
A thread
www.biorxiv.org/content/10.6...
Lots of tools out there in the "AI for Science" space. I don't want something to slop-write my papers and "do my research" for me. But I have a ton of PDFs in Zotero, and I'd love an AI thing to help me understand what's in there. I found it today blog.stephenturner.us/p/zotero-con... 🧵 1/
This is figure 2, which shows that within-cell-type changes are associated with each exposure.
A single-cell epigenomic atlas of human immune cells highlights cell-type-specific features associated with genetic or environmental exposures, according to a paper in Nature Genetics. go.nature.com/4taJRJT 🧬 🧪
Happy to share our latest work on the epigenetic basis of trained immunity in hematopoietic stem cells! @bcmhouston.bsky.social @texaschildrens.bsky.social
Fantastic read. How a billionaire saved himself (for now) from cancer.
Not everyone has resources like Sid.
centuryofbio.com/p/sid
This imposes a bigger question on how we can bring therapeutics to every patient.
We wrote a review of representation learning methods of single-cell RNA-seq data, where we compare factor models, autoencoders, contrastive learning, and foundation models 🎉
rnajournal.cshlp.org/content/earl...
Very early days, but delighted that our recent review on reevaluation of aging hematopoiesis published in Experimental Hematology, official journal of @isehsociety.bsky.social is classified as highly cited by web of science. Open access here: www.exphem.org/article/S030...
OpenAI and Anthropic launch life sciences research and healthcare connectors doi.org/10.59350/t7h...
I think I learned more from @andrew.heiss.phd about Positron (and generally automating my life on MacOS) in one hour than I have in the past year, from his talk on the @posit.co data science lab yesterday. Talk will be posted on YouTube soon. www.andrewheiss.com/blog/2026/01... #Rstats
My "Friends don't let friends make bad graphs" repo is approaching 7k stars on GitHub. As of this moment, 6962, to be exact. 38 more to go to 7000.
github.com/cxli233/Frie...
