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1/6 Today we highlight a new in situ method from the Sten Linnarsson lab called EEL-FISH. The authors set out to speed up imaging time to profile large tissue sections and reduce background, all while maintaining highly multiplexed gene capture. biorxiv.org/content/10.110…

Some thoughts on the passing of a hero, Paul Farmer of Partners In Health . In the early 2000s I was having a mid-life "crisis". I'd been politically involved from high school through my postdoc, but then a faculty job and two kids changed everything 1/n

Our new preprint, led by YUHAN HAO, introduces bridge integration: cross-modality alignment via a multiomic 'bridge' dataset. We map single-cell ATAC-seq, methylation, CUT&Tag and CyTOF profiles onto scRNA-seq references- scaling to millions of cells. biorxiv.org/content/10.110…

We've released a Seurat update with support for imaging-based spatial technologies! Our new vignette shows how to download, analyze, and explore public datasets from Vizgen (MERFISH), @nanostringtech (SMI), and Akoya Biosciences (CODEX). Check it out at: satijalab.org/seurat/article…

Congratulations to all the authors and architects of the Human Lung Cell Atlas! You can now upload and map your datasets directly to their reference using Azimuth at azimuth.hubmapconsortium.org

We've released an Azimuth API that lets you process, map, and annotate your scRNA-seq dataset with a single R command. Just needs the raw counts matrix as input, and accepts Seurat objects, AnnData (h5ad), or hdf5 files. Check out the vignette at: satijalab.github.io/azimuth/articl…

Happy to share our spatial atlas of the mouse central nervous system at molecular resolution using STARmap PLUS method and ClusterMap (rdcu.be/cWLg4) pipeline led by Hailing Shi, Yichun He, Yiming Zhou in collaboration with Jia Liu. biorxiv.org/content/10.110…

Applications are open for the Center for Integrated Cellular Analysis summer internship program! Open to undergrads who are interested in learning about single cell genomics and computational biology, and doing summer research in NYC. No previous experience required. Learn more at: multimodalintegration.org/usrp

New preprint w/Anshul Kundaje (anshulkundaje@bluesky) introducing CPA-Perturb-seq! We systematically perturb regulators of cleavage and polyadenylation, and explore post-transcriptional changes at single-cell resolution. Led by Madeline Kowalski harm and Johannes Linder (🧵) biorxiv.org/content/10.110…

Interested in single cell genomics but need help getting started? Check out my lab's Single Cell Genomics Day on April 7. Talks will feature recent exciting computational and experimental advances and will be livestreamed at satijalab.org/scgd. Please RT/spread the word!

We are excited to introduce Phospho-seq, our approach for profiling intracellular protein and cell signaling dynamics alongside additional molecular modalities in single cells! Check out @JBlairSci's preprint at biorxiv.org/content/10.110…

Austin Hartman And, of course, really incredible work by @JBlairSci

We are recruiting a postdoc to join the lab in Singapore! We are looking for either a computational or experimental scientist interested in single-cell methods. Please get in touch via email if you’d like to find out more stuartlab.org

Out on bioRxiv, I'm excited to share our latest deep dive into the world of mitochondrial genetics using single-cell genomics. Grateful to have worked with LeifLudwig, Ansu Satpathy, and many others. biorxiv.org/content/10.110… Thread here: 1/n

Today our Human Lung Cell Atlas (HLCA) paper came out in Nature Medicine nature.com/articles/s4159…! The HLCA includes 2.4M cells from 486 individuals and 49 datasets. Check out this tweetorial to learn more about how we built it, and how you can use it (1/21)

Some big news: I’m absolutely delighted to announce that I will be starting my group this fall in the Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center in New York City! clareaulab.com 1/

1/2 Interested in adding intracellular proteins to your single-cell sequencing experiments? Sign up to receive our (free) Phospho-seq starter kit through our Tech Sharing program from Center for Integrated Cellular Analysis Preprint: biorxiv.org/content/10.110… Request your starter kit: multimodalintegration.org/techsharing

Happy to share our preprint comparing spatial transcriptomics methods! biorxiv.org/content/10.110…

Want to hear about the latest updates/new techniques in single cell and spatial genomics? Check out the full agenda for our Single Cell Genomics Day on Friday, 3/29. All talks will be live-streamed (no registration required) at satijalab.org/scgd