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We have released Azimuth references for human heart, tonsil, and adipose tissue! You can map your own scRNA-seq datasets to 11 different references for automated processing, annotation, visualization, and marker discovery at azimuth.hubmapconsortium.org

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

1/8 Today we highlight exciting work from Alex Predeus 🇺🇦, Matthew Young, et al. at Wellcome Sanger Institute. They introduce inactiveXX, a method to accurately predict X-inactivation states of cells from single-cell transcriptomes. biorxiv.org/content/10.110…

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've been working on Seurat v5 for two years and are excited to share it with you soon! In a webinar w/10x Genomics and Science Magazine on 3/29, I'll introduce new methods to analyze spatial/multimodal datasets that scale to tens of millions of cells: view6.workcast.net/register?cpak=…

Happy to present my recent work - a cluster-free method for DE testing, leveraging overlapping neighbourhoods in the graph representation of sc-data (aka miloDE): biorxiv.org/content/10.110… . A little thread below describes the motivation and suggestions on interpreting the results.

Gesmira Molla and Yuhan Hao overview strategies for massively scalable single-cell analysis #singlecellgenomicsday

On October 23, we will submit Seurat v5 to CRAN, and once accepted it will become the default version for new installs. A few notes on v5 below:

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 & computational biology, and doing summer research in NYC. No previous experience required. Learn more at: multimodalintegration.org/usrp

We compared six commercial + academic multiplexed in-situ gene expression profiling technologies. Check out our preprint, led by Austin Hartman. Takeaway when evaluating spatial tech: consider both sensitivity and specificity! biorxiv.org/cgi/content/sh…

Want to hear about the latest updates/new techniques in single cell and spatial genomics? Check out my lab's eighth annual Single Cell Genomics Day on March 29. Keynotes from IdoAmitLab Jason Buenrostro and Xiaowei Zhuang. Please RT/spread the word! satijalab.org/scgd