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Using in situ spatial transcriptomics? Try Proseg, @danielcjones’s new cell segmentation method based on probabilistic and Cellular Potts modeling. Great for Vizgen Merscope, 10x Genomics Xenium, and @nanostringtech CosMx data. Preprint & code: (1/n) doi.org/10.1101/2024.0…

Very happy to share our latest pre-print studying T cell dynamics in multiple myeloma disease evolution 🧵1/10. medrxiv.org/content/10.110…

We recently benchmarked Fluent BioSciences PIPseq using the v4PLUS T-20 kit. We processed two healthy donor PBMCs in replicate and chose their DSP-Methanol fixation and freezing option since this is often desired for flexible experiment planning. (1/7)

Earlier this week we carried out a preliminary analysis of our first 10x Genomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.

What did we #learn after #sequencing #5million #Tcells #scRNA and #TCRseq with @lisa_wagar Andreas Tiffeau-Mayer Suhas Sureshchandra and funding agency Wellcome Leap STLChildrensHospital -Tissue determinants of the human T cell receptor repertoire. biorxiv.org/content/10.110…

Preprint alert! A spatial atlas of human gastro-intestinal acute GVHD reveals epithelial and immune dynamics underlying disease pathophysiology biorxiv.org/cgi/content/sh…. We examined how immune cells are organized in the gut and what happens to them in GVHD. TL;DR Timing is key!

Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA or Protein), multimodal (RNA and Protein), super cheap! NO SEQUENCING! 10x Genomics @nanostringtech Akoya Biosciences Bruker

1/ 🚨 Hot off the press! 🚨Our new paper, led by Andreas Obers & Maximilien Evrard, is now live in Immunity! 🧬 Curious how CD8+ tissue-resident memory T cells (TRM) adopt their fate in different organs? Let’s dive in! 🧵👇 authors.elsevier.com/c/1jw~j_OR~yiO…

Are you an early career scientist who wants to pursue a research project in the lab of a Fred Hutch Computational Biologist mentor? If yes, then the #MahanFellowship is for you. Apply by Dec. 20, 2024! Learn more: apply.interfolio.com/157470

Join us in accelerating groundbreaking discoveries in #infectiousdiseases and #immunology! Fred Hutch is seeking a scientific leader for the Bezos Family Distinguished Scholar in Viruses and Vaccines faculty position. Learn more and apply: bit.ly/488PkH4

What factors enable CAR-Ts to respond to checkpoint blockade, and can they be engineered to be more sensitive to enhancement? We explore this question in our lab’s first pre-print, led by MSTP student AJ Snyder with great collaborations with Evan Newell and Scott Furlan. 1/

Just released today in Nature Methods. If you haven't tried Proseg's cell segmentation method on your spatial transcriptomic data yet, maybe you should. See how it stacks up to other methods with data from multiple platforms. nature.com/articles/s4159…

Cell simulation as cell segmentation | Nature Methods nature.com/articles/s4159…

Proseg is a segmentation tool for single-cell spatial transcriptomics data that uses unsupervised probabilistic modeling of transcript spatial distribution, for accurate segmentation without multimodal staining. nature.com/articles/s4159…

This has been a massive undertaking since I started #chualabnccs 7y ago! So pleased to see our work published Cell where we posit a novel model that #TIME delineates progression trajectories of distinct #NPC phenotypes: cell.com/cell-reports-m… Thanks to everyone and

We are pleased to share our work evaluating some of the latest single-cell platforms, including updated chemistries, in two separate experiments using peripheral blood mononuclear cells (PBMCs). biorxiv.org/cgi/content/sh…

New from @FH_IIRC Evan Newell Fred Hutch Innovation Lab “Cell simulation as cell segmentation,” a novel approach that improves accuracy in identifying tumor-infiltrating immune cells from spatial transcriptomics data. Faster, more precise boundaries across platforms nature.com/articles/s4159…

Excited to share our study in Science Immunology dissecting the immune landscape of psoriatic arthritis (PsA)—with a new finding: immunoproteasome overactivity drives treatment resistance🧵 Led by Reut Tzemach,Chamutal Gur,T. San Phan,Eyal David & team. (1/11) science.org/doi/10.1126/sc…