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🤩Excited to share our Nature Methods comment on “Unlocking the Power of Spatial Omics with AI” nature.com/articles/s4159… co-authored with Kyle Coleman and Amelia Schroeder Dept. of Biostatistics, Epidemiology & Informatics. Big thanks to Rita Strack for inviting us to contribute.

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics👍 genomebiology.biomedcentral.com/articles/10.11…

Many #SpatialTranscriptomics tools are out there! Which performs best? Which runs fastest? A nice resource here😆👇 16 clustering methods SpatialPCA DR.SC SpaGCN BANKSY GraphST STAGATE SEDR PRECAST conST DeepST CCST BASS ADEPT SpaceFlow BayesSpace ConGI 10

Now out - WebAtlas pipeline for visualizing and processing integrated single cell and spatial transcriptomics data ⁦Nature Methods⁩ ⁦Omer Ali Bayraktar⁩ ⁦Haniffa Lab⁩ ⁦Shila Ghazanfar⁩ ⁦Human Cell Atlas⁩ github.com/haniffalab/web… nature.com/articles/s4159…

A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data nature.com/articles/s4146…

Mapping cellular interactions from spatially resolved transcriptomics data nature.com/articles/s4159… (read free: rdcu.be/dSTC5) Spacia software: github.com/yunguan-wang/S… 🧬🖥️

SpatialOne: end-to-end analysis of visium data at scale academic.oup.com/bioinformatics… 🧬🖥️ github.com/Sanofi-Public/…

We've been awarded an NIH R01 grant to further improve ShinyGO! 🎉 - Thank you for using it and citing our paper! - These support letters were essential! - This means the annotation databases will be updated for at least 5 years, also benefiting iDEP users. - Feel free to

CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics nature.com/articles/s4159…

New preprint from Luciane T Kagohara 🇧🇷🧬👩🏻‍🔬👩🏻‍💻 @FertigLab Dr. Elizabeth Jaffee Won Jin Ho Ashley Kiemen Ashi_W & colleagues Johns Hopkins Kimmel Cancer Center Convergence Institute Spatial multi-omics reveal intratumoral humoral immunity niches associated with tertiary lymphoid structures in #PancreaticCancer immunotherapy

STAMP Single-Cell Transcriptomics Analysis & Multimodal Profiling through Sequencing-free, Imaging-based #SpatialOmics system CosMx Xenium Single-cell suspension cytospinned to slides 100 ~ >1M cells ⏫cell capture ⏬doublets Able to identify ultra-rare cell population

Thrilled to share our back-to-back two Nature nature papers on the unexpected role of type 2 immunity against cancer. We found that interleukin 4 (Fc–IL-4), a type 2 cytokine, reinvigorates exhausted T cells to potentiate anticancer immunotherapy w/ Yugang GUO Rong Fan(1/11)

Excited to share this preprint on TNC, Wnt, and thyroid cancer! Thanks Matthew Loberg for helping me with this!

We are excited to share our new work out today in Nature Cell Biology uncovering a new Achilles heel of pancreatic cancer. Myc is a key driver of PDAC and predicts poor survival. Thus, we asked the question of how Myc protein levels are regulated in PDAC. 👉 rdcu.be/d8xLT 🎉

We are excited to share our recent pre-print exploring cancer-associated fibroblast (CAF) phenotypes as thyroid cancers progress from treatable well-differentiated tumors to highly lethal anaplastic thyroid cancer! Vivian Weiss Heather Hartmann Megan Tigue '16 biorxiv.org/content/10.110…

Spotiphy enables single-cell spatial whole transcriptomics across an entire section | Nature Methods nature.com/articles/s4159…

Congratulations to Matthew Loberg for the awesome poster presentation at AACR. Thanks also to our fantastic collaborative team.

Congrats Megan Tigue '16 !! Can't wait to see where this project goes!