iiinova — where your digital self keeps evolving

Reposted by Jovan Tanevski

Saez-Rodriguez Group @saezlab.bsky.social · 17/12/2025

See 👇 our new manuscript introducing SpaCEy, an explainable method for predicting clinical outcomes from spatial omics data 🧬 📄 Paper: www.biorxiv.org/content/10.6... 💻 Code repo: github.com/saezlab/SpaCEy

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Reposted by Jovan Tanevski

Loan Vulliard @lvulliard.bsky.social · 08/10/2025

🧭 Colorectal cancer doesn’t follow a single path. Using spatial proteomics on ~500 tumors, we found distinct trajectories from early to late stage, involving the whole tumor microenvironment and its metabolic state. 📄 Preprint: arxiv.org/abs/2510.05083 #SpatialBiology #CRC #ImageBasedProfiling 1/5

arxiv.org

Robust multicellular programs dissect the complex tumor microenvironment and track disease progression in colorectal adenocarcinomas

Colorectal cancer (CRC) is highly heterogeneous, with five-year survival rates dropping from $\sim$90% in localized disease to $\sim$15% with distant metastases. Disease progression is shaped not only...

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Reposted by Jovan Tanevski

Saez-Rodriguez Group @saezlab.bsky.social · 15/09/2025

Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics. 🔗 Manuscript: www.biorxiv.org/content/10.1... 💻 Code: partipy.readthedocs.io

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Jovan Tanevski @tanevski.bsky.social · 22/07/2025

🎉 Such a great work by everyone involved in this major push forward in spatial multiplexing and next-generation pathology. I‘m glad to have been able to contribute to this effort and shed a light on the discovery of sub-cellular to tissue level organization patterns by xAI based on this technology.

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Reposted by Jovan Tanevski

Saez-Rodriguez Group @saezlab.bsky.social · 07/05/2025

The latest version of the Kasumi manuscript is now published in Nature Comms www.nature.com/articles/s41... Kasumi identifies patterns in tissue patches, enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level

nature.com

Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications

Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...

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Reposted by Jovan Tanevski

Alastair Lamb @lambalastair.bsky.social · 29/04/2025

Brilliant session focused entirely on spatial multiomics @theaacr.bsky.social #AUA25 Well said @tanevski.bsky.social "Cancer is a spatial disease-spatialomics is the future of cancer science"! Wonderful composite spatial data from Linghua Wang @mdanderson.bsky.social www.nature.com/articles/s41...

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Jovan Tanevski @tanevski.bsky.social · 22/04/2025

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

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Jovan Tanevski @tanevski.bsky.social · 15/04/2025

@chiaraschiller.bsky.social did an amazing job describing the landscape of methods for pairwise-association analysis in immediate spatial neighborhoods. Addressing limitations she proposes COZI and shows its ability to consistently recover directional cell-type associations and generate new insights

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