RT @saezlab: The latest version of Kasumi is now published in Nature Comms Kasumi identifies patterns in tissue pat….

This work was led by @FCeccarelli96 in collaboration with @pl219_Cambridge, @SeanHoldenAI, @saezlab and Tanevski Lab.

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We demonstrate TOAST on intra-, intersample, and temporal alignment in:.🧠 Human cortical layers (Visium).🧫 Axolotl regeneration (Stereo-seq).🐭 Locallization in mouse embryo development (seqFISH).🎯 Various cancer types (IMC).… with state-of-the-art efficiency and performance.

TOAST quantifies spatial coherence using entropy in local neighborhoods—favoring alignments that keep the order of local spatial compositions. It also preserves neighborhood consistency—aligning spots with similar gene expression in the spatial neighborhood.

Alignment is an important step for data integration that can help gain insights into mechanisms, progression and structural changes in disease. When the spatial context is available it *has to* complement molecular similarity to yield more biologically plausible mappings.

🚨 New preprint: "Topography Aware Optimal Transport for Alignment of Spatial Omics Data".We present our new alignment framework TOAST

RT @felixjhartmann: Together with @tanevski and @drbetge, we are looking for a computational postdoc interested in the combination of model….

RT @saezlab: 📣 The much-revised manuscript of LIANA+, our all-in-one solution to study cell-cell communication from single-cell, spatial, a….

RT @natgabrielli: Tomorrow at BioQuant : Dissecting and overcoming different shades of cancer immune evasion by Benjamin Izar. Join us! Sup….

RT @saezlab: Our workflow, FLOP, exploring the impact of filtering, normalization, and differential expression on functional analysis is no….

I am particularly happy for this publication. It is a milestone in my recently started transition to a group leader. I am grateful to everyone involved - @Arezou_Rahimi for her amazing work and trust, @JulioSaezRod for his continuous support and the great collaboration with @GSK.

In a very busy area with many great methods, we took a step forward. We generalize on localization and deconvolution and introduce new tasks, bridging information between samples and across modalities. We offer a flexible and scalable solution while achieving the best performance.

🚨 We are looking for a PhD student 🚨 to join the Tanevski Lab and @DenisSchapiro Lab at the Heidelberg University Hospital, working at the intersection of machine learning and spatial omics as part of the Translational Spatial Profiling Center. Please RT

RT @emblebi: We welcome Julio Saez-Rodriguez @JulioSaezRod as our new Head of Research!. Associate Director for EMBL-EBI Services Jo McEnty….

Check it out here (project number 71) or contact me directly. Please RT 🙂.

If this sounds interesting to you and you happen to look for a new position, with @felixjhartmann we are hiring an interinstitutional postdoc to work with us in Heidelberg on capturing and exploring higher order tissue organization from highly multiplexed omics data.

If you like MISTy you'll really like Kasumi Kasumi is a multi-view explainable representation learning approach, capturing localized relationship-based patterns in tissues across conditions aiming towards facilitating translation.

RT @sbi2_org: We have great scientific sessions lined up this year including "Artificial Intelligence / Machine Learning: Data Integration….

Amazing work by @DanielBDimitrov extending LIANA to now include also CCC approaches aimed at spatial data. I’m happy that i was able to help by showcasing MISTy. Huge thanks to @psl_schaefer for the adaptation, bringing MISTy to the Python leaning part of our community.

RT @saezlab: Integrating single-cell & spatial omics with different resolutions is key to understand tissue structure & function 🧬🔬 We had….