DESpace2: a novel framework to compare spatial expression patterns between conditions (e.g., healthy vs. diseased), from spatial omics data. Aim: identifying genes with distinct spatial structures (DSP) between groups of samples. 1/3

RT @BoyanSlat: Excited to announce that @TheOceanCleanup is massively scaling up Interceptor projects in the coming years!. ✅30 Cities. ✅St….

RT @TheOceanCleanup: IMPACT UPDATE: In the first half of 2025, we caught more trash than in all of 2024 combined! This adds up to over 30,0….

We incorporated the approach within DESpace Bioconductor package, with a novel dedicated vignette. bioRxiv: Bioc Package: DSP Vignette: Work from Peiying Cai (PhD at UZH), @markrobinsonca and myself. 3/3

Input: multi-sample multi-condition spatial omics data, and pre-computed spatial clusters/domains. Analysis:.- pseudo-bulk counts within each spatial cluster;.- compare (via edgeR) spatial expression structures among 2+ groups of samples;.- identify DSP genes. 2/3

RT @TheOceanCleanup: BREAKING: The Ocean Cleanup just announced the next big step in scaling Interceptor deployments worldwide: a 30-city p….

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RT @TheOceanCleanup: 2024 was 🤯

RT @KVittingSeerup: There is still a bit more than a week for people to apply 😉.

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Many thanks to all co-authors:.- Joel Meili (former MSc student at.@markrobinsonca.lab).- Peiying Cai (PhD student at.@markrobinsonca.lab).- @CSoneson.- @DongzeHe.- @hrksrkr.- @AleAviP.- @nomad421.- @markrobinsonca.

*DifferentialRegulation* out in Biostatistics: A Bayesian hierarchical method to identify differences in splicing dynamics (i.e. gene regulation) between conditions. It works on bulk and single-cell RNA-seq. Also on Bioconductor:

RT @tiberi_simone: *NEW pre-print*. IsoBayes: a Bayesian approach for single-isoform proteomics inference. A stati….

Key ideas:. - allocating peptide-level data to the protein isoform(s) each peptide maps to. -> hence going from peptide- to protein-level data. - enhance the available data by integrating MS and (short or long) RNA-seq data via informative priors. -> improving accuracy.

I thank all the people contributed to this work. In particular, I want to mention:.- Jordy Bollon, for performing most of the analyses;.- Michael Shortreed, for his proteomics support;.- Gloria Sheynkman, for the idea of the project, and for coordinating the biological analyses.

*NEW pre-print*. IsoBayes: a Bayesian approach for single-isoform proteomics inference. A statistical method to study proteins at the isoform-level, from mass spectrometry data. Available on Bioconductor 👇.

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DESpace final version now in Bionformatics: Huge congrats to Peiying Cai (@markrobinsonca lab) for her hard work and persistence.

Further details:.- 12 month position;.- net salary ~1,420 euros per month.