Group leader - computational biomedical discovery - @UniHeidelberg, @uniklinik_hd. Associate - knowledge technologies - @JSI_SLO. Visitor - @emblebi.
Heidelberg, Germany
Joined December 2008
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Spatial omics is moving beyond mapping tissues toward discoveries that advance biomedicine and ultimately benefit patients. For us, the route there is tissue representation learning and the discovery of spatial biomarkers 🧵
nature.com/articles/s41467-0…
Spatial biomarkers are small sets of markers whose spatial organization associates with clinical outcomes. SpaCEy, now in @NatureComms, learns tissue representations guided by progression and survival, and its explainer extracts the biomarkers behind each prediction.
@ahmet_rifaioglu led this work, supported by Egle Ervin, @a_sarig_ , Deniz Germen, @BodenmillerLab and co-supervised by @JulioSaezRod and me.
Code: github.com/saezlab/SpaCEy
Jovan Tanevski retweeted
Meet the Speakers | STOC GM2
🎙 Deng Ziqing – BGI Research Beijing
Advancement & Future Directions of the STOC Infection Working Group
🎙 Jovan Tanevski – Heidelberg University
Context-Aware Framework for Multimodal Integration & Tissue Dynamics
🔗 stocgeneralmeeting.com/
Ending the year on a high note 🎉 Happy to share our latest preprint: SpaCEy biorxiv.org/content/10.64898…
We’ve been cooking this with @ahmet_rifaioglu for quite some time, and we’re excited to finally share the paper.
See more below.
See 👇 our new manuscript introducing SpaCEy, an explainable method for predicting clinical outcomes from spatial omics data 🧬
📄 Paper: biorxiv.org/content/10.64898…
💻 Code repo: github.com/saezlab/SpaCEy
Jovan Tanevski retweeted
The latest version of Kasumi is now published in Nature Comms nature.com/articles/s41467-0… 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
🚨 New preprint: "Topography Aware Optimal Transport for Alignment of Spatial Omics Data"
We present our new alignment framework TOAST biorxiv.org/content/10.1101/…
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.
This work was led by @FCeccarelli96 in collaboration with @pl219_Cambridge, @SeanHoldenAI, @saezlab and Tanevski Lab.
Jovan Tanevski retweeted
Together with @tanevski and @drbetge, we are looking for a computational postdoc interested in the combination of modeling tissue organization patterns from spatial proteomics data in a highly clinically relevant cancer context. Funding available: health-life-sciences.de/oppo…
Jovan Tanevski retweeted
📣 The much-revised manuscript of LIANA+, our all-in-one solution to study cell-cell communication from single-cell, spatial, and multi-omics technologies, is now published in @NatureCellBio nature.com/articles/s41556-0…
Jovan Tanevski retweeted
Tomorrow at BioQuant : Dissecting and overcoming different shades of cancer immune evasion by Benjamin Izar. Join us! Supported by @ResearchLifesci
Hosted by: @DenisSchapiro , @JulioSaezRod and @tanevski
Organised by MULTI-SPACE
bioquant.uni-heidelberg.de/e…
Jovan Tanevski retweeted
Our workflow, FLOP, exploring the impact of filtering, normalization, and differential expression on functional analysis is now published in @NAR_Open. doi.org/10.1093/nar/gkae552
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
1/n Our multi-objective optimization framework for transferring features across single-cell and different resolutions of spatial omics DOT is now published @NatureComms 🎉, freely available as an open source R implementation at saezlab.github.io/DOT/
doi.org/10.1038/s41467-024-4…
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
🚨 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 karriere.klinikum.uni-heidel…
Jovan Tanevski retweeted
We welcome Julio Saez-Rodriguez @JulioSaezRod as our new Head of Research!
Associate Director for EMBL-EBI Services Jo McEntyre @jomcentyre has been promoted to Deputy Director of EMBL-EBI & Rolf Apweiler is stepping back to Associate Director as he looks towards retirement.
If you like MISTy doi.org/10.1186/s13059-022-0…, you'll really like Kasumi doi.org/10.1101/2024.03.06.5…. Kasumi is a multi-view explainable representation learning approach, capturing localized relationship-based patterns in tissues across conditions aiming towards facilitating translation
Local heterogeneity of tissues can define their function and predict clinical outcomes. We introduce Kasumi 💻biorxiv.org/content/10.1101/… to identify spatially localized neighborhoods of intra and intercellular relationships from spatial omics persistent across samples & conditions
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.
Check it out here health-life-sciences.de/jobs… (project number 71) or contact me directly. Please RT 🙂