Play MISTy for me, says someone with spatial omics data to find relationships between markers in. It's a machine learning method from Jovan Tanevski, Saez-Rodriguez Group & co. It's demonstrated on mass cytometry and spatial transcriptomics data from breast cancer genomebiology.biomedcentral.com/articles/10.11…

Still possible to apply for PhD/Postdoc to work with us Universitätsklinikum Heidelberg - pls consider doing so and/or retweeting 🙏

#Postdoc + #PhD positions available in our lab in a new endeavor - funded by the NOMIS Foundation and supported by Treutlein lab, Gray Camp and Svante Pääbo - to unravel the evolutionary impact of de novo genes in primates! Details here: zmbh.uni-heidelberg.de/Kaessmann/open… Please RT!

📄 Knowledge graphs (KGs) are a key technology in biomedicine, but can be hard to create/share/reuse. To make KGs as accessible as possible we developed the #opensource framework BioCypher: nature.com/articles/s4158…, now peer-reviewed Nature Biotechnology. 🧵👇 1/

Integrating single-cell & spatial omics with different resolutions is key to understand tissue structure & function 🧬🔬 We had tackled this using multi-objective optimization - we just updated our paper and implemented an #rstats package arxiv.org/abs/2301.01682

📣 Introducing LIANA+: an all-in-one cell-cell communication (CCC) framework 🧬 Many tools exist, yet they use various syntaxes and are tailored for a specific purpose LIANA+ harmonises and extends existing methods, enabling their synergistic applications tinyurl.com/lianaplus

We are recruiting a PhD student on machine learning methods to analyze spatially resolved omics data in human disease within ELLIS #ELLISPhD programme

1) Are you interested in computational approaches to study the immune system 🔎🦠by integrating single-cell + spatial multi-omics data with prior knowledge? Check our review 📖out now in Nature Immunology nature.com/articles/s4159… 🧵

Local heterogeneity of tissues can define their function and predict clinical outcomes. We introduce Kasumi 💻biorxiv.org/content/10.110… to identify spatially localized neighborhoods of intra and intercellular relationships from spatial omics persistent across samples & conditions

🧵1/10 We’re thrilled to share our latest paper, Bicycle, a novel approach for inferring cyclic causal relationships from observational and interventional data! This work addresses a critical gap in understanding complex biological networks.

We welcome Julio Saez-Rodriguez Julio Saez-Rodriguez as our new Head of Research! Associate Director for EMBL-EBI Services Jo McEntyre Jo McEntyre has been promoted to Deputy Director of EMBL-EBI & Rolf Apweiler is stepping back to Associate Director as he looks towards retirement.

🚨 We are looking for a PhD student 🚨 to join the Tanevski Lab and Denis 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-heidelberg.de/index.php?ac=j…

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭In collaboration with the Zhang lab BCMHouston, we performed a comprehensive evaluation of kinase activity inference tools to help answer that question tinyurl.com/yc56axsv 🧵⬇️

📣 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 Nature Cell Biology nature.com/articles/s4155…

👉Consider joining us for a post-doc at EMBL-EBI & AstraZenecaUK as part of the EAZPOD program to study multicellular mechanisms associated with #cancer treatment resistance! #postdoc ebi.ac.uk/research/postd…

📢 Introducing CORNETO: a unified, knowledge-driven framework for multi-sample network learning & modeling via constrained optimization, supporting a wide variety of network methods and prior knowledge 💻Code: github.com/saezlab/corneto 📜Paper: doi.org/10.1101/2024.1… 🧵👇

This was a close collaboration with Lucas Schirmer, led by Celia Lerma Martin and our Pau Badia i Mompel. Congrats to them and all the other co-authors: Ricardo O. Ramirez Flores, Patricia Sekol, Philipp Schäfer, Christian J. Riedl, …

#Postdoc or #PhD position jointly hosted in our lab and that of Alexander Sasse @LXandR_ to investigate the evolution of gene regulation at the single-cell level across primates/mammals using state-of-the-art deep learning approaches: home.kaessmannlab.org/openPositions Please RT!

We will be at the inaugural #ESSB conference this week in Berlin, presenting with Maria Puschhof a talk on multi-modal whole brain tumor profiling, Philipp Schäfer with Jovan Tanevski a poster on analyzing cross-condition/temporal spatial data [1/2]

Postdoc position in our group at EMBL-EBI , analyzing single cell data to better understand and treat neurodegen diseases, collab with Andrew Bassett , Mo Lotfollahi, Omer Ali Bayraktar M Strauss and others Open Targets . Deadline 20/07. Please share🙏: embl.wd103.myworkdayjobs.com/en-US/EMBL/job…