How to link single-cell diversity and the emergence and maintenance of robust multicellular processes in developed tissues? 🤔

What can we learn about multicellular coordination in tissues from single-cell omics data?

Read about our view: arxiv.org/abs/2403.06753

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

Our study integrating functional proteomics, phosphoproteomics and transcriptomics using COSMOS is out in Mol Syst Biol 🧬🧫
You can find it here: tinyurl.com/COSMOS-TPP
More information in the thread below 👇

📢 Join us as our Daniel Dimitrov presents “Modelling Cross-Conditional Intercellular Mechanisms” with LIANA+ (liana-py.readthedocs.io) at MMPU’s 30th Public Research Day 🗓️ March 5, 2023 ⏰ 16:30 📍 BioQuant Heidelberg.

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… 🧵

Are you looking to apply Large Language Models to biomedical questions? You may want to take a look at our new framework (biochatter.org) and the updated preprint (arxiv.org/abs/2305.06488). 🧵👇

Register to listen March 7th to our Julio Saez-Rodriguez talk about 'large-scale models of signaling from prior knowledge and omics: where we are and where we may go to', along w Ruth Huttenhain 's talk on spatially resolved signaling

If you do image analysis, check these recommendations & pitfalls - Congrats Lena Maier-Hein Annika Reinke Paul F. Jäger Minu Dietlinde Tizabi + rest of the team and thanks for involving our Julio Saez-Rodriguez

Our Julio Saez-Rodriguez will give #biomedx #lunchtalk Thursday, January 25, 11 AM Communication Center DKFZ   #Heidelberg about 'Knowledge-Based Machine Learning to Extract Disease Mechanisms from Omics Data' bio.mx/news/events/

Congrats Markus Rinschen and team and thanks for involving us! Glad our Aurelien Dugourd R. Fallegger Julio Saez-Rodriguez could help to analyse this multi-omics data to understand the effect of SGLT2 inhibitors

#spatial technologies advance v rapidly - See 👇 Mol Syst Biol from Theodore Alexandrov Sinem Saka & our Julio Saez-Rodriguez review & perspective on major challenges & opportunities, incl. computationally

Congrats Rebekka Schneider Hélène Gleitz Stephani Schmitz and thanks for involving our Aurelien Dugourd Julio Saez-Rodriguez in the analysis of this very interesting data.

Join us in beautiful Heidelberg as Staff
jobrxiv.org/job/heidelberg…
or to do your #PhD
jobrxiv.org/job/heidelberg…
analyzing cutting-edge Spatial omics to understand host-microbiome interactions in disease 🔍 pls RT 🙏

Thanks to funding from DFG public | @[email protected] 🙏 we will soon be recruiting developers to extend our prior knowledge frameworks BioCypher (biocypher.org) and OmniPath (omnipathdb.org): ssc.uni-heidelberg.de/en/newsroom/tw….

first European Research Council (ERC) funding after 7 applications and 5 interviews❗ so, if you did not get it, don’t give up! And, if you can, get as awesome partners as Stefania Giacomello Eduardo Villablanca Zeller Group 😄 Very thankful to them, many Saez-Rodriguez Group members & all others that helped us🙏

Accurate Transcription Factor (TF) activity estimation is key to interpret #transcriptomics data 🧬💡 In collaboration with NTNU and BSC-CNS, we present a high-confidence collection of signed regulons for >1000 TFs: academic.oup.com/nar/advance-ar…, now peer-reviewed @NAR_open 🧵⬇️

Results in diff expression analysis can vary depending on the processing pipeline used, but to what extent do they affect gene set enrichment?🤔 To answer this we present FLOP, a #nextflow workflow to perform & contrast RNA-seq results 🖥️ doi.org/10.1101/2023.0… 👇🧵

📣 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

Different omics provide complementarity information - we explored how to integrate them to understand PARP inhibition in ovarian cancer using our multi-omics network framework COSMOS in our latest work led by Mira Burtscher (tinyurl.com/579fehuy)

We’ll be at #ISMBECCB2023 !👇
Ece Kartal Predicting HF from microbiome🫀🦠
Pau Badia i Mompel Evaluation of gene regulatory nets🧬
Julio Saez-Rodriguez Knowledge-based machine learning🖥️
Loan Vulliard Tumor metabolic environment imaging📸
@TimTheRose MS annotation using metabolic nets✍️