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While reaching for cookies, we stumbled on a treat of a different kind: DIGGER 2.0 for exploring the functional role of protein interactions in #AlternativeSplicing! ☃️🍪
Now supporting the mouse interactome and the functional enrichment tool NEASE #CoSyAdventcalender

👉 exbio.wzw.tum.de/digger/

🐉 Have you ever met a DRaCOoN? This season’s new species doesn’t breathe fire, it reveals pathway-level changes in gene co-expression across conditions. A Python tool + web app with built-in benchmarking for robust #Transcriptomics analysis. #CoSyAdventcalender

☕ Grab a cup of hot chocolate and enjoy our next holiday reading!
Our study shows that exercise therapy and education (GLA:D®) lead to real, measurable improvements for people with #KneeOsteoarthritis beyond normal fluctuations over time. #CoSyAdventcalender

🔗 www.mdpi.com/2077-0383/14...

FedscGen: privacy-preserving federated batch effect correction of single-cell RNA sequencing data - Genome Biology Single-cell RNA-seq data from clinical samples often suffer from batch effects, but data sharing is limited due to genomic privacy concerns. We present FedscGen, a privacy-preserving communication-eff...

🎄✨ Today’s #CoSyAdventCalender highlight: FedscGen!
A federated, privacy-preserving way to correct batch effects in distributed #scRNAseq datasets.

🔗 genomebiology.biomedcentral.com/articles/10....

Privacy-preserving multicenter differential protein abundance analysis with FedProt - Nature Computational Science In this Resource, the authors present FedProt, a tool that enables privacy-preserving, federated differential protein abundance analysis across multiple institutions. Its results match the results of ...

Are you ready for the next #CoSyAdventcalender reading?
Say hello to FedProt, a privacy-preserving tool for multi-center differential protein analysis. #Proteomics #FederatedLearning

🔗 www.nature.com/articles/s43...

Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE Abstract. Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on i

You better watch out, you better not bias …
We tested 17 normalization + 2 batch correction methods in proteomics and built PRONE to reveal how much they change results. Normalization matters and so does picking the right one. #CoSyAdventcalender

academic.oup.com/bib/article/...

To Implement or Not to Implement? A Commentary on the Pitfalls of Judging the Value and Risks of Personalized Prognostic Statistical Models Prognostic models in medicine have garnered significant attention, with established guidelines governing their development. However, there remains a lack of clarity regarding the appropriate circumsta...

❄️ Not every snowflake becomes a snowman and not every model belongs in the clinic. We mapped 16 scenarios to judge when a prognostic model is “good enough to build or deploy, using a structured benefit-risk approach. #PrognosticModels #HealthcareAI #CoSyAdventcalender

👉 jmir.org/2025/1/e69341

Meta-analysis of genomic characteristics for antiviral influenza defective interfering particle prioritization Abstract. Defective interfering particles (DIPs) are viral deletion mutants that hamper virus replication and are, thus, potent novel antiviral agents. To

Oh the viruses may be frightful, but the DIPs are so delightful …This year we explored defective interfering particles (DIPs), viral mutants that block viral replication and could become novel #antivirals. #CoSyAdventcalender
Learn more: academic.oup.com/nargab/artic...

@mathbiotanja.bsky.social

🎁 This holiday season, we unwrap one of our highlights: @daibetes.bsky.social !
By combining privacy-perserving #AI & virtual twins, the project is working to transform #Type2DiabetesCare
#CoSyAdventcalender

Transcription factor prediction using protein 3D secondary structures AbstractMotivation. Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if th

🎄 The first light on our holiday research tree: StrucTFactor! This deep learning method predicts #TranscriptionFactors using 3D structure, shining 17% brighter than existing methods. ✨
#CoSyAdventcalender

🎁 Learn more: academic.oup.com/bioinformati...

The holiday season is here! 🎄 Cookies, chocolate … and research! This advent calendar serves up our research highlights from 2025, a sweet countdown of computational biomedicine highlights. 🍪📄 → Follow us for daily advent calendar posts!
#CoSyAdventcalender #Bioinformatics