CoSy.Bio
@cosybio-uhh.bsky.social
Computational Systems Biomedicine research group at the University Hamburg
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/
Now supporting the mouse interactome and the functional enrichment tool NEASE #CoSyAdventcalender
👉 exbio.wzw.tum.de/digger/
Home | DIGGER
exbio.wzw.tum.de
December 23, 2025 at 12:28 PM
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/
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
December 18, 2025 at 6:42 PM
🐉 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...
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...
www.mdpi.com
December 17, 2025 at 5:49 PM
☕ 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...
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...
🎄✨ Today’s #CoSyAdventCalender highlight: FedscGen!
A federated, privacy-preserving way to correct batch effects in distributed #scRNAseq datasets.
🔗 genomebiology.biomedcentral.com/articles/10....
A federated, privacy-preserving way to correct batch effects in distributed #scRNAseq datasets.
🔗 genomebiology.biomedcentral.com/articles/10....
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...
genomebiology.biomedcentral.com
December 16, 2025 at 7:11 PM
🎄✨ Today’s #CoSyAdventCalender highlight: FedscGen!
A federated, privacy-preserving way to correct batch effects in distributed #scRNAseq datasets.
🔗 genomebiology.biomedcentral.com/articles/10....
A federated, privacy-preserving way to correct batch effects in distributed #scRNAseq datasets.
🔗 genomebiology.biomedcentral.com/articles/10....
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...
Say hello to FedProt, a privacy-preserving tool for multi-center differential protein analysis. #Proteomics #FederatedLearning
🔗 www.nature.com/articles/s43...
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 ...
www.nature.com
December 15, 2025 at 12:04 PM
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...
Say hello to FedProt, a privacy-preserving tool for multi-center differential protein analysis. #Proteomics #FederatedLearning
🔗 www.nature.com/articles/s43...
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/...
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/...
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
academic.oup.com
December 11, 2025 at 6:44 PM
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/...
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/...
❄️ 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
👉 jmir.org/2025/1/e69341
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...
jmir.org
December 10, 2025 at 4:29 PM
❄️ 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
👉 jmir.org/2025/1/e69341
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
Learn more: academic.oup.com/nargab/artic...
@mathbiotanja.bsky.social
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
academic.oup.com
December 9, 2025 at 3:53 PM
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
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
By combining privacy-perserving #AI & virtual twins, the project is working to transform #Type2DiabetesCare
#CoSyAdventcalender
December 8, 2025 at 11:35 AM
🎁 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
By combining privacy-perserving #AI & virtual twins, the project is working to transform #Type2DiabetesCare
#CoSyAdventcalender
🎄 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...
#CoSyAdventcalender
🎁 Learn more: academic.oup.com/bioinformati...
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
academic.oup.com
December 1, 2025 at 12:37 PM
🎄 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...
#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
#CoSyAdventcalender #Bioinformatics
December 1, 2025 at 8:39 AM
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
#CoSyAdventcalender #Bioinformatics
We present FedscGen, a federated, #PrivacyPreserving method (built on scGen) batch-effect correction tool to help analyze distributed #scRNAseq datasets.
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
October 6, 2025 at 11:56 AM
We present FedscGen, a federated, #PrivacyPreserving method (built on scGen) batch-effect correction tool to help analyze distributed #scRNAseq datasets.
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
✨ Congratulations to Faren, the winner of the Young Investigator Award #RExPO25! This is a truly well-deserved recognition of her outstanding research and impact. 👏 @repo4eu.bsky.social
September 29, 2025 at 10:21 AM
✨ Congratulations to Faren, the winner of the Young Investigator Award #RExPO25! This is a truly well-deserved recognition of her outstanding research and impact. 👏 @repo4eu.bsky.social
#Acne and other #SkinDisorders are often linked to the sebaceous gland (SG). We provide a detailed molecular map of the human SG, revealing dynamic differentiation of sebocytes and identifying new #GeneMarkers, providing a valuable reference for future research.
www.jidonline.org/article/S002...
www.jidonline.org/article/S002...
September 22, 2025 at 12:28 PM
#Acne and other #SkinDisorders are often linked to the sebaceous gland (SG). We provide a detailed molecular map of the human SG, revealing dynamic differentiation of sebocytes and identifying new #GeneMarkers, providing a valuable reference for future research.
www.jidonline.org/article/S002...
www.jidonline.org/article/S002...
🚀🦠 Exciting discussions at the @microb-ai-ome.bsky.social Steering Committee Meeting in Vienna! Great to see progress at the intersection of #MicrobiomeResearch and #AI!
September 15, 2025 at 11:24 AM
🚀🦠 Exciting discussions at the @microb-ai-ome.bsky.social Steering Committee Meeting in Vienna! Great to see progress at the intersection of #MicrobiomeResearch and #AI!
Studying #BoneTissue proteins can be likened to finding a needle in a haystack of collagen. Our new protocol eliminates collagen interference without the use of enzymes, yielding 68% more proteins identified. #proteomics
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
September 11, 2025 at 1:11 PM
Studying #BoneTissue proteins can be likened to finding a needle in a haystack of collagen. Our new protocol eliminates collagen interference without the use of enzymes, yielding 68% more proteins identified. #proteomics
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
We introduce DRaCOoN 🐉: a Python package and web tool designed for pathway-level #DifferentialCoexpression analysis. It features a unique benchmarking framework and demonstrates robust performance across various #Transcriptomics datasets.
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
September 8, 2025 at 9:54 AM
We introduce DRaCOoN 🐉: a Python package and web tool designed for pathway-level #DifferentialCoexpression analysis. It features a unique benchmarking framework and demonstrates robust performance across various #Transcriptomics datasets.
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
Presenting DIGGER 2.0: we extended our #AlternativeSplicing software DIGGER with new functionalities, including support of the mouse interactome and NEASE for #EnrichmentAnalysis! Check it out here: exbio.wzw.tum.de/digger/
August 21, 2025 at 11:32 AM
Presenting DIGGER 2.0: we extended our #AlternativeSplicing software DIGGER with new functionalities, including support of the mouse interactome and NEASE for #EnrichmentAnalysis! Check it out here: exbio.wzw.tum.de/digger/
When is "good enough" actually good enough for #PrognosticModels? Our commentary tackles this question with a structured analysis of 16 scenarios + practical approaches for development decisions for healthcare-related prognostic models.
www.jmir.org/2025/1/e69341
www.jmir.org/2025/1/e69341
August 7, 2025 at 9:01 AM
When is "good enough" actually good enough for #PrognosticModels? Our commentary tackles this question with a structured analysis of 16 scenarios + practical approaches for development decisions for healthcare-related prognostic models.
www.jmir.org/2025/1/e69341
www.jmir.org/2025/1/e69341
Defective interfering particles (DIPs) as potential novel #Antivirals! Our meta-analysis of 20 #Influenza datasets provides insights for selecting candidates for antiviral treatment design.
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
July 28, 2025 at 8:27 AM
Defective interfering particles (DIPs) as potential novel #Antivirals! Our meta-analysis of 20 #Influenza datasets provides insights for selecting candidates for antiviral treatment design.
academic.oup.com/nargab/artic...
academic.oup.com/nargab/artic...
We compared various models predicting changes in #KneePain of #Osteoarthritis patients due to participation in supervised education and exercise and propose a concise 6-variable model for personalized prediction.
rehab.jmir.org/2025/1/e60162
rehab.jmir.org/2025/1/e60162
July 21, 2025 at 7:46 AM
We compared various models predicting changes in #KneePain of #Osteoarthritis patients due to participation in supervised education and exercise and propose a concise 6-variable model for personalized prediction.
rehab.jmir.org/2025/1/e60162
rehab.jmir.org/2025/1/e60162
Introducing DREAMER, a groundbreaking tool that identifies mechanisms of #AdverseDrugReactions (ADRs) by linking drug and disease phenotypes to protein interaction networks. Here, DREAMER revealed #MolecularMechanisms behind 67 ADRs.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
June 30, 2025 at 11:46 AM
Introducing DREAMER, a groundbreaking tool that identifies mechanisms of #AdverseDrugReactions (ADRs) by linking drug and disease phenotypes to protein interaction networks. Here, DREAMER revealed #MolecularMechanisms behind 67 ADRs.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Join CoSy.Bio in Hamburg!
We are looking for a System Administrator to support our team.
🔧 Linux/macOS | HPC | Automation | Bioinformatics
📍 Hamburg
🗓️ Apply by June 27
🔗 www.stepstone.de/stellenangeb...
We are looking for a System Administrator to support our team.
🔧 Linux/macOS | HPC | Automation | Bioinformatics
📍 Hamburg
🗓️ Apply by June 27
🔗 www.stepstone.de/stellenangeb...
www.stepstone.de
June 23, 2025 at 11:11 AM
Join CoSy.Bio in Hamburg!
We are looking for a System Administrator to support our team.
🔧 Linux/macOS | HPC | Automation | Bioinformatics
📍 Hamburg
🗓️ Apply by June 27
🔗 www.stepstone.de/stellenangeb...
We are looking for a System Administrator to support our team.
🔧 Linux/macOS | HPC | Automation | Bioinformatics
📍 Hamburg
🗓️ Apply by June 27
🔗 www.stepstone.de/stellenangeb...
We wrapped up a productive @daibetes.bsky.social Steering Committee Meeting last week in Boston!
Great discussions on how privacy-preserving #AI can advance #DiabetesResearch and #PersonalizedPatientCare.
Great discussions on how privacy-preserving #AI can advance #DiabetesResearch and #PersonalizedPatientCare.
June 10, 2025 at 12:47 PM
We wrapped up a productive @daibetes.bsky.social Steering Committee Meeting last week in Boston!
Great discussions on how privacy-preserving #AI can advance #DiabetesResearch and #PersonalizedPatientCare.
Great discussions on how privacy-preserving #AI can advance #DiabetesResearch and #PersonalizedPatientCare.
Soluble guanylate cyclase (sGC) protects cells from #OxidativeStress. Our research shows ta cGMP-dependent reduction of #ReactiveOxygenSpecies (ROS) upon soluble guanylate cyclase activation via a downregulation of NOX4/5 via NF-κB. Our findings have significant implications for #StrokeRecovery!
June 2, 2025 at 12:16 PM
Soluble guanylate cyclase (sGC) protects cells from #OxidativeStress. Our research shows ta cGMP-dependent reduction of #ReactiveOxygenSpecies (ROS) upon soluble guanylate cyclase activation via a downregulation of NOX4/5 via NF-κB. Our findings have significant implications for #StrokeRecovery!