This work was motivated by settings with scarce data such as rare diseases. It turned into multi-dimensional puzzles and alignement problems that we really enjoyed solving! Congrats to Daniel Lepe-Soltero, the postdoc who led this work. Link -> arxiv.org/abs/2503.18856

Very happy to share MODIS - a new Multi-Omics Data Integration method for Small and unpaired datasets! We solve a long-standing problem in the field: how to perform data integration for small unpaired datasets Our solution: learning with class imbalance on both reference and target datasets!

Link to the preprint -> www.biorxiv.org/content/10.1...

Very happy to introduce jsPCA, a fast and interpretable computational framework for spatial transcriptomics that simultaneously identifies spatial domains and variable genes across multi-slice and multi-sample data.

Excited to share David Hirst's PhD work! 🧬 When you only have a few datasets available for multi-omics integration, for instance because you work on rare diseases, one solution is Transfer Learning. Introducing #MOTL - now available in Genome Biology! doi.org/10.1186/s130...

🚨 We're hiring! NCMBM @ncmbm.bsky.social is looking for 2 new group leaders to join our vibrant research community. Ready to build your own group with strong support and a solid startup package? Interested and attending #ISMBECCB2025? Let’s connect! 🔗 www.jobbnorge.no/en/available...

👋 We wrap up our #NetBio track 2025 with announcing the #Cytoscape network visualization competition winners (woobox.com/b9poce) Congrats: 1: Alejandra Paulina Perez Gonzalez 2. Michael Costanzo 3. Jong Chan Lim 👏👏👏 Exciting to have Alejandra and Jong in the audience and congrats to Michael!

🎉 And now it is time to introduce our last and shared keynote with the Microbiome COSI: @fionabrinkman.bsky.social is talking about "Microbiome multitudes and metadata madness" connecting the #Microbiome and #NetworkBiology communities! #ISMBECCB2025

✨ And it's already time for the last selected #NetBio talk! Piotr Sliwa is presenting "Multilayer Networks Identify Clinically Relevant Patient Endotypes in COVID-19 and Sepsis" #ISMBECCB2025 #NetworkBiology

#NetBio talks are continuing in room 1B: Dongmin Bang is presenting his proceeding paper on "MixingDTA: Improved Drug-Target Affinity Prediction by Extending Mixup with Guilt-By-Association" doi.org/10.1093/bioi... #ISMBECCB2025 #NetworkBiology

🔊 Nicoleta Siminea just presented her work on "Interactome-based computational solutions to support personalized drug therapy decisions in glioblastoma" at the #NetBio track at #ISMBECCB2025!

🎤 Next up is Terence Egbelo He is sharing his research on "Improving Target-Adverse Event Association Prediction by Mitigating Topological Imbalance in Knowledge Graphs" with the #NetBio audience! ✨ #ISMBECCB2025 #NetworkBiology #KnowledgeGraphs

✨Johannes Kersting just presented his cool #Nextflow Pipeline for Network-Based Disease Module Identification and Drug Repurposing nf-co.re/diseasemodul... github.com/nf-core/dise... #ISMBECCB2025 #NetworkBiology #NetBio

📣Last speaker of the #NetBio morning session: Samuele Firmani is presenting GATE (Graph Antiviral Target Explorer) to predict disease genes in viral infections with Message Passing Neural Networks" #ISMBECCB2025 #NetworkBiology

🎤 Next #NetBio talk: Erik Sonnhammer presents #FunCoup6, an upgrade to the functional association network database, now with enhanced regulatory links, a redesigned interface, and powerful new tools for comparative interactomics and disease module analysis. funcoup.org #ISMBECCB2025 #NetworkBiology

🔊 Next in #NetBio at #ISMBECCB2025 Dewei Hu presents: SPACE: STRING proteins as complementary embeddings Cross-species network embeddings meet protein function prediction, leveraging STRING across 1,300+ eukaryotes. A powerful complement to sequence embeddings! #NetworkBiology

⌛It's already time for our last #NetBio speaker of today: ✨🔊We are excited to welcome our 2nd keynote speaker Jan Baumbach talking about "Quantum computing for network medicine-based epistatic disease mechanism mining - Fake it till you make it?" ✨ #ISMBECCB2025 #NetworkBiology

🎤 Next talk at #NetBio is by Aritra Bose from IBM Research presenting their work on "Quantum Random Walks for Biomarker Discovery in Biomolecular Networks". #ISMBECCB2025 #NetworkBiology

After lots of #NetBio discussions over coffee, we are now starting the last session for today: Lucas Gillenwater is presenting his #ISMBECCB2025 proceeding paper "GRACKLE: An interpretable matrix factorization approach for biomedical representation learning". doi.org/10.1093/bioi... #NetworkBiology

🎤 Next talk at #NetBio: @beatrizurda.bsky.social: Disentangling the genetic and non-genetic origin of disease co-occurrences #ISMBECCB2025 #NetworkBiology

🎙️Next #NetBio talk: Kivilcim Ozturk uncovers how mutations in intrinsically disordered regions (IDRs) disrupt protein interactions in cancer, revealing potential cellular vulnerabilities. #ISMBECCB2025 #NetworkBiology

🔊 Now presenting in our #NetBio track: Ibrahim Alsaggaf introduces Sup-EGsCL, a contrastive learning method using enhanced Gaussian noise augmentation to better predict gene longevity effects from protein-protein interaction networks. github.com/ibrahimsagga... #ISMBECCB2025 #NetworkBiology

🚨 Excited to announce our first keynote for #NetBio 2025: Laura Cantini (@cantinilab.bsky.social)! She is sharing cutting-edge work on multi-modal learning for single-cell data integration, tackling how to combine diverse omics and spatial data to unlock new insights into cellular heterogeneity.

📢 Next up: @SaniyaKhullar presents NetREm, a powerful new method revealing how transcription factors coordinate gene regulation across cell types. From immune cells to Alzheimer’s brains, NetREm maps regulatory networks with real-world validation. #ISMBECCB2025 #NetworkBiology

📢 Next up at #NetBio: We're excited to welcome Mayra Luisa Ruiz Tejada Segura presenting: "Nichesphere: A Method to Identify Disease-Specific Physical Cell-Cell Interactions and Communication Networks" #ISMBECCB2025 #NetworkBiology

🧬Excited to welcome Giulia Cesaro to present #CellGOSSIP, a novel strategy to decode cell-specific intracellular signaling from noisy single-cell data using personalized network propagation. 🎯 Reveal hidden pathway dynamics and functional cell states! #ISMBECCB2025 #NetworkBiology #NetBio

Our #NetBio track will continue in a few minutes in room 1B with another set of great talks! Have you already seen our new logo ✨👏? Thanks @romanayanez.bsky.social for the beautiful design 🥰!

🔊 Up next at #NetBio: Sindhura Kommu presents her work on "Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning." She couldn’t join us onsite in Liverpool, but is connecting live to share her research ✨! #ISMBECCB2025 #NetworkBiology

✨ @anaisbaudot.bsky.social is opening #NetBio 2025 to a full conference hall here in Liverpool. Exciting to see many network enthusiasts in one room! 👏 #ISMBECCB2025 #NetworkBiology

It's an honor to be recognized for advocating for what you believe "that everyone belongs in computational biology and that all ideas are valued equally, recognizing that diversity of thought and background drives scientific excellence" doi.org/10.1093/bioi...

I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Who else is going?

Our group @ebi.embl.org‬ is a host for the ARISE2 MSCA-funded post-doc fellowship, in collab with @bioimagearchive.bsky.social‬ and ‪@scilifelab.se (esp. A Mezger and S. Giacomello) to support the development of next-gen spatial data infrastructures. Apply by 30/09 www.embl.org/training/ari...

🔬 A new study by #IRBBarcelona reveals the limitations of current methods used to study cell communication. 📰 #GenomeBiology ✍️ @epareja10.bsky.social @ptck72.bsky.social ➡️ bit.ly/4kvcD2a 📌 DOI: 10.1186/s13059-025-03677-5 #IRBScience 🧪 🧵👇

Lancement de l’école thématique Organoides : modéliser des systèmes multicellulaires à Nantes du 7 au 11 Juillet 2025 @cnrsbiologie.bsky.social @inserm.fr @insermgrandouest.bsky.social #organoids #research avec Maxime Mahé et Vincent Flacher

First day of « École thématique #organoids » With ground-breaking talks! thanks to Drs. Isabelle Dupin, Vincent Guen, Jean Baptiste Dupont, Olivier Goureau and Xavier Gidrol @cnrsbiologie.bsky.social @inserm.fr @insermgrandouest.bsky.social @cea @institutducerveau.bsky.social

Second day!!! Amazing talks #organoids from Drs. Stéphane Nedelec, Diana Passaro, Emily Tubbs and Audrey Ferrand! Follows by hands-on training at Micropicell 🧫🔬Nantes University @cnrs.fr @inserm.fr @insermgrandouest.bsky.social @NantesUniversity @institutcochin.bsky.social @ferrandlab.bsky.social

What a nice week at CIRM in Marseille for the workshop "Mathematics of Single-Cell Data Analysis", organized by PEPR Digital Health and PEPR MathVives. So many exciting mathematical approaches covering GRN inference, statistical testing and optimal transport. Looking forward to the next edition!

Do you have experience in mechanistic modelling of biological systems and want to do a postdoc with an interdisciplinary team on developing Digital Twins for rare disease? We have the job for you! Check it out below - deadline July 13th, online interviews 24th July.

Today’s Impromptu Seminar at CeMM featured @epetsalaki.bsky.social (@ebi.embl.org‬), who shared her lab’s work on context-specific signalling using network modelling & machine learning. From melanoma resistance to MASLD, a fascinating session—thank you, Evangelia & @ar-abdelfattah.bsky.social!

If EMBL-EBI managed data resources have ever saved you time & effort, this is your chance to give back! Fill in a 15-minute survey to help us: 🌍Demonstrate the real-world impact of our resources 🤓Understand your needs 🌟Secure continued funding Closes 16 July www.surveymonkey.com/r/QGFMBH8?ch...

Exciting opportunity at the forefront of network biology, multiomics, AI and DT. Deadline 13th July! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

I, Rahuman Sheriff @biomodels.bsky.social and Ellie McDonagh from @opentargets.org @ebi.embl.org are looking for an enthusiastic postdoc with skills in executable modelling to create Digital Twins for rare disease (CZI-funded project).

@netsciconf.bsky.social crossing Holland on my way to Maastricht for @netbiomed2025.bsky.social Join us tomorrow at FASOS for a great day of network biomedicine talks!

Our latest work - MODIS: Multi-Omics Data Integration for Small and Unpaired Datasets - was in Singapore for the www.lmrl.org workshop at ICLR. Congrats Daniel Lepe-Soltero!! Preprint: arxiv.org/abs/2503.18856

Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.

📢 Applications for EMBL Sabbatical Visitor fellowships are open! An opportunity for senior scientists to receive up to 15000 € to foster collaboration, share knowledge and expertise while based at any of the EMBL’s six sites. 📩 Apply until 15 June 2025. www.embl.org/about/info/s...

Join our lab to study transcriptional regulation in mouse germ cells and embryonic stem cells at @haskoliislands.bsky.social in beautiful Reykjavík! Apply here: tinyurl.com/34y6jcrd #epigenetics #TranscriptionFactors #transcriptomics #stemCells #pluripotency

For those who prefer matrix factorization to auto-encoders, we previously proposed "MOTL: enhancing multi-omics matrix factorization with transfer learning" ;) www.biorxiv.org/content/10.1...

Very happy to share our new preprint "MODIS: Multi-Omics Data Integration for Small and Unpaired Datasets"! We proposed a new coupled variational auto-encoder architecture to solve the problem of data integration for small and unpaired datasets (diagonal integration) arxiv.org/abs/2503.18856