Correlation is not causation. In our new perspective, we connect systems biology, causal reasoning, and machine learning to inform future approaches in systems biology and molecular medicine in the wake of current deep learning advances: doi.org/10.1038/s44320… 🧵👇

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 🧵⬇️

Understanding complex diseases requires approaches that jointly analyze omic data across multiple biological layers. In our new preprint, we merge data-driven multiomic factor analysis with systematic integration of mechanistic knowledge using COSMOS+ 🧵👇 doi.org/10.1101/2024.0…

link.springer.com/book/10.1007/9… Mühendislik öğrencileri için programlamaya giriş kitabımız yayınlandı. Bayilerinizden ısrarla isteyiniz...

📣 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…

Post-doc opening to join our lab EMBL-EBI #EMBLEBIresearch to develop/apply #bioinformatics methods to study cellular organization, int/extra cell networks to extract disease mechanisms from sc and spatial multiomic data, with Yvan Saeys, supp by Chan Zuckerberg Initiative 👇embl.org/jobs/position/…

📢 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… 🧵👇

Our work with Lucas Schirmer in multiple sclerosis (MS) is out today in Nature Neuroscience. We investigated lesion progression and cell-cell communication events in MS using snRNA-seq and spatial transcriptomics 🧠 See below ⬇️ nature.com/articles/s4159…

TÜBİTAK 2247-C STAR programı kapsamında grubumuza (Hacettepe Biyolojik Veri Bilimi Lab.) katılmak için bir adet lisans öğrencisi kontenjanı mevcut. Proje bilgileri: Proje başlığı: "Üretken Derin Öğrenme Ile Yeni Protein Dizilerinin Moleküler İşlev Odaklı Otomatik Tasarımı" ++

We are excited to announce an opening for a PhD student to join our research team at Uniklinik Heidelberg. If you are passionate about unraveling the molecular mechanisms underlying metabolic disorders, please apply at: karriere.klinikum.uni-heidelberg.de/index.php?ac=j… Deutsches Zentrum für Diabetesforschung (DZD) Helmholtz Diabetes Center (HDC)

🚀"Signals and Systems: Theory and Practical Explorations with Python" by our faculty members Fatos Yarman Vural (Fatos Tunay Yarman Vural) and Emre Akbas (Emre Akbas) is out from Wiley! Learn more at wiley.com/en-us/Signals+…

The latest version of Kasumi is now published in Nature Comms nature.com/articles/s4146… Kasumi identifies patterns in tissue patches enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level

🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with Omer Ali Bayraktar , Oliver Stegle and Moritz Mall groups. Preprint at end🧵👇

Great effort by Omer Ali Bayraktar, Stegle Lab & Moritz Mall labs in unravelling GBM cell state variability and spatial organisation at single-cell multimodal resolution. Happy that we could also contribute to this fantastic study! #Glioblastoma #SingleCell #SpatialOmics

Great work by Omer Ali Bayraktar , Oliver Stegle , and Moritz Mall ! Happy that our Ahmet Rifaioğlu contributed to this study by mapping CCC events between spatially co-localized TME and malignant cells using LIANA+ 🧠 github.com/saezlab/liana-…

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab BCMHouston, is now out Nature Communications 🔬 tinyurl.com/4twuc6z4

🚨Job Alert! 🔬 PhD Position in Bioinformatics! Join my group at Heidelberg University to study AML dormancy & therapy resistance using multi-omics & single-cell data. 📷Apply or share: karriere.klinikum.uni-heidelberg.de/index.php?ac=j…

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: nature.com/articles/s4225… 📖 News & Views: nature.com/articles/s4225… 💻 Code: corneto.org 🧵 Thread 👇

Great to see that this work is out! Glad to have been part of this effort!

🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳 📖biorxiv.org/content/10.110… 🔍 Explore: explore.omnipathdb.org OmniPath integrates 160+ resources for multi-omics analysis & modeling 🧶⬇️