Seppe De Winter

Happy to share CREsted, our latest package on enhancer modeling! CREsted allows for training sequence-based deep learning models from scATAC-seq data, enhancer decoding and enhancer design through a variety of methods. Check out the GitHub here: github.com/aertslab/CREst…. [1/9]

@dagarfield @steinaerts The recording is available on YouTube, please enjoy! youtube.com/live/QW63LLd1X…

@steinaerts speaking of...y'all do any recordings of your recent training/intro on SCENIC as part of this set of questions? I do love me some SCENIC.

Very excited to announce our new preprint together with Nikolai Hecker! Dive into our findings on the conserved regulatory codes shaping cell identity across species. 🧬 [1/n] biorxiv.org/content/10.110…

Excited to announce our upcoming webinar on SCENIC+: a Python package for constructing enhancer-driven gene regulatory networks from single-cell multiomics data! Join us on March 26th, 5pm CET. Register here: forms.gle/cVP3tW17fnJY4b…

🤖🧬In a new breakthrough, the team of @steinaerts (@_VIB_AI, @CBD_VIB) designed an AI model to guide the creation of synthetic DNA sequences. The study enhances our understanding of gene regulation and holds great potential for gene therapy. Read more: vibbio.tech/3t5sZdv

Exciting news! Our latest research on "Cell type directed design of synthetic enhancers" has been published in @Nature. We've harnessed deep learning to design enhancers with cell-type specificity. Find our paper here: nature.com/articles/s4158…. Highlights below: [1/n]

📣 We're excited to announce the opening of multiple faculty positions! Do you use and/or develop artificial intelligence methods and mechanistic mathematical models to address fundamental questions in biology? We'd love to hear from you. (Please share far and wide 🙏)

Binnen één week is het zover: Dag van de Wetenschap! 👨‍🔬 Op welke activiteit(en) mogen we jou verwachten? dagvandewetenschap.be #DVDW2023

So how did we, @AdrianRanga1 lab, manage to bring order to neural tube domains inside hPSC-derived human neural tube (NT) organoids? Read our newest story about local mechanical forces, you will find our approach to be very “attractive”. DOI: doi.org/10.1038/s41467…

Proud to announce our systematic scATAC-seq benchmark in @NatureBiotech! The @steinaerts lab teamed up with @hoheyn and 9 other labs/companies to investigate performance differences and possible fragment biases between current scATAC-seq methods. nature.com/articles/s4158… 1/n

Beyond proud to share my first (co-)first author manuscript out today in #Nature, where we describe the inhibition of epithelial-to-mesenchymal transition (#EMT) by pharmacological targeting of netrin-1 (1/23) nature.com/articles/s4158…

Are you at #ISMBECCB2023? Wanna hear about designing cell type specific enhancers guided by deep learning models? Visit my poster today (B-346) and my talk tomorrow (17h20) at @ISCB_RegSys COSI!

How can we evaluate Gene Regulatory Network? 🔍 I'll present our strategies today at #ISMBECCB2023 If you are interested come to poster 338

p.s. We also created a YouTube video together with @CBD_VIB youtube.com/watch?v=K-D2nN…

Last but not least, big thank you to all our amazing colleagues who have helped a lot in this project: @Bravo_Potato, Gert, Nikolai, @irina_M, Valerie, @S_Poovathingal, @Wouters_J_, @SaraAibar and @steinaerts. And thank you to @dkv_scientific for the beautiful logo. 🧵9/9🧵

I am happy to communicate that SCENIC+ was published in @naturemethods. SCENIC+ is a workflow to infer enhancer-driven gene regulatory networks from scRNA-seq and scATAC-seq data. This work was done together with @Bravo_Potato at @steinaerts lab! 🧵1/9🧵 nature.com/articles/s4159…