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This is now out! And here is an animation that shows a smooth interpolation from a linear visualization (PCA) to GraphDR (with increasing regularization parameter). Colors indicate annotated cell types. nature.com/articles/s4159…

Kathy Chen’s paper for sequence-based global map of regulatory activity is now out (nature.com/articles/s4158…)! Congratulations to all co-authors Aaron Wong Olga Troyanskaya. Thanks to Anshul Kundaje (anshulkundaje@bluesky) and Wouter Meuleman for the News & Views!

↘️First preprint from my lab! We introduce a new #GNN method that capitalizes on complementary information in *multiple* PPI networks for #cancer gene prediction. SOTA performance+ #XAI for bio insights. Fantastic work done by Michail Chatzianastasis. Feedback welcome!

Excited to share our new work about the sequence basis of transcription initiation in human. We showed that simple rules can explain most human promoters, offering fresh insights into transcription initiation and gene regulation biorxiv.org/content/10.110…

Glad to share our new preprint on sequence basis of transcription initiation, showing that simple rules can explain the majority of human promoters! Checkout Kseniia Dudnyk's thread on how sequence can help understand the biology of transcription initiation:

Unleash the power of #DNA foundation models with #NLP #LLMs - check out our new method LINGO! We steer the NLP linguistic knowledge for #genome understanding, with just genomic-specific adapters & no pretraining! feedback welcome :) arxiv.org/abs/2402.08075

In light of the recent discussions on UMAP, I'd like to bring to attention this alternative that avoids many issues of UMAP/tSNE: GraphDR can be considered an enhanced PCA that contracts points toward each other based on high dimensional similarity, works well in 2D / 3D / more

Princeton Precision Health is hiring! Be part of our interdisciplinary team leveraging AI and big data to revolutionize human health and health policy! #PrecisionMedicine