🔬Can whole-slide Hematoxylin and eosin (H&E) stained histology images predict gene expression profiles in single-cell spatial omics? #spatial #SingleCell
Introduce our latest paper, BLEEP (Bi-modaL Embedding for Expression Prediction): a state-of-the-art tool predicting spatial gene expression profiles purely from histology images.
👉 Paper: https://t.co/YZjfKRBao5
👉 Code: https://t.co/rG31TXrx8U
Compared to alternatives, it offers superior correlation & captures the variance of original expression profiles more effectively.
Understanding molecular mechanisms behind tissue architecture is key to unraveling disease pathways & formulating effective treatments. Yet, gene expression profiling is often a costly, lengthy process.
BLEEP is a game-changing bi-modal embedding framework. It uses a contrastive learning approach to create a low-dimensional joint embedding space from paired image & expression profiles at micrometer resolution. This space serves as a reference for predicting expression in unknown image patches from whole-slide H&E stained histology images.
Benchmarked on a human liver tissue dataset from the 10x Visium platform, BLEEP outperforms ST-Net & His2Gene in terms of gene expression correlation & variance.
All the credits go to the amazing PHD student Ronald (@RonaldXie1 ), who is co-supervised by @garybader1 and myself. @pmcc_ai@VectorInst@UofT_TCAIREM@DonnellyCentre@UHN
CFP: The Symposium on Artificial Intelligence for Learning Health Systems (SAIL) is a new annual conference on AI for clinical medicine. SAIL will be held in Puerto Rico on May 9-12, 2023. https://t.co/CXxjqvg8FH #bioinformatics#artificialintelligence
Gene regulatory network reconstruction from scRNAseq: Greatly reduced false positives using multivariate transfer entropy. Great work by Guangzheng and @JunilKim_caleb. Collaboration with @kedar_natarajan
https://t.co/bWVU2N2Vec
In our new study we chart human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution (RNA + ATAC) @CellCellPress https://t.co/jqTWLOZEIu
We updated our database and now list 385 postdoc fellowship opportunities (w/ description, deadline, amount, eligibility, etc).
Getting one means a lot more freedom to do the work you want to do.
It is great to see an algorithmic development (TENET) leads to finding a new factor important for autophagy. Great work by @JunilKim_caleb in collaboration with Sunghee Baek and Dongha Kim.
scRNAseq analysis revealed the role for Shank3 neural stem cells and the association with autism. Collaboration with Jongphil Kim.
https://t.co/5YC7P9zQvJ
What an exciting week for CUT&Tag!!! After we published spatial-CUT&Tag in Science last week, Prof. Xiaowei Zhang lab demonstrated combining CUT&Tag and MERFISH to image, for example, 127 target H3K4me3 loci or 139 H3K27ac loci in mouse brain. Very cool!
https://t.co/BWddFt1Kdb
We’re excited to have this approach by @Morteza31846588 & @EllaKarjalainen published. A great collaboration with @KjwonL@HelinLab and the Grønbæk lab @UCPH_BRIC