CAST enables physical alignment of spatial omics data across replicates, techs, modalities at single-cell resolution. Such accurate alignment enables spatial atlas searching, unbiased DEG identification, and reconstruction of spatial multi-omics. DM for questions and collabs!

My guidelines for exploratory data analysis

Synthesizing RNA can be as fun as LEGO puzzles! This work is co-led by my incredible colleagues @LDangliang and @AbhiAditham . Huge thanks to my supervisor @WangXiaoLab for such amazing ideas. We are also grateful for the editor, reviewers, and all collaborators along the way.

Chapter 2 of branched RNA: chemically modified branched cap for multi-capped mRNA and capped circular RNA (QRNA)--the cellular translation machinery is surprisingly tolerant of unnatural structures! Beyond enhanced performance, the mechanism is intriguing: rdcu.be/dUQKX

Happy to share CAST as the "BLAST" tool for spatial omics, searching and aligning similar patterns across datasets while revealing their differences with prototype demo of querying new data against reference spatial atlas and comparative spatial studies👇rdcu.be/dULBj

Excited to share Deep-STARmap and Deep-RIBOmap! We enabled spatial transcriptomic and translatomic mapping of >1K genes in 200 µm thick tissue and neuron morphology co-profiling. Thanks @WangXiaoLab for unwavering support; Jennifer for human skin study! biorxiv.org/content/10.1101/…

The field of #ComputationalBiology has changed dramatically in the last few years with #GenerativeAI. I'm excited to be recording my lectures again this year, and to be teaching with the awesome @EjAlm. You can find the first lecture here: piped.video/1zZSPeKGRzw and more will be coming in the playlist below. Fall 2024: piped.video/playlist?list=PL… Spring 2021: piped.video/watch?v=0jWOZoTs… Fall 2020: piped.video/watch?v=CTPs5HEL… #CompBio #DeepLearning #MachineLearning #Genomics #Therapeutics #RepresenationLearning #Chemistry #ProteinFolding #ClinicalRecords #SingleCell

With the growing availability of spatial omics data from different techniques, CAST offers a computational tool for reconstructing single-cell multi-omic profiles and downstream analysis in a spatially resolved manner. @WangXiaoLab nature.com/articles/s41592-0…

Search and match across spatial omics samples at single-cell resolution nature.com/articles/s41592-0…

Spatial omics technology is transforming our understanding of in situ RNA biology. We are grateful for the opportunity to publish this review in @MolecularCell. We hope this will be a useful resource for the community. @HailingShi @nemo08061 @WangXiaoLab

Online Now: Spatial omics advances for in situ RNA biology dlvr.it/TD8Y9t

NOW AVAILABLE - The #BICAN webinar highlighting new information about the whole mouse brain atlas is now available for replay. Watch: piped.video/l5NHSLk6O-A?si=JFJP… #studyBRAIN @USBrainAlliance @Nature

It has been a great pleasure working on this project in which the the initial idea came from creative insights on a protein structure. Huge thanks to @HaotianDu4, Possu and everyone❤️❤️❤️

Very excited to share my first paper on TRACeR platform! (and I registered a twitter account for it🫣)

How do we uncover cell-cell interactions from #SpatialTranscriptomics data? Excited to share Niche-DE (doi.org/10.1186/s13059-023-0…). Niche-DE asks how does a cell’s transcriptome depend on its spatial neighbors, by identifying Niche-Differentially Expressed genes. 1/9

Thrilled to see our work finally online! We utilized in situ spatial transcriptomic method STARmap PLUS to map 1.09 million cells in the adult mouse central nervous system at molecular resolution and identified previously unknown tissue architectures. nature.com/articles/s41586-0…

Love napari but missing some ImageJ functions? Look no further than napari-imagej, which provides an accessible and comprehensive solution to ImageJ ecosystem access from napari. nature.com/articles/s41592-0…

Excited to share an update of our STalign tool that physically aligns #spatialtranscriptomics data using image varifolds for molecular + compositional comparisons at matched locations Preprint: biorxiv.org/content/10.1101/… New #Jupiter notebooks: jef.works/STalign/ 🧵👇(1/n)

CAST: Search and Match across Spatial Omics Samples at Single-cell Resolution biorxiv.org/content/10.1101/…