PyGWalker for visualizing dataframes in jupyternotebook with simple drag-and-drop operations github.com/Kanaries/pygwa…

Thrilled to see a landmark tool from The Yu Lab St. Jude Research: NetBID2, out in Nature Communications! Kudos to Xinran Dong, the GOAT in the lab and the BEST R programmer I've worked with. Unhappy with your RNA-seq DE/GSEA results? Give NetBID2 a try! nature.com/articles/s4146… #hiddendriver

NetBID2 provides comprehensive hidden driver analysis | Nature Communications nature.com/articles/s4146…

High-resolution spatial multi-omics reveals cell-type specific nuclear compartments | bioRxiv biorxiv.org/content/10.110…

1/ Spatial Genomics is very excited to announce the launch of Gene Positioning System (GenePS), the first confocal end-to-end solution for spatial multiomics assays based on seqFISH technology! Please retweet! Check out more info at spatialgenomics.com/product/ #GenePS #seqFISH

3/ Interact with the kidney data in a Minerva story exploring these high quality results! Have fun visualizing the cell types, genes and transcripts at the highest resolution one can get! kidneyviewer.spatialgenomics.com

I’m just an average researcher. But something I’ve learned in 30 years of being a researcher is that if you’ve convinced yourself at age 25 that you can teach others how to be great researchers, you’ve still got a lot to learn.

Why spatial? What can we learn from spatial transcriptomic analysis that we can't learn otherwise? Excited to present our collaboration with McMahon Lab led by Michal Polonsky and Louisa Gerhardt : doi.org/10.1101/2023.1…

Just posted a preprint on our new spatial genomic recording system, baseMEMOIR. biorxiv.org/content/10.110… Motivation: Cells divide, differentiate, and migrate to form exquisitely organized tissues. Reconstructing the dynamic histories of individual cells, including their lineage

By characterizing B-cells’ developmental stages, St. Jude scientists designed and tested a drug combination to effectively treat resistant B-cell leukemia and reduce side effects. Learn more about the research by @Jiyang_Yu and @JunJYang. bit.ly/4avBOh1

Thrilled to see this out on the Solar ECLIPSE day! A perfect extension of our T-ALL study (go.nature.com/3VVICQN, translated into many trials) to B-ALL, and of systems pharmacology from bulk to single-cell. Targeting developmental origins is one way to guide cancer treatments!

Thanks so much, @NCIsysbio , for the wonderful tweetorial of our recent work and for the wonderful support to our #NCICSBC U01 grant with Jun Yang St. Jude Research (reporter.nih.gov/search/2JHO4aT…), which motivated us to extend the idea from T-ALL to B-ALL. Much appreciated!!

Our new preprint with S.Yoshida and B.Simons! Led by Arun Chakravorty, we leverage spatial information to resolve temporal dynamics in spermatogenesis! biorxiv.org/content/10.110… Also check out a complementary preprint by S.Y. and B.S using live imaging! biorxiv.org/content/10.110… (1/10)

New tool developed by St. Jude researchers improves RNA-seq analysis by addressing transcriptome size differences. ReDeconv reduces errors caused by flawed assumptions in existing approaches. ow.ly/V1y750USBA1

St. Jude scientists leveraged findings about how cancer cells reduce the effectiveness of immunotherapy to suggest a combination treatment to reduce leukemia relapse. Read more: ow.ly/VhTj50V69eE

Kudos to Jiyuan Yang, a postdoc in The Yu Lab, for his amazing transformation from plant biology to spatial & computational wizard—truly a #Transformer! Fantastic collaborations w Kaibo Liu and his former #ML star student Ziqian Zheng (UW–Madison) & Junmin Peng St. Jude Research.

scMINER enhances clustering and reveals regulatory networks and hidden biological drivers Jiyang Yu The Yu Lab St. Jude Research #BiotechNatureComms   doi.org/10.1038/s41467…

A milestone paper from The Yu Lab. What a ride, saw this tool from its infancy to a full fledged package. Proud to be able to contribute to the team’s efforts. nature.com/articles/s4146… Congratulations to the team who lead the effort and to my mentor Jiyang Yu

Nice blog post by Qingfei Pan and Sarah August for thoughts behind our recently-published scMINER tool St. Jude Research The Yu Lab (nature.com/articles/s4146…): communities.springernature.com/posts/catching…