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Trick or treat? For this Halloween, our treat for those who are analyzing single-cell RNA-seq data is - TreeCorTreat biorxiv.org/content/10.110…

Lineage barcoding approaches were limited to measuring static features of development. Preprints from us & Tanja Stadler group change that by measuring progenitor dynamics in development. A key: time-scaled phylogenies. dlvr.it/SK0DG1 dlvr.it/SK0DF7 Hongkai Ji

#vaccination diversifies the #SARSCoV2-specific T cell repertoire in patients with a prior history of #COVID. Shout out to Arbor Dykema, @BezaWoldemeskel, and Hongkai Ji for leading the charge and bringin’ it on home! #Immunology #genomics sciencedirect.com/science/articl…

Our study showing that Hedgehog signaling is essential for maintaining the early foregut and larynx by preventing EMT was published: doi.org/10.7554/eLife.… eLife - the journal. This was led by recent UTexasILS graduate Janani Ramachandran with help from Hongkai Ji Hongkai Ji and Aaron Zorn.

PRECAST - a data integration method for integrating multiple spatial transcriptomics datasets by aligning shared embeddings of biological effects while accounting for batch effects. nature.com/articles/s4146…

Excited to share Lamian - a statistical framework for differential pseudotemporal trajectory analysis across biological conditions using single-cell RNA-seq data from multiple samples. Wenpin Hou zhicheng ji Zeyu Chen E. John Wherry Stephanie Hicks, PhD rdcu.be/dqMlh

Some thoughts about the publication ecosystem in statistics and biostatistics: rdcu.be/dBtBB

Big thanks to UCSC Genome Browser for integrating FUNCODE into the UCSC Genome Browser!

Exciting collaboration with Christina Jackson, MD, Drew Pardoll, Chetan Bettegowda, Vasan Yegnasubramani, and many others - now published in Science! Grateful for the contributions of our current and past group members: Runzhe Li, zhicheng ji, Wenpin Hou, and Wentao Zhan. #TeamScience

Zeng et al. developed a mutation-associated neoantigen (MANA) score, based on the expression of ENTPD1, CXCL13, and IL7R, that can identify neoantigen- and tumor-associated antigen-specific TILs across cancers. bit.ly/4hIhgFB  jhubiostat  Hongkai Ji  Kellie N. Smith