Johnny X. Yu

The paper introduces Rhaister, a perturbation-response predictor that uses summary statistics to predict drug responses, outperforming virtual-cell models in speed and accuracy.

This study uses GENEVA to analyze drug response variations in cancer cells, revealing mitochondrial activation's role in KRAS inhibition and EMT as a resistance mechanism.

The paper introduces Tahoe-x1, a large-scale perturbation-trained single-cell foundation model with 3 billion parameters, achieving state-of-the-art performance in cancer-related tasks.

This study uses single-cell lineage tracing and RNAseq to identify pre-existing resistant tumor subclones in lung cancer models and their transcriptional programs, revealing mechanisms of therapy resistance.

A 100-million-cell atlas: 50 cancer lines pooled as spheroid villages, treated with 379 drugs at several doses, profiled by combinatorial-barcoding scRNA-seq and embedded with a 10-dimensional scVI model.

The paper systematically identifies post-transcriptional regulatory modules by integrating multimodal data on RBP interactions and functions.

The paper identifies 245 putative RNA structural switches in the human transcriptome using a computational and experimental approach, validates one with DMS-MaPseq and cryo-EM, and shows its regulation by trans factors and nonsense-mediated decay.

This study develops hPSC-derived enteric ganglioids to model human ENS development and function, identifying drug candidates and PDGFR inhibition as key factors in NO neuron specification.

The paper identifies RBMS1 as a suppressor of colon cancer metastasis by stabilizing its mRNA targets, showing its clinical relevance in patient survival.