Yuxuan Song

Inferring gene regulatory networks from single-cell perturbation data by optimizing causal reach of latent mediator dynamics

CausalODE infers gene regulatory networks from single-cell perturbation data by optimizing causal reach, capturing transient dynamics, and modeling latent protein levels, outperforming existing methods on real datasets.

CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data

CytoSignal detects and quantifies ligand-receptor signaling interactions at cellular resolution from spatial transcriptomic data, enabling spatial gradient analysis and temporal dynamics prediction.

Nuclear Speckles Regulate Splicing During Muscle Stem Cell Activation and Aging

The paper investigates how nuclear speckles regulate splicing and stem cell function in muscle stem cells during activation, injury, and aging.

Predicting the Structural Impact of Human Alternative Splicing

The paper predicts the structural impact of human alternative splicing using AlphaFold2 on over 11,000 isoforms and identifies structural changes across multiple metrics.

PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations

PerturbNet predicts cell state changes from unseen chemical and genetic perturbations using deep learning and perturbation response data.