Huanhuan Xia

Phenotype-Guided In Silico Molecular Generation Using Large Language Models

GEMGen generates small molecules from transcriptomic data to phenocopy gene knockdown effects and identify novel inhibitors.

FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling

FlexRibbon is a pretrained protein model that jointly learns from sequences and structures, achieving state-of-the-art performance in mutation-rich settings.

Directing cellular transitions on gene graph-enhanced cell state manifold

CellNavi predicts driver genes for cell state transitions using a deep learning framework that integrates gene graphs with transcriptomics data across diverse cell types and perturbations.

CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms

CREaTor models cis-regulatory patterns using attention mechanisms and RNA-seq/ChIP-seq data, outperforming existing methods in predicting cCRE-gene interactions across cell types.