10 papers
MetaGEM: Bottom-Up Reconstruction of Genome-Scale Metabolic Networks via Deep Enzyme-Metabolite Anchoring
Weiyu Xiao, Jiangbin Zheng, Stan Z. Li
Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homol…
TCRTransBench: A Comprehensive Benchmark for Bidirectional TCR-Peptide Sequence Generation
Yiming Wang, Weiyu Xiao, Jiangbin Zheng +1
T-cell receptor (TCR) interactions with antigenic peptides underpin adaptive immunity and are pivotal for personalized immunotherapy and vaccine development. Despite recent progres…
Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges
Changxi Chi, Yufei Huang, Jun Xia +4
Predicting single-cell perturbation outcomes directly advances gene function analysis and facilitates drug candidate selection, making it a key driver of both basic and translation…
Multimodal Regression for Enzyme Turnover Rates Prediction
Bozhen Hu, Cheng Tan, Siyuan Li +4
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most org…
DapPep: Domain Adaptive Peptide-agnostic Learning for Universal T-cell Receptor-antigen Binding Affinity Prediction
Jiangbin Zheng, Qianhui Xu, Ruichen Xia +1
Identifying T-cell receptors (TCRs) that interact with antigenic peptides provides the technical basis for developing vaccines and immunotherapies. The emergent deep learning metho…
Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design
Jiangbin Zheng, Ge Wang, Han Zhang +1
Computational protein design (CPD) offers transformative potential for bioengineering, but current deep CPD models, focused on universal domains, struggle with function-specific de…