114 citations · 347 across the 17 of their papers we have counts for
5 papers · 1 filter
Multi-Scale Representation Learning for Protein Fitness Prediction
Zuobai Zhang, Pascal Notin, Yining Huang +5
Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experime…
Cell-ontology guided transcriptome foundation model
Xinyu Yuan, Zhihao Zhan, Zuobai Zhang +5
Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale s…
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu, Zuobai Zhang, Bozitao Zhong +2
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations…
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan +3
Protein function annotation is an important yet challenging task in biology. Recent deep learning advancements show significant potential for accurate function prediction by learni…
Structure-Informed Protein Language Model
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan +3
Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language model…