5 citations · 13 across the 11 of their papers we have counts for
11 papers
ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks
Dongxin Ye, Fang Hu, Han Hu +6
Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biolo…
Self-evolving AI agents for protein discovery and directed evolution
Yang Tan, Lingrong Zhang, Mingchen Li +5
Protein scientific discovery is bottlenecked by the manual orchestration of information and algorithms, while general agents are insufficient in complex domain projects. VenusFacto…
Fast and Interpretable Protein Substructure Alignment via Optimal Transport
Zhiyu Wang, Bingxin Zhou, Jing Wang +4
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure…
VenusX: Unlocking Fine-Grained Functional Understanding of Proteins
Yang Tan, Wenrui Gou, Bozitao Zhong +3
Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many b…
VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data
Liang Zhang, Hua Pang, Chenghao Zhang +11
In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (…
Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model
Yang Tan, Ruilin Wang, Banghao Wu +2
Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other…
Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection
Song Li, Yang Tan, Song Ke +2
Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely…
Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion
Yutong Hu, Yang Tan, Andi Han +3
The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared t…
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?
Yang Tan, Lirong Zheng, Bozitao Zhong +2
Deep learning has become a crucial tool in studying proteins. While the significance of modeling protein structure has been discussed extensively in the literature, amino acid type…
ProtSolM: Protein Solubility Prediction with Multi-modal Features
Yang Tan, Jia Zheng, Liang Hong +1
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs…
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction
Yang Tan, Bingxin Zhou, Yuanhong Jiang +2
Directed evolution plays an indispensable role in protein engineering that revises existing protein sequences to attain new or enhanced functions. Accurately predicting the effects…