📃 Publications

NovoBench: Benchmarking Deep Learning-based De Novo Sequencing Methods in Proteomics

Jingbo Zhou†, Shaorong Chen†, Jun Xia†, Sizhe Liu, Tianze Ling, Wenjie Du, Yue Liu, Jianwei Yin, Stan Z. Li

Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module

Jingbo Zhou†, Yixuan Du†, Ruqiong Zhang†, Jun Xia, Zhizhi Yu, Zelin Zang, Di Jin, Carl Yang, Rui Zhang, Stan Z. Li

AdaNovo: Adaptive De Novo Peptide Sequencing with Conditional Mutual Information

Jun Xia†, Shaorong Chen†, Jingbo Zhou†, Xiaojun Shan, Wenjie Du, Zhangyang Gao, Cheng Tan, Bozhen Hu, Jiangbin Zheng, Stan Z. Li

Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo

Jun Xia†, Sizhe Liu†, Jingbo Zhou†, Shaorong Chen, hongxin xiang, Zicheng Liu, Yue Liu, Stan Z. Li
🔥 NeurIPS 2024 AIDrugX Spotlight

ReNovo: Retrieval-Based De Novo Mass Spectrometry Peptide Sequencing

Shaorong Chen†, Jun Xia†, Jingbo Zhou†, Lecheng Zhang, Zhangyang Gao, Bozhen Hu, Cheng Tan, Wenjie Du, Stan Z. Li

Regressor-guided Diffusion Model for De Novo Peptide Sequencing with Explicit Mass Control

Shaorong Chen, Jingbo Zhou, Jun Xia

A comprehensive and systematic review for deep learning-based de novo peptide sequencing

Jun Xia†, Jingbo Zhou†, Shaorong Chen†, Tianze Ling†, Stan Z. Li

MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging

Siyuan Li, Zicheng Liu, Kai Yu, Chang Yu, Jingbo Zhou, Anna Wang, Qirong Yang, yucheng guo, Xiaoming Zhang, Stan Z. Li

PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation

Jiabei Cheng, Changxi Chi, Jingbo Zhou, Hongyi Xin, Jun Xia

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

Changxi Chi, Xia Jun, Jingbo Zhou, Jiabei Cheng, Chang Yu, Stan Z. Li

NodeReg: Mitigating the Imbalance and Distribution Shift Effects in Semi-Supervised Node Classification via Norm Consistency

Shenzhi Yang, Jun Xia, Jingbo Zhou, Xingkai Yao, Xiaofang Zhang