2025

Artificial Intelligence for Bone-Theory, Methods, and Applications

Yuan et al. Advanced Intelligent Discovery. 2025.

Accurate Immune Protein Structure Prediction by Large Language Model and Transfer Learning

Tian Zhu#, Milong Ren#, ..., Jian Zhang*, Dongbo Bu*, Haicang Zhang*. bioRxiv. 2025.

Multi-objective antibody design with constrained preference optimization

Milong Ren, Zaikai He, Haicang Zhang*. 2025. ICLR.

Learning to Design Greedy Algorithm for NP-Complete Problems

Ding et al. Theoretical Computer Science. 2025.

ILETIA-An AI enhanced method for individualized trigger-oocyte pickup interval estimation of progestin-primed ovarian stimulation protocol

Wu et al. arXiv. 2025.

2024

A survey on deep learning-based algorithms for the traveling salesman problem

Sui et al. Frontiers of Computer Science. 2024.

GPCR-BSD,a database of binding sites of human G-protein coupled receptors under diverse states

Liu et al.BMC Bioinformatics. 2024.

Return of genetic research results in 21,532 individuals with autism

Wright et al. Genetics in Medicine. 2024.

CarbonNovo-Joint Design of Protein Structure and Sequence Using a Unified Energy-based Model

Milong Ren, Tian Zhu, Haicang Zhang*. ICML. 2024.

Antibody Design Using a Score-based Diffusion Model Guided by Evolutionary, Physical and Geometric Constraints

Tian Zhu, Milong Ren, Haicang Zhang*. ICML. 2025

Accurate and robust protein sequence design with CarbonDesign

Milong Ren, Chungong Yu, Dongbo Bu*, Haicang Zhang*. Nature Machine Intelligence. 2024.

2023

A complete mass spectrometry-based immunopeptidomics pipeline for neoantigen identification and validation

Tran et al. bioRxiv. 2023.

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang*. NeuIPS. 2023.

Protein Structure Prediction-Challenges, Advances, and the Shift of Research Paradigms

Bin Huang#, Lupeng Kong#, Chao Wang#, ..., Haicang Zhang*, Chungong Yu*, Wei-Mou Zheng*, Dongbo Bu*. Genomics, Proteomics & Bioinformatics. 2023.

Accurate and efficient protein sequence design through learning concise local environment of residues

Huang et al. Bioinformatics. 2023.

2022

Predicting functional effect of missense variants using graph attention neural networks

Haicang Zhang, Michelle S Xu, Xiao Fan, Wendy K Chung, Yufeng Shen*. Nature Machine Intelligence. 2022.

Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

Zhou et al. Nature Genetics. 2022.

Microblog-HAN, A micro-blog rumor detection model based on heterogeneous graph attention network

Bi et al. PLOS One. 2022.

2021

FALCON2- a web server for high-quality prediction of protein tertiary structures

Kong et al. BMC Bioinformatics. 2021

MVP predicts the pathogenicity of missense variants by deep learning

Hongjian Qi#, Haicang Zhang#, Yige Zhao#, Chen Chen#, John J Long, Wendy K Chung, Yongtao Guan, Yufeng Shen*. Nature Communications. 2021.

2020

Template-based prediction of protein structure with deep learning

Haicang Zhang*, Yufeng Shen*.

Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data

Chen et al. bioRxiv. 2020.

2019

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun*, Wei-Mou Zheng*, Dongbo Bu*. BMC Bioinformatics. 2019.

Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes

Feliciano et al. NPJ genomic medicine. 2019.

Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling

Want et al. BMC Bioinformtics. 2019.

2018

A Survey on Algorithms for Protein Tertiary Structure Prediction

Want et al. Chinese Journal of Computers. 2018.

2017

Improving protein fold recognition by extracting fold-specific features from predicted residue–residue contacts

Zhu et al. Bioinformatics. 2017.

A Survey on Algorithms for Protein Contact Prediction

Haicang Zhang#, Yujuan Gao#, Minghua Deng, Weimou Zheng, Dongbo Bu*. Journal of Computer Research and Development. 2017.

Improving prediction of burial state of residues by exploiting correlation among residues

Gong et al. BMC Bioinformatics. 2017.

2016

Insights into the transmission of respiratory infectious diseases through empirical human contact networks

Huang et al. Scientific Reports. 2016.

Improving residue–residue contact prediction via low-rank and sparse decomposition of residue correlation matrix

Haicang Zhang#, Yujuan Gao#, ..., Wei-Mou Zheng*, Dongbo Bu*. Biochemical and Biophysical Research Communications. 2016.

FALCON@home, a high-throughput protein structure prediction server based on remote homologue recognition

Chao Wang#, Haicang Zhang#, ..., Shuai Cheng Li*, Dongbo Bu*. Bioinformatics. 2016.

2014

On the inapproximability of minimizing cascading failures under the deterministic threshold model

Nie et al. Information Processing Letters. 2014.