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Shuangjia Zheng
Assistant Professor, School of Artificial Intelligence, Shanghai Jiaotong University
Assistant Professor, Global Institute of Future Technology (GIFT), Shanghai Jiao Tong University
Joined
February 2021
Names
Shuangjia Zheng
(Preferred)
,
SHUANGJIA ZHENG
Emails
****@mail2.sysu.edu.cn
(Confirmed)
,
****@gmail.com
(Confirmed)
,
****@sjtu.edu.cn
(Confirmed)
Personal Links
Homepage
Google Scholar
DBLP
ORCID
Semantic Scholar
Career & Education History
Assistant Professor
School of Artificial Intelligence,
Shanghai Jiaotong University
(sjtu.edu.cn)
2025
–
Present
Assistant Professor
Global Institute of Future Technology (GIFT),
Shanghai Jiao Tong University
(sjtu.edu.cn)
2023
–
Present
PhD student
SUN YAT-SEN UNIVERSITY
(sysu.edu.cn)
2020
–
2023
Advisors, Relations & Conflicts
PhD Advisor
Yuedong Yang
2020
–
2023
Expertise
Deep learning
Present
Drug discovery
Present
Protein Modeling
Present
Foundation Modeling
Present
Multi-agents
Present
Publications
Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design
Zichen Wang
,
Runze Ma
,
Xiaoliang Shi
,
Zhongyue Zhang
,
Shuangjia Zheng
GEM 2026
Readers:
Everyone
VCWorld: A Biological World Model for Virtual Cell Simulation
Zhijian Wei
,
Runze Ma
,
Zichen Wang
,
Zhongmin Li
,
Shuotong Song
,
Shuangjia Zheng
ICLR 2026 Poster
Readers:
Everyone
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction
Zhongmin Li
,
Runze Ma
,
Jiahao Tan
,
TAN Chengzi
,
Shuangjia Zheng
Submitted to ICLR 2026
Readers:
Everyone
Self-Tooling Agent: Dynamically Extending Agent Capabilities through Scientific Tool Synthesis and Invocation
Shiyang Feng
,
Shuaiyu Zhang
,
Songtao Huang
,
Xiaohan He
,
Bin Wang
,
Shuangjia Zheng
,
Bo Zhang
,
LEI BAI
Submitted to ICLR 2026
Readers:
Everyone
EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization
Dingyi Rong
,
Haotian Lu
,
Wenzhuo Zheng
,
Fan Zhang
,
Shuangjia Zheng
,
Ning Liu
ICLR 2026 Conference Withdrawn Submission
Readers:
Everyone
Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design
Nianzu Yang
,
Songlin Jiang
,
Jian Ma
,
Huaijin Wu
,
Shuangjia Zheng
,
Wengong Jin
,
Junchi Yan
NeurIPS 2025 poster
Readers:
Everyone
RiboFlow: Conditional De Novo RNA Co-Design via Synergistic Flow Matching
Runze Ma
,
Zhongyue Zhang
,
Zichen Wang
,
Will Hua
,
Jiahua Rao
,
Zhuomin Zhou
,
Shuangjia Zheng
NeurIPS 2025 poster
Readers:
Everyone
Accurately Predicting Protein Mutational Effects via a Hierarchical Many-Body Attention Network
Dahao Xu
,
Jiahua Rao
,
Mingming Zhu
,
Jixian Zhang
,
Wei Lu
,
Shuangjia Zheng
,
Yuedong Yang
NeurIPS 2025 poster
Readers:
Everyone
Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design
Nianzu Yang
,
Jian Ma
,
Songlin Jiang
,
Huaijin Wu
,
Shuangjia Zheng
,
Wengong Jin
,
Junchi Yan
GEM
Readers:
Everyone
AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions
Wei Lu
,
Jixian Zhang
,
Jiahua Rao
,
Zhongyue Zhang
,
Shuangjia Zheng
AIDrugX Poster
Readers:
Everyone
View all 63 publications
Co-Authors
Atanas Patronov
Bin Wang
Binghong Chen
Bo Zhang
Bozitao Zhong
Chang Wen
Chao Zhao
Chaochao Yan
Chengtao Li
Chenqing Hua
Cohen Ethan
Connor W. Coley
Dahao Xu
Dahong Qian
Daiguo Deng
Dinghuai Zhang
Dingyi Rong
Doina Precup
Fan Zhang
Fenglong Gu
Guy Wolf
Haifeng Hu
Haitao Ai
Hanlin Gan
Haotian Lu
View all 123 co-authors