Publications

AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories

Xue Xia*, Chengkai Yao*, Mingyu Tsoi, Xinjie Mao, Wenxuan Huang, Jiaqi Wei, Hao Wu, Cheng Tan, Lang Yu, Yuejin Yang, Siqi Sun#, Zhangyang Gao#

arXiv 2026 (Preprint)

Paper

Structure-guided taxonomic placement of divergent RNA viruses with ViraClass

Sheng Xu*, Wenxuan Huang*, Shutong Yue*, Weiqiang Bai, Shiyang Feng, Xiaohan He, Bo Zhang, Qiantai Feng, Edward Holmes, Weifeng Shi#, Siqi Sun#

2026 (Under Review)

Paper

Benchmarking virtual cell models for in-the-wild perturbation response

Xinjie Mao*, Songming Zhang*, Qianhong Wen*, Xiangyu Wen*, Kedu Jin, Hao Wu, Shuizhou Chen, Yuqiang Li, Lei Bai, Qi Liu, Ning Ding, Siqi Sun#, Zhangyang Gao#

arXiv 2026 (Under Review)

Paper

SCALE: Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

Shuizhou Chen, Lang Yu, Kedu Jin, Songming Zhang, Hao Wu, Wenxuan Huang, Sheng Xu, Quan Qian, Qin Chen, Lei Bai, Siqi Sun#, Zhangyang Gao#

arXiv 2026 (Preprint)

Paper

ViraHInter: a dual-modal artificial intelligence framework for predicting virus-host interactions

Weiqiang Bai, Fei Wang, Jialin Wang, Sheng Xu, Lifeng Qiao, Juan Li, Zhuyi Guo, Xiangyun Hou, Lei Bai, Bowen Zhou, Edward C. Holmes, Weifeng Shi#, Siqi Sun#

arXiv 2026 (Under Review)

Paper

Structure-based discovery of small molecules that allosterically modulate RNA function

Zhiling Pan*, Hao Wu*, Han Hu*, Jian Zou*, Haiyun Ma*, Hongshan Ni*, Liu Wang, Jiaqi Zhao, Xiaoqi Sun, Jiayu Dong, Sheng Xu, Yu Cheng, Ling Liu#, Ke Zheng#, Siqi Sun#, Zhaoming Su#

Research Square 2026 (Under Review)

Paper

A genome-scale language model uncovers animal viruses with zoonotic potential

Sheng Xu*, Shutong Yue*, Juan Li*, Xiang Zhang, Moujian Guo, Jiaqi Wei, Fei Wang, Tao Hu, Yuhe Song, Wanli Ouyang, Edward C. Holmes, Siqi Sun#, Weifeng Shi#

2025 (Under Review)

Paper

Fitness aligned structural modeling enables scalable virtual screening with AuroBind

Zhongyue Zhang*, Jiahua Rao*, Jie Zhong, Weiqiang Bai, Dongxue Wang, Shaobo Ning, Lifeng Qiao, Sheng Xu, Runze Ma, Will Hua, Jack Xiaoyu Chen, Odin Zhang, Wei Lu, Hanyi Feng, He Yang, Xinchao Shi, Rui Li, Wanli Ouyang, Xinzhu Ma, Jiahao Wang, Jixian Zhang, Jia Duan, Siqi Sun#, Jian Zhang#, Shuangjia Zheng#

arXiv 2025 (Under Review)

Paper

MassNet: billion-scale AI-friendly mass spectral corpus enables robust de novo peptide sequencing

A Jun*, Xiang Zhang*, Xiaofan Zhang*, Jiaqi Wei*, Te Zhang, Yamin Deng, Pu Liu, Zongxiang Nie, Yi Chen, Nanqing Dong, Zhiqiang Gao#, Siqi Sun#, Tiannan Guo#

bioRxiv 2025 (Under Review)

Paper

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Zhongyue Zhang*, Zijie Qiu*, Yingcheng Wu*, Shuya Li*, Dingyan Wang, Zhuomin Zhou, Duo An, Yuhan Chen, Yu Li, Yongbo Wang, Chubin Ou, Zichen Wang, Jack Xiaoyu Chen, Bo Zhang, Yusong Hu, Wenxin Zhang, Zhijian Wei, Runze Ma, Qingwu Liu, Bo Dong, Yuexi He, Qiantai Feng, Lei Bai#, Qiang Gao#, Siqi Sun#, Shuangjia Zheng#

bioRxiv 2025 (Under Review)

Paper

Accurate de novo sequencing of the modified proteome with OmniNovo

Yuhan Chen, Shang Qu, Zhiqiang Gao, Yuejin Yang, Xiang Zhang, Sheng Xu, Xinjie Mao, Liujia Qian, Jiaqi Wei, Zijie Qiu, Chenyu You, Lei Bai, Ning Ding#, Tiannan Guo#, Bowen Zhou#, Siqi Sun#

arXiv 2025 (Under Review)

Paper

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation: Application in De Novo Peptide Sequencing

Xiang Zhang*, Jiaqi Wei*, Zijie Qiu, Sheng Xu, Zhi Jin, ZhiQiang Gao, Nanqing Dong, Siqi Sun#

NeurIPS 2025

Paper

Cryo-EM reveals mechanisms of natural RNA multivalency

Liu Wang*, Jiahao Xie*, Tao Gong*, Hao Wu*, Yifan Tu*, Xin Peng*, Sitong Shang*, Xinyu Jia, Haiyun Ma, Jian Zou, Sheng Xu, Xin Zheng, Dong Zhang, Yang Liu, Chong Zhang, Yongbo Luo, Zirui Huang, Bin Shao, Binwu Ying, Yu Cheng, Siqi Sun#, Xuedong Zhou#, Zhaoming Su#

Science, 2025

Paper

Retrieval is Not Enough: Enhancing RAG through Test-Time Critique and Optimization

Jiaqi Wei*, Hao Zhou*, Xiang Zhang*, Di Zhang, Zijie Qiu, Noah Wei, Jinzhe Li, Wanli Ouyang, Siqi Sun#

NeurIPS 2025

Paper

Fast, sensitive detection of protein homologs using deep dense retrieval

Liang Hong*, Zhihang Hu*, Siqi Sun*,#, Xiangru Tang, Jiuming Wang, Qingxiong Tan, Liangzhen Zheng, Sheng Wang, Sheng Xu, Irwin King, Mark Gerstein#, Yu Li#

Nature Biotechnology, 2025

Paper

Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing

Zijie Qiu*, Jiaqi Wei*, Xiang Zhang*, Sheng Xu, Kai Zou, Zhi Jin, Zhiqiang Gao, Nanqing Dong, Siqi Sun#

ICML 2025

Paper

Benchmarking all-atom biomolecular structure prediction with FoldBench

Sheng Xu*, Qiantai Feng*, Lifeng Qiao, Hao Wu, Tao Shen, Yu Cheng#, Shuangjia Zheng#, Siqi Sun#

Nature Communications, 2025

Paper

Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing

Xiang Zhang*, Jiaqi Wei*, Zijie Qiu, Sheng Xu, Nanqing Dong, Zhiqiang Gao, Siqi Sun#

ICML 2025

Paper

π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing

Xiang Zhang*, Tianze Ling*, Zhi Jin*, Sheng Xu*, Zhiqiang Gao, Boyan Sun, Zijie Qiu, Jiaqi Wei, Nanqing Dong, Guangshuai Wang, Guibin Wang, Leyuan Li, Muhammad Abdul-Mageed, Laks V.S. Lakshmanan, Fuchu He, Wanli Ouyang#, Cheng Chang#, Siqi Sun#

Nature Communications, 2025

Paper

PriFold: Biological Priors Improve RNA Secondary Structure Predictions

Chenchen Yang*, Hao Wu*, Tao Shen, Kai Zou, Siqi Sun#

AAAI 2025

Paper

Accurate RNA 3D structure prediction using a language model-based deep learning approach

Tao Shen*, Zhihang Hu*, Siqi Sun*,#, Di Liu, Felix Wong, Jiuming Wang, Jiayang Chen, Yixuan Wang, Liang Hong, Jin Xiao, Mark Gerstein, Yu Li#

Nature Methods, 2024

Paper

MSA Generation with Seqs2Seqs Pretraining: Advancing Protein Structure Predictions

Le Zhang*, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun#

NeurIPS 2024

Paper

Accurate prediction of antibody function and structure using bio-inspired antibody language model

Hongtai Jing*, Zhengtao Gao, Sheng Xu, Tao Shen, Zhangzhi Peng, Shwai He, Tao You, Shuang Ye#, Wei Lin#, Siqi Sun#

Briefings in Bioinformatics, 2024

Paper

ContraNovo: a contrastive learning approach to enhance de novo peptide sequencing

Zhi Jin*, Sheng Xu*, Xiang Zhang*, Tianze Ling, Nanqing Dong, Wanli Ouyang, Zhiqiang Gao, Cheng Chang#, Siqi Sun#

AAAI 2024

Paper

Crossbind: Collaborative cross-modal identification of protein nucleic-acid-binding residues

Linglin Jing*, Sheng Xu*, Yifan Wang, Yuzhe Zhou, Tao Shen, Zhigang Ji, Hui Fang, Zhen Li, Siqi Sun#

AAAI 2024

Paper