Sheng Xu is currently a PhD student at Fudan University, advised by Prof. Siqi Sun. Before that, he obtained his masters degree at the Department of Computer Science and Engineering (CSE) at the Chinese University of Hong Kong (CUHK), supervised by Prof. Yu Li. He did his bachelors at East China Normal University (ECNU), advised by Prof. Qin Li.

Recent News

• January 2024, SSBlazer is accepted by Genome Biology (IF=12.3)🎉!
• December 2023, two papers are accepted by AAAI-24🎉!
• September 2023, begin Ph.D. study at IICS, Fudan University.

Research Interests

My research is centered on the integration of artificial intelligence with molecular biology. Specifically, I focus on the study of RNA-protein interaction, noncoding RNA and precision medicine like T cell therapy. My objective is to leverage the power of AI to better understand these complex biological phenomena and to develop innovative, tailored therapeutics for disease treatment.

Publications

(*equal contribution, #corresponding)

• 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, 2024.
  [Paper]

• RTM-align: an improved RNA alignment tool with enhanced short sequence performance via post-standardization and fragment alignment
  Zijie Qiu*, Sheng Xu*, Junkang Wei, Tao Shen, Siqi Sun#. bioRxiv Preprint, 2024.
  [Preprint]

• Pi-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, Nanqing Dong, Guangshuai Wang, Guibin Wang, Leyuan Li, Muhammad Abdul Mageed, Laks V.S. Lakshmanan, Wanli Ouyang#, Cheng Chang#, Siqi Sun#. bioRxiv Preprint, 2024.
  [Preprint]

• 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]

• SSBlazer: A genome-wide nucleotide-resolution model for predicting single-strand break sites
  Sheng Xu*, Junkang Wei*#, Siqi Sun, Jizhou Zhang, Ting-Fung Chan, Yu Li#. Genome Biology, 2024.
  [Paper] [Server] [Code]

• 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-24, 2024.
  [Preprint] [Code]

• 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-24, 2024.
  [Preprint] [Code]

• AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction
  Zhongju Yuan, Tao Shen, Sheng Xu, Leiye Yu, Ruobing Ren#, Siqi Sun#. arXiv Preprint, 2023.
  [Preprint]

• AcrNET: Predicting Anti-CRISPR with Deep Learning
  Yunxiang Li*, Yumeng Wei*, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li#. Bioinformatics, 2023.
  [Paper] [Server] [Code]