Yuedong Yang

Scopus Author ID ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 52

Top Venues

Journal of chemical information and modeling

The Journal of experimental medicine

Nature computational science

Nucleic acids research

Griffith University - Gold Coast Campus

University of Science and Technology of China (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Griffith University - Gold Coast Campus Jun 01 2013 - Jun 30 2017

Australia

Research Fellow :: Institute for Glycomics

Indiana University School of Informatics and Computing May 01 2011 - Jun 01 2013

United States

Research Assistant Professor

Indiana University School of Medicine Sep 20 2006 - May 01 2011

United States

Postdoc :: Center of Computational Biology and Bioinformatics

Education History

University of Science and Technology of China Sep 01 2000 - Jul 01 2006

China

PHD

University of Science and Technology of China Sep 01 1996 - Jul 01 2000

China

BSC

Publications

Zhen Qin, Ruining Wang, Ping Hou, Yuanyuan Zhang, Qianmu Yuan, Ying Wang, Yuedong Yang, Tao Xu
TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation. The Journal of experimental medicine 221 (3) (2024)
Qianmu Yuan, Chong Tian, Yuedong Yang
Genome-scale annotation of protein binding sites via language model and geometric deep learning. eLife 13 (2024)
Zhen Qin, Ruining Wang, Ping Hou, Yuanyuan Zhang, Qianmu Yuan, Ying Wang, Yuedong Yang, Tao Xu
TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation. The Journal of experimental medicine 221 (3) (2024)
Jiahua Rao, Jiancong Xie, Qianmu Yuan, Deqin Liu, Zhen Wang, Yutong Lu, Shuangjia Zheng, Yuedong Yang
A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions. Nature communications 15 (1) (2024)
Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. Journal of chemical information and modeling 64 (3) (2024)
Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang
Deciphering cell types by integrating scATAC-seq data with genome sequences. Nature computational science 4 (4) (2024)
Sheng Chen, Junjie Xie, Renlong Ye, David Daqiang Xu, Yuedong Yang
Structure-aware dual-target drug design through collaborative learning of pharmacophore combination and molecular simulation. Chemical science 15 (27) (2024)
Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. Journal of chemical information and modeling 64 (7) (2024)
Zhen Qin, Ruining Wang, Ping Hou, Yuanyuan Zhang, Qianmu Yuan, Ying Wang, Yuedong Yang, Tao Xu
TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation. The Journal of experimental medicine 221 (3) (2024)
Sheng Chen, Junjie Xie, Renlong Ye, David Daqiang Xu, Yuedong Yang
Structure-aware dual-target drug design through collaborative learning of pharmacophore combination and molecular simulation. Chemical science 15 (27) (2024)
Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. Journal of chemical information and modeling (2024)
Qianmu Yuan, Chong Tian, Yuedong Yang
Genome-scale annotation of protein binding sites via language model and geometric deep learning. eLife 13 (2024)
Qianmu Yuan, Chong Tian, Yidong Song, Peihua Ou, Mingming Zhu, Huiying Zhao, Yuedong Yang
GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic acids research (2024)
Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang
Deciphering cell types by integrating scATAC-seq data with genome sequences. Nature computational science 4 (4) (2024)
Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. Journal of chemical information and modeling 64 (3) (2024)
Qianmu Yuan, Chong Tian, Yuedong Yang
Genome-scale annotation of protein binding sites via language model and geometric deep learning. eLife 13 (2024)
Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. Journal of chemical information and modeling 64 (3) (2024)
Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang
Deciphering cell types by integrating scATAC-seq data with genome sequences. Nature computational science (2024)
Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. Journal of chemical information and modeling (2024)
Qianmu Yuan, Chong Tian, Yidong Song, Peihua Ou, Mingming Zhu, Huiying Zhao, Yuedong Yang
GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic acids research 52 (W1) (2024)
Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. Journal of chemical information and modeling 64 (6) (2024)
Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. Journal of chemical information and modeling 64 (3) (2024)
Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. Journal of chemical information and modeling 64 (7) (2024)
Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. Journal of chemical information and modeling 64 (6) (2024)
Yidong Song, Qianmu Yuan, Sheng Chen, Yuansong Zeng, Huiying Zhao, Yuedong Yang
Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures. Nature communications 15 (1) (2024)
Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. Journal of chemical information and modeling 64 (6) (2024)
Qianmu Yuan, Chong Tian, Yidong Song, Peihua Ou, Mingming Zhu, Huiying Zhao, Yuedong Yang
GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic acids research 52 (W1) (2024)
Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. Journal of chemical information and modeling (2024)
Zhen Qin, Ruining Wang, Ping Hou, Yuanyuan Zhang, Qianmu Yuan, Ying Wang, Yuedong Yang, Tao Xu
TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation. The Journal of experimental medicine 221 (3) (2024)
Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. Journal of chemical information and modeling 64 (7) (2024)
Ken Chen, Yue Zhou, Maolin Ding, Yu Wang, Zhixiang Ren, Yuedong Yang
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Briefings in bioinformatics 25 (3) (2024)
Zhen Qin, Ruining Wang, Ping Hou, Yuanyuan Zhang, Qianmu Yuan, Ying Wang, Yuedong Yang, Tao Xu
TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation. The Journal of experimental medicine 221 (3) (2024)
Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang
Deciphering cell types by integrating scATAC-seq data with genome sequences. Nature computational science 4 (4) (2024)
Ken Chen, Yue Zhou, Maolin Ding, Yu Wang, Zhixiang Ren, Yuedong Yang
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Briefings in bioinformatics 25 (3) (2024)
Yuansong Zeng, Mai Luo, Ningyuan Shangguan, Peiyu Shi, Junxi Feng, Jin Xu, Ken Chen, Yutong Lu, Weijiang Yu, Yuedong Yang
Deciphering cell types by integrating scATAC-seq data with genome sequences. Nature computational science (2024)
Qianmu Yuan, Chong Tian, Yidong Song, Peihua Ou, Mingming Zhu, Huiying Zhao, Yuedong Yang
GPSFun: geometry-aware protein sequence function predictions with language models. Nucleic acids research 52 (W1) (2024)
Miles McGibbon, Steven Shave, Jie Dong, Yumiao Gao, Douglas R Houston, Jiancong Xie, Yuedong Yang, Philippe Schwaller, Vincent Blay
From intuition to AI: evolution of small molecule representations in drug discovery. Briefings in bioinformatics 25 (1) (2023)
Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W Coley, Yuedong Yang, Ruibo Wu
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP. Nature communications 13 (1) (2022)
Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang
Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. Journal of chemical information and modeling 62 (5) (2022)
Bing He, Shuning Liu, Mengxin Xu, Yunqi Hu, Kexin Lv, Yuanyuan Wang, Yong Ma, Yanmei Zhai, Xinyu Yue, Lin Liu, Hongjie Lu, Siwei Zhou, Pengbin Li, Guoqin Mai, Xiaoping Huang, Chenhang Li, Shifeng Chen, Shupei Ye, Pingsen Zhao, Yuedong Yang, Xinhua Li, Yusheng Jie, Mang Shi, Jingyi Yang, Yuelong Shu, Yao-Qing Chen
Comparative global B cell receptor repertoire difference induced by SARS-CoV-2 infection or vaccination via single-cell V(D)J sequencing. Emerging microbes & infections 11 (1) (2022)
Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang
DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. Journal of chemical information and modeling (2022)
Ziwang Huang, Liang Li, Xiang Zhang, Ying Song, Jianwen Chen, Huiying Zhao, Yutian Chong, Hejun Wu, Yuedong Yang, Jun Shen, Yunfei Zha
A coarse-refine segmentation network for COVID-19 CT images. IET image processing 16 (2) (2021)
Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang
Meta Learning for Low-Resource Molecular Optimization. Journal of chemical information and modeling 61 (4) (2021)
Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang
Deep scaffold hopping with multimodal transformer neural networks. Journal of cheminformatics 13 (1) (2021)
Bing He, Shuning Liu, Yuanyuan Wang, Mengxin Xu, Wei Cai, Jia Liu, Wendi Bai, Shupei Ye, Yong Ma, Hengrui Hu, Huicui Meng, Tao Sun, Yanling Li, Huanle Luo, Mang Shi, Xiangjun Du, Wenjing Zhao, Shoudeng Chen, Jingyi Yang, Haipeng Zhu, Yusheng Jie, Yuedong Yang, De-Ying Guo, Qiao Wang, Yuwen Liu, Huimin Yan, Man-Li Wang, Yao-Qing Chen
Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq. Signal transduction and targeted therapy 6 (1) (2021)
Xuan Lv, Jianwen Chen, Yutong Lu, Zhiguang Chen, Nong Xiao, Yuedong Yang
Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. Journal of chemical information and modeling 60 (4) (2020)
Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. Journal of cheminformatics 11 (1) (2019)
Sheng Chen, Zhe Sun, Lihua Lin, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao, Yuedong Yang
To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. Journal of chemical information and modeling 60 (1) (2019)
Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. Journal of chemical information and modeling 60 (1) (2019)
Bailing Zhou, Yuedong Yang, Jian Zhan, Xianghua Dou, Jihua Wang, Yaoqi Zhou
Predicting functional long non-coding RNAs validated by low throughput experiments. RNA biology 16 (11) (2019)
Zanxia Cao, Yunqiang Bian, Guodong Hu, Liling Zhao, Zhenzhen Kong, Yuedong Yang, Jihua Wang, Yaoqi Zhou
Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. International journal of molecular sciences 19 (3) (2018)
Huiying Zhao, Dale R Nyholt, Yuanhao Yang, Jihua Wang, Yuedong Yang
Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks. Scientific reports 7 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Yuedong Yang