Jianyang Zeng

ORCID

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 31

Top Venues

Duke University, Durham, NC, USA (PHD)

Education History

Duke University, Durham, NC, USA

PHD

Publications

Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao, Jianyang Zeng
Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. Nat. Mac. Intell. 5 (4) (2023)
Siqin Zhang, Kuo Yang, Zhenhong Liu, Xinxing Lai, Zhen Yang, Jianyang Zeng, Shao Li
DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms. Briefings Bioinform. 24 (1) (2023)
Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma
Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Briefings Bioinform. 23 (5) (2022)
Han Li, Dan Zhao, Jianyang Zeng
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. KDD (2022)
Yaosen Min, Ye Wei, Peizhuo Wang, Nian Wu, Stefan Bauer, Shuxin Zheng, Yu Shi, Yingheng Wang, Dan Zhao, Ji Wu, Jianyang Zeng
Predicting the protein-ligand affinity from molecular dynamics trajectories. CoRR (2022)
Han Li, Dan Zhao, Jianyang Zeng
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. CoRR (2022)
Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao, Jianyang Zeng
Full-length ribosome density prediction by a multi-input and multi-output model. PLoS Comput. Biol. 17 (3) (2021)
Xuan He, Sai Zhang, Yanqing Zhang, Zhixin Lei, Tao Jiang, Jianyang Zeng
Characterizing RNA Pseudouridylation by Convolutional Neural Networks. Genom. Proteom. Bioinform. 19 (5) (2021)
Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
Predicting MHC-peptide binding affinity by differential boundary tree. Bioinform. 37 (Supplement) (2021)
Hailin Hu, Xianggen Liu, An Xiao, Yangyang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song, Jianyang Zeng
Riboexp: an interpretable reinforcement learning framework for ribosome density modeling. Briefings Bioinform. 22 (5) (2021)
Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng
MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and Proteins. RECOMB (2020)
Lixiang Hong, Jinjian Lin, Shuya Li, Fangping Wan, Hui Yang, Tao Jiang, Dan Zhao, Jianyang Zeng
A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories. Nat. Mach. Intell. 2 (6) (2020)
Rong Ma, Yi Li, Chenxing Li, Fangping Wan, Hailin Hu, Wei Xu, Jianyang Zeng
Secure multiparty computation for privacy-preserving drug discovery. Bioinform. 36 (9) (2020)
Yan Hu, Ziqiang Wang, Hailin Hu, Fangping Wan, Lin Chen, Yuanpeng Xiong, Xiaoxia Wang, Dan Zhao, Weiren Huang, Jianyang Zeng
ACME: pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks. Bioinform. 35 (23) (2019)
Hao Chen, Dipan Shaw, Jianyang Zeng, Dongbo Bu, Tao Jiang
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. Bioinform. 35 (14) (2019)
Hongfei Cui, Hailin Hu, Jianyang Zeng, Ting Chen
DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. BMC Bioinform. (24) (2019)
Hailin Hu, An Xiao, Sai Zhang, Yangyang Li, Xuanling Shi, Tao Jiang, Linqi Zhang, Lei Zhang, Jianyang Zeng
DeepHINT: understanding HIV-1 integration via deep learning with attention. Bioinform. 35 (10) (2019)
Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng
Metagenomic binning through low-density hashing. Bioinform. 35 (2) (2019)
Fangping Wan, Yue Zhu, Hailin Hu, Antao Dai, Xiaoqing Cai, Ligong Chen, Haipeng Gong, Tian Xia, Dehua Yang, Ming-Wei Wang, Jianyang Zeng
Drug Screening. Genom. Proteom. Bioinform. 17 (5) (2019)
Fangping Wan, Lixiang Hong, An Xiao, Tao Jiang, Jianyang Zeng
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions. Bioinform. 35 (1) (2019)
Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng
TITER: predicting translation initiation sites by deep learning. Bioinform. 33 (14) (2017)
Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, Jianyang Zeng
A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. RECOMB (2017)
Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng
ROSE: A Deep Learning Based Framework for Predicting Ribosome Stalling. RECOMB (2017)
Sai Zhang, Muxuan Liang, Zhongjun Zhou, Chen Zhang, Ning Chen, Ting Chen, Jianyang Zeng
Elastic restricted Boltzmann machines for cancer data analysis. Quant. Biol. 5 (2) (2017)
Dapeng Xiong, Jianyang Zeng, Haipeng Gong
A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy. Bioinform. 33 (17) (2017)
Feng Wang, Huichao Gong, Gaochao liu, Meijing Li, Chuangye Yan, Tian Xia, Xueming Li, Jianyang Zeng
DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM. CoRR (2016)
Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce Randall Donald, Jianyang Zeng, Wei Xu
cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. J. Comput. Biol. 23 (9) (2016)
Yichao Zhou, Yuexin Wu, Jianyang Zeng
Computational Protein Design Using AND/OR Branch-and-Bound Search. J. Comput. Biol. 23 (6) (2016)
Suiqian Luo, Pingzhong Tang, Chenggang Wu, Jianyang Zeng
Approximation of barter exchanges with cycle length constraints. CoRR (2016)
Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng
Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. RECOMB (2016)
Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. J. Comput. Biol. 23 (5) (2016)
Yichao Zhou, Yuexin Wu, Jianyang Zeng
Computational Protein Design Using AND/OR Branch-and-Bound Search. RECOMB (2015)
Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng
Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. RECOMB (2015)
Yichao Zhou, Jianyang Zeng
Massively Parallel A* Search on a GPU. AAAI (2015)
Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng
An efficient parallel algorithm for accelerating computational protein design. Bioinform. 30 (12) (2014)
Yichao Zhou, Yuexin Wu, Jianyang Zeng
Computational Protein Design Using AND/OR Branch-and-Bound Search. CoRR (2014)
Yuhao Wang, Jianyang Zeng
Predicting drug-target interactions using restricted Boltzmann machines. Bioinform. 29 (13) (2013)
Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. RECOMB (2011)
Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald
Protein Loop Closure Using Orientational Restraints from NMR Data. RECOMB (2011)
Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald
A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. J. Comput. Biol. 18 (11) (2011)
Jianyang Zeng, Pei Zhou, Bruce Randall Donald
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. RECOMB (2010)
Jianyang Zeng, Wen-Jing Hsu
Conflict-free container routing in mesh yard layouts. Robotics Auton. Syst. 56 (5) (2008)
Jianyang Zeng, Wen-Jing Hsu
Optimal Routing in a Small-World Network. J. Comput. Sci. Technol. 21 (4) (2006)
Jianyang Zeng, Wen-Jing Hsu
Optimal Routing in a Small-World Network. PDCAT (2005)
Jianyang Zeng, Wen-Jing Hsu, Suiping Zhou
Construction of Scale-Free Networks with Partial Information. COCOON (2005)
Jianyang Zeng, Wen-Jing Hsu
ReCord: A Distributed Hash Table with Recursive Structure. PDCAT (2005)
Jianyang Zeng, Wen-Jing Hsu, Jiangdian Wang
Near Optimal Routing in a Small-World Network with Augmented Local Awareness. ISPA (2005)
Jianyang Zeng, Wen-Jing Hsu, Yahong Hu
Looking Further Ahead Reveals An Even Smaller World CoRR (2004)
Jianyang Zeng, Wen-Jing Hsu
ReCord: A Distributed Hash Table with Recursive Structure CoRR (2004)
Jianyang Zeng, Wen-Jing Hsu
Conflict-free routing of AGVs on the mesh topology based on a discrete-time model. ICRA (2003)

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Publication Activity (10 Years)

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Jianyang Zeng