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ORCIDJianyang Zeng 0001
Person information
- affiliation: Westlake University, School of Engineering, Hangzhou, China
- affiliation: Tsinghua University, Institute for Interdisciplinary Information Sciences, Beijing, China
- affiliation (PhD 2011): Duke University, Department of Computer Science, Durham, NC, USA
Other persons with the same name
- Jianyang Zeng 0002 — Nanyang Technological University, Singapore
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Books and Theses
- 2011
[b1]Jianyang Zeng:
Novel Algorithms for Automated NMR Assignment and Protein Structure Determination. Duke University, Durham, NC, USA, 2011
Journal Articles
- 2024
- [j32]Tingzhong Tian
, Shuya Li, Meng Fang, Dan Zhao, Jianyang Zeng:
MolSHAP: Interpreting Quantitative Structure-Activity Relationships Using Shapley Values of R-Groups. J. Chem. Inf. Model. 64(7): 2236-2249 (2024) - [j31]Chang Liu, Kaimin Xiao, Cuinan Yu, Yipin Lei, Kangbo Lyu, Tingzhong Tian, Dan Zhao, Fengfeng Zhou, Haidong Tang, Jianyang Zeng:
A probabilistic knowledge graph for target identification. PLoS Comput. Biol. 20(4): 1011945 (2024) - [j30]Khalid Usman, Fangping Wan, Dan Zhao, Jian Peng, Jianyang Zeng:
Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset. IEEE ACM Trans. Comput. Biol. Bioinform. 21(6): 1784-1793 (2024) - 2023
- [j29]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) - [j28]Han Li, Xuan He, Lawrence Kurowski, Ruotian Zhang, Dan Zhao, Jianyang Zeng:
Improving comparative analyses of Hi-C data via contrastive self-supervised learning. Briefings Bioinform. 24(4) (2023) - [j27]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): 395-407 (2023) - [j26]Yuanpeng Xiong, Xuan He, Dan Zhao, Tao Jiang, Jianyang Zeng:
DeepRCI: predicting RNA-chromatin interactions via deep learning with multi-omics data. Quant. Biol. 11(3): 275-286 (2023) - 2022
- [j25]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) - 2021
- [j24]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) - [j23]Peiyuan Feng, Jianyang Zeng, Jianzhu Ma:
Predicting MHC-peptide binding affinity by differential boundary tree. Bioinform. 37(Supplement): 254-261 (2021) - [j22]Xuan He, Sai Zhang, Yanqing Zhang, Zhixin Lei, Tao Jiang, Jianyang Zeng:
Characterizing RNA Pseudouridylation by Convolutional Neural Networks. Genom. Proteom. Bioinform. 19(5): 815-833 (2021) - [j21]Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma:
Modeling gene regulatory networks using neural network architectures. Nat. Comput. Sci. 1(7): 491-501 (2021) - [j20]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) - 2020
- [j19]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): 2872-2880 (2020) - [j18]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): 347-355 (2020) - 2019
- [j17]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): 104-111 (2019) - [j16]Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng:
Metagenomic binning through low-density hashing. Bioinform. 35(2): 219-226 (2019) - [j15]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): 1660-1667 (2019) - [j14]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): i284-i294 (2019) - [j13]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): 4946-4954 (2019) - [j12]Hongfei Cui, Hailin Hu, Jianyang Zeng, Ting Chen:
DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. BMC Bioinform. 20-S(24): 678 (2019) - [j11]Fangping Wan, Yue Zhu, Hailin Hu, Antao Dai, Xiaoqing Cai, Ligong Chen, Haipeng Gong, Tian Xia, Dehua Yang, Ming-Wei Wang, Jianyang Zeng:
DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. Genom. Proteom. Bioinform. 17(5): 478-495 (2019) - 2017
- [j10]Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng:
TITER: predicting translation initiation sites by deep learning. Bioinform. 33(14): i234-i242 (2017) - [j9]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): 2675-2683 (2017) - [j8]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): 159-172 (2017) - 2016
- [j7]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): 300-310 (2016) - [j6]Yichao Zhou, Yuexin Wu, Jianyang Zeng:
Computational Protein Design Using AND/OR Branch-and-Bound Search. J. Comput. Biol. 23(6): 439-451 (2016) - [j5]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): 737-749 (2016) - 2015
- [j4]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): 928-937 (2015) - 2014
- [j3]Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng:
An efficient parallel algorithm for accelerating computational protein design. Bioinform. 30(12): 255-263 (2014) - 2013
- [j2]Yuhao Wang, Jianyang Zeng:
Predicting drug-target interactions using restricted Boltzmann machines. Bioinform. 29(13): 126-134 (2013) - 2011
- [j1]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): 1661-1679 (2011)
Conference and Workshop Papers
- 2024
- [c15]Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang:
PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. RECOMB 2024: 377-380 - 2022
- [c14]Han Li, Dan Zhao, Jianyang Zeng:
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. KDD 2022: 857-867 - 2020
- [c13]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: 259-260 - 2017
- [c12]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: 383-384 - [c11]Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng:
ROSE: A Deep Learning Based Framework for Predicting Ribosome Stalling. RECOMB 2017: 402-403 - 2016
- [c10]Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng:
Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. RECOMB 2016: 255-257 - 2015
- [c9]Yichao Zhou, Jianyang Zeng:
Massively Parallel A* Search on a GPU. AAAI 2015: 1248-1255 - [c8]Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng:
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. RECOMB 2015: 108-121 - [c7]Yichao Zhou, Yuexin Wu, Jianyang Zeng:
Computational Protein Design Using AND/OR Branch-and-Bound Search. RECOMB 2015: 354-366 - 2011
- [c6]Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald:
Protein Loop Closure Using Orientational Restraints from NMR Data. RECOMB 2011: 483-498 - [c5]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: 563-578 - 2010
- [c4]Jianyang Zeng, Pei Zhou, Bruce Randall Donald:
A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. RECOMB 2010: 550-570 - 2005
- [c3]Jianyang Zeng, Wen-Jing Hsu:
ReCord: A Distributed Hash Table with Recursive Structure. PDCAT 2005: 16-20 - [c2]Jianyang Zeng, Wen-Jing Hsu:
Optimal Routing in a Small-World Network. PDCAT 2005: 610-614 - 2003
- [c1]Jianyang Zeng, Wen-Jing Hsu:
Conflict-free routing of AGVs on the mesh topology based on a discrete-time model. ICRA 2003: 3510-3516
Informal and Other Publications
- 2024
- [i8]Yipin Lei, Xu Wang, Meng Fang, Han Li, Xiang Li, Jianyang Zeng:
PepGB: Facilitating peptide drug discovery via graph neural networks. CoRR abs/2401.14665 (2024) - 2022
- [i7]Han Li, Dan Zhao, Jianyang Zeng:
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. CoRR abs/2206.03364 (2022) - [i6]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 abs/2208.10230 (2022) - 2016
- [i5]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 abs/1605.01838 (2016) - [i4]Suiqian Luo, Pingzhong Tang, Chenggang Wu, Jianyang Zeng:
Approximation of barter exchanges with cycle length constraints. CoRR abs/1605.08863 (2016) - 2014
- [i3]Yichao Zhou, Yuexin Wu, Jianyang Zeng:
Computational Protein Design Using AND/OR Branch-and-Bound Search. CoRR abs/1412.3138 (2014) - 2004
- [i2]Jianyang Zeng, Wen-Jing Hsu:
ReCord: A Distributed Hash Table with Recursive Structure. CoRR cs.DC/0410074 (2004) - [i1]Jianyang Zeng, Wen-Jing Hsu, Yahong Hu:
Looking Further Ahead Reveals An Even Smaller World. CoRR cs.DM/0409017 (2004)
Coauthor Index
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