Jianyang Zeng - RankMe

57 papers A* 3B 10C 2Journal 41

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	A probabilistic knowledge graph for target identification. PLoS Comput. Biol. Chang Liu, Kaimin Xiao, Cuinan Yu, Yipin Lei, Kangbo Lyu, Tingzhong Tian, Dan Zhao, Fengfeng Zhou, Haidong Tang, Jianyang Zeng
2024	J	`jnl`	Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset. IEEE ACM Trans. Comput. Biol. Bioinform. Khalid Usman, Fangping Wan, Dan Zhao, Jian Peng, Jianyang Zeng
2024	J	`jnl`	DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug's expression perturbation and treatment effectiveness. Bioinform. Shuyue Fan, Kuo Yang, Kezhi Lu, Xin Dong, Xianan Li, Qiang Zhu, Shao Li, Jianyang Zeng, Xuezhong Zhou
2024	J	`jnl`	MolSHAP: Interpreting Quantitative Structure-Activity Relationships Using Shapley Values of R-Groups. J. Chem. Inf. Model. Tingzhong Tian, Shuya Li, Meng Fang, Dan Zhao, Jianyang Zeng
2024	B	`conf`	PRS-Net: Interpretable Polygenic Risk Scores via Geometric Learning. RECOMB Han Li, Jianyang Zeng, Michael P. Snyder, Sai Zhang
2024	J	`jnl`	PepGB: Facilitating peptide drug discovery via graph neural networks. CoRR Yipin Lei, Xu Wang, Meng Fang, Han Li, Xiang Li, Jianyang Zeng
2023	J	`jnl`	Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. Nat. Mac. Intell. Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao, Jianyang Zeng
2023	J	`jnl`	DeepRCI: predicting RNA-chromatin interactions via deep learning with multi-omics data. Quant. Biol. Yuanpeng Xiong, Xuan He, Dan Zhao, Tao Jiang, Jianyang Zeng
2023	J	`jnl`	DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms. Briefings Bioinform. Siqin Zhang, Kuo Yang, Zhenhong Liu, Xinxing Lai, Zhen Yang, Jianyang Zeng, Shao Li
2023	J	`jnl`	Improving comparative analyses of Hi-C data via contrastive self-supervised learning. Briefings Bioinform. Han Li, Xuan He, Lawrence Kurowski, Ruotian Zhang, Dan Zhao, Jianyang Zeng
2022	J	`jnl`	Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Briefings Bioinform. Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma
2022	A*	`conf`	KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. KDD Han Li, Dan Zhao, Jianyang Zeng
2022	J	`jnl`	KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction. CoRR Han Li, Dan Zhao, Jianyang Zeng
2022	J	`jnl`	Predicting the protein-ligand affinity from molecular dynamics trajectories. CoRR Yaosen Min, Ye Wei, Peizhuo Wang, Nian Wu, Stefan Bauer, Shuxin Zheng, Yu Shi, Yingheng Wang, Dan Zhao, Ji Wu, Jianyang Zeng
2021	J	`jnl`	Characterizing RNA Pseudouridylation by Convolutional Neural Networks. Genom. Proteom. Bioinform. Xuan He, Sai Zhang, Yanqing Zhang, Zhixin Lei, Tao Jiang, Jianyang Zeng
2021	J	`jnl`	Full-length ribosome density prediction by a multi-input and multi-output model. PLoS Comput. Biol. Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao, Jianyang Zeng
2021	J	`jnl`	Modeling gene regulatory networks using neural network architectures. Nat. Comput. Sci. Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma
2021	J	`jnl`	Predicting MHC-peptide binding affinity by differential boundary tree. Bioinform. Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
2021	J	`jnl`	Riboexp: an interpretable reinforcement learning framework for ribosome density modeling. Briefings Bioinform. Hailin Hu, Xianggen Liu, An Xiao, Yangyang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song, Jianyang Zeng
2020	J	`jnl`	A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories. Nat. Mach. Intell. Lixiang Hong, Jinjian Lin, Shuya Li, Fangping Wan, Hui Yang, Tao Jiang, Dan Zhao, Jianyang Zeng
2020	B	`conf`	MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and Proteins. RECOMB Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng
2020	J	`jnl`	Secure multiparty computation for privacy-preserving drug discovery. Bioinform. Rong Ma, Yi Li, Chenxing Li, Fangping Wan, Hailin Hu, Wei Xu, Jianyang Zeng
2019	J	`jnl`	ACME: pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks. Bioinform. Yan Hu, Ziqiang Wang, Hailin Hu, Fangping Wan, Lin Chen, Yuanpeng Xiong, Xiaoxia Wang, Dan Zhao, Weiren Huang, Jianyang Zeng
2019	J	`jnl`	DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. Bioinform. Hao Chen, Dipan Shaw, Jianyang Zeng, Dongbo Bu, Tao Jiang
2019	J	`jnl`	DeepCPI: A Deep Learning-based Framework for Large-scale Genom. Proteom. Bioinform. Fangping Wan, Yue Zhu, Hailin Hu, Antao Dai, Xiaoqing Cai, Ligong Chen, Haipeng Gong, Tian Xia, Dehua Yang, Ming-Wei Wang, Jianyang Zeng
2019	J	`jnl`	DeepHINT: understanding HIV-1 integration via deep learning with attention. Bioinform. Hailin Hu, An Xiao, Sai Zhang, Yangyang Li, Xuanling Shi, Tao Jiang, Linqi Zhang, Lei Zhang, Jianyang Zeng
2019	J	`jnl`	DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. BMC Bioinform. Hongfei Cui, Hailin Hu, Jianyang Zeng, Ting Chen
2019	J	`jnl`	Metagenomic binning through low-density hashing. Bioinform. Yunan Luo, Yun William Yu, Jianyang Zeng, Bonnie Berger, Jian Peng
2019	J	`jnl`	NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions. Bioinform. Fangping Wan, Lixiang Hong, An Xiao, Tao Jiang, Jianyang Zeng
2017	B	`conf`	A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. RECOMB Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, Jianyang Zeng
2017	J	`jnl`	A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy. Bioinform. Dapeng Xiong, Jianyang Zeng, Haipeng Gong
2017	J	`jnl`	Elastic restricted Boltzmann machines for cancer data analysis. Quant. Biol. Sai Zhang, Muxuan Liang, Zhongjun Zhou, Chen Zhang, Ning Chen, Ting Chen, Jianyang Zeng
2017	B	`conf`	ROSE: A Deep Learning Based Framework for Predicting Ribosome Stalling. RECOMB Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng
2017	J	`jnl`	TITER: predicting translation initiation sites by deep learning. Bioinform. Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng
2016	J	`jnl`	Approximation of barter exchanges with cycle length constraints. CoRR Suiqian Luo, Pingzhong Tang, Chenggang Wu, Jianyang Zeng
2016	J	`jnl`	Computational Protein Design Using AND/OR Branch-and-Bound Search. J. Comput. Biol. Yichao Zhou, Yuexin Wu, Jianyang Zeng
2016	J	`jnl`	Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. J. Comput. Biol. Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng
2016	J	`jnl`	DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM. CoRR Feng Wang, Huichao Gong, Gaochao Liu, Meijing Li, Chuangye Yan, Tian Xia, Xueming Li, Jianyang Zeng
2016	B	`conf`	Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. RECOMB Yunan Luo, Jianyang Zeng, Bonnie Berger, Jian Peng
2016	J	`jnl`	cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. J. Comput. Biol. Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce Randall Donald, Jianyang Zeng, Wei Xu
2015	B	`conf`	Computational Protein Design Using AND/OR Branch-and-Bound Search. RECOMB Yichao Zhou, Yuexin Wu, Jianyang Zeng
2015	B	`conf`	Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. RECOMB Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng
2015	J	`jnl`	Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach. IEEE ACM Trans. Comput. Biol. Bioinform. Muxuan Liang, Zhizhong Li, Ting Chen, Jianyang Zeng
2015	A*	`conf`	Massively Parallel A* Search on a GPU. AAAI Yichao Zhou, Jianyang Zeng
2014	J	`jnl`	An efficient parallel algorithm for accelerating computational protein design. Bioinform. Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng
2014	J	`jnl`	Computational Protein Design Using AND/OR Branch-and-Bound Search. CoRR Yichao Zhou, Yuexin Wu, Jianyang Zeng
2013	J	`jnl`	Predicting drug-target interactions using restricted Boltzmann machines. Bioinform. Yuhao Wang, Jianyang Zeng
2011	B	`conf`	A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. RECOMB Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald
2011	J	`jnl`	A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. J. Comput. Biol. Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald
2011	—	`—`	Novel Algorithms for Automated NMR Assignment and Protein Structure Determination. Jianyang Zeng
2011	B	`conf`	Protein Loop Closure Using Orientational Restraints from NMR Data. RECOMB Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald
2010	B	`conf`	A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. RECOMB Jianyang Zeng, Pei Zhou, Bruce Randall Donald
2005	C	`conf`	Optimal Routing in a Small-World Network. PDCAT Jianyang Zeng, Wen-Jing Hsu
2005	C	`conf`	ReCord: A Distributed Hash Table with Recursive Structure. PDCAT Jianyang Zeng, Wen-Jing Hsu
2004	J	`jnl`	Looking Further Ahead Reveals An Even Smaller World CoRR Jianyang Zeng, Wen-Jing Hsu, Yahong Hu
2004	J	`jnl`	ReCord: A Distributed Hash Table with Recursive Structure CoRR Jianyang Zeng, Wen-Jing Hsu
2003	A*	`conf`	Conflict-free routing of AGVs on the mesh topology based on a discrete-time model. ICRA Jianyang Zeng, Wen-Jing Hsu