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Zhaofeng YE
Zhaofeng YE
School of Medicine, Tsinghua University
Verified email at tsinghua.org.cn
Title
Cited by
Cited by
Year
Predicting protein targets for drug-like compounds using transcriptomics
NA Pabon, Y Xia, SK Estabrooks, Z Ye, AK Herbrand, E S, RM Biondi, ...
PLoS computational biology 14 (12), e1006651, 2018
502018
Tensorcircuit: a quantum software framework for the nisq era
SX Zhang, J Allcock, ZQ Wan, S Liu, J Sun, H Yu, XH Yang, J Qiu, Z Ye, ...
Quantum 7, 912, 2023
362023
Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge
Z Ye, MP Baumgartner, BM Wingert, CJ Camacho
Journal of computer-aided molecular design 30, 695-706, 2016
262016
A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells
J Li, S Garavaglia, Z Ye, A Moretti, OV Belyaeva, A Beiser, M Ibrahim, ...
Communications Biology 4 (1), 1420, 2021
222021
Symmetry breaking during homodimeric assembly activates an E3 ubiquitin ligase
Z Ye, PG Needham, SK Estabrooks, SK Whitaker, BL Garcia, S Misra, ...
Scientific reports 7 (1), 1789, 2017
222017
Defining the Kv2. 1–syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant
CY Yeh, Z Ye, A Moutal, S Gaur, AM Henton, S Kouvaros, JL Saloman, ...
Proceedings of the National Academy of Sciences 116 (31), 15696-15705, 2019
102019
Improved the Protein Complex Prediction with Protein Language Models
B Chen, Z Xie, J Qiu, Z Ye, J Xu, J Tang
bioRxiv, 2022.09. 15.508065, 2022
92022
SPLDExtraTrees: robust machine learning approach for predicting kinase inhibitor resistance
ZY Yang, ZF Ye, YJ Xiao, CY Hsieh, SY Zhang
Briefings in Bioinformatics 23 (3), bbac050, 2022
82022
MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection
Z Wang, Y Zhong, Z Ye, L Zeng, Y Chen, M Shi, Z Yuan, Q Zhou, M Qian, ...
Nucleic Acids Research 50 (1), 46-56, 2022
82022
MetalProGNet: a structure-based deep graph model for metalloprotein–ligand interaction predictions
D Jiang, Z Ye, CY Hsieh, Z Yang, X Zhang, Y Kang, H Du, Z Wu, J Wang, ...
Chemical Science 14 (8), 2054-2069, 2023
52023
ScaffComb: A Phenotype‐Based Framework for Drug Combination Virtual Screening in Large‐Scale Chemical Datasets
Z Ye, F Chen, J Zeng, J Gao, MQ Zhang
Advanced Science 8 (24), 2102092, 2021
52021
Improved the heterodimer protein complex prediction with protein language models
B Chen, Z Xie, J Qiu, Z Ye, J Xu, J Tang
Briefings in Bioinformatics, bbad221, 2023
32023
Multi-task bioassay pre-training for protein-ligand binding affinity prediction
J Yan, Z Ye, Z Yang, C Lu, S Zhang, Q Liu, J Qiu
Briefings in Bioinformatics 25 (1), bbad451, 2024
22024
Development of a 32-gene signature using machine learning for accurate prediction of inflammatory bowel disease
S Yu, M Zhang, Z Ye, Y Wang, X Wang, YG Chen
Cell Regeneration 12 (1), 1-13, 2023
12023
A mutation-induced drug resistance database (MdrDB)
Z Yang, Z Ye, J Qiu, R Feng, D Li, C Hsieh, J Allcock, S Zhang
Communications Chemistry 6 (1), 123, 2023
12023
Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform
JP Mailoa, Z Ye, J Qiu, CY Hsieh, S Zhang
arXiv preprint arXiv:2301.00984, 2023
12023
MdrDB: Mutation-induced drug resistance DataBase
Z Yang, Z Ye, J Qiu, R Feng, D Li, C Hsieh, J Allcock, SY Zhang
bioRxiv, 2022.10. 20.513118, 2022
2022
Proteome-scale detection of drug-target interactions using correlations in transcriptomic perturbations
NA Pabon, Y Xia, SK Estabrooks, Z Ye, AK Herbrand, E S, RM Biondi, ...
bioRxiv, 254367, 2018
2018
IDENTIFICATION OF NOVEL INHIBITORS OF UBIQUITINATION THAT IMPROVE RESCUE OF F508DEL-CFTR BY VX-809
J Goeckeler-Fried, SK Estabrooks, A Chiang, W Chung, Z Ye, RA Denny, ...
PEDIATRIC PULMONOLOGY 51, 206-206, 2016
2016
Improve the Protein Complex Prediction with Protein
B Chen, Z Xie, J Xu, J Qiu, Z Ye, J Tang
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