Yaoqi Zhou

71 papers C 1Journal 69Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.
Briefings Bioinform.
He Wang, Yikun Zhang, Jie Chen, Jian Zhan, Yaoqi Zhou
2025 J jnl
A Comparative Review of RNA Language Models.
CoRR
He Wang, Yikun Zhang, Jie Chen, Jian Zhan, Yaoqi Zhou
2025 J jnl
Benchmarking the methods for predicting base pairs in RNA-RNA interactions.
Bioinform.
Mei Lang, Thomas Litfin, Ke Chen, Jian Zhan, Yaoqi Zhou
2024 J jnl
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search.
Genom. Proteom. Bioinform.
Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou
2023 J jnl
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Nucleic Acids Res.
Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
2023 J jnl
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.
Briefings Bioinform.
Bailing Zhou, Maolin Ding, Jing Feng, Baohua Ji, Pingping Huang, Junye Zhang, Xue Yu, Zanxia Cao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
2023 J jnl
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model.
Briefings Bioinform.
Yidong Song, Qianmu Yuan, Sheng Chen, Ken Chen, Yaoqi Zhou, Yuedong Yang
2023 J jnl
SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network.
PLoS Comput. Biol.
Xing Zhang, Hongmei Yin, Fei Ling, Jian Zhan, Yaoqi Zhou
2022 J jnl
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.
Bioinform.
Jaswinder Singh, Kuldip K. Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou
2022 J jnl
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
Briefings Bioinform.
Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan
2022 J jnl
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.
Bioinform.
Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou
2021 J jnl
De novo protein design by an energy function based on series expansion in distance and orientation dependence.
Bioinform.
Shide Liang, Zhixiu Li, Jian Zhan, Yaoqi Zhou
2021 — conf
DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks.
BIBM
Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang
2021 J jnl
DescribePROT: database of amino acid-level protein structure and function predictions.
Nucleic Acids Res.
Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan
2021 J jnl
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments.
Nucleic Acids Res.
Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
2021 J jnl
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.
Bioinform.
Jaswinder Singh, Kuldip K. Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin, Yaoqi Zhou
2021 J jnl
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks.
J. Chem. Inf. Model.
Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou
2021 J jnl
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.
Bioinform.
Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip K. Paliwal, Yaoqi Zhou
2021 J jnl
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning.
Bioinform.
Jaspreet Singh, Thomas Litfin, Kuldip K. Paliwal, Jaswinder Singh, Anil Kumar Hanumanthappa, Yaoqi Zhou
2021 C conf
SPOT-1D2: Improving Protein Secondary Structure Prediction using High Sequence Identity Training Set and an Ensemble of Recurrent and Residual-convolutional Neural Networks.
CIBCB
Jaspreet Singh, Jaswinder Singh, Kuldip K. Paliwal, Andrew Busch, Yaoqi Zhou
2021 J jnl
Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network.
Bioinform.
Anil Kumar Hanumanthappa, Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou
2021 J jnl
Structure-aware protein-protein interaction site prediction using deep graph convolutional network.
Bioinform.
Qianmu Yuan, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
2020 J jnl
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State.
J. Comput. Biol.
Tongchuan Zhang, Guodong Hu, Yuedong Yang, Jihua Wang, Yaoqi Zhou
2020 J jnl
Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
Database J. Biol. Databases Curation
Peter Brown, Yaoqi Zhou
2020 J jnl
GM-DockZn: a geometry matching-based docking algorithm for zinc proteins.
Bioinform.
Kai Wang, Nan Lyu, Hongjuan Diao, Shujuan Jin, Tao Zeng, Yaoqi Zhou, Ruibo Wu
2020 J jnl
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning.
J. Comput. Biol.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2020 J jnl
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning.
Bioinform.
Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou
2020 J jnl
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map.
J. Comput. Chem.
Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang
2019 J jnl
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state.
J. Cheminformatics
Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
2019 J jnl
Improved fragment sampling for ab initio protein structure prediction using deep neural networks.
Nat. Mach. Intell.
Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong
2019 J jnl
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.
Bioinform.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2019 J jnl
Large expert-curated database for benchmarking document similarity detection in biomedical literature search.
Database J. Biol. Databases Curation
Peter Brown, RELISH Consortium, Yaoqi Zhou
2019 J jnl
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.
Genom. Proteom. Bioinform.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou
2019 J jnl
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites.
J. Chem. Inf. Model.
Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2019 J jnl
SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties.
Bioinform.
Ghazaleh Taherzadeh, Abdollah Dehzangi, Maryam Golchin, Yaoqi Zhou, Matthew P. Campbell
2018 J jnl
Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures.
J. Chem. Inf. Model.
Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou
2018 J jnl
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.
Bioinform.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2018 J jnl
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning.
J. Chem. Inf. Model.
Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip K. Paliwal, Yuedong Yang, Yaoqi Zhou
2018 J jnl
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.
Nucleic Acids Res.
Bailing Zhou, Huiying Zhao, Jia-Feng Yu, Chengang Guo, Xianghua Dou, Feng Song, Guodong Hu, Zanxia Cao, Yuanxu Qu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
2018 J jnl
Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures.
BMC Bioinform.
Jianzhao Gao, Yuedong Yang, Yaoqi Zhou
2018 J jnl
Predicting lysine-malonylation sites of proteins using sequence and predicted structural features.
J. Comput. Chem.
Ghazaleh Taherzadeh, Yuedong Yang, Hao-Dong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
2018 J jnl
Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning.
J. Comput. Chem.
Rhys Heffernan, Kuldip K. Paliwal, James G. Lyons, Jaswinder Singh, Yuedong Yang, Yaoqi Zhou
2018 J jnl
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
Briefings Bioinform.
Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou
2018 J jnl
Structure-based prediction of protein- peptide binding regions using Random Forest.
Bioinform.
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
2017 J jnl
A heuristic for the time constrained asymmetric linear sum assignment problem.
J. Comb. Optim.
Peter Brown, Yuedong Yang, Yaoqi Zhou, Wayne J. Pullan
2017 J jnl
Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.
Bioinform.
Rhys Heffernan, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou
2017 J jnl
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins.
BMC Bioinform.
Jia-Feng Yu, Xianghua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang
2017 J jnl
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.
Bioinform.
Jack Hanson, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou
2017 J jnl
LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction.
Bioinform.
Tong Wang, Yuedong Yang, Yaoqi Zhou, Haipeng Gong
2017 J jnl
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.
Bioinform.
Thomas Litfin, Yaoqi Zhou, Yuedong Yang
2016 J jnl
Effective protein conformational sampling based on predicted torsion angles.
J. Comput. Chem.
Yuedong Yang, Yaoqi Zhou
2016 J jnl
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.
Bioinform.
Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou
2016 J jnl
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.
Bioinform.
Rhys Heffernan, Abdollah Dehzangi, James G. Lyons, Kuldip K. Paliwal, Alok Sharma, Jihua Wang, Abdul Sattar, Yaoqi Zhou, Yuedong Yang
2016 J jnl
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks.
Bioinform.
Jianzhao Gao, Yuedong Yang, Yaoqi Zhou
2016 J jnl
SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.
J. Comput. Chem.
Yuedong Yang, Jian Zhan, Yaoqi Zhou
2016 J jnl
Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines.
J. Chem. Inf. Model.
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
2016 J jnl
Sequence-based prediction of protein-peptide binding sites using support vector machine.
J. Comput. Chem.
Ghazaleh Taherzadeh, Yuedong Yang, Tuo Zhang, Alan Wee-Chung Liew, Yaoqi Zhou
2016 J jnl
sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections.
J. Comput. Chem.
Md. Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou
2015 J jnl
DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels.
Bioinform.
Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou
2014 J jnl
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction.
J. Comput. Chem.
Huiying Zhao, Yuedong Yang, Mark von Itzstein, Yaoqi Zhou
2014 J jnl
LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains.
J. Comput. Chem.
Shide Liang, Chi Zhang, Yaoqi Zhou
2014 J jnl
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.
J. Comput. Chem.
James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip K. Paliwal, Abdul Sattar, Yaoqi Zhou, Yuedong Yang
2012 J jnl
SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles.
J. Comput. Chem.
Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, Yaoqi Zhou
2011 J jnl
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates.
Bioinform.
Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou
2011 J jnl
In-silico prediction of disorder content using hybrid sequence representation.
BMC Bioinform.
Marcin J. Mizianty, Tuo Zhang, Bin Xue, Yaoqi Zhou, A. Keith Dunker, Vladimir N. Uversky, Lukasz A. Kurgan
2011 J jnl
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.
J. Comput. Chem.
Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley
2010 J jnl
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.
Bioinform.
Huiying Zhao, Yuedong Yang, Yaoqi Zhou
2005 J jnl
Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function.
J. Bioinform. Comput. Biol.
Hongzhi Li, Yaoqi Zhou
2005 J jnl
SCUD: Fast structure clustering of decoys using reference state to remove overall rotation.
J. Comput. Chem.
Hongzhi Li, Yaoqi Zhou
2005 J jnl
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
Bioinform.
Hongyi Zhou, Yaoqi Zhou
2005 J jnl
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations.
Nucleic Acids Res.
Hongyi Zhou, Chi Zhang, Song Liu, Yaoqi Zhou