Yuedong Yang

发表

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto‐encoder deep neural network

Kuldip K. Paliwal, James G. Lyons, Abdollah Dehzangi, 2014, J. Comput. Chem..

Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks

Yaoqi Zhou, Yuedong Yang, Jianzhao Gao, 2016, Bioinform..

Communicative Representation Learning on Attributed Molecular Graphs

Yuedong Yang, Zhang-Hua Fu, Ying Song, 2020, IJCAI.

sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections

Yaoqi Zhou, Yuedong Yang, Avdesh Mishra, 2016, J. Comput. Chem..

SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks.

James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, 2017, Methods in molecular biology.

Joints Parameters Identification in Numerical Modeling of Structural Dynamics

Yuedong Yang, Fengchong Lan, Jiqing Chen, 2018 .

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Kuldip K. Paliwal, Rhys Heffernan, Yaoqi Zhou, 2016, Briefings Bioinform..

SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity

Yaoqi Zhou, Yuedong Yang, Jian Zhan, 2016, J. Comput. Chem..

Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks pdf

Yuedong Yang, Jun Xu, Shuangjia Zheng, 2019, ArXiv.

Predicting functional long non-coding RNAs validated by low throughput experiments

Yuedong Yang, Bailing Zhou, Jian Zhan, 2019 .

LSA: a local-weighted structural alignment tool for pharmaceutical virtual screening

Jun Xu, Yuedong Yang, Yutong Lu, 2019, RSC advances.

To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map.

Yuedong Yang, Yutong Lu, Xun Liu, 2019, Journal of chemical information and modeling.

LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction

Tong Wang, Yaoqi Zhou, Yuedong Yang, 2016, Bioinform..

Carbohydrate‐binding protein identification by coupling structural similarity searching with binding affinity prediction

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2014, J. Comput. Chem..

Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network

Yuedong Yang, Xiang Zhou, Yutong Lu, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning

Yaoqi Zhou, Yuedong Yang, Jack Hanson, 2020, J. Comput. Biol..

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

Lukasz A. Kurgan, Yaoqi Zhou, Yuedong Yang, 2012, J. Comput. Chem..

Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning–based neural network

Yuedong Yang, Xiang Zhou, Ching-Hsing Luo, 2020, GigaScience.

An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles

Yaoqi Zhou, Yuedong Yang, Beisi Xu, 2009, Proteins.

SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2014, Methods in molecular biology.

Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting

Yuedong Yang, Nong Xiao, Zhiguang Chen, 2020, J. Chem. Inf. Model..

Single‐sequence‐based prediction of protein secondary structures and solvent accessibility by deep whole‐sequence learning

Jaswinder Singh, Kuldip K. Paliwal, James G. Lyons, 2018, J. Comput. Chem..

Accurate Prediction of Genome-wide RNA Secondary Structure Profile Based On Extreme Gradient Boosting

Yuedong Yang, Yaobin Ke, Yutong Lu, 2019, bioRxiv.

Predicting lysine‐malonylation sites of proteins using sequence and predicted structural features

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2018, J. Comput. Chem..

Knowledge-based Recurrent Attentive Neural Network for Small Object Detection

Nanning Zheng, Yuedong Yang, Shitao Chen, 2018 .

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

Kuldip K. Paliwal, Rhys Heffernan, Yaoqi Zhou, 2017, Bioinform..

QBMG: quasi-biogenic molecule generator with deep recurrent neural network

Jun Xu, Yuedong Yang, Xin Yan, 2019, Journal of Cheminformatics.

Effective protein conformational sampling based on predicted torsion angles

Yaoqi Zhou, Yuedong Yang, Yaoqi Zhou, 2016, J. Comput. Chem..

Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning

Rhys Heffernan, Yaoqi Zhou, Yuedong Yang, 2018, J. Chem. Inf. Model..

Investigation into Improvement for Anti-Rollover Propensity of SUV

Yuedong Yang, Fei Xiong, Fengchong Lan, 2017 .

Structure‐based prediction of protein‐ peptide binding regions using Random Forest

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2018, Bioinform..

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

A heuristic for the time constrained asymmetric linear sum assignment problem

Yaoqi Zhou, Yuedong Yang, Peter Brown, 2017, J. Comb. Optim..

SPOT‐Fold: Fragment‐Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map

Yuedong Yang, Yutong Lu, Kuldip Paliwal, 2020, J. Comput. Chem..

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2017, Nucleic Acids Res..

Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks

Kuldip K. Paliwal, Yaoqi Zhou, Yuedong Yang, 2018, Bioinform..

Publisher Correction: Predicting drug–protein interaction using quasi-visual question answering system

Yuedong Yang, Shuangjia Zheng, Sheng Chen, 2020 .

All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2020, J. Comput. Biol..

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

Yaoqi Zhou, Yuedong Yang, Yutong Lu, 2019, Journal of Cheminformatics.

Improving protein disorder prediction by deep bidirectional long short‐term memory recurrent neural networks

Yaoqi Zhou, Yuedong Yang, Kuldip Paliwal, 2016, Bioinform..

Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network

Yuedong Yang, Xiang Zhou, Yutong Lu, 2020, bioRxiv.

Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2016, J. Chem. Inf. Model..

Computational Prediction of Carbohydrate‐Binding Proteins and Binding Sites

Yaoqi Zhou, Yuedong Yang, Ghazaleh Taherzadeh, 2018, Current protocols in protein science.

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

Yaoqi Zhou, Yuedong Yang, Jianzhao Gao, 2018, BMC Bioinformatics.

View-invariant action recognition using interest points

Aimin Hao, Qinping Zhao, Yuedong Yang, 2008, MIR '08.

B‐factor profile prediction for RNA flexibility using support vector machines

Yaoqi Zhou, Yuedong Yang, Jian Zhan, 2018, J. Comput. Chem..

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2010, Bioinform..

An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer

Yuedong Yang, Yutong Lu, Zhiguang Chen, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins

Kuldip K. Paliwal, James G. Lyons, Abdollah Dehzangi, 2016, Bioinform..

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic

Yaoqi Zhou, Yuedong Yang, Peter Brown, 2016, Bioinform..

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

Yaoqi Zhou, Yuedong Yang, Kuldip Paliwal, 2018, Bioinform..

SPOT‐ligand 2: improving structure‐based virtual screening by binding‐homology search on an expanded structural template library

Yaoqi Zhou, Yuedong Yang, Thomas Litfin, 2017, Bioinform..

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

Yunlong Liu, Abdul Sattar, Yaoqi Zhou, 2015, Bioinform..

An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer

Yuedong Yang, Yutong Lu, Zhiguang Chen, 2020, bioRxiv.

Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space

Haiyan Liu, Yuedong Yang, Yuedong Yang, 2006, J. Comput. Chem..

Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models

James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, 2015, IEEE Transactions on NanoBioscience.

Sequence‐based prediction of protein–peptide binding sites using support vector machine

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2016, J. Comput. Chem..

SPIN2: Predicting sequence profiles from protein structures using deep neural networks

James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, 2018, Proteins.

DTW-Curve for Classification of Logically Similar Motions

Qinping Zhao, Yuedong Yang, Weihe Wu, 2008, GRAPP.

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

Yuedong Yang, Shuangjia Zheng, Huiying Zhao, 2020, bioRxiv.

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

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2011, Bioinform..

To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map

Yuedong Yang, Yutong Lu, Zhe Sun, 2019, bioRxiv.

SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites

Yaoqi Zhou, Yuedong Yang, Thomas Litfin, 2019, J. Chem. Inf. Model..

Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism

Yuedong Yang, Xin Yan, Jun Xu, 2018, J. Chem. Inf. Model..

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

Yuedong Yang, Shuangjia Zheng, Huiying Zhao, 2021, Journal of Cheminformatics.

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Yuedong Yang, Huiying Zhao, Guodong Hu, 2020, Nucleic Acids Res..

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

Yuedong Yang, Olivier Lichtarge, Giovanni Minervini, 2017, Human mutation.

Discriminating between disease-causing and neutral non-frameshifting micro-INDELs by support vector machines by means of integrated sequence- and structure-based features

Yuedong Yang, Matthew Mort, Yaoqi Zhou, 2013 .

The role of semidisorder in temperature adaptation of bacterial FlgM proteins.

Yuedong Yang, Yaoqi Zhou, Zanxia Cao, 2013, Biophysical journal.

Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome

Yuedong Yang, Sarath Chandra Janga, Huiying Zhao, 2014, Proteins.

Prediction of RNA binding proteins comes of age from low resolution to high resolution.

Yuedong Yang, Huiying Zhao, Yaoqi Zhou, 2013, Molecular bioSystems.

Investigating DNA‐, RNA‐, and protein‐based features as a means to discriminate pathogenic synonymous variants

Yuedong Yang, Bela Stantic, Ping Zhang, 2017, Human mutation.

Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction

Yuedong Yang, Jian Zhan, Yaoqi Zhou, 2017, RNA.

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution

Yuedong Yang, Matthew Mort, Weixing Feng, 2017, Human Genetics.

Predicting functional long non-coding RNAs validated by low throughput experiments

Yuedong Yang, Jian Zhan, Xianghua Dou, 2019, bioRxiv.

Charting the Unexplored RNA-binding Protein Atlas of the Human Genome

Yuedong Yang, Sarath Chandra Janga, Heng Zhu, 2000 .

Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Yuedong Yang, Shesheng Zhang, Yaoqi Zhou, 2009, Structure.

Natural protein sequences are more intrinsically disordered than random sequences

Yuedong Yang, Jia-Feng Yu, Yaoqi Zhou, 2016, Cellular and Molecular Life Sciences.

Structural basis for SUMO‐E2 interaction revealed by a complex model using docking approach in combination with NMR data

Yuedong Yang, Jiahai Zhang, Yuedong Yang, 2005, Proteins.

Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

Yuedong Yang, Huiying Zhao, Yaoqi Zhou, 2011, RNA biology.

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome

Yuedong Yang, Huiying Zhao, Yaoqi Zhou, 2014, PloS one.

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

Yuedong Yang, Matthew Mort, Huiying Zhao, 2013, Genome Biology.

Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles

Yuedong Yang, Jian Zhan, Yaoqi Zhou, 2014, Proteins.