List of works - Yuedong Yang

A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information

scientific article published on 25 November 2022

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

scientific article published on 9 May 2008

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

scholarly article by Jack Hanson published in June 2018

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

scientific article published on 30 March 2020

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

scientific article published on 20 July 2015

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

scientific article published on August 2009

B-factor profile prediction for RNA flexibility using support vector machines.

scientific article published on 21 November 2017

Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.

scientific article published on 16 March 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

scientific article

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

scientific article published on 15 September 2014

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

scientific article

Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites

scientific article published on 14 August 2018

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

scientific article published on 7 January 2015

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

scientific article

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

scientific article published on 07 August 2019

Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images

scientific article published on 11 March 2021

Deep learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) with CT images

scientific article (preprint)

Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP

scientific article published on 10 June 2022

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

scientific article published on 29 August 2018

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

scientific article

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

scientific article

Effective protein conformational sampling based on predicted torsion angles.

scientific article

Energy functions in de novo protein design: current challenges and future prospects

scientific article published on 28 February 2013

Enrichment of SNPs in Functional Categories Reveals Genes Affecting Complex Traits.

scientific article

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

scientific article published on 8 September 2016

Experimentally Validated Plant lncRNAs in EVLncRNAs Database

article

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

scientific article

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

scientific article published in October 2006

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

scientific article

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

scientific article published in February 2018

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

scientific article

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

scientific article published on 06 February 2019

Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

scientific article

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

scientific article published on 22 December 2016

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

scientific article

Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

scientific article

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

scientific article published on 01 July 2020

Infectivity of Plasmodium falciparum in Malaria-Naive Individuals Is Related to Knob Expression and Cytoadherence of the Parasite

scientific article published on 05 July 2016

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

scientific article published on 25 June 2017

Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10.

scientific article

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

scientific article

Natural protein sequences are more intrinsically disordered than random sequences

scientific article published on 22 January 2016

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

scientific article

Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks

scientific article published on 24 December 2019

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

scientific article

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

scientific article published on 26 July 2019

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

scientific article published on 14 May 2018

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

scientific article published on 22 August 2016

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

scientific article

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

scientific article published on October 2013

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

scientific article published on 17 January 2019

Quantitative mapping of genetic similarity in human heritable diseases by shared mutations

scientific article published on 17 October 2017

Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq

scientific article published on 17 May 2021

Retrieval-based Knowledge Augmented Vision Language Pre-training

scientific article published on 27 October 2023

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

scientific article published in January 2017

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

scientific article published on 6 March 2018

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

scientific article published on 2 November 2011

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

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

scientific article published on 14 February 2019

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

scientific article published on January 2014

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

scientific article

Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides

scientific article published on 27 September 2018

Sequence and Structure Analysis of Biological Molecules Based on Computational Methods

scientific article published on 5 July 2015

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

scientific article published on 13 September 2016

Sequence-based prediction of protein-peptide binding sites using support vector machine.

scientific article published on 2 February 2016

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

scientific article

Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr

scientific article published on 31 January 2005

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

scientific article published in August 2008

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

scientific article

Structural insights into the histone H1-nucleosome complex

scientific article

Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA.

scientific article

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

scientific article

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

scientific article

Structure-based prediction of protein-peptide binding regions using Random Forest.

scientific article published on 26 September 2017

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

scientific article published on 16 March 2017

Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana

scientific article published on May 2012

The role of semidisorder in temperature adaptation of bacterial FlgM proteins

scientific article published on December 2013

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

scientific article published on 20 December 2019

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

scientific article published on 31 January 2018

Transition state ensemble for the folding of B domain of protein A: a comparison of distributed molecular dynamics simulations with experiments

scientific article published in December 2005

Trends in template/fragment-free protein structure prediction

scientific article

YesU from Bacillus subtilis preferentially binds fucosylated glycans

scientific article published in Scientific Reports

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

scientific article published on 5 February 2016

List of works by Yuedong Yang

A Drug Combination Prediction Framework Based on Graph Convolutional Network and Heterogeneous Information

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

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

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

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

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

B-factor profile prediction for RNA flexibility using support vector machines.

Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.

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

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

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

Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites

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

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

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

Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images

Deep learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) with CT images

Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP

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

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

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

Effective protein conformational sampling based on predicted torsion angles.

Energy functions in de novo protein design: current challenges and future prospects

Enrichment of SNPs in Functional Categories Reveals Genes Affecting Complex Traits.

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

Experimentally Validated Plant lncRNAs in EVLncRNAs Database

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

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

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

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

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

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

Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

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

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

Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

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

Infectivity of Plasmodium falciparum in Malaria-Naive Individuals Is Related to Knob Expression and Cytoadherence of the Parasite

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

Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10.

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

Natural protein sequences are more intrinsically disordered than random sequences

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks

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

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

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

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

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

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

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

Quantitative mapping of genetic similarity in human heritable diseases by shared mutations

Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq

Retrieval-based Knowledge Augmented Vision Language Pre-training

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

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

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

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

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

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

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

Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides

Sequence and Structure Analysis of Biological Molecules Based on Computational Methods

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

Sequence-based prediction of protein-peptide binding sites using support vector machine.

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

Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from Neurexin and Bcr

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

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

Structural insights into the histone H1-nucleosome complex

Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA.

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

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

Structure-based prediction of protein-peptide binding regions using Random Forest.

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana

The role of semidisorder in temperature adaptation of bacterial FlgM proteins

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

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes