Yaoqi Zhou

Research.com Recognitions

• 2025 - Research.com Computer Science in Australia Leader Award
• 2022 - Research.com Computer Science in Australia Leader Award

Overview

Best Publications

• 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.

  Rhys Heffernan;Yuedong Yang;Kuldip K. Paliwal;Yaoqi Zhou

  455
  Citations

• Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

  Shicai Xu;Jian Zhan;Baoyuan Man;Shouzhen Jiang

  438
  Citations

• 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

  Yuedong Yang;Eshel Faraggi;Huiying Zhao;Yaoqi Zhou

  431
  Citations

• RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.

  Jaswinder Singh;Jack Hanson;Kuldip Paliwal;Yaoqi Zhou

  425
  Citations

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

  Rhys Heffernan;Kuldip Paliwal;James Lyons;Abdollah Dehzangi

  407
  Citations

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

  Jack Hanson;Yuedong Yang;Kuldip K. Paliwal;Yaoqi Zhou

  315
  Citations

• Protein binding site prediction using an empirical scoring function

  Shide Liang;Chi Zhang;Song Liu;Yaoqi Zhou

  312
  Citations

• Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments

  Hongyi Zhou;Yaoqi Zhou

  294
  Citations

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

  Eshel Faraggi;Tuo Zhang;Tuo Zhang;Yuedong Yang;Yuedong Yang;Lukasz A. Kurgan;Lukasz A. Kurgan

  290
  Citations

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

  Yuedong Yang;Jianzhao Gao;Jihua Wang;Rhys Heffernan

  281
  Citations

• Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition

  Hongyi Zhou;Yaoqi Zhou

  228
  Citations

• 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

  Jack Hanson;Kuldip K. Paliwal;Thomas Litfin;Yuedong Yang

  223
  Citations

• Folding rate prediction using total contact distance.

  Hongyi Zhou;Yaoqi Zhou

  223
  Citations

• SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

  Tuo Zhang;Eshel Faraggi;Bin Xue;A. Keith Dunker

  205
  Citations

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

  Jack Hanson;Kuldip K. Paliwal;Thomas Litfin;Yuedong Yang;Yuedong Yang

  197
  Citations

• Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training

  Ofer Dor;Yaoqi Zhou

  189
  Citations

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

  Yuedong Yang;Rhys Heffernan;Kuldip Paliwal;James Lyons

  187
  Citations

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

  James G. Lyons;Abdollah Dehzangi;Abdollah Dehzangi;Rhys Heffernan;Alok Sharma;Alok Sharma

  180
  Citations

• Structure-aware protein-protein interaction site prediction using deep graph convolutional network.

  Qianmu Yuan;Jianwen Chen;Huiying Zhao;Yaoqi Zhou

  178
  Citations

• SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

  Jack Hanson;Kuldip K. Paliwal;Thomas Litfin;Yaoqi Zhou

  164
  Citations

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

  Sarel J. Fleishman;Sarel J. Fleishman;Timothy A. Whitehead;Eva Maria Strauch;Jacob E. Corn;Jacob E. Corn

  156
  Citations

• Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network.

  Eshel Faraggi;Bin Xue;Bin Xue;Yaoqi Zhou;Yaoqi Zhou

  150
  Citations