Yaoqi Zhou

Scopus Author ID ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 34

Top Venues

Journal of computational chemistry

Journal of chemical information and modeling

Bioinformatics (Oxford, England)

PloS one

Griffith University - Gold Coast Campus

Stony Brook University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Griffith University - Gold Coast Campus Jun 01 2013

Australia

Research Leader :: Institute for Glycomics

Indiana University-Purdue University Indianapolis Jun 01 2006 - May 31 2013

United States

Professor :: School of Informatics

University at Buffalo Jul 01 2000 - May 31 2006

United States

Assistant and Associate Professor :: Physiology and Biophysics

Education History

Stony Brook University Sep 01 1985 - Apr 30 1990

United States

PHD :: Chemistry

University of Science and Technology of China Sep 01 1979 - Jun 30 1984

China

BSC :: Modern Chemistry

Publications

Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. Genomics, proteomics & bioinformatics 22 (1) (2024)
Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. Genomics, proteomics & bioinformatics 22 (1) (2024)
Yaoqi Zhou, Thomas Litfin, Jian Zhan
3 = 1 + 2: how the divide conquered de novo protein structure prediction and what is next? National science review 10 (12) (2023)
Bailing Zhou, Baohua Ji, Congcong Shen, Xia Zhang, Xue Yu, Pingping Huang, Ru Yu, Hongmei Zhang, Xianghua Dou, Qingshuai Chen, Qiangcheng Zeng, Xiaoxin Wang, Zanxia Cao, Guodong Hu, Shicai Xu, Huiying Zhao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic acids research (2023)
Yikun Zhang, Mei Lang, Jiuhong Jiang, Zhiqiang Gao, Fan Xu, Thomas Litfin, Ke Chen, Jaswinder Singh, Xiansong Huang, Guoli Song, Yonghong Tian, Jian Zhan, Jie Chen, Yaoqi Zhou
Multiple sequence alignment-based RNA language model and its application to structural inference. Nucleic acids research (2023)
Xing Zhang, Hongmei Yin, Fei Ling, Jian Zhan, Yaoqi Zhou
SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network. PLoS computational biology 19 (12) (2023)
Jaswinder Singh, Kuldip Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. Bioinformatics (Oxford, England) 38 (16) (2022)
Xin Chen, Ke Chen, Zhaoyong Zhang, Peilan Wei, Lu Zhang, Yunxia Xu, Qili Lun, Yanhong Ma, Fang Wu, Ying Zhang, Yanqun Wang, Jincun Zhao, Yaoqi Zhou, Jian Zhan, Wei Xu
Investigating Derivatives of Tanshinone IIA Sulfonate Sodium and Chloroxine for Their Inhibition Activities against the SARS-CoV-2 Papain-like Protease. ACS omega 7 (51) (2022)
Na Liu, Yichi Zhang, Yingshou Lei, Rui Wang, Meimiao Zhan, Jianbo Liu, Yuhao An, Yaoqi Zhou, Jian Zhan, Feng Yin, Zigang Li
Design and Evaluation of a Novel Peptide-Drug Conjugate Covalently Targeting SARS-CoV-2 Papain-like Protease. Journal of medicinal chemistry 65 (1) (2022)
Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip Paliwal, Yaoqi Zhou
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. Bioinformatics (Oxford, England) 38 (7) (2022)
Xin Chen, Ke Chen, Zhaoyong Zhang, Peilan Wei, Lu Zhang, Yunxia Xu, Qili Lun, Yanhong Ma, Fang Wu, Ying Zhang, Yanqun Wang, Jincun Zhao, Yaoqi Zhou, Jian Zhan, Wei Xu
Investigating Derivatives of Tanshinone IIA Sulfonate Sodium and Chloroxine for Their Inhibition Activities against the SARS-CoV-2 Papain-like Protease. ACS omega 7 (51) (2022)
Anil Kumar Hanumanthappa, Jaswinder Singh, Kuldip Paliwal, Jaspreet Singh, Yaoqi Zhou
Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. Bioinformatics (Oxford, England) 36 (21) (2021)
Shujuan Jin, Jian Zhan, Yaoqi Zhou
Argonaute proteins: structures and their endonuclease activity. Molecular biology reports 48 (5) (2021)
Peng Xiong, Ruibo Wu, Jian Zhan, Yaoqi Zhou
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement. Nature communications 12 (1) (2021)
Jaswinder Singh, Kuldip Paliwal, Jaspreet Singh, Yaoqi Zhou
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks. Journal of chemical information and modeling 61 (6) (2021)
Wyatt T Clark, Laura Kasak, Constantina Bakolitsa, Zhiqiang Hu, Gaia Andreoletti, Giulia Babbi, Yana Bromberg, Rita Casadio, Roland L Dunbrack, Lukas Folkman, Colby T Ford, David Jones, Panagiostis Katsonis, Kunal Kundu, Olivier Lichtarge, Pier Luigi Martelli, Sean D Mooney, Conor Nodzak, Lipika R Pal, Predrag Radivojac, Castrense Savojardo, Xinghua Shi, Yaoqi Zhou, Aneeta Uppal, Qifang Xu, Yizhou Yin, Vikas Pejaver, Meng Wang, Liping Wei, John Moult, Guoying Karen Yu, Steven E Brenner, Jonathan H LeBowitz
Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Human mutation 40 (9) (2020)
Aimee Tan, Luke V Blakeway, null Taha, Yuedong Yang, Yaoqi Zhou, John M Atack, Ian R Peak, Kate L Seib
Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease. PloS one 15 (6) (2020)
Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. Journal of cheminformatics 11 (1) (2019)
Zanxia Cao, Xiumei Zhang, Chunling Wang, Lei Liu, Liling Zhao, Jihua Wang, Yaoqi Zhou
Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations. The Journal of chemical physics 150 (8) (2019)
Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. Journal of computational chemistry 41 (8) (2019)
Thomas Litfin, Yuedong Yang, Yaoqi Zhou
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. Journal of chemical information and modeling 59 (2) (2019)
Jaswinder Singh, Jack Hanson, Kuldip Paliwal, Yaoqi Zhou
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nature communications 10 (1) (2019)
Bailing Zhou, Yuedong Yang, Jian Zhan, Xianghua Dou, Jihua Wang, Yaoqi Zhou
Predicting functional long non-coding RNAs validated by low throughput experiments. RNA biology 16 (11) (2019)
Rhys Heffernan, Kuldip Paliwal, James Lyons, Jaswinder Singh, Yuedong Yang, Yaoqi Zhou
Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. Journal of computational chemistry 39 (26) (2018)
Zanxia Cao, Yunqiang Bian, Guodong Hu, Liling Zhao, Zhenzhen Kong, Yuedong Yang, Jihua Wang, Yaoqi Zhou
Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids. International journal of molecular sciences 19 (3) (2018)
Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip Paliwal, Yuedong Yang, Yaoqi Zhou
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. Journal of chemical information and modeling 58 (9) (2018)
Liling Zhao, Zanxia Cao, Yunqiang Bian, Guodong Hu, Jihua Wang, Yaoqi Zhou
Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers. International journal of molecular sciences 19 (4) (2018)
Joe Tiralongo, Oren Cooper, Tom Litfin, Yuedong Yang, Rebecca King, Jian Zhan, Huiying Zhao, Nicolai Bovin, Christopher J Day, Yaoqi Zhou
YesU from Bacillus subtilis preferentially binds fucosylated glycans. Scientific reports 8 (1) (2018)
Ghazaleh Taherzadeh, Yuedong Yang, Haodong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. Journal of computational chemistry 39 (22) (2018)
James O'Connell, Zhixiu Li, Jack Hanson, Rhys Heffernan, James Lyons, Kuldip Paliwal, Abdollah Dehzangi, Yuedong Yang, Yaoqi Zhou
SPIN2: Predicting sequence profiles from protein structures using deep neural networks. Proteins 86 (6) (2018)
Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang
B-factor profile prediction for RNA flexibility using support vector machines. Journal of computational chemistry 39 (8) (2017)
Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. BMC bioinformatics 18 (1) (2017)
Clara Jegousse, Yuedong Yang, Jian Zhan, Jihua Wang, Yaoqi Zhou
Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA. PloS one 12 (9) (2017)
Yuedong Yang, Jian Zhan, Yaoqi Zhou
SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. Journal of computational chemistry 37 (18) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Yaoqi Zhou