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2020 – today
- 2024
[j67]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. Genom. Proteom. Bioinform. 22(1) (2024)- 2023
- [j66]Bailing Zhou, Maolin Ding, Jing Feng, Baohua Ji, Pingping Huang, Junye Zhang, Xue Yu, Zanxia Cao, Yuedong Yang, Yaoqi Zhou, Jihua Wang:
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. Briefings Bioinform. 24(1) (2023) - [j65]Yidong Song, Qianmu Yuan, Sheng Chen, Ken Chen, Yaoqi Zhou, Yuedong Yang:
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. Briefings Bioinform. 24(4) (2023) - [j64]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:
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51(W1): 62-69 (2023) - [j63]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 Comput. Biol. 19(12) (2023) - 2022
- [j62]Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan:
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Briefings Bioinform. 23(3) (2022) - [j61]Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou:
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. Bioinform. 38(7): 1888-1894 (2022) - [j60]Jaswinder Singh, Kuldip K. 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. Bioinform. 38(16): 3900-3910 (2022) - 2021
- [j59]Anil Kumar Hanumanthappa, Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou:
Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. Bioinform. 36(21): 5169-5176 (2021) - [j58]Jaswinder Singh, Kuldip K. Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin, Yaoqi Zhou:
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. Bioinform. 37(17): 2589-2600 (2021) - [j57]Jaspreet Singh, Thomas Litfin, Kuldip K. Paliwal, Jaswinder Singh, Anil Kumar Hanumanthappa, Yaoqi Zhou:
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. 37(20): 3464-3472 (2021) - [j56]Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip K. Paliwal, Yaoqi Zhou:
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. Bioinform. 37(20): 3494-3500 (2021) - [j55]Shide Liang, Zhixiu Li, Jian Zhan, Yaoqi Zhou:
De novo protein design by an energy function based on series expansion in distance and orientation dependence. Bioinform. 38(1): 86-93 (2021) - [j54]Qianmu Yuan, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang:
Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinform. 38(1): 125-132 (2021) - [j53]Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou:
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks. J. Chem. Inf. Model. 61(6): 2610-2622 (2021) - [j52]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:
DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 49(Database-Issue): D298-D308 (2021) - [j51]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:
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 49(Database-Issue): D86-D91 (2021) - [c2]Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang:
DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM 2021: 118-124 - [c1]Jaspreet Singh, Jaswinder Singh, Kuldip K. Paliwal, Andrew Busch, Yaoqi Zhou:
SPOT-1D2: Improving Protein Secondary Structure Prediction using High Sequence Identity Training Set and an Ensemble of Recurrent and Residual-convolutional Neural Networks. CIBCB 2021: 1-7 - 2020
- [j50]Peter Brown, Yaoqi Zhou:
Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database J. Biol. Databases Curation 2020 (2020) - [j49]Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou:
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. Bioinform. 36(4): 1107-1113 (2020) - [j48]Kai Wang, Nan Lyu, Hongjuan Diao, Shujuan Jin, Tao Zeng, Yaoqi Zhou, Ruibo Wu:
GM-DockZn: a geometry matching-based docking algorithm for zinc proteins. Bioinform. 36(13): 4004-4011 (2020) - [j47]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. J. Comput. Biol. 27(5): 796-814 (2020) - [j46]Tongchuan Zhang, Guodong Hu, Yuedong Yang, Jihua Wang, Yaoqi Zhou:
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. J. Comput. Biol. 27(6): 856-867 (2020) - [j45]Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. J. Comput. Chem. 41(8): 745-750 (2020)
2010 – 2019
- 2019
- [j44]Peter Brown, RELISH Consortium, Yaoqi Zhou:
Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database J. Biol. Databases Curation 2019: baz085 (2019) - [j43]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
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. 35(14): 2403-2410 (2019) - [j42]Ghazaleh Taherzadeh, Abdollah Dehzangi, Maryam Golchin, Yaoqi Zhou, Matthew P. Campbell:
SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties. Bioinform. 35(20): 4140-4146 (2019) - [j41]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou:
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. Genom. Proteom. Bioinform. 17(6): 645-656 (2019) - [j40]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. J. Cheminformatics 11(1): 52:1-52:11 (2019) - [j39]Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. J. Chem. Inf. Model. 59(2): 924-930 (2019) - [j38]Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong:
Improved fragment sampling for ab initio protein structure prediction using deep neural networks. Nat. Mach. Intell. 1(8): 347-355 (2019) - 2018
- [j37]Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou:
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Briefings Bioinform. 19(3): 482-494 (2018) - [j36]Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang:
Structure-based prediction of protein- peptide binding regions using Random Forest. Bioinform. 34(3): 477-484 (2018) - [j35]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. Bioinform. 34(23): 4039-4045 (2018) - [j34]Jianzhao Gao, Yuedong Yang, Yaoqi Zhou:
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. 19(1): 29:1-29:8 (2018) - [j33]Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang:
B-factor profile prediction for RNA flexibility using support vector machines. J. Comput. Chem. 39(8): 407-411 (2018) - [j32]Ghazaleh Taherzadeh, Yuedong Yang, Hao-Dong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou:
Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. J. Comput. Chem. 39(22): 1757-1763 (2018) - [j31]Rhys Heffernan, Kuldip K. Paliwal, James G. Lyons, Jaswinder Singh, Yuedong Yang, Yaoqi Zhou:
Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. J. Comput. Chem. 39(26): 2210-2216 (2018) - [j30]Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip K. Paliwal, Yuedong Yang, Yaoqi Zhou:
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. J. Chem. Inf. Model. 58(9): 2033-2042 (2018) - [j29]Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou:
Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures. J. Chem. Inf. Model. 58(11): 2369-2376 (2018) - [j28]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:
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 46(Database-Issue): D100-D105 (2018) - 2017
- [j27]Tong Wang, Yuedong Yang, Yaoqi Zhou, Haipeng Gong:
LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. Bioinform. 33(5): 677-684 (2017) - [j26]Jack Hanson, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou:
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinform. 33(5): 685-692 (2017) - [j25]Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinform. 33(8): 1238-1240 (2017) - [j24]Rhys Heffernan, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou:
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. 33(18): 2842-2849 (2017) - [j23]Jia-Feng Yu, Xianghua 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 Bioinform. 18(1): 206:1-206:5 (2017) - [j22]Peter Brown, Yuedong Yang, Yaoqi Zhou, Wayne J. Pullan:
A heuristic for the time constrained asymmetric linear sum assignment problem. J. Comb. Optim. 33(2): 551-566 (2017) - 2016
- [j21]Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou:
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinform. 32(3): 370-377 (2016) - [j20]Rhys Heffernan, Abdollah Dehzangi, James G. Lyons, Kuldip K. Paliwal, Alok Sharma, Jihua Wang, Abdul Sattar, Yaoqi Zhou, Yuedong Yang:
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinform. 32(6): 843-849 (2016) - [j19]Jianzhao Gao, Yuedong Yang, Yaoqi Zhou:
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. Bioinform. 32(24): 3768-3773 (2016) - [j18]Yuedong Yang, Yaoqi Zhou:
Effective protein conformational sampling based on predicted torsion angles. J. Comput. Chem. 37(11): 976-980 (2016) - [j17]Md. Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou:
sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. J. Comput. Chem. 37(12): 1119-1124 (2016) - [j16]Ghazaleh Taherzadeh, Yuedong Yang, Tuo Zhang, Alan Wee-Chung Liew, Yaoqi Zhou:
Sequence-based prediction of protein-peptide binding sites using support vector machine. J. Comput. Chem. 37(13): 1223-1229 (2016) - [j15]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. J. Comput. Chem. 37(18): 1734-1739 (2016) - [j14]Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang:
Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. J. Chem. Inf. Model. 56(10): 2123 (2016) - 2015
- [j13]Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou:
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. 31(10): 1599-1606 (2015) - 2014
- [j12]Shide Liang, Chi Zhang, Yaoqi Zhou:
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. 35(4): 335-341 (2014) - [j11]James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip K. Paliwal, Abdul Sattar, Yaoqi Zhou, Yuedong Yang:
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J. Comput. Chem. 35(28): 2040-2046 (2014) - [j10]Huiying Zhao, Yuedong Yang, Mark von Itzstein, Yaoqi Zhou:
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. J. Comput. Chem. 35(30): 2177-2183 (2014) - 2012
- [j9]Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, Yaoqi Zhou:
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. 33(3): 259-267 (2012) - 2011
- [j8]Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou:
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. 27(15): 2076-2082 (2011) - [j7]Marcin J. Mizianty, Tuo Zhang, Bin Xue, Yaoqi Zhou, A. Keith Dunker, Vladimir N. Uversky, Lukasz A. Kurgan:
In-silico prediction of disorder content using hybrid sequence representation. BMC Bioinform. 12: 245 (2011) - [j6]Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley:
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J. Comput. Chem. 32(8): 1680-1686 (2011) - 2010
- [j5]Huiying Zhao, Yuedong Yang, Yaoqi Zhou:
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinform. 26(15): 1857-1863 (2010)
2000 – 2009
- 2005
- [j4]Hongyi Zhou, Yaoqi Zhou:
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinform. 21(18): 3615-3621 (2005) - [j3]Hongzhi Li, Yaoqi Zhou:
Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function. J. Bioinform. Comput. Biol. 3(5): 1151-1170 (2005) - [j2]Hongzhi Li, Yaoqi Zhou:
SCUD: Fast structure clustering of decoys using reference state to remove overall rotation. J. Comput. Chem. 26(11): 1189-1192 (2005) - [j1]Hongyi Zhou, Chi Zhang, Song Liu, Yaoqi Zhou:
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. 33(Web-Server-Issue): 193-197 (2005)
Coauthor Index
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