Jianyi Yang

40 papers Journal 38Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
RNA language model and graph attention network for RNA and small molecule binding sites prediction.
Bioinform.
Saisai Sun, Jianyi Yang, Lin Gao, Pengyong Li, Yumeng Liu
2025 J jnl
Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning.
J. Chem. Inf. Model.
Qiuyi Lyu, Hong Wei, Shuaishuai Chen, Zhenling Peng, Jianyi Yang
2024 J jnl
FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.
Genom. Proteom. Bioinform.
Junhai Qi, Chenjie Feng, Yulin Shi, Jianyi Yang, Fa Zhang, Guojun Li, Renmin Han
2024 J jnl
Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions.
Genom. Proteom. Bioinform.
Hong Wei, Wenkai Wang, Zhenling Peng, Jianyi Yang
2024 J jnl
RNA threading with secondary structure and sequence profile.
Bioinform.
Zongyang Du, Zhenling Peng, Jianyi Yang
2023 J jnl
A unified approach to protein domain parsing with inter-residue distance matrix.
Bioinform.
Kun Zhu, Hong Su, Zhenling Peng, Jianyi Yang
2023 J jnl
CryoAlign: feature-based method for global and local 3D alignment of EM density maps.
CoRR
Bintao He, Fa Zhang, Chenjie Feng, Jianyi Yang, Xin Gao, Renmin Han
2022 J jnl
On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang
2022 J jnl
Single-sequence protein structure prediction using supervised transformer protein language models.
Nat. Comput. Sci.
Wenkai Wang, Zhenling Peng, Jianyi Yang
2022 J jnl
Toward the assessment of predicted inter-residue distance.
Bioinform.
Zongyang Du, Zhenling Peng, Jianyi Yang
2021 J jnl
Human host status inference from temporal microbiome changes via recurrent neural networks.
Briefings Bioinform.
Xingjian Chen, Lingjing Liu, Weitong Zhang, Jianyi Yang, Ka-Chun Wong
2021 J jnl
Improved estimation of model quality using predicted inter-residue distance.
Bioinform.
Lisha Ye, Peikun Wu, Zhenling Peng, Jianzhao Gao, Jian Liu, Jianyi Yang
2021 J jnl
RNA Flexibility Prediction With Sequence Profile and Predicted Solvent Accessibility.
IEEE ACM Trans. Comput. Biol. Bioinform.
Hong Wei, Boling Wang, Jianyi Yang, Jianzhao Gao
2021 J jnl
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks.
Bioinform.
Saisai Sun, Wenkai Wang, Zhenling Peng, Jianyi Yang
2021 J jnl
Recognition of small molecule-RNA binding sites using RNA sequence and structure.
Bioinform.
Hong Su, Zhenling Peng, Jianyi Yang
2020 J jnl
CATHER: a novel threading algorithm with predicted contacts.
Bioinform.
Zongyang Du, Shuo Pan, Qi Wu, Zhenling Peng, Jianyi Yang
2020 J jnl
Protein contact prediction using metagenome sequence data and residual neural networks.
Bioinform.
Qi Wu, Zhenling Peng, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang
2019 J jnl
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles.
Bioinform.
Saisai Sun, Qi Wu, Zhenling Peng, Jianyi Yang
2019 J jnl
Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods.
Bioinform.
Hong Su, Mengchen Liu, Saisai Sun, Zhenling Peng, Jianyi Yang
2018 J jnl
A large-scale comparative assessment of methods for residue-residue contact prediction.
Briefings Bioinform.
Qiqige Wuyun, Wei Zheng, Zhenling Peng, Jianyi Yang
2018 J jnl
COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking.
Nucleic Acids Res.
Qi Wu, Zhenling Peng, Yang Zhang, Jianyi Yang
2018 J jnl
CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction.
Bioinform.
Qiaozhen Meng, Zhenling Peng, Jianyi Yang
2018 J jnl
Improving Sequence-Based Prediction of Protein-Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method.
J. Chem. Inf. Model.
Zijuan Zhao, Zhenling Peng, Jianyi Yang
2018 J jnl
mTM-align: a server for fast protein structure database search and multiple protein structure alignment.
Nucleic Acids Res.
Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang
2018 J jnl
mTM-align: an algorithm for fast and accurate multiple protein structure alignment.
Bioinform.
Runze Dong, Zhenling Peng, Yang Zhang, Jianyi Yang
2017 J jnl
An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier.
Bioinform.
Jiaqi Xia, Zhenling Peng, Dawei Qi, Hongbo Mu, Jianyi Yang
2017 J jnl
DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method.
Bioinform.
Qi Wu, Zu-Guo Yu, Jianyi Yang
2017 J jnl
Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions.
J. Chem. Inf. Model.
Yang Li, Jianyi Yang
2016 J jnl
Recognizing metal and acid radical ion-binding sites by integrating
Bioinform.
Xiuzhen Hu, Qiwen Dong, Jianyi Yang, Yang Zhang
2015 J jnl
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations.
Bioinform.
Wallace K. B. Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey R. Brender, Junguk Hur, Arzucan Özgür, Yang Zhang
2015 J jnl
I-TASSER server: new development for protein structure and function predictions.
Nucleic Acids Res.
Jianyi Yang, Yang Zhang
2013 J jnl
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.
Nucleic Acids Res.
Jianyi Yang, Ambrish Roy, Yang Zhang
2013 J jnl
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment.
Bioinform.
Jianyi Yang, Ambrish Roy, Yang Zhang
2012 J jnl
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.
Nucleic Acids Res.
Ambrish Roy, Jianyi Yang, Yang Zhang
2011 — conf
A Consensus Approach to Predicting Protein Contact Map via Logistic Regression.
ISBRA
Jianyi Yang, Xin Chen
2010 J jnl
An improved classification of G-protein-coupled receptors using sequence-derived features.
BMC Bioinform.
Zhen-Ling Peng, Jianyi Yang, Xin Chen
2010 J jnl
Constructing Consensus Genetic Maps in Comparative Analysis.
J. Comput. Biol.
Xin Chen, Jianyi Yang
2010 J jnl
Prediction of protein structural classes for low-homology sequences based on predicted secondary structure.
BMC Bioinform.
Jianyi Yang, Zhen-Ling Peng, Xin Chen
2008 J jnl
Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides.
BMC Bioinform.
Jianyi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, Li-Qian Zhou
2008 — conf
Protein Structure Classification Based on Chaos Game Representation and Multifractal Analysis.
ICNC (4)
Jianyi Yang, Zu-Guo Yu, Vo Anh