Protein Structure Classification Based on Chaos Game Representation and Multifractal Analysis. - Jianyi Yang 002; Zu-Guo Yu; Vo Anh (ICNC (4), 2008)

Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides. - Jianyi Yang 002; Yu Zhou; Zu-Guo Yu; Vo Anh; Li-Qian Zhou (BMC Bioinform., 2008)

An improved classification of G-protein-coupled receptors using sequence-derived features. - Zhen-Ling Peng; Jianyi Yang 002; Xin Chen 037 (BMC Bioinform., 2010)

Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. - Jianyi Yang 002; Zhen-Ling Peng; Xin Chen 037 (BMC Bioinform., 2010)

Constructing Consensus Genetic Maps in Comparative Analysis. - Xin Chen 037; Jianyi Yang 002 (J. Comput. Biol., 2010)

A Consensus Approach to Predicting Protein Contact Map via Logistic Regression. - Jianyi Yang 002; Xin Chen 037 (ISBRA, 2011)

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. - Ambrish Roy; Jianyi Yang 002; Yang Zhang 040 (Nucleic Acids Res., 2012)

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. - Jianyi Yang 002; Ambrish Roy; Yang Zhang 040 (Bioinform., 2013)

BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. - Jianyi Yang 002; Ambrish Roy; Yang Zhang 040 (Nucleic Acids Res., 2013)

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. - Wallace K. B. Chan; Hongjiu Zhang; Jianyi Yang 002; Jeffrey R. Brender; Junguk Hur; Arzucan Özgür; Yang Zhang 040 (Bioinform., 2015)

I-TASSER server: new development for protein structure and function predictions. - Jianyi Yang 002; Yang Zhang 040 (Nucleic Acids Res., 2015)

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. - Xiuzhen Hu; Qiwen Dong; Jianyi Yang 002; Yang Zhang 040 (Bioinform., 2016)

DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method. - Qi Wu 016; Zu-Guo Yu; Jianyi Yang 002 (Bioinform., 2017)

An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier. - Jiaqi Xia; Zhenling Peng; Dawei Qi; Hongbo Mu; Jianyi Yang 002 (Bioinform., 2017)

Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions. - Yang Li 042; Jianyi Yang 002 (J. Chem. Inf. Model., 2017)

A large-scale comparative assessment of methods for residue-residue contact prediction. - Qiqige Wuyun; Wei Zheng 013; Zhenling Peng; Jianyi Yang 002 (Briefings Bioinform., 2018)

mTM-align: an algorithm for fast and accurate multiple protein structure alignment. - Runze Dong; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Bioinform., 2018)

CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction. - Qiaozhen Meng; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2018)

Improving Sequence-Based Prediction of Protein-Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method. - Zijuan Zhao; Zhenling Peng; Jianyi Yang 002 (J. Chem. Inf. Model., 2018)

mTM-align: a server for fast protein structure database search and multiple protein structure alignment. - Runze Dong; Shuo Pan; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Nucleic Acids Res., 2018)

COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. - Qi Wu 016; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Nucleic Acids Res., 2018)

Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods. - Hong Su; Mengchen Liu; Saisai Sun; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2019)

Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles. - Saisai Sun; Qi Wu 016; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2019)

CATHER: a novel threading algorithm with predicted contacts. - Zongyang Du; Shuo Pan; Qi Wu 016; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2020)

Protein contact prediction using metagenome sequence data and residual neural networks. - Qi Wu 016; Zhenling Peng; Ivan Anishchenko; Qian Cong; David Baker 001; Jianyi Yang 002 (Bioinform., 2020)

Human host status inference from temporal microbiome changes via recurrent neural networks. - Xingjian Chen; Lingjing Liu; Weitong Zhang; Jianyi Yang 002; Ka-Chun Wong (Briefings Bioinform., 2021)

Recognition of small molecule-RNA binding sites using RNA sequence and structure. - Hong Su; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2021)

RNA inter-nucleotide 3D closeness prediction by deep residual neural networks. - Saisai Sun; Wenkai Wang; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2021)

Improved estimation of model quality using predicted inter-residue distance. - Lisha Ye; Peikun Wu; Zhenling Peng; Jianzhao Gao; Jian Liu; Jianyi Yang 002 (Bioinform., 2021)

RNA Flexibility Prediction With Sequence Profile and Predicted Solvent Accessibility. - Hong Wei; Boling Wang; Jianyi Yang 002; Jianzhao Gao (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Toward the assessment of predicted inter-residue distance. - Zongyang Du; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2022)

Single-sequence protein structure prediction using supervised transformer protein language models. - Wenkai Wang; Zhenling Peng; Jianyi Yang 002 (Nat. Comput. Sci., 2022)

On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions. - Yajun Dai; Yang Li 042; Liping Wang; Zhenling Peng; Jianyi Yang 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

CryoAlign: feature-based method for global and local 3D alignment of EM density maps. - Bintao He; Fa Zhang 001; Chenjie Feng; Jianyi Yang 002; Xin Gao 001; Renmin Han (CoRR, 2023)

A unified approach to protein domain parsing with inter-residue distance matrix. - Kun Zhu 023; Hong Su; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2023)

FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval. - Junhai Qi; Chenjie Feng; Yulin Shi; Jianyi Yang 002; Fa Zhang 001; Guojun Li; Renmin Han (Genom. Proteom. Bioinform., 2024)

Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions. - Hong Wei; Wenkai Wang; Zhenling Peng; Jianyi Yang 002 (Genom. Proteom. Bioinform., 2024)

RNA threading with secondary structure and sequence profile. - Zongyang Du; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2024)