A two-stage classifier for identification of protein-protein interface residues. - Changhui Yan; Drena Dobbs; Vasant G. Honavar (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. - Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan; Changhui Yan; Vasant G. Honavar; Kai-Ming Ho; Cai-Zhuang Wang; Yungok Ihm; Haibo Cao; Xun Gu; Drena Dobbs (BMC Bioinform., 2004)

Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach. - Changhui Yan; Vasant G. Honavar; Drena Dobbs (Neural Comput. Appl., 2004)

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and Rna Binding Sites in Rev Proteins of Hiv-1 and Eiav Agree with Experimental Data - Michael Terribilini; Jae-Hyung Lee; Changhui Yan; Robert L. Jernigan; Susan Carpenter; Vasant G. Honavar; Drena Dobbs (CoRR, 2005)

A Hidden Markov Model Approach to Identifying HTH Motifs Using Protein Sequence and Predicted Solvent Accessibility. - Changhui Yan; Jing Hu 001 (CIBCB, 2006)

A Hidden Markov Model Approach to Model Protein Sequence and Structural Information: Identification of Helix-Turn-Helix DNA-Binding Motif. - Changhui Yan (GrC, 2006)

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data. - Michael Terribilini; Jae-Hyung Lee; Changhui Yan; Robert L. Jernigan; Susan Carpenter (Pacific Symposium on Biocomputing, 2006)

Predicting DNA-binding sites of proteins from amino acid sequence. - Changhui Yan; Michael Terribilini; Feihong Wu; Robert L. Jernigan; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2006)

Predicting Protein Subcelluar Localizations Using Weighted Euclidian Distance. - Jing Hu 001; Changhui Yan (BIBE, 2007)

Toward The Recognition Code Of Protein-DNA Recognition. - Juan Shan; Yuxuan Wang; Changhui Yan (BIBE, 2007)

Mining sequence features for DNA-binding site prediction. - Jing Hu 001; Changhui Yan (CIBCB, 2008)

Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information. - Jing Hu 001; Changhui Yan (BMC Bioinform., 2008)

Discrimination of outer membrane proteins with improved performance. - Changhui Yan; Jing Hu 001; Yingfeng Wang (BMC Bioinform., 2008)

A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes. - Jing Hu 001; Changhui Yan (Comput. Biol. Chem., 2008)

Protein subcelluar localisation prediction with improved performance. - Jing Hu 001; Changhui Yan (Int. J. Funct. Informatics Pers. Medicine, 2008)

Discrimination of disease-related non-synonymous single nucleotide polymorphisms using multi-scale RBF kernel fuzzy support vector machine. - Wen Ju; Juan Shan; Changhui Yan; Heng-Da Cheng (Pattern Recognit. Lett., 2009)

A Comparison between Transmembrane Helices and Reentrant Loops. - Changhui Yan; Jingru Luo (BIBE, 2010)

Exploring structural modeling of proteins for kernel-based enzyme discrimination. - Marco A. Alvarez; Changhui Yan (CIBCB, 2010)

A shortest-path graph kernel for estimating gene product semantic similarity. - Marco A. Alvarez; Xiaojun Qi; Changhui Yan (J. Biomed. Semant., 2011)

A Graph-Based Semantic Similarity Measure for the gene Ontology. - Marco A. Alvarez; Changhui Yan (J. Bioinform. Comput. Biol., 2011)

A nearest neighbor method for predicting solenoid proteins. - Wen Cheng; Malinda Sanjaka; Changhui Yan (GrC, 2012)

A new protein graph model for function prediction. - Marco A. Alvarez; Changhui Yan (Comput. Biol. Chem., 2012)

Graph methods for protein-nucleotide interactions. - Changhui Yan; Wen Cheng (BCB, 2014)

Graph methods for predicting the function of chemical compounds. - Ya Zhu; Changhui Yan (GrC, 2014)

A graph kernel method for DNA-binding site prediction. - Changhui Yan; Yingfeng Wang (BMC Syst. Biol., 2014)

Mining graph patterns in the protein-RNA interfaces. - Wen Cheng; Changhui Yan (BIBM, 2015)

Mining structure patterns on the protein-DNA interfaces. - Qing Sun; Changhui Yan (BIBM, 2016)

A Graph Approach to Mining Biological Patterns in the Binding Interfaces. - Wen Cheng; Changhui Yan (J. Comput. Biol., 2017)

An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis. - Yuan Liu; Yongchao Ma; Evan Salsman; Frank A. Manthey; Elias M. Elias; Xuehui Li; Changhui Yan (J. Bioinform. Comput. Biol., 2019)

A Novel Spatial Feature For Predicting Lysine Malonylation Sites Using Machine Learning. - Yuan Liu; Changhui Yan (BIBM, 2020)

Impacts of reference selection on the assembly of suspicious coronavirus genome. - Yuan Liu; Changhui Yan (J. Bioinform. Comput. Biol., 2021)

Evolution Of SARS-CoV-2 In The Presence Of Vaccines. - Vishwajeet Marathe; Changhui Yan (BIBM, 2022)

Detection of Violent Scenes in Cartoon Movies Using a Deep Learning Approach. - Noreen Fayyaz Khan; Sareer Ul Amin; Zahoor Jan; Changhui Yan (IEEE Access, 2024)

VirusT5: Harnessing Large Language Models to Predicting SARS-CoV-2 Evolution. - Vishwajeet Marathe; Deewan Bajracharya; Changhui Yan (CoRR, 2024)