Hybrid Methods to Select Informative Gene Sets in Microarray Data Classification. - Pengyi Yang; Zili Zhang 001 (Australian Conference on Artificial Intelligence, 2007)

A Hybrid Approach to Selecting Susceptible Single Nucleotide Polymorphisms for Complex Disease Analysis. - Pengyi Yang; Zili Zhang 001 (BMEI (1), 2008)

A Clustering Based Hybrid System for Mass Spectrometry Data Analysis. - Pengyi Yang; Zili Zhang 001 (PRIB, 2008)

An Ensemble of Classifiers with Genetic Algorithm Based Feature Selection. - Zili Zhang 001; Pengyi Yang (IEEE Intell. Informatics Bull., 2008)

Multiagent Framework for Bio-data Mining. - Pengyi Yang; Li Tao; Liang Xu; Zili Zhang 001 (RSKT, 2009)

An Embedded Two-Layer Feature Selection Approach for Microarray Data Analysis. - Pengyi Yang; Zili Zhang 001 (IEEE Intell. Informatics Bull., 2009)

An Agent-Based Hybrid System for Microarray Data Analysis. - Zili Zhang 001; Pengyi Yang; Xindong Wu 001; Chengqi Zhang (IEEE Intell. Syst., 2009)

Genetic Algorithm-Based Multi-objective Optimisation for QoS-Aware Web Services Composition. - Li Li 006; Pengyi Yang; Ling Ou; Zili Zhang 001; Peng Cheng 011 (KSEM, 2010)

A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. - Penghao Wang; Pengyi Yang; Jonathan Arthur; Jean Yee Hwa Yang (Bioinform., 2010)

A genetic ensemble approach for gene-gene interaction identification. - Pengyi Yang; Joshua Wing Kei Ho; Albert Y. Zomaya; Bing Bing Zhou (BMC Bioinform., 2010)

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data. - Pengyi Yang; Bing Bing Zhou; Zili Zhang 001; Albert Y. Zomaya (BMC Bioinform., 2010)

A clustering based hybrid system for biomarker selection and sample classification of mass spectrometry data. - Pengyi Yang; Zili Zhang 001; Bing Bing Zhou; Albert Y. Zomaya (Neurocomputing, 2010)

Sample Subset Optimization for Classifying Imbalanced Biological Data. - Pengyi Yang; Zili Zhang 001; Bing Bing Zhou; Albert Y. Zomaya (PAKDD (2), 2011)

Gene-gene interaction filtering with ensemble of filters. - Pengyi Yang; Joshua Wing Kei Ho; Jean Yee Hwa Yang; Bing Bing Zhou (BMC Bioinform., 2011)

OCAP: an open comprehensive analysis pipeline for iTRAQ. - Penghao Wang; Pengyi Yang; Jean Yee Hwa Yang (Bioinform., 2012)

Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator. - Pengyi Yang; Jie Ma; Penghao Wang; Yunping Zhu; Bing Bing Zhou; Jean Yee Hwa Yang (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Ensemble-Based Wrapper Methods for Feature Selection and Class Imbalance Learning. - Pengyi Yang; Wei Liu 007; Bing Bing Zhou; Sanjay Chawla; Albert Y. Zomaya (PAKDD (1), 2013)

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. - Pengyi Yang; Ellis Patrick; Shi-Xiong Tan; Daniel J. Fazakerley; James G. Burchfield; Christopher Gribben; Matthew J. Prior; David E. James; Yee Hwa Yang (Bioinform., 2014)

Sample Subset Optimization Techniques for Imbalanced and Ensemble Learning Problems in Bioinformatics Applications. - Pengyi Yang; Paul D. Yoo; Juanita I. Fernando; Bing Bing Zhou; Zili Zhang 001; Albert Y. Zomaya (IEEE Trans. Cybern., 2014)

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. - Pengyi Yang; Xiaofeng Zheng; Vivek Jayaswal; Guang Hu; Jean Yee Hwa Yang; Raja Jothi (PLoS Comput. Biol., 2015)

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. - Pengyi Yang; Sean J. Humphrey; David E. James; Yee Hwa Yang; Raja Jothi (Bioinform., 2016)

NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity. - Chang Lu; Jun Wang 035; Zili Zhang 001; Pengyi Yang; Guo-Xian Yu (Comput. Biol. Chem., 2016)

Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. - Katie Wilkins; Mehedi Hassan; Margherita Francescatto; Jakob B. Jespersen; R. Gonzalo Parra; Bart Cuypers; Dan F. DeBlasio; Alexander Junge; Anupama Jigisha; Farzana Rahman; Griet Laenen; Sander Willems; et al. (BMC Bioinform., 2016)

Positive unlabeled learning via wrapper-based adaptive sampling. - Pengyi Yang; Wei Liu 007; Jean Yee Hwa Yang (IJCAI, 2017)

Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. - Pengyi Yang; Andrew J. Oldfield; Taiyun Kim; Andrian Yang; Jean Yee Hwa Yang; Joshua Wing Kei Ho (Bioinform., 2017)

New Parallel Algorithms for All Pairwise Computation on Large HPC Clusters. - Tao Tang; Hao Wu; Wei Bao 001; Pengyi Yang; Dong Yuan 001; Bing Bing Zhou (PDCAT, 2019)

Impact of similarity metrics on single-cell RNA-seq data clustering. - Taiyun Kim; Irene Rui Chen; Yingxin Lin; Andy Yi-Yang Wang; Jean Yee Hwa Yang; Pengyi Yang (Briefings Bioinform., 2019)

scDC: single cell differential composition analysis. - Yue Cao; Yingxin Lin; John T. Ormerod; Pengyi Yang; Jean Yee Hwa Yang; Kitty K. Lo (BMC Bioinform., 2019)

An Uncertainty Visual Analytics Framework for fMRI Functional Connectivity. - Michael de Ridder; Karsten Klein 001; Jean Yee Hwa Yang; Pengyi Yang; Jim Lagopoulos; Ian B. Hickie; Max Bennett; Jinman Kim (Neuroinformatics, 2019)

AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications. - Pengyi Yang; John T. Ormerod; Wei Liu 007; Chendong Ma; Albert Y. Zomaya; Jean Yee Hwa Yang (IEEE Trans. Cybern., 2019)

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis. - Thomas Andrew Geddes; Taiyun Kim; Lihao Nan; James G. Burchfield; Jean Yee Hwa Yang; Dacheng Tao; Pengyi Yang (BMC Bioinform., 2019)

CiteFuse enables multi-modal analysis of CITE-seq data. - Hani Jieun Kim; Yingxin Lin; Thomas Andrew Geddes; Jean Yee Hwa Yang; Pengyi Yang (Bioinform., 2020)

Ensemble deep learning in bioinformatics. - Yue Cao; Thomas Andrew Geddes; Jean Yee Hwa Yang; Pengyi Yang (Nat. Mach. Intell., 2020)

Feature selection revisited in the single-cell era. - Pengyi Yang; Hao Huang; Chunlei Liu (CoRR, 2021)

Uncovering cell identity through differential stability with Cepo. - Hani Jieun Kim; Kevin Y. X. Wang; Carissa Chen; Yingxin Lin; Patrick P. L. Tam; David M. Lin; Jean Y. H. Yang; Pengyi Yang (Nat. Comput. Sci., 2021)

Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. - Di Xiao; Hani Jieun Kim; Ignatius Pang; Pengyi Yang (Bioinform., 2022)

scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. - Yue Cao; Yingxin Lin; Ellis Patrick; Pengyi Yang; Jean Yee Hwa Yang (Bioinform., 2022)

Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. - Yue Cao; Shila Ghazanfar; Pengyi Yang; Jean Y. H. Yang (Briefings Bioinform., 2023)

Interpretable deep learning in single-cell omics. - Manoj M. Wagle; Siqu Long; Carissa Chen; Chunlei Liu; Pengyi Yang (CoRR, 2024)