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  		  Articles
  • Sean J. Humphrey, Guang Yang, Pengyi Yang, Daniel J. Fazakerley, Jacqueline Stockli, Jean Y. Yang, and David E James, Dynamic adipocyte phosphoproteome reveals Akt directly regulates mTORC2, Cell Metabolism, In Press, Corrected Proof [fulltext]

  • Pengyi Yang, Paul D. Yoo, Juanita Fernando, Bing B. Zhou, Zili Zhang, and Albert Y. Zomaya, Sample subset optimization techniques for imbalanced and ensemble learning problems in bioinformatics applications, IEEE Transactions on Cybernetics, accepted (note: previously known as IEEE Transactions on Systems, Man, and Cybernetics Part B: Cybernetics; Acceptance rate: ~7%) [manuscript]

    Practical contribution: this study unify several of our previous work on imbalanced sampling and ensemble learning. This includes (1) Yang et al., A particle swarm based hybrid system for imbalanced medical data sampling, BMC Genomics, 10(Suppl 3):S34, 2009; and (2) Yang et al., Sample subsets optimization for classifying imbalanced biological data, In: Proceedings of PAKDD, LNAI 6635, 333-344, 2011.
    Source code available from:     https://code.google.com/p/sample-subset-optimization/
  • Pengyi Yang, Sean J. Humphrey, Daniel J. Fazakerley, Matthew J. Prior, Guang Yang, David E. James, and Jean Yee-Hwa Yang, Re-Fraction: a machine learning approach for deterministic identification of protein homologs and splice variants in large-scale MS-based proteomics, Journal of Proteome Research, 11(5):3035-3045, 2012. [fulltext] [manuscript]

    Available from: http://code.google.com/p/re-fraction/
  • Penghao Wang, Pengyi Yang, Jean Yee-Hwa Yang, OCAP: An Open Comprehensive Analysis Pipeline for iTRAQ, Bioinformatics, 28(10):1404-1405, 2012. [fulltext]

    Available from: http://code.google.com/p/ocap/
  • Pengyi Yang, Jia Ma, Penghao Wang, Yunping Zhu, Bing B. Zhou, Yee Hwa Yang, Improving X!Tandem on peptide identification from mass spectrometry by self-boosted Percolator, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5):1273-1280, 2012. [manuscript]

    Practical contribution: providing a complete pipeline for processing X!Tandem database search results. Access the software from: http://code.google.com/p/self-boosted-percolator/
  • Pengyi Yang, Joshua W.K. Ho, Yee Hwa Yang, Bing B. Zhou, Gene-gene interaction filtering with ensemble of filters, BMC Bioinformatics, 12(Suppl 1):S10, 2011. [fulltext], [presentation video]

    Practical contribution: providing a filtering approach that is more robust and more powerful in filtering gene-gene interaction from GWA dataset. Capable of filtering millions of SNPs. Access the software from: http://code.google.com/p/ensemble-of-filters/
  • Pengyi Yang, Yee Hwa Yang, Bing B. Zhou, Albert Y. Zomaya, A review of ensemble methods in bioinformatics, Current Bioinformatics, vol. 5, pp. 296-308, 2010. [fulltext] [manuscript]
  • Pengyi Yang, Joshua W.K. Ho, Albert Y. Zomaya, Bing B. Zhou, A genetic ensemble approach for gene-gene interaction identification, BMC Bioinformatics, 11:524, 2010. (highly accessed). [fulltext] [software]

    Practical contribution: providing a useful approach for pinpoint gene-gene interaction from filtered GWA dataset. It is now re-implemented with parallel execution capacity, which offers many folds of speedup. Access the software from: http://code.google.com/p/genetic-ensemble-snpx/
  • Paul D. Yoo, Yung S. Ho, Jason Ng, Michael Charleston, Nitin K. Saksena, Pengyi Yang, Albert Y. Zomaya, Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 Profiles, BMC Genomics, 11(Suppl 4):S22, 2010. [fulltext] [dataset]
  • Penghao Wang, Pengyi Yang, Jonathan Arthur, Jean Yee Hwa Yang, A dynamic wavelet-based algorithm for pre-processing mass spectrometry data, Bioinformatics, vol. 26, no. 18, pp. 2242-2249, 2010. [fulltext] [software]

    Practical contribution: providing a software for spectrum prefiltering of mass spectrometry data. Access the software from: http://code.google.com/p/dywave/
  • Pengyi Yang, Zili Zhang, Bing B. Zhou, Albert Y. Zomaya, A clustering based hybrid system for biomarker selection and sample classification of mass spectrometry data, Neurocomputing, vol. 73, pp. 2317-2331, 2010. [fulltext] [software]
  • Pengyi Yang, Bing B. Zhou, Zili Zhang, Albert Y. Zomaya, A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data, BMC Bioinformatics, 11(Suppl 1):S5, 2010. [fulltext] [software]
  • Pengyi Yang, Liang Xu, Bing B. Zhou, Zili Zhang, Albert Y. Zomaya, A particle swarm based hybrid system for imbalanced medical data sampling, BMC Genomics, 10(Suppl 3):S34, 2009. [fulltext] [software]

    Practical contribution: providing a software for sampling from imbalanced data using sample subset optimization technique: http://code.google.com/p/imbalanced-data-sampling/

  • Pengyi Yang and Zili Zhang, An embedded two-layer feature selection approach for microarray data analysis, IEEE Intelligent Informatics Bulletin, vol. 10, pp. 24-32, 2009. [pdf]
  • Zili Zhang, Pengyi Yang, Xindong Wu and Chengqi Zhang, An agent-based hybrid system for microarray data analysis, IEEE Intelligent Systems, vol. 24, no. 5, pp. 53-63, 2009. [pdf]
  • Zili Zhang and Pengyi Yang, An ensemble of classifiers with genetic algorithm based feature selection, IEEE Intelligent Informatics Bulletin, vol. 9, pp. 18-24, 2008. [pdf]

Proceedings

  • Pengyi Yang, Wei Liu, Bing B. Zhou, Sanjay Chawla, Albert Y. Zomaya, Ensemble-based wrapper methods for feature selection and class imbalance learning, In: Proceedings of the 17th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), LNAI 7818, 544-555, 2013. [fulltext], [manuscript]

  • Pengyi Yang, Zili Zhang, Bing B. Zhou, Albert Y. Zomaya, Sample subsets optimization for classifying imbalanced biological data, In: Proceedings of the 15th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), LNAI 6635, 333-344, 2011. [fulltext], [manuscript]

    • Practical contribution: build the theoretical foundation for sample subset optimization (SSO) technique, which is utilized for sampling from imbalanced data: http://code.google.com/p/imbalanced-data-sampling/

  • Li Li, Pengyi Yang, Ling Qu, Zili Zhang, Peng Cheng, Genetic algorithm-based multi-objective optimisation for QoS-Aware web services composition, In: Proceedings of the 4th International Conference on Knowledge Science, Engineering and Management, LNAI 6291, pp. 549-554, 2010. [fulltext]
  • Pengyi Yang, Li Tao, Liang Xu and Zili Zhang, Multiagent framework for bio-data mining, In: Proceedings of the 4th Rough Set and Knowledge Technology, LNCS 5589, pp. 200-207, 2009. [published version (pdf)], [full version (pdf)]
  • Pengyi Yang and Zili Zhang, A clustering based hybrid system for mass spectrometry data analysis, In: Proceedings of Pattern Recognition in Bioinformatics (PRIB), LNBI 5265, pp. 98-109, 2008. (PRIB 2008 Travel Award Paper). [pdf]
  • Pengyi Yang and Zili Zhang, A hybrid approach to selecting susceptible single nucleotide polymorphisms for complex disease analysis, In: Proceedings of BioMedical and Engineering Informatics, IEEE, pp. 214-218, 2008. [pdf]
  • Pengyi Yang and Zili Zhang, Hybrid methods to select informative gene sets in microarray data classification, In: Proceedings of the 20th Australian Conference on Artificial Intelligence, LNAI 4830, pp. 811-815, 2007. [pdf]

Book Chapters

  • Pengyi Yang, Yee Hwa Yang, Bing B. Zhou, Albert Y. Zomaya, Stability of feature selection algorithms and ensemble feature selection methods in bioinformatics, In: Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Wiley-Blackwell, John Wiley & Sons Ltd., New Jersey, USA, 2013. [ manuscript pdf]

Posters

  • Pengyi Yang, Penghao Wang, Bing B. Zhou, Yee Hwa Yang, Studying false positive identifications in target-decoy search of mass spectrometry-based proteomics, Human Proteome World Congress 2010 (HUPO), Sydney, Australia.
  • Pengyi Yang and Bing B. Zhou, A clustering based hybrid system for mass spectrometry data analysis, EII PhD School 2009, The University of Queensland, Brisbane, Australia. (Highly Commended Award poster) [pdf]