Notations:


✢: Co-first author
†: Corresponding/Co-corresponding author

Key publications


Cinghu, S.✢, Yang, P.✢, Kosak, J., Conway, A., Kumar, D., Oldfield, A., Adelman, K. & Jothi, R. (2017) Intragenic enhancers attenuate host gene expression. Molecular Cell, 68(1), 104–117. [Full Text], [PDF]
• highlighted in Nature Reviews Genetics, doi:10.1038/nrg.2017.90, 2017. [fulltext]
• also highlighted in Nature Reviews Molecular Cell Biology, doi:10.1038/nrm.2017.111, 2017. [fulltext]

Yang, P.†, Oldfield, A., Kim, T., Yang, A., Yang, J. & Ho, J.† (2017) Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. Bioinformatics, 33(13), 1916–1920. [Full Text], [PDF]

Yang, P.†, Humphrey, S., James, D., Yang, J. & Jothi, R.† (2016). Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinformatics, 32(2), 252-259. [Pubmed], [PDF], [Predictions]

Oldfield, A.✢, Yang, P.✢, Conway, A., Cinghu, S., Freudenberg, J., Yellaboina, S. & Jothi, R. (2014). Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors. Molecular Cell, 55(5), 708-722. [Pubmed], [PDF]

Yang, P.✢, Patrick, E.✢, Tan, S., Fazakerley, D., Burchfield, J., Gribben, C., Prior, M., James, D. & Yang, J. (2014). Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. Bioinformatics, 30(6), 808-814. [Pubmed], [PDF]

Humphrey, S., Yang, G., Yang, P., Fazakerley, D. J., Stöckli, J., Yang, J. & James, D. (2013). Dynamic adipocyte phosphoproteome reveals that Akt directly regulates mTORC2. Cell Metabolism, 17(6), 1009-1020. [Pubmed], [PDF]

All publications


2018

Systems biology:
Fazakerley, DJ., Chaudhuri, R., Yang, P., Maghzal, GJ., Thomas, KC., Krycer, JR., Humphrey, SJ., Parker, BL., Fisher-Wellman, KH., Meoli, CC., Hoffman, NJ., Diskin, C., Burchfield, JG., Cowley, MJ., Kaplan, W., Modrusan, Z., Kolumam, G., Yang, JYH, Chen, DL., Samocha-Bonet, D., Greenfield, JR., Hoehn, KL., Stocker, R. & James, DE. (2018) Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. eLIFE, 7, e32111. [Full Text]

Methodology and tools:
Yang, P.†, Ormerod, J., Liu, W., Ma, C., Zomaya, A., Yang, J.(2018) AdaSampling for positive-unlabeled and label noise learning with bioinformatics applications. IEEE Transactions on Cybernetics, accepted. doi:10.1109/TCYB.2018.2816984 [PDF], [Repo]

2017

Systems biology:
Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Speed, T., Yang J.†, Yang, P.† (2017) Housekeeping genes, revisited at the single-cell level. doi: https://doi.org/10.1101/229815 [PDF], [human HK genes] [mouse HK genes]

Cinghu, S.✢, Yang, P.✢, Kosak, J., Conway, A., Kumar, D., Oldfield, A., Adelman, K. & Jothi, R. (2017) Intragenic enhancers attenuate host gene expression. Molecular Cell, 68(1), 104–117. [Full Text], [PDF]

Norris, DM.✢, Yang, P.✢, Krycer JR., Fazakerley DJ, James, DE. & Burchfield JG.† (2017) An improved Akt reporter reveals intra- and inter- cellular heterogeneity and oscillations in signal transduction. Journal of Cell Science, 130, 2757-2766. [PDF]

Yang, P.†, Oldfield, A., Kim, T., Yang, A., Yang, J. & Ho, J.† (2017) Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. Bioinformatics, 33(13), 1916–1920. [Full Text], [PDF]

Methodology and tools:
Yang, P., Liu, W. & Yang, J. (2017) Positive unlabeled learning via wrapper-based adaptive sampling. Proceedings of the 26th International Joint Conference on Artificial Intelligence (IJCAI), Pre-print [PDF]

2016

Systems biology:
Zheng, X., Yang, P., Lackford, B., Bennett, B., Wang, L., Li, H., Wang, Y., Miao, Y., Foley, J., Fargo, D., Jin, Y., Williams, C., Jothi, R. & Hu, G. (2016) CNOT3-dependent mRNA deadenylation safeguards the pluripotent state. Stem Cell Reports, 7(5), 897-910. [Text], [PDF]

Minard, A., Tan, S., Yang, P., Fazakerley, D., Domanova, W., Parker, B., Humphrey, S., Jothi, R., Stöckli. J. & James. D. (2016) mTORC1 is a major regulatory node in the FGF21 signaling network in adipocytes. Cell Reports, 17(1), 29-36. [Pubmed]

Methodology and tools:
Yang, P., Patrick, E., Humphrey, S., Ghazanfar, S., James, D., Jothi, R. & Yang, J. (2016). KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis. Proteomics, 16(13), 1868-1871. [Text], [Online tool]

Yang, P.†, Humphrey, S., James, D., Yang, J. & Jothi, R.† (2016). Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinformatics, 32(2), 252-259. [Pubmed], [PDF], [Predictions]

Lu, C., Wang, J., Zhang, Z., Yang, P. & Yu, G. (2016). NoisyGOA: Noisy GO annotations prediction using taxonomic and semantic similarity. Computational Biology and Chemistry, 65, 203-211.

Domanova, W., Krycer, J., Chaudhuri, R., Yang, P., Vafaee, F., Fazakerley, D., Humphrey, S., James, D. & Kuncic, Z., (2016). Unraveling kinase activation dynamics using kinase-substrate relationships from temporal large-scale phosphoproteomics studies. PLoS One, 11(6), e0157763.

2015

Systems biology:
Pathania, R., Ramachandran, S., Elangovan, S., Padia, R., Yang, P., Cinghu, S., Veeranan-Karmegam, R., Fulzele, S., Pei, L., Chang, C., Choi, J., Shi, H., Manicassamy, S., Prasad, P., Sharma, S., Ganapathy, V., Jothi, R. & Thangaraju, M. (2015). DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nature Communications, 6, 6910. [Pubmed]

Hoffman, N., Parker, B., Chaudhuri, R., Fisher-Wellman, K., Kleinert, M., Humphrey, S., Yang, P., Holliday, M., Trefely, S., Fazakerley, D., Stockli, J., Burchfield, J., Jensen, T., Jothi, R., Kiens, B., Wojtaszewski, J., Richter, E. & James, D. (2015). Global phosphoproteomic analysis of human skeletal muscle reveals a network of exercise-regulated kinases and AMPK substrates. Cell Metabolism, 22(5), 922-935. [Pubmed]

Methodology and tools:
Yang, P.†, Zheng, X., Jayaswal, V., Hu, G., Yang, J. & Jothi, R. (2015). Knowledge-based analysis for detecting key signaling events from time-series phosphoproteomics data. PLoS Computational Biology, 11(8), e1004403. [Pubmed], [PDF]

2014

Systems biology:
Oldfield, A.✢, Yang, P.✢, Conway, A., Cinghu, S., Freudenberg, J., Yellaboina, S. & Jothi, R. (2014). Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors. Molecular Cell, 55(5), 708-722. [Pubmed], [PDF]

Ma, X., Yang, P., Kaplan, W., Lee, B., Wu, L., Yang, J., Yasunaga, M., Sato, K., Chisholm, D. & James, D. (2014). ISL1 regulates peroxisome proliferator-activated receptor γ activation and early adipogenesis via bone morphogenetic protein 4-dependent and -independent mechanisms. Molecular and Cellular Biology, 34(19), 3607-3617. [Pubmed]

Lackford, B., Yao, C., Charles, G., Weng, L., Zheng, X., Choi, E., Xie, X., Wan, J., Xing, Y., Freudenberg, J., Yang, P., Jothi, R., Hu, G. & Shi, Y. (2014). Fip1 regulates mRNA alternative polyadenylation to promote stem cell self‐renewal. EMBO Journal, 33(8), 878-889. [Pubmed]

Methodology and tools:
Yang, P.✢, Patrick, E.✢, Tan, S., Fazakerley, D., Burchfield, J., Gribben, C., Prior, M., James, D. & Yang, J. (2014). Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. Bioinformatics, 30(6), 808-814. [Pubmed], [PDF]

Yang, P.†, Yoo, P., Fernando, J., Zhou, B., Zhang, Z. & Zomaya, A. (2014). Sample subset optimization techniques for imbalanced and ensemble learning problems in bioinformatics applications. IEEE Transactions on Cybernetics, 44(3), 445-455. [IEEE Xplore] [PDF] [Software]

2013

Systems biology:
Humphrey, S., Yang, G., Yang, P., Fazakerley, D. J., Stöckli, J., Yang, J. & James, D. (2013). Dynamic adipocyte phosphoproteome reveals that Akt directly regulates mTORC2. Cell Metabolism, 17(6), 1009-1020. [Pubmed], [PDF]

Methodology and tools:
Yang, P., Liu, W., Zhou, B., Chawla, S. & Zomaya, A. (2013). 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),  Lecture Notes in Artificial Intelligence 7818, Springer Berlin Heidelberg, 544-555. [Text]

Yang, P., Yang, J., Zhou, B. & Zomaya. A. (2013). 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, New Jersey, USA, 333-352. [PDF]

2012

Yang, P., Humphrey, S., Fazakerley, D., Prior, M., Yang, G., James, D. & Yang, J. (2012). Re-fraction: a machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics. Journal of Proteome Research, 11(5), 3035-3045. [Pubmed], [PDF]

Yang, P.†, Ma, J., Wang, P., Zhu, Y., Zhou, B. & Yang, J. (2012). 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. [Pubmed], [PDF]

Wang, P., Yang, P. & Yang, J. (2012). OCAP: an open comprehensive analysis pipeline for iTRAQ. Bioinformatics, 28(10), 1404-1405. [Pubmed]

2011

Yang, P.✢, †, Ho, J.✢, Yang, J. & Zhou, B. (2011). Gene-gene interaction filtering with ensemble of filters. BMC Bioinformatics, 12, S10. [Pubmed]

Yang, P., Zhang, Z., Zhou, B. & Zomaya, A. (2011). Sample subset optimization for classifying imbalanced biological data. In Proceedings of the 15th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD),  Lecture Notes in Artificial Intelligence 6635, Springer Berlin Heidelberg, 333-344. [Text]

2010

Yang, P.†, Ho, J., Zomaya, A. & Zhou, B. (2010). A genetic ensemble approach for gene-gene interaction identification. BMC Bioinformatics, 11(1), 524. [Pubmed]

Wang, P., Yang, P., Arthur, J. & Yang, J. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [Pubmed]

Yoo, P., Ho, Y., Ng, J., Charleston, M., Saksena, N., Yang, P. & Zomaya, A. (2010). Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles. BMC Genomics, 11, S22. [Pubmed]

Yang, P.†, Zhang, Z., Zhou, B. & Zomaya, A. (2010). A clustering based hybrid system for biomarker selection and sample classification of mass spectrometry data. Neurocomputing, 73(13), 2317-2331. [Text]

Yang, P.†, Zhou, B., Zhang, Z. & Zomaya, A. (2010). A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data. BMC Bioinformatics, 11, S5. [Pubmed]

Yang, P., Yang, J., Zhou, B. & Zomaya, A. (2010). A review of ensemble methods in bioinformatics. Current Bioinformatics, 5(4), 296-308. [Text], [PDF]

Li, L., Yang, P., Ou, L., Zhang, Z. & Cheng, P. (2010). 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 (KSEM), Lecture Notes in Computer Science 6291, Springer Berlin Heidelberg, 549-554. [Text]

2009

Yang, P.†, Xu, L., Zhou, B., Zhang, Z. & Zomaya, A. (2009). A particle swarm based hybrid system for imbalanced medical data sampling. BMC Genomics, 10, S34. [Pubmed]

Zhang, Z., Yang, P., Wu, X. & Zhang, C. (2009). An agent-based hybrid system for microarray data analysis. IEEE Intelligent Systems, 24(5), 53-63. [PDF]

Yang, P.† & Zhang, Z. (2009). An embedded two-layer feature selection approach for microarray data analysis. IEEE Intelligent Informatics Bulletin, 10(1), 24-32. [PDF]

Yang, P., Tao, L., Xu, L. & Zhang, Z. (2009). Multiagent framework for bio-data mining. In Proceedings of the 4th Rough Sets and Knowledge Technology (RSKT), Lecture Notes in Computer Science 5589, Springer Berlin Heidelberg, 200-207. [Text]

2008

Zhang, Z. & Yang, P.† (2008). An ensemble of classifiers with genetic algorithm-based feature selection. IEEE Intelligent Informatics Bulletin, 9(1), 18-24. [PDF]

Yang, P. & Zhang, Z. (2008). A clustering based hybrid system for mass spectrometry data analysis. In Proceedings of the 3rd Pattern Recognition in Bioinformatics (PRIB), Lecture Notes in Bioinformatics 5265, Springer Berlin Heidelberg, 98-109. [Text]

Yang, P. & Zhang, Z. (2008). A hybrid approach to selecting susceptible single nucleotide polymorphisms for complex disease analysis. In Proceedings of BioMedical Engineering and Informatics (BMEI), IEEE, 214-218. [PDF]

2007

Yang, P. & Zhang, Z. (2007). Hybrid methods to select informative gene sets in microarray data classification. In Proceedings of the 20th Australian Joint Conference on Artificial Intelligence (AI), Lecture Notes in Artificial Intelligence 4830, Springer Berlin Heidelberg, 811-815. [Text]