Associate Professor Jean Yang

F07 - Carslaw Building
The University of Sydney

Telephone 9351 3012
Fax 9351 4534

Website Personal web page

Teaching and supervision

Timetable

Selected grants

2013

  • Vertically integrated statistical modelling in multi-layered omics studies; Yang Y, Muller S, Mann G; Australian Research Council (ARC)/Discovery Projects (DP).

2012

  • Heads or tails - which did echinoderms lose in the evolution of radial symmetry?; Wray G, Byrne M, Yang Y; Australian Research Council (ARC)/Discovery Projects (DP).

2010

  • New statistical methods for identifying microRNA regulatory network.; Yang Y; Australian Research Council (ARC)/Future Fellowships (FT).

2009

  • Functional Genomics to Predict and Enhance Response to Interferon; George J, Suppiah V, Kingston D, Bahlo M, Yang Y, McKay F, Booth D, Stewart G, Bahlo M; Australian Research Council (ARC)/Linkage Projects (LP).
  • Statistical and computational methods using a multiscale approach for protein identification and quantification; Yang Y, Raimondo M, Stewart M, Arthur J; Australian Research Council (ARC)/Discovery Projects (DP).

2007

  • Statistical methods and tools for integrative microarray analysis; Yang Y; Australian Research Council (ARC)/Discovery Projects (DP).
  • Statistical methods for identifying regulatory microRNA from gene expression data; Yang Y; University of Sydney/Newly Appointed Staff.

2006

  • Advanced Bioinformatics Teaching Facility; Arthur J, Triccas J, Jermiin L, Charleston M, Yang Y, Britton W; DVC Research/Teaching Equipment Grant (Sesqui).

Selected publications

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Book Chapters

  • Yang, Y. (2008). Microarrays - Planning your experiment. In Ronald J.A. Trent (Eds.), Clinical Bioinformatics: Methods in Molecular Medicine, (pp. 71-85). New Jersey: Humana Press.
  • Yang, Y., Paquet, A. (2005). Preprocessing Two-Color Spotted Arrays. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (Eds.), Bioinformatics and Computational Biology Solutions using R and Bioconductor, (pp. 49-70). New York: Springer.
  • Yang, Y., Speed, T. (2003). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger (Eds.), The Analysis of Gene Expression Data: Methods and Software, (pp. 73-101). New York: Springer.
  • Yang, Y., Speed, T. (2003). Design and Analysis of Comparative Microarray Experiments. In T. P. Speed (Eds.), Statistical Analysis of Gene Expression Microarray Data, (pp. 35-92). Chapman & Hall.
  • Yang, Y., Thorne, N. (2003). Normalization for Two-color cDNA Microarray Data. In Darlene R Goldstein (Eds.), Science and Statistics: A Festschrift for Terry Speed, (pp. 403-418). Beachwood, Ohio: Institute of Mathematical Statistics.
  • Smyth, G., Yang, Y., Speed, T. (2003). Statistical issues in cDNA microarray data analysis. In M. J. Brownstein and A. B. Khodursky (Eds.), Functional Genomics: Methods and Protocols, (pp. 111-136). New Jersey: Humana Press.
  • Ball, C., Chen, Y., Panavally, S., Sherlock, G., Speed, T., Spellman, P., Yang, Y. (2002). An introduction to microarray bioinformatics. In D. Bowtell and J. Sambrook (Eds.), DNA Microarrays: A Molecular Cloning Manual, (pp. 509-602). New York: Cold Spring Harbor Laboratory Press.

Journals

  • Oates, J., Casikar, I., Campain, A., Muller, S., Yang, Y., Reid, S., Condous, G. (2013). A prediction model for viability at the end of the first trimester after a single early pregnancy evaluation. Australian and New Zealand Journal of Obstetrics and Gynaecology, 53(1), 51-57. [More Information]
  • Mann, G., Pupo, G., Campain, A., Carter, C., Schramm, S., Pianova, S., Gerega, S., Desilva, C., Lai, K., Wilmott, J., Hersey, P., Kefford, R., Thompson, J., Yang, Y., Scolyer, R., et al (2013). BRAF Mutation, NRAS Mutation, and the Absence of an Immune-Related Expressed Gene Profile Predict Poor Outcome in Patients with Stage III Melanoma. The Journal of Investigative Dermatology, 133(2), 509-517. [More Information]
  • Strbenac, D., Armstrong, N., Yang, Y. (2013). Correction: Detection and classification of peaks in 5' cap RNA sequencing data. BMC Genetics, 14(1), Art. 767-1. [More Information]
  • Strbenac, D., Armstrong, N., Yang, Y. (2013). Detection and classification of peaks in 5’ cap RNA sequencing data. BMC Genomics, 14(Suppl 5), 1-11. [More Information]
  • Chung, S., Shen, W., Jayawardana, K., Wang, P., Yang, Y., Shackel, N., Gillies, M. (2013). Differential gene expression profiling after conditional müller-cell ablation in a novel transgenic model. Investigative Ophthalmology and Visual Science, 54(3), 2142-2152. [More Information]
  • Schramm, S., Li, S., Jayaswal, V., Fung, D., Campain, A., Pang, C., Scolyer, R., Yang, Y., Mann, G., Wilkins, M. (2013). Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden. Pigment Cell and Melanoma Research, 26(5), 708-722. [More Information]
  • Humphrey, S., Yang, G., Yang, P., Fazakerley, D., Stockli, J., Yang, Y., James, D. (2013). Dynamic adipocyte phosphoproteome reveals that akt directly regulates mTORC2. Cell Metabolism, 17(6), 1009-1020. [More Information]
  • Patrick, E., Buckley, M., Yang, Y. (2013). Estimation of data-specific constitutive exons with RNA-Seq data. BMC Bioinformatics, 14(31), 1-10. [More Information]
  • Patrick, E., Buckley, M., Lin, D., Yang, Y. (2013). Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information. BMC Genomics, 14(Suppl 1), S1-S9. [More Information]
  • Schramm, S., Jayaswal, V., Goel, A., Li, S., Yang, Y., Mann, G., Wilkins, M. (2013). Molecular interaction networks for the analysis of human disease: utility, limitations, and considerations. Proteomics, 13(23-24), 3393-3405. [More Information]
  • Neff, C., Yang, Y. (2013). Shark bites and public attitudes: Policy implications from the first before and after shark bite survey. Marine Policy, 38, 545-547. [More Information]
  • Jayaswal, V., Schramm, S., Mann, G., Wilkins, M., Yang, Y. (2013). VAN: an R package for identifying biologically perturbed networks via differential variability analysis. BMC Research Notes, 6(1), 1-9. [More Information]
  • Yang, Y., Markus, M., Mangs, H., Raitskin, O., Sperling, R., Morris, B. (2013). ZRANB2 localizes to supraspliceosomes and influences the alternative splicing of multiple genes in the transcriptome. Molecular Biology Reports, 40(9), 5381-5395. [More Information]
  • Yang, P., Ma, J., Wang, P., Zhu, Y., Zhou, B., Yang, Y. (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. [More Information]
  • Jayaswal, V., Lutherborrow, M., Yang, Y. (2012). Measures of Association for Identifying MicroRNA-mRNA Pairs of Biological Interest. PLoS One, 7(1), e29612-1-e29612-10. [More Information]
  • Bryant, A., Palma, C., Jayaswal, V., Yang, Y., Lutherborrow, M., Ma, D. (2012). miR-10a is aberrantly overexpressed in Nucleophosmin1 mutated acute myeloid leukaemia and its suppression induces cell death. Molecular Cancer, 11(8), 1-9. [More Information]
  • Wang, P., Yang, P., Yang, Y. (2012). OCAP: an open comprehensive analysis pipeline for iTRAQ. Bioinformatics, 28(10), 1404-1405. [More Information]
  • Yang, P., Humphrey, S., Fazakerley, D., Prior, M., Yang, G., James, D., Yang, Y. (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. [More Information]
  • Schramm, S., Campain, A., Scolyer, R., Yang, Y., Mann, G. (2012). Review and Cross-Validation of Gene Expression Signatures and Melanoma Prognosis. The Journal of Investigative Dermatology, 132(2), 274-283. [More Information]
  • Loi, T., Campain, A., Bryant, A., Molloy, T., Lutherborrow, M., Turner, J., Yang, Y., Ma, D. (2011). Discriminating lymphomas and reactive lymphadenopathy in lymph node biopsies by gene expression profiling. BMC Medical Genomics, 4(27), 1-10. [More Information]
  • Lutherborrow, M., Bryant, A., Jayaswal, V., Agapiou, D., PALMA, C., Yang, Y., Ma, D. (2011). Expression Profiling of Cytogenetically Normal Acute Myeloid Leukemia Identifies MicroRNAs that Target Genes Involved in Monocytic Differentiation. American Journal Of Hematology, 86(1), 2-11. [More Information]
  • Marques, F., Campain, A., Tomaszewski, M., Zukowska-Szczechowska, E., Yang, Y., Charchar, F., Morris, B. (2011). Gene Expression Profiling Reveals Renin mRNA Overexpression in Human Hypertensive Kidneys and a Role for MicroRNAs. Hypertension, 58(6), 1093-1098. [More Information]
  • Yang, P., Ho, J., Yang, Y., Zhou, B. (2011). Gene-gene interaction filtering with ensemble of filters. BMC Bioinformatics, 12(Supp 1: S10), 1-10. [More Information]
  • Marques, F., Campain, A., Davern, P., Yang, Y., Head, G., Morris, B. (2011). Genes Influencing Circadian Differences in Blood Pressure in Hypertensive Mice. PLoS One, 6(4), e19203-1-e19203-9. [More Information]
  • Wu, J., Dwyer, D., Dyer, W., Yang, Y., Wang, B., Saksena, N. (2011). Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease. Retrovirology, 8(18), 1-21. [More Information]
  • Marques, F., Campain, A., Davern, P., Yang, Y., Head, G., Morris, B. (2011). Global identification of the genes and pathways differentially expressed in hypothalamus in early and established neurogenic hypertension. Physiological Genomics, 43(12), 766-771. [More Information]
  • Jayaswal, V., Lutherborrow, M., Ma, D., Yang, Y. (2011). Identification of microRNA-mRNA modules using microarray data. BMC Genomics, 12(138), 1-32. [More Information]
  • Collinson, E., Wimmer-Kleikamp, S., Gerega, S., Yang, Y., Parish, C., Dawes, I., Stocker, R. (2011). The Yeast Homolog of Heme Oxygenase-1 Affords Cellular Antioxidant Protection via the Transcriptional Regulation of Known Antioxidant Genes. Journal of Biological Chemistry, 286(3), 2205-2214. [More Information]
  • Peters, T., Bulger, D., Loi, T., Yang, Y., Ma, D. (2011). Two-Step Cross-Entropy Feature Selection For Microarrays-Power Through Complementarity. IEEE - ACM Transactions on Computational Biology and Bioinformatics, 8(4), 1148-1151. [More Information]
  • Wang, P., Yang, P., Arthur, J., Yang, Y. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [More Information]
  • Yang, P., Yang, Y., Zhou, B., Zomaya, A. (2010). A Review of Ensemble Methods in Bioinformatics. Current Bioinformatics, 5(4), 296-308.
  • Jensen, S., Apisiridej, S., Kwong, S., Yang, Y., Skurray, R., Firth, N. (2010). Analysis of the prototypical Staphylococcus aureus multiresistance plasmid pSK1. Plasmid, 64(3), 135-142. [More Information]
  • Campain, A., Yang, Y. (2010). Comparison study of microarray meta-analysis methods. BMC Bioinformatics, 11(408), 1-11.
  • Marques, F., Campain, A., Yang, Y., Morris, B. (2010). Meta-Analysis of Genome-Wide Gene Expression Differences in Onset and Maintenance Phases of Genetic Hypertension. Hypertension, 56(2), 319-324. [More Information]
  • Karim, R., Gerega, S., Yang, Y., Spillane, A., Carmalt, H., Scolyer, R., Lee, C. (2010). p16 and pRb immunohistochemical expression increases with increasing tumour grade in mammary phyllodes tumours. Histopathology, 56(7), 868-875. [More Information]
  • Jayaswal, V., Lutherborrow, M., Ma, D., Yang, Y. (2009). Identification of microRNAs with regulatory potential using a matched microRNA -mRNA time-course data. Nucleic Acids Research, 37(8), e60-e60. [More Information]
  • Karim, R., Gerega, S., Yang, Y., Spillane, A., Carmalt, H., Scolyer, R., Lee, C. (2009). Phyllodes tumours of the breast: a clinicopathological analysis of 65 cases from a single institution. The Breast, 18(3), 165-170. [More Information]
  • Karim, R., Gerega, S., Yang, Y., Horvath, L., Spillane, A., Carmalt, H., Scolyer, R., Lee, C. (2009). Proteins from the Wnt pathway are involved in the pathogenesis and progression of mammary phyllodes tumours. Journal of Clinical Pathology, 62(11), 1016-1020. [More Information]
  • Karim, R., Li, W., Sanki, A., Colman, M., Yang, Y., Thompson, J., Scolyer, R. (2009). Reduced p16 and increased cyclin D1 and pRb expression are correlated with progression in cutaneous melanocytic tumors. International Journal of Surgical Pathology, 17(5), 361-367. [More Information]
  • Lewis, C., Yang, Y., Huang, X., Banerjee, S., Balckburn, M., Baluk, P., McDonald, D., Blackwell, T., Nagabhushanam, V., Peters, W., et al (2008). Disease specific gene expression profiling in multiple models of lung disease. American Journal of Respiratory and Critical Care Medicine, 177(4), 376-387.
  • Kechris, K., Yang, Y., Yeh, R. (2008). Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. BMC Genomics, 9(SUPPL. 2, Article number 551), 1-15.
  • Wu, J., Dwyer, D., Dyer, W., Yang, Y., Wang, B., Saksena, N. (2008). Transcriptional profiles in CD8+ T cells from HIV+ progressors on HAART are characterized by coordinated up-regulation of oxidative phosphorylation enzymes and interferon responses. Virology, 380(1), 124-135. [More Information]
  • Xiao, Y., Segal, M., Yang, Y., Yeh, R. (2007). A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics, 23(12), 1459-1467.
  • Winn, V., Haimov-Kochman, R., Paquet, A., Yang, Y., Madhusudhan, M., Gormley, M., Feng, K., Bernlohr, D., McDonagh, S., Pereira, L., et al (2007). Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology, 148(3), 1059-1079.
  • Woodruff, P., Boushey, H., Dolganov, G., Barker, C., Yang, Y., Donnelly, S., Ellwanger, A., Sidhu, S., Dao-Pick, T., Pantoja, C., et al (2007). Genome-wide profiling identifies elpithelial cell genes associated with asthma and with treatment response to corticosteroids. Proceedings of the National Academy of Sciences (PNAS), 104(40), 15858-15863.
  • Williams, E., Xiao, Y., Sickles, H., Shafer, P., Yona, G., Yang, Y., Lin, D. (2007). Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers. BMC Developmental Biology, 7(article no. 48), 1-15.
  • Woodruff, P., Koth, L., Yang, Y., Rodriguez, M., Favoreto, S., Dolganov, G., Paquet, A., Erle, D. (2005). A distinctive alveolar macrophage activation state induced by cigarette smoking. American Journal of Respiratory and Critical Care Medicine, 172(11), 1383-1392.
  • Xiao, Y., Yang, Y., Burckin, T., Shiue, L., Hartzog, G., Segal, M. (2005). Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing. PLoS Computational Biology, 1(4), e39-0276-e39-0288. [More Information]
  • Kuperman, D., Lewis, C., Woodruff, P., Rodriguez, M., Yang, Y., Dolganov, G., Fahy, J., Erle, D. (2005). Dissecting asthma using focused transgenic modeling and functional genomics. Journal of Allergy and Clinical Immunology, 116(2), 305-311. [More Information]
  • Gonzalez, R., Griffin, C., Yang, Y., Allen, L., Tigue, Z., Dobbs, L. (2005). Freshly isolated rat alveolar type I cells, type II cells, and cultured type II cells have distinct molecular phenotypes. American Journal of Physiology: Lung Cellular and Molecular Physiology, 288(1), L179-L189.
  • Yang, Y., Xiao, Y., Segal, M. (2005). Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics, 21(7), 1084-1093.
  • Barker, C., Griffin, C., Dolganov, G., Hanspers, K., Yang, Y., Erle, D. (2005). Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics, 6(57), 57- 1-57- 8.
  • Xiao, Y., Segal, M., Yang, Y. (2005). Stepwise Normalization of Two-Channel Spotted Microarrays. Statistical Applications in Genetics and Molecular Biology, 4(1), 4-1-4-29.
  • Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Yang, Y., et al (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biology, 5(10), R80.1-R80.16.
  • Rodriguez, M., Paquet, A., Yang, Y., Erle, D. (2004). Differential gene expression by integrin ß7+ and ß7-memory T helper cells. BMC Immunology, 5(13), 1-11.
  • Lin, D., Yang, Y., Scolnick, J., Brunet, L., Marsh, H., Peng, V., Okazaki, Y., Hayashizaki, Y., Speed, T., Ngai, J. (2004). Spatial patterns of gene expression in the olfactory bulb. Proceedings of the National Academy of Sciences (PNAS), 101(34), 12718-12723.
  • Diaz, E., Yang, Y., Ferreira, T., Loh, K., Okazaki, Y., Hayashizaki, Y., Tessier-Lavigne, M., Speed, T., Ngai, J. (2003). Analysis of gene expression in the developing mouse retina. Proceedings of the National Academy of Sciences (PNAS), 100(9), 5491-5496.
  • Erle, D., Yang, Y. (2003). Asthma investigators begin to reap the fruits of genomics. Genome Biology, 4(11), 232.1-232.3.
  • Yang, Y., Buckley, M., Dudoit, S., Speed, T. (2002). Comparison of methods for image analysis on cDNA microarray data. Journal of Computational and Graphical Statistics, 11(1), 108-136.
  • Yang, Y., Speed, T. (2002). Design issues for cDNA microarray experiments. Nature Reviews Genetics, 3(8), 579-588.
  • Speed, T., Yang, Y. (2002). Direct versus indirect designs for cDNA microarray experiments. Sankhya: The Indian Journal of Statistics, 64(Series A, Pt. 3), 707-721.
  • Diaz, E., Ge, Y., Yang, Y., Loh, K., Serafini, T., Okazaki, Y., Hayashizaki, Y., Speed, T., Ngai, J., Scheiffele, P. (2002). Molecular Analysis of Gene Expression in the Developing Pontocerebellar Projection System. Neuron, 36(3), 417-434.
  • Yang, Y., Dudoit, S., Luu, P., Lin, D., Peng, V., Ngai, J., Speed, T. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, 30(4), e15.
  • Dudoit, S., Yang, Y., Callow, M., Speed, T. (2002). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica, 12, 111-139.
  • Yang, Y., Buckley, M., Speed, T. (2001). Analysis of cDNA microarray images. Briefings in Bioinformatics, 2(4), 341-349.

Conferences

  • Wang, P., Yang, Y., Raftery, M., Zhong, L., Wilson, S. (2013). Latin Square Dataset for Evaluating the Accuracy of Mass Spectrometry-based Protein Identification and Quantification. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2013), Piscataway, United States: (IEEE) Institute of Electrical and Electronics Engineers. [More Information]

Magazine / Newspaper Articles

  • Dudoit, S., Yang, Y., Bolstad, B. (2002). Using R for the Analysis of DNA Microarray Data. R News.

2013

  • Oates, J., Casikar, I., Campain, A., Muller, S., Yang, Y., Reid, S., Condous, G. (2013). A prediction model for viability at the end of the first trimester after a single early pregnancy evaluation. Australian and New Zealand Journal of Obstetrics and Gynaecology, 53(1), 51-57. [More Information]
  • Mann, G., Pupo, G., Campain, A., Carter, C., Schramm, S., Pianova, S., Gerega, S., Desilva, C., Lai, K., Wilmott, J., Hersey, P., Kefford, R., Thompson, J., Yang, Y., Scolyer, R., et al (2013). BRAF Mutation, NRAS Mutation, and the Absence of an Immune-Related Expressed Gene Profile Predict Poor Outcome in Patients with Stage III Melanoma. The Journal of Investigative Dermatology, 133(2), 509-517. [More Information]
  • Strbenac, D., Armstrong, N., Yang, Y. (2013). Correction: Detection and classification of peaks in 5' cap RNA sequencing data. BMC Genetics, 14(1), Art. 767-1. [More Information]
  • Strbenac, D., Armstrong, N., Yang, Y. (2013). Detection and classification of peaks in 5’ cap RNA sequencing data. BMC Genomics, 14(Suppl 5), 1-11. [More Information]
  • Chung, S., Shen, W., Jayawardana, K., Wang, P., Yang, Y., Shackel, N., Gillies, M. (2013). Differential gene expression profiling after conditional müller-cell ablation in a novel transgenic model. Investigative Ophthalmology and Visual Science, 54(3), 2142-2152. [More Information]
  • Schramm, S., Li, S., Jayaswal, V., Fung, D., Campain, A., Pang, C., Scolyer, R., Yang, Y., Mann, G., Wilkins, M. (2013). Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden. Pigment Cell and Melanoma Research, 26(5), 708-722. [More Information]
  • Humphrey, S., Yang, G., Yang, P., Fazakerley, D., Stockli, J., Yang, Y., James, D. (2013). Dynamic adipocyte phosphoproteome reveals that akt directly regulates mTORC2. Cell Metabolism, 17(6), 1009-1020. [More Information]
  • Patrick, E., Buckley, M., Yang, Y. (2013). Estimation of data-specific constitutive exons with RNA-Seq data. BMC Bioinformatics, 14(31), 1-10. [More Information]
  • Patrick, E., Buckley, M., Lin, D., Yang, Y. (2013). Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information. BMC Genomics, 14(Suppl 1), S1-S9. [More Information]
  • Wang, P., Yang, Y., Raftery, M., Zhong, L., Wilson, S. (2013). Latin Square Dataset for Evaluating the Accuracy of Mass Spectrometry-based Protein Identification and Quantification. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2013), Piscataway, United States: (IEEE) Institute of Electrical and Electronics Engineers. [More Information]
  • Schramm, S., Jayaswal, V., Goel, A., Li, S., Yang, Y., Mann, G., Wilkins, M. (2013). Molecular interaction networks for the analysis of human disease: utility, limitations, and considerations. Proteomics, 13(23-24), 3393-3405. [More Information]
  • Neff, C., Yang, Y. (2013). Shark bites and public attitudes: Policy implications from the first before and after shark bite survey. Marine Policy, 38, 545-547. [More Information]
  • Jayaswal, V., Schramm, S., Mann, G., Wilkins, M., Yang, Y. (2013). VAN: an R package for identifying biologically perturbed networks via differential variability analysis. BMC Research Notes, 6(1), 1-9. [More Information]
  • Yang, Y., Markus, M., Mangs, H., Raitskin, O., Sperling, R., Morris, B. (2013). ZRANB2 localizes to supraspliceosomes and influences the alternative splicing of multiple genes in the transcriptome. Molecular Biology Reports, 40(9), 5381-5395. [More Information]

2012

  • Yang, P., Ma, J., Wang, P., Zhu, Y., Zhou, B., Yang, Y. (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. [More Information]
  • Jayaswal, V., Lutherborrow, M., Yang, Y. (2012). Measures of Association for Identifying MicroRNA-mRNA Pairs of Biological Interest. PLoS One, 7(1), e29612-1-e29612-10. [More Information]
  • Bryant, A., Palma, C., Jayaswal, V., Yang, Y., Lutherborrow, M., Ma, D. (2012). miR-10a is aberrantly overexpressed in Nucleophosmin1 mutated acute myeloid leukaemia and its suppression induces cell death. Molecular Cancer, 11(8), 1-9. [More Information]
  • Wang, P., Yang, P., Yang, Y. (2012). OCAP: an open comprehensive analysis pipeline for iTRAQ. Bioinformatics, 28(10), 1404-1405. [More Information]
  • Yang, P., Humphrey, S., Fazakerley, D., Prior, M., Yang, G., James, D., Yang, Y. (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. [More Information]
  • Schramm, S., Campain, A., Scolyer, R., Yang, Y., Mann, G. (2012). Review and Cross-Validation of Gene Expression Signatures and Melanoma Prognosis. The Journal of Investigative Dermatology, 132(2), 274-283. [More Information]

2011

  • Loi, T., Campain, A., Bryant, A., Molloy, T., Lutherborrow, M., Turner, J., Yang, Y., Ma, D. (2011). Discriminating lymphomas and reactive lymphadenopathy in lymph node biopsies by gene expression profiling. BMC Medical Genomics, 4(27), 1-10. [More Information]
  • Lutherborrow, M., Bryant, A., Jayaswal, V., Agapiou, D., PALMA, C., Yang, Y., Ma, D. (2011). Expression Profiling of Cytogenetically Normal Acute Myeloid Leukemia Identifies MicroRNAs that Target Genes Involved in Monocytic Differentiation. American Journal Of Hematology, 86(1), 2-11. [More Information]
  • Marques, F., Campain, A., Tomaszewski, M., Zukowska-Szczechowska, E., Yang, Y., Charchar, F., Morris, B. (2011). Gene Expression Profiling Reveals Renin mRNA Overexpression in Human Hypertensive Kidneys and a Role for MicroRNAs. Hypertension, 58(6), 1093-1098. [More Information]
  • Yang, P., Ho, J., Yang, Y., Zhou, B. (2011). Gene-gene interaction filtering with ensemble of filters. BMC Bioinformatics, 12(Supp 1: S10), 1-10. [More Information]
  • Marques, F., Campain, A., Davern, P., Yang, Y., Head, G., Morris, B. (2011). Genes Influencing Circadian Differences in Blood Pressure in Hypertensive Mice. PLoS One, 6(4), e19203-1-e19203-9. [More Information]
  • Wu, J., Dwyer, D., Dyer, W., Yang, Y., Wang, B., Saksena, N. (2011). Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease. Retrovirology, 8(18), 1-21. [More Information]
  • Marques, F., Campain, A., Davern, P., Yang, Y., Head, G., Morris, B. (2011). Global identification of the genes and pathways differentially expressed in hypothalamus in early and established neurogenic hypertension. Physiological Genomics, 43(12), 766-771. [More Information]
  • Jayaswal, V., Lutherborrow, M., Ma, D., Yang, Y. (2011). Identification of microRNA-mRNA modules using microarray data. BMC Genomics, 12(138), 1-32. [More Information]
  • Collinson, E., Wimmer-Kleikamp, S., Gerega, S., Yang, Y., Parish, C., Dawes, I., Stocker, R. (2011). The Yeast Homolog of Heme Oxygenase-1 Affords Cellular Antioxidant Protection via the Transcriptional Regulation of Known Antioxidant Genes. Journal of Biological Chemistry, 286(3), 2205-2214. [More Information]
  • Peters, T., Bulger, D., Loi, T., Yang, Y., Ma, D. (2011). Two-Step Cross-Entropy Feature Selection For Microarrays-Power Through Complementarity. IEEE - ACM Transactions on Computational Biology and Bioinformatics, 8(4), 1148-1151. [More Information]

2010

  • Wang, P., Yang, P., Arthur, J., Yang, Y. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [More Information]
  • Yang, P., Yang, Y., Zhou, B., Zomaya, A. (2010). A Review of Ensemble Methods in Bioinformatics. Current Bioinformatics, 5(4), 296-308.
  • Jensen, S., Apisiridej, S., Kwong, S., Yang, Y., Skurray, R., Firth, N. (2010). Analysis of the prototypical Staphylococcus aureus multiresistance plasmid pSK1. Plasmid, 64(3), 135-142. [More Information]
  • Campain, A., Yang, Y. (2010). Comparison study of microarray meta-analysis methods. BMC Bioinformatics, 11(408), 1-11.
  • Marques, F., Campain, A., Yang, Y., Morris, B. (2010). Meta-Analysis of Genome-Wide Gene Expression Differences in Onset and Maintenance Phases of Genetic Hypertension. Hypertension, 56(2), 319-324. [More Information]
  • Karim, R., Gerega, S., Yang, Y., Spillane, A., Carmalt, H., Scolyer, R., Lee, C. (2010). p16 and pRb immunohistochemical expression increases with increasing tumour grade in mammary phyllodes tumours. Histopathology, 56(7), 868-875. [More Information]

2009

  • Jayaswal, V., Lutherborrow, M., Ma, D., Yang, Y. (2009). Identification of microRNAs with regulatory potential using a matched microRNA -mRNA time-course data. Nucleic Acids Research, 37(8), e60-e60. [More Information]
  • Karim, R., Gerega, S., Yang, Y., Spillane, A., Carmalt, H., Scolyer, R., Lee, C. (2009). Phyllodes tumours of the breast: a clinicopathological analysis of 65 cases from a single institution. The Breast, 18(3), 165-170. [More Information]
  • Karim, R., Gerega, S., Yang, Y., Horvath, L., Spillane, A., Carmalt, H., Scolyer, R., Lee, C. (2009). Proteins from the Wnt pathway are involved in the pathogenesis and progression of mammary phyllodes tumours. Journal of Clinical Pathology, 62(11), 1016-1020. [More Information]
  • Karim, R., Li, W., Sanki, A., Colman, M., Yang, Y., Thompson, J., Scolyer, R. (2009). Reduced p16 and increased cyclin D1 and pRb expression are correlated with progression in cutaneous melanocytic tumors. International Journal of Surgical Pathology, 17(5), 361-367. [More Information]

2008

  • Lewis, C., Yang, Y., Huang, X., Banerjee, S., Balckburn, M., Baluk, P., McDonald, D., Blackwell, T., Nagabhushanam, V., Peters, W., et al (2008). Disease specific gene expression profiling in multiple models of lung disease. American Journal of Respiratory and Critical Care Medicine, 177(4), 376-387.
  • Yang, Y. (2008). Microarrays - Planning your experiment. In Ronald J.A. Trent (Eds.), Clinical Bioinformatics: Methods in Molecular Medicine, (pp. 71-85). New Jersey: Humana Press.
  • Kechris, K., Yang, Y., Yeh, R. (2008). Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. BMC Genomics, 9(SUPPL. 2, Article number 551), 1-15.
  • Wu, J., Dwyer, D., Dyer, W., Yang, Y., Wang, B., Saksena, N. (2008). Transcriptional profiles in CD8+ T cells from HIV+ progressors on HAART are characterized by coordinated up-regulation of oxidative phosphorylation enzymes and interferon responses. Virology, 380(1), 124-135. [More Information]

2007

  • Xiao, Y., Segal, M., Yang, Y., Yeh, R. (2007). A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics, 23(12), 1459-1467.
  • Winn, V., Haimov-Kochman, R., Paquet, A., Yang, Y., Madhusudhan, M., Gormley, M., Feng, K., Bernlohr, D., McDonagh, S., Pereira, L., et al (2007). Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology, 148(3), 1059-1079.
  • Woodruff, P., Boushey, H., Dolganov, G., Barker, C., Yang, Y., Donnelly, S., Ellwanger, A., Sidhu, S., Dao-Pick, T., Pantoja, C., et al (2007). Genome-wide profiling identifies elpithelial cell genes associated with asthma and with treatment response to corticosteroids. Proceedings of the National Academy of Sciences (PNAS), 104(40), 15858-15863.
  • Williams, E., Xiao, Y., Sickles, H., Shafer, P., Yona, G., Yang, Y., Lin, D. (2007). Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers. BMC Developmental Biology, 7(article no. 48), 1-15.

2005

  • Woodruff, P., Koth, L., Yang, Y., Rodriguez, M., Favoreto, S., Dolganov, G., Paquet, A., Erle, D. (2005). A distinctive alveolar macrophage activation state induced by cigarette smoking. American Journal of Respiratory and Critical Care Medicine, 172(11), 1383-1392.
  • Xiao, Y., Yang, Y., Burckin, T., Shiue, L., Hartzog, G., Segal, M. (2005). Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing. PLoS Computational Biology, 1(4), e39-0276-e39-0288. [More Information]
  • Kuperman, D., Lewis, C., Woodruff, P., Rodriguez, M., Yang, Y., Dolganov, G., Fahy, J., Erle, D. (2005). Dissecting asthma using focused transgenic modeling and functional genomics. Journal of Allergy and Clinical Immunology, 116(2), 305-311. [More Information]
  • Gonzalez, R., Griffin, C., Yang, Y., Allen, L., Tigue, Z., Dobbs, L. (2005). Freshly isolated rat alveolar type I cells, type II cells, and cultured type II cells have distinct molecular phenotypes. American Journal of Physiology: Lung Cellular and Molecular Physiology, 288(1), L179-L189.
  • Yang, Y., Xiao, Y., Segal, M. (2005). Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics, 21(7), 1084-1093.
  • Barker, C., Griffin, C., Dolganov, G., Hanspers, K., Yang, Y., Erle, D. (2005). Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics, 6(57), 57- 1-57- 8.
  • Yang, Y., Paquet, A. (2005). Preprocessing Two-Color Spotted Arrays. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (Eds.), Bioinformatics and Computational Biology Solutions using R and Bioconductor, (pp. 49-70). New York: Springer.
  • Xiao, Y., Segal, M., Yang, Y. (2005). Stepwise Normalization of Two-Channel Spotted Microarrays. Statistical Applications in Genetics and Molecular Biology, 4(1), 4-1-4-29.

2004

  • Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Yang, Y., et al (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biology, 5(10), R80.1-R80.16.
  • Rodriguez, M., Paquet, A., Yang, Y., Erle, D. (2004). Differential gene expression by integrin ß7+ and ß7-memory T helper cells. BMC Immunology, 5(13), 1-11.
  • Lin, D., Yang, Y., Scolnick, J., Brunet, L., Marsh, H., Peng, V., Okazaki, Y., Hayashizaki, Y., Speed, T., Ngai, J. (2004). Spatial patterns of gene expression in the olfactory bulb. Proceedings of the National Academy of Sciences (PNAS), 101(34), 12718-12723.

2003

  • Diaz, E., Yang, Y., Ferreira, T., Loh, K., Okazaki, Y., Hayashizaki, Y., Tessier-Lavigne, M., Speed, T., Ngai, J. (2003). Analysis of gene expression in the developing mouse retina. Proceedings of the National Academy of Sciences (PNAS), 100(9), 5491-5496.
  • Erle, D., Yang, Y. (2003). Asthma investigators begin to reap the fruits of genomics. Genome Biology, 4(11), 232.1-232.3.
  • Yang, Y., Speed, T. (2003). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger (Eds.), The Analysis of Gene Expression Data: Methods and Software, (pp. 73-101). New York: Springer.
  • Yang, Y., Speed, T. (2003). Design and Analysis of Comparative Microarray Experiments. In T. P. Speed (Eds.), Statistical Analysis of Gene Expression Microarray Data, (pp. 35-92). Chapman & Hall.
  • Yang, Y., Thorne, N. (2003). Normalization for Two-color cDNA Microarray Data. In Darlene R Goldstein (Eds.), Science and Statistics: A Festschrift for Terry Speed, (pp. 403-418). Beachwood, Ohio: Institute of Mathematical Statistics.
  • Smyth, G., Yang, Y., Speed, T. (2003). Statistical issues in cDNA microarray data analysis. In M. J. Brownstein and A. B. Khodursky (Eds.), Functional Genomics: Methods and Protocols, (pp. 111-136). New Jersey: Humana Press.

2002

  • Ball, C., Chen, Y., Panavally, S., Sherlock, G., Speed, T., Spellman, P., Yang, Y. (2002). An introduction to microarray bioinformatics. In D. Bowtell and J. Sambrook (Eds.), DNA Microarrays: A Molecular Cloning Manual, (pp. 509-602). New York: Cold Spring Harbor Laboratory Press.
  • Yang, Y., Buckley, M., Dudoit, S., Speed, T. (2002). Comparison of methods for image analysis on cDNA microarray data. Journal of Computational and Graphical Statistics, 11(1), 108-136.
  • Yang, Y., Speed, T. (2002). Design issues for cDNA microarray experiments. Nature Reviews Genetics, 3(8), 579-588.
  • Speed, T., Yang, Y. (2002). Direct versus indirect designs for cDNA microarray experiments. Sankhya: The Indian Journal of Statistics, 64(Series A, Pt. 3), 707-721.
  • Diaz, E., Ge, Y., Yang, Y., Loh, K., Serafini, T., Okazaki, Y., Hayashizaki, Y., Speed, T., Ngai, J., Scheiffele, P. (2002). Molecular Analysis of Gene Expression in the Developing Pontocerebellar Projection System. Neuron, 36(3), 417-434.
  • Yang, Y., Dudoit, S., Luu, P., Lin, D., Peng, V., Ngai, J., Speed, T. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, 30(4), e15.
  • Dudoit, S., Yang, Y., Callow, M., Speed, T. (2002). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica, 12, 111-139.
  • Dudoit, S., Yang, Y., Bolstad, B. (2002). Using R for the Analysis of DNA Microarray Data. R News.

2001

  • Yang, Y., Buckley, M., Speed, T. (2001). Analysis of cDNA microarray images. Briefings in Bioinformatics, 2(4), 341-349.

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