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

2014

  • Towards real time data sharing to support patient-centred care, quality health delivery, improvement programmes, performance management and research; Morris J, Roberts C, Simpson S, Kay J, Venkatesh S, Fazekas B, Arthur J, Feng D, Holmes E, James D, Yang J, Engel A; NSW Ministry of Health, Office for Health and Medical Research/Bioinformatics Collaborative Grants Program.

2013

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

2012

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

2010

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

2009

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

2007

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

2006

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

Selected publications

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Book Chapters

  • Yang, J. (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, J., 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, J., 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, J., 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, J., 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, J., 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, J. (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

  • Yang, P., Patrick, E., Tan, S., Fazakerley, D., Burchfield, J., Prior, M., James, D., Yang, J., Gribben, C. (2014). Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. Bioinformatics, 30(6), 808-814.
  • O'Connor, K., Parnell, G., Patrick, E., Ahlenstiel, G., Suppiah, V., van der Poorten, D., Read, S., Leung, R., Douglas, M., Yang, J., Stewart, G., Liddle, C., George, J., Booth, D. (2014). Hepatic metallothionein expression in chronic hepatitis C virus infection is IFNL3 genotype-dependent. Genes and Immunity, 15(2), 88-94. [More Information]
  • 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 Activation and Early Adipogenesis via Bone Morphogenetic Protein 4-Dependent and -Independent Mechanisms. Molecular and Cellular Biology, 34(19), 3607-3617. [More Information]
  • Wygoda, J., Yang, J., Byrne, M., Wray, G. (2014). Transcriptomic analysis of the highly derived radial body plan of a sea urchin. Genome Biology and Evolution, 6(4), 964-973. [More Information]
  • Oates, J., Casikar, I., Campain, A., Mueller, S., Yang, J., 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, J., 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, J. (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, J. (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, J., 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, J., 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, J., 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, J. (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, J. (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, J., 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, J. (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, J. (2013). VAN: an R package for identifying biologically perturbed networks via differential variability analysis. BMC Research Notes, 6(1), 1-9. [More Information]
  • Yang, J., Markus, A., Mangs, A., 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, 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. [More Information]
  • Jayaswal, V., Lutherborrow, M., Yang, J. (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, J., 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, J. (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, 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. [More Information]
  • Schramm, S., Campain, A., Scolyer, R., Yang, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J. (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, J., 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, J., 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, J. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [More Information]
  • Yang, P., Yang, J., 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, J., Skurray, R., Firth, N. (2010). Analysis of the prototypical Staphylococcus aureus multiresistance plasmid pSK1. Plasmid, 64(3), 135-142. [More Information]
  • Campain, A., Yang, J. (2010). Comparison study of microarray meta-analysis methods. BMC Bioinformatics, 11(408), 1-11.
  • Marques, F., Campain, A., Yang, J., 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, J., 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, J. (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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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) of the United States of America, 104(40), 15858-15863.
  • Williams, E., Xiao, Y., Sickles, H., Shafer, P., Yona, G., Yang, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., Erle, D. (2005). Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics, 6(57), 57- 1-57- 8.
  • Xiao, Y., Segal, M., Yang, J. (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, J., 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, J., Erle, D. (2004). Differential gene expression by integrin ß7+ and ß7-memory T helper cells. BMC Immunology, 5(13), 1-11.
  • Lin, D., Yang, J., 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) of the United States of America, 101(34), 12718-12723.
  • Diaz, E., Yang, J., 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) of the United States of America, 100(9), 5491-5496.
  • Erle, D., Yang, J. (2003). Asthma investigators begin to reap the fruits of genomics. Genome Biology, 4(11), 232.1-232.3.
  • Yang, J., 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, J., Speed, T. (2002). Design issues for cDNA microarray experiments. Nature Reviews Genetics, 3(8), 579-588.
  • Speed, T., Yang, J. (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, J., 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, J., 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, J., Callow, M., Speed, T. (2002). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica, 12, 111-139.
  • Yang, J., Buckley, M., Speed, T. (2001). Analysis of cDNA microarray images. Briefings in Bioinformatics, 2(4), 341-349.

Conferences

  • Wang, P., Yang, J., 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, J., Bolstad, B. (2002). Using R for the Analysis of DNA Microarray Data. R News.

2014

  • Yang, P., Patrick, E., Tan, S., Fazakerley, D., Burchfield, J., Prior, M., James, D., Yang, J., Gribben, C. (2014). Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. Bioinformatics, 30(6), 808-814.
  • O'Connor, K., Parnell, G., Patrick, E., Ahlenstiel, G., Suppiah, V., van der Poorten, D., Read, S., Leung, R., Douglas, M., Yang, J., Stewart, G., Liddle, C., George, J., Booth, D. (2014). Hepatic metallothionein expression in chronic hepatitis C virus infection is IFNL3 genotype-dependent. Genes and Immunity, 15(2), 88-94. [More Information]
  • 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 Activation and Early Adipogenesis via Bone Morphogenetic Protein 4-Dependent and -Independent Mechanisms. Molecular and Cellular Biology, 34(19), 3607-3617. [More Information]
  • Wygoda, J., Yang, J., Byrne, M., Wray, G. (2014). Transcriptomic analysis of the highly derived radial body plan of a sea urchin. Genome Biology and Evolution, 6(4), 964-973. [More Information]

2013

  • Oates, J., Casikar, I., Campain, A., Mueller, S., Yang, J., 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, J., 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, J. (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, J. (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, J., 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, J., 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, J., 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, J. (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, J. (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, J., 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, J., 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, J. (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, J. (2013). VAN: an R package for identifying biologically perturbed networks via differential variability analysis. BMC Research Notes, 6(1), 1-9. [More Information]
  • Yang, J., Markus, A., Mangs, A., 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, 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. [More Information]
  • Jayaswal, V., Lutherborrow, M., Yang, J. (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, J., 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, J. (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, 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. [More Information]
  • Schramm, S., Campain, A., Scolyer, R., Yang, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J. (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, J., 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, J., 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, J. (2010). A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data. Bioinformatics, 26(18), 2242-2249. [More Information]
  • Yang, P., Yang, J., 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, J., Skurray, R., Firth, N. (2010). Analysis of the prototypical Staphylococcus aureus multiresistance plasmid pSK1. Plasmid, 64(3), 135-142. [More Information]
  • Campain, A., Yang, J. (2010). Comparison study of microarray meta-analysis methods. BMC Bioinformatics, 11(408), 1-11.
  • Marques, F., Campain, A., Yang, J., 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, J., 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, J. (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, J., 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, J., 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, J., 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, J., 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, J. (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, J., 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, J., 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, J., 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, J., 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, J., 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) of the United States of America, 104(40), 15858-15863.
  • Williams, E., Xiao, Y., Sickles, H., Shafer, P., Yona, G., Yang, J., 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, J., 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, J., 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, J., 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, J., 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, J., 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, J., Erle, D. (2005). Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics, 6(57), 57- 1-57- 8.
  • Yang, J., 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, J. (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, J., 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, J., Erle, D. (2004). Differential gene expression by integrin ß7+ and ß7-memory T helper cells. BMC Immunology, 5(13), 1-11.
  • Lin, D., Yang, J., 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) of the United States of America, 101(34), 12718-12723.

2003

  • Diaz, E., Yang, J., 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) of the United States of America, 100(9), 5491-5496.
  • Erle, D., Yang, J. (2003). Asthma investigators begin to reap the fruits of genomics. Genome Biology, 4(11), 232.1-232.3.
  • Yang, J., 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, J., 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, J., 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, J., 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, J. (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, J., 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, J., Speed, T. (2002). Design issues for cDNA microarray experiments. Nature Reviews Genetics, 3(8), 579-588.
  • Speed, T., Yang, J. (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, J., 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, J., 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, J., 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, J., Bolstad, B. (2002). Using R for the Analysis of DNA Microarray Data. R News.

2001

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

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