2025

• Wang, C., Chan, A., Fu, X., Ghazanfar, S., Kim, J., Patrick, E., Yang, J. (2025). Benchmarking the translational potential of spatial gene expression prediction from histology. Nature Communications, 16(1), Article 1544 - 1-Article 1544 - 17. [More Information]
• Yin, D., Cao, Y., Chen, J., Mak, C., Yu, K., Zhang, J., Li, J., Lin, Y., Ho, J., Yang, J. (2025). Scope+: An open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels. Bioinformatics, 41(1).

2024

• Philipoff, A., Lin, Y., Teixeira-Pinto, A., Gately, R., Craig, J., Opdam, H., Chapman, J., Pleass, H., Rogers, N., Davies, C., Yang, J., Wong, G., et al (2024). Antecedent Cardiac Arrest Status of Donation After Circulatory Determination of Death (DCDD) Kidney Donors and the Risk of Delayed Graft Function After Kidney Transplantation: A Cohort Study. Transplantation, 108(10), 2117-2126.
• Fu, X., Lin, Y., Lin, D., Mechtersheimer, D., Wang, C., Ameen, F., Ghazanfar, S., Patrick, E., Kim, J., Yang, J. (2024). BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data. Nature Communications, 15(Article 509), 1-17. [More Information]
• Tran, A., Wang, A., Mickaill, J., Strbenac, D., Larance, M., Vernon, S., Grieve, S., Figtree, G., Patrick, E., Yang, J. (2024). Construction and optimization of multi-platform precision pathways for precision medicine. Scientific Reports, 14(Article 4248), 1-11.
• Lin, Y., Wu, T., Chen, X., Wan, S., Chao, B., Xin, J., Yang, J., Wong, W., Wang, Y. (2024). Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE. Genome Research, 34(1), 119-133. [More Information]
• Robertson, H., Kim, H., Li, J., Robertson, N., Robertson, P., Jimenez-Vera, E., Ameen, F., Tran, A., Trinh, K., O'Connell, P., Yang, J., Rogers, N., Patrick, E. (2024). Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas. Nature Medicine, 30, 3748-3757.
• Fiorenza, S., Zheng, Y., Purushe, J., Bock, T., Sarthy, J., Janssens, D., Sheih, A., Kimble, E., Kirchmeier, D., Phi, T., Yang, J., Turtle, C., et al (2024). Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion. Nature Communications, 15(Article 8309).
• Mechtersheimer, D., Ding, W., Xu, X., Kim, S., M Sue, C., Cao, Y., Yang, J. (2024). IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits. Bioinformatics, 41(1), 1-8.
• Dakic, A., Wu, J., Wang, T., Huynh, K., Mellett, N., Duong, T., Beyene, H., Yang, J., Figtree, G., Simes, R., et al (2024). Imputation of plasma lipid species to facilitate integration of lipidomic datasets. Nature Communications, 15(1), 1540. [More Information]
• Wu, J., Giles, C., Dakic, A., Beyene, H., Huynh, K., Wang, T., Meikle, T., Olshansky, G., Salim, A., Duong, T., Zhu, D., Yang, J., Grieve, S., Wilson, A., Chow, C., Vernon, S., Gray, M., Figtree, G., et al (2024). Lipidomic Risk Score to Enhance Cardiovascular Risk Stratification for Primary Prevention. Journal of the American College of Cardiology, 84(5), 434-446.
• Ribeiro, R., Senior, A., Simpson, S., Tan, J., Raubenheimer, D., Le Couteur, D., Macia, L., Holmes, A., Eberhard, J., O'Sullivan, J., Koay, Y., Kanjrawi, A., Yang, J., Kim, T., Gosby, A. (2024). Rapid benefits in older age from transition to whole food diet regardless of protein source or fat to carbohydrate ratio: Arandomised control trial. Aging Cell, 23(11), e14276. [More Information]
• Lim, S., Lin, Y., Lee, D., Pedersen, B., Stewart, A., Scolyer, R., Long, G., Yang, J., Rizos, H. (2024). Single-cell RNA sequencing reveals melanoma cell state-dependent heterogeneity of response to MAPK inhibitors. EBioMedicine, 107(105308).
• Koay, Y., Liu, R., McIntosh, B., Vigder, N., Lauren, S., Bai, A., Tomita, S., Li, D., Harney, D., Hunter, B., Zhang, Y., Yang, J., Bannon, P., Philp, A., Larance, M., Lal, S., O'Sullivan, J., et al (2024). The Efficacy of Risk Factor Modification Compared to NAD+ Repletion in Diastolic Heart Failure. JACC: Basic to Translational Science, 9(6), 733-750. [More Information]
• Bate, K., Genetzakis, E., Vescovi, J., Gray, M., Celermajer, D., McGuire, H., Grieve, S., Vernon, S., Cartland, S., Yang, J., Kavurma, M., Figtree, G. (2024). Vascular Cytokines and Atherosclerosis: Differential Serum Levels of TRAIL, IL-18, and OPG in Obstructive Coronary Artery Disease. Biomolecules, 14, 1119. [More Information]

2023

• Zhang, Y., Deng, D., Mueller, S., Wong, G., Yang, J. (2023). A Multi-Step Precision Pathway for Predicting Allograft Survival in Heterogeneous Cohorts of Kidney Transplant Recipients. Transplant International, 36, 11338-1-11388-8. [More Information]
• Lin, Y., Cao, Y., Wood, E., Patrick, E., Yang, J. (2023). Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Nature Communications, 14.
• Cao, Y., Ghazanfar, S., Yang, P., Yang, J. (2023). Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. Briefings in Bioinformatics, 24(3). [More Information]
• Gupta, R., Strbenac, D., Satgunaseelan, L., Cheung, V., Narayanappa, H., Ashford, B., Mitchell, J., Thind, A., Palme, C., Ch'ng, S., Low, T., Willet, C., Chew, T., Yang, J., Clark, J., et al (2023). Comparing Genomic Landscapes of Oral and Cutaneous Squamous Cell Carcinoma of the Head and Neck: Quest for Novel Diagnostic Markers. Modern Pathology, 36(8), 100190. [More Information]
• Fu, X., Patrick, E., Yang, J., Feng, D., Kim, J. (2023). Deep multimodal graph-based network for survival prediction from highly multiplexed images and patient variables. Computers in Biology and Medicine, 154. [More Information]
• Lay, A., Dupuy, A., Hagimola, L., Tieng, J., Larance, M., Zhang, Y., Yang, J., Kong, Y., Chiu, J., Gray, E., Maclean, J., Hofma, B., Jackson, S., Hogg, P., Passam, F., et al (2023). Endoplasmic reticulum protein 5 attenuates platelet endoplasmic reticulum stress and secretion in a mouse model. Blood Advances, 7(9), 1650-1665. [More Information]
• Yu, L., Liu, C., Yang, J., Yang, P. (2023). Ensemble deep learning of embeddings for clustering multimodal single-cell omics data. Bioinformatics, 39(6).
• Kim, D., Tran, A., Kim, H., Lin, Y., Yang, J., Yang, P. (2023). Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data. Npj Systems Biology And Applications, 9.
• Kim, D., Tran, A., Kim, H., Lin, Y., Yang, J., Yang, P. (2023). Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data. Npj Systems Biology And Applications, 9(51). [More Information]
• Kott, K., Chan, A., Vernon, S., Hansen, T., Kim, T., De Dreu, M., Gunasegaran, B., Murphy, A., Patrick, E., Psaltis, P., Grieve, S., Yang, J., Fazekas de St Groth, B., McGuire, H., Figtree, G. (2023). Mass cytometry analysis reveals altered immune profiles in patients with coronary artery disease. Clinical & Translational Immunology, 12(11), e1462-1-e1462-18. [More Information]
• Xu, X., Lubomski, M., Holmes, A., Sue, C., Davis, R., Mueller, S., Yang, J. (2023). NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions. Microbiome, 11(1). [More Information]
• Chan, A., Wu, S., Vernon, S., Tang, O., Figtree, G., Liu, T., Yang, J., Patrick, E. (2023). Overcoming cohort heterogeneity for the prediction of subclinical cardiovascular disease risk. iScience, 26(5), Article 106633 - 1-Article 106633 - 17. [More Information]
• Martinez, A., Chung, A., Huang, S., Bisogni, A., Lin, Y., Cao, Y., Williams, E., Kim, J., Yang, J., Lin, D. (2023). Pcdh19 mediates olfactory sensory neuron coalescence during postnatal stages and regeneration. iScience, 26(11), 108220-1-108220-18. [More Information]
• Hao, J., Zou, J., Zhang, J., Chen, K., Wu, D., Cao, W., Shang, G., Yang, J., Wong-Lin, K., Sun, H., et al (2023). scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data. Briefings in Bioinformatics, 24(2). [More Information]
• Kott, K., Genetzakis, E., Gray, M., Hansen, P., McGuire, H., Yang, J., Grieve, S., Vernon, S., Figtree, G. (2023). Serum Soluble Lectin-like Oxidized Low-Density Lipoprotein Receptor-1 (sLOX-1) Is Associated with Atherosclerosis Severity in Coronary Artery Disease. Biomolecules, 13(8), 1187-17 pages. [More Information]
• Zhang, Y., Hu, A., Lin, Y., Cao, Y., Muller, S., Wong, G., Yang, J. (2023). simKAP: simulation framework for the kidney allocation process with decision making model. Scientific Reports, 13(Article 16367), 1-9.
• Cao, Y., Tran, A., Kim, H., Robertson, N., Lin, Y., Torkel, M., Yang, P., Patrick, E., Ghazanfar, S., Yang, J. (2023). Thinking process templates for constructing data stories with SCDNEY. F1000Research, 12, 261-1-261-18. [More Information]
• Lin, Y., McDonald, S., Yang, J., Lim, W., Wong, G., Teixeira-Pinto, A., Craig, J., Opdam, H., Chapman, J., Pleass, H., et al (2023). Trajectories of systolic blood pressure decline in kidney transplant donors prior to circulatory death and delayed graft function. Clinical Kidney Journal, 16(7), 1170-1179. [More Information]

2022

• Lin, Y., Yang, J. (2022). 3D reconstruction of spatial expression. Nature Methods, 19(5), 526-527. [More Information]
• Yu, L., Cao, Y., Yang, J., Yang, P. (2022). Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data. Genome Biology, 23(1). [More Information]
• Tran, A., Yang, P., Yang, J., Ormerod, J. (2022). Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era. Briefings in Functional Genomics, 21(4), 270-279. [More Information]
• Wang, K., Pupo, G., Tembe, V., Patrick, E., Strbenac, D., Schramm, S., Thompson, J., Scolyer, R., Mueller, S., Tarr, G., Mann, G., Yang, J. (2022). Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine. npj Digital Medicine, 5(1), 85-1-85-10. [More Information]
• Au, E., Wong, G., Howard, K., Chapman, J., Castells, A., Roger, S., Bourke, M., Macaskill, P., Turner, R., Lim, W., Pollock, C., Jaure, A., Teixeira-Pinto, A., Yang, J., Kieu, A., James, L., et al (2022). Factors Associated With Advanced Colorectal Neoplasia in Patients With CKD. American Journal of Kidney Diseases, 79(4), 549-560. [More Information]
• Havula, E., Ghazanfar, S., Lamichane, N., Francis, D., Hasygar, K., Liu, Y., Alton, L., Johnstone, J., Needham, E., Pulpitel, T., Clark, T., Niranjan, H., Shang, V., Tong, V., Jiwnani, N., Audia, G., Neely, G., Yang, J., Simpson, S., Senior, A., et al (2022). Genetic variation of macronutrient tolerance in Drosophila melanogaster. Nature Communications, 13(1637), 1-16. [More Information]
• Vernon, S., Kott, K., Hansen, T., Finemore, M., Baumgart, K., Bhindi, R., Yang, J., Hansen, P., Nicholls, S., Celermajer, D., Ward, M., Van Nunen, S., Grieve, S., Figtree, G. (2022). Immunoglobulin E Sensitization to Mammalian Oligosaccharide Galactose-á-1,3 (á-Gal) Is Associated With Noncalcified Plaque, Obstructive Coronary Artery Disease, and ST-Segment-Elevated Myocardial Infarction. Arteriosclerosis, Thrombosis, and Vascular Biology, 42(3), 352-361. [More Information]
• Lin, Y., Teixeira-Pinto, A., Opdam, H., Chapman, J., Craig, J., Rogers, N., Pleass, H., Davies, C., McDonald, S., Yang, J., Wong, G., et al (2022). Nonutilization of Kidneys from Donors after Circulatory Determinant of Death. Transplantation Direct, 8(6), E1331-E1331. [More Information]
• Lubomski, M., Xu, X., Holmes, A., Mueller, S., Yang, J., Davis, R., Sue, C. (2022). Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease. Frontiers in Aging Neuroscience, 14, 881872-1-881872-16. [More Information]
• Lin, Y., Loo, L., Tran, A., Lin, D., Moreno, C., Hesselson, D., Neely, G., Yang, J. (2022). Scalable workflow for characterization of cell-cell communication in COVID-19 patients. PLoS Computational Biology, 18(10), 1010495-1-1010495-19. [More Information]
• Cao, Y., Lin, Y., Patrick, E., Yang, P., Yang, J. (2022). scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. Bioinformatics, 38(20), 4745-4753. [More Information]
• Lin, Y., Wu, T., Wan, S., Yang, J., Wong, W., Wang, Y. (2022). scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning. Nature Biotechnology, 40(5), 703-710. [More Information]
• Tran, A., Yang, P., Yang, J., Ormerod, J. (2022). scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model. NAR Genomics and Bioinformatics, 4(1), 1-11. [More Information]
• Zhang, Y., Wong, G., Mann, G., Mueller, S., Yang, J. (2022). SurvBenchmark: Comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. GigaScience, 11, 1-13. [More Information]
• Lubomski, M., Xu, X., Holmes, A., Mueller, S., Yang, J., Davis, R., Sue, C. (2022). The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies. Frontiers in Aging Neuroscience, 14(May 17 2022), 875261-1-875261-24. [More Information]
• Coorey, G., Figtree, G., Fletcher, D., Snelson, V., Vernon, S., Winlaw, D., Grieve, S., McEwan, A., Yang, J., Qian, P., Orchard, J., Kim, J., Patel, S., Redfern, J., et al (2022). The health digital twin to tackle cardiovascular disease—a review of an emerging interdisciplinary field. npj Digital Medicine, 5(1), 1-12. [More Information]
• Lubomski, M., Xu, X., Holmes, A., Yang, J., Sue, C., Davis, R. (2022). The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease. Journal of Neurology, 269(2), 780-795. [More Information]
• Satgunaseelan, L., Strbenac, D., Tadi, S., Nguyen, K., Wykes, J., Palme, C., Low, T., Yang, J., Clark, J., Gupta, R. (2022). Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma. Cancers, 14(21), 5213-1-5213-16. [More Information]
• Satgunaseelan, L., Strbenac, D., Willet, C., Chew, T., Sadsad, R., Wykes, J., Low, T., Cooper, W., Lee, C., Palme, C., Yang, J., Clark, J., Gupta, R. (2022). Whole genome duplication in oral squamous cell carcinoma in patients younger than 50 years: implications for prognosis and adverse clinicopathological factors. Genes Chromosomes and Cancer, 61(9), 561-571. [More Information]

2021

• Cao, Y., Yang, P., Yang, J. (2021). A benchmark study of simulation methods for single-cell RNA sequencing data. Nature Communications, 12(1), 6911. [More Information]
• Way, G., Greene, C., Carninci, P., Carvalho, B., de Hoon, M., Finley, S., Gosline, S., Le Cao, K., Lee, J., Marchionni, L., Yang, J., et al (2021). A field guide to cultivating computational biology. PLoS Biology, 19(10), e3001419. [More Information]
• Kim, T., Tang, O., Vernon, S., Kott, K., Koay, Y., Park, J., James, D., Grieve, S., Speed, T., Yang, P., Figtree, G., John, O., Yang, J. (2021). A hierarchical approach to removal of unwanted variation for large-scale metabolomics data. Nature Communications, 12(1), 4992-1-4992-10. [More Information]
• Kott, K., Morel-Kopp, M., Vernon, S., Takagi, Y., Di Bartolo, B., Peter, K., Yang, J., Grieve, S., Ward, C., Figtree, G. (2021). Association of global coagulation profiles with cardiovascular risk factors and atherosclerosis: A sex disaggregated analysis from the bioheart-ct study. Journal of the American Heart Association, 10(20), e020604. [More Information]
• Su, X., Zhao, L., Shi, Y., Zhang, R., Long, Q., Bai, S., Luo, Q., Lin, Y., Zou, X., Ghazanfar, S., Yang, P., Yang, J., et al (2021). Clonal evolution in liver cancer at single-cell and single-variant resolution. Journal of Hematology and Oncology, 14(1), 22-26. [More Information]
• He, J., Lin, Y., Meng, M., Li, J., Yang, J., Wang, H. (2021). Construction of a Human Cell Landscape of COVID-19 Infection at Single-cell Level. Aging and Disease, 12(3), 705-709. [More Information]
• Koay, Y., Stanton, K., Kienzle, V., Li, M., Yang, J., Celermajer, D., O'Sullivan, J. (2021). Effect of chronic exercise in healthy young male adults: a metabolomic analysis. Cardiovascular Research, 117(2), 613-622. [More Information]
• Francis, D., Ghazanfar, S., Havula, E., Krycer, J., Strbenac, D., Senior, A., Minard, A., Geddes, T., Nelson, M., Weiss, F., Stoeckli, J., Yang, J., James, D. (2021). Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes. G3: Genes, Genomes, Genetics, 11(10), jkab171. [More Information]
• Cao, Y., Alexander, S., Chapman, J., Craig, J., Wong, G., Yang, J. (2021). Integrative Analysis of Prognostic Biomarkers for Acute Rejection in Kidney Transplant Recipients. Transplantation, 105(6), 1225-1237. [More Information]
• Hu, A., Stewart, C., Craig, J., Wyburn, K., Pleass, H., Kanellis, J., Lim, W., Yang, J., Wong, G. (2021). Jurisdictional inequalities in deceased donor kidney allocation in Australia. Kidney International, 100(1), 49-54. [More Information]
• Vernon, S., Tang, O., Kim, T., Chan, A., Kott, K., Park, J., Hansen, T., Koay, Y., Grieve, S., O'Sullivan, J., Yang, J., Figtree, G. (2021). Metabolic Signatures in Coronary Artery Disease: Results from the BioHEART-CT Study. Cells, 10(5), 980. [More Information]
• Dutta, S., Li, D., Wang, A., Ishak, M., Cook, K., Farnham, M., Dissanayake, H., Cistulli, P., Hunyor, I., Liu, R., Wilcox, I., Koay, Y., Yang, J., Lal, S., O'Sullivan, J. (2021). Metabolite signatures of heart failure, sleep apnoea, their interaction, and outcomes in the community. ESC Heart Failure, 8(6), 5392-5402. [More Information]
• Schafer, S., Wang, K., Sundling, F., Yang, J., Liu, A., Nanan, R. (2021). Modelling maternal and perinatal risk factors to predict poorly controlled childhood asthma. PloS One, 16(5), e0252215-1-e0252215-8. [More Information]
• Satgunaseelan, L., Porazinski, S., Strbenac, D., Istadi, A., Willet, C., Chew, T., Sadsad, R., Palme, C., Lee, J., Boyer, M., Yang, J., Clark, J., Gupta, R., et al (2021). Oral Squamous Cell Carcinoma in Young Patients Show Higher Rates of EGFR Amplification: Implications for Novel Personalized Therapy. Frontiers in Oncology, 11, 750852. [More Information]
• Koay, Y., Chen, Y., Wali, J., Luk, A., Li, M., Doma, H., Reimark, R., Zaldivia, M., Habtom, H., Franks, A., Fusco-Allison, G., Yang, J., Holmes, A., Simpson, S., O'Sullivan, J., et al (2021). Plasma levels of trimethylamine-N-oxide can be increased with 'healthy' and 'unhealthy' diets and do not correlate with the extent of atherosclerosis but with plaque instability. Cardiovascular Research, 117(2), 435-449. [More Information]
• Coorey, C., Sharma, A., Mueller, S., Yang, J. (2021). Prediction modeling—part 2: using machine learning strategies to improve transplantation outcomes. Kidney International, 99(4), 817-823. [More Information]
• Eastwood, J., Wang, A., Khanlari, S., Montgomery, A., Yang, J. (2021). Psychosocial stratification of antenatal indicators to guide population-based programs in perinatal depression. BMC Pregnancy and Childbirth, 21(1), 277-1-277-12. [More Information]
• Byrne, M., Koop, D., Strbenac, D., Cisternas, P., Yang, J., Davidson, P., Wray, G. (2021). Transcriptomic analysis of Nodal-and BMP-associated genes during development to the juvenile seastar in Parvulastra exigua (Asterinidae). Marine Genomics, 59, 100857. [More Information]
• Zhang, Y., Wong, G., Yang, J. (2021). Trash or Treasure: Rescuing Discard Kidneys. Transplantation, 105(9), 1914-1915. [More Information]
• Sutherland, K., Almeida, F., Kim, T., Brown, E., Knapman, F., Ngiam, J., Yang, J., Bilston, L., Cistulli, P. (2021). Treatment usage patterns of oral appliances for obstructive sleep apnea over the first 60 days: A cluster analysis. The Journal of Clinical Sleep Medicine, 17(9), 1785-1792. [More Information]
• Chan, A., Jiang, W., Blyth, E., Yang, J., Patrick, E. (2021). treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data. Genome Biology, 22(1), 324-1-324-14. [More Information]
• Kim, H., Wang, K., Chen, C., Lin, Y., Tam, P., Lin, D., Yang, J., Yang, P. (2021). Uncovering cell identity through differential stability with Cepo. Nature Computational Science, 1(12), 784-790. [More Information]

2020

• Hewavisenti, R., Ferguson, A., Wang, K., Jones, D., Gebhardt, T., Edwards, J., Zhang, M., Britton, W., Yang, J., Hong, A., Palendira, M. (2020). CD103+ tumor-resident CD8+ T cell numbers underlie improved patient survival in oropharyngeal squamous cell carcinoma. Journal for ImmunoTherapy of Cancer, 8 (Open Access)(1), 1-8. [More Information]
• Kim, H., Lin, Y., Geddes, T., Yang, J., Yang, P. (2020). CiteFuse enables multi-modal analysis of CITE-seq data. Bioinformatics, 36(14), 4137-4143. [More Information]
• Li, M., Parker, B., Pearson, E., Hunter, B., Cao, J., Koay, Y., Guneratne, O., James, D., Yang, J., Lal, S., O'Sullivan, J. (2020). Core functional nodes and sex-specific pathways in human ischaemic and dilated cardiomyopathy. Nature Communications, 11(1), 2843. [More Information]
• Romanes, S., Ormerod, J., Yang, J. (2020). Diagonal Discriminant Analysis With Feature Selection for High-Dimensional Data. Journal of Computational and Graphical Statistics, 29(1), 114-127. [More Information]
• Cao, Y., Geddes, T., Yang, J., Yang, P. (2020). Ensemble deep learning in bioinformatics. Nature Machine Intelligence, 2(September 2020), 500-508. [More Information]
• Krishnan, A., Teixeira-Pinto, A., Lim, W., Howard, K., Chapman, J., Castells, A., Roger, S., Bourke, M., Macaskill, P., Williams, G., Sen, S., Turner, R., Jaure, A., Yang, J., Williams, N., Au, E., Kieu, A., James, L., Francis, A., Wong, G., et al (2020). Health-Related Quality of Life in People Across the Spectrum of CKD. Kidney International Reports, 5(12), 2264-2274. [More Information]
• Ghazanfar, S., Lin, Y., Su, X., Lin, D., Patrick, E., Han, Z., Marioni, J., Yang, J. (2020). Investigating higher-order interactions in single-cell data with scHOT. Nature Methods, 17(8), 799-806. [More Information]
• Xu, X., Solon-Biet, S., Senior, A., Raubenheimer, D., Simpson, S., Fontana, L., Mueller, S., Yang, J. (2020). LC-N2G: a local consistency approach for nutrigenomics data analysis. BMC Bioinformatics, 21(1), 530. [More Information]
• Su, X., Long, Q., Bo, J., Shi, Y., Zhao, L., Lin, Y., Luo, Q., Ghazanfar, S., Zhang, C., Liu, Q., Yang, J., et al (2020). Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma. The Prostate, 80(6), 508-517. [More Information]
• Campbell, P., Getz, G., Korbel, J., Stuart, J., Jennings, J., Stein, L., Perry, M., Nahal-Bose, H., Ouellette, B., Li, C., deFazio, A., Chiew, Y., Tembe, V., Mann, G., et al (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82-93. [More Information]
• Bailey, M., Meyerson, W., Dursi, L., Wang, L., Dong, G., Liang, W., Weerasinghe, A., Li, S., Burke, H., Chiew, Y., Chou, A., Dagg, R., De Paoli-Iseppi, R., Gill, A., Hayward, N., Hersey, P., Jakrot, V., Kakavand, H., Kench, J., Kennedy, C., Mann, G., Pupo, G., Samra, J., Schramm, S., Scolyer, R., Tembe, V., Vilain, R., Yang, J., deFazio, A., et al (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1), 1-27. [More Information]
• Lin, Y., Cao, Y., Kim, H., Salim, A., Speed, T., Lin, D., Yang, P., Yang, J. (2020). scClassify: sample size estimation and multiscale classification of cells using single and multiple reference. Molecular Systems Biology, 16(Open access), e9389-1-e9389-16. [More Information]
• Li, C., Prokopec, S., Sun, R., Yousif, F., Schmitz, N., Al-Shahrour, F., Atwal, G., Bailey, P., Biankin, A., Burke, H., et al (2020). Sex differences in oncogenic mutational processes. Nature Communications, 11(1), 4330. [More Information]
• Poulos, R., Hains, P., Shah, R., Lucas, N., Xavier, D., Manda, S., Anees, A., Koh, J., Mahboob, S., Wittman, M., Williams, S., Sykes, E., Hecker, M., Dausmann, M., Wouters, M., Yang, J., deFazio, A., Balleine, R., Tully, B., Reddel, R., Robinson, P., Zhong, Q., et al (2020). Strategies to enable large-scale proteomics for reproducible research. Nature Communications, 11(1), 3793. [More Information]
• Lau, M., Ghazanfar, S., Parkin, A., Cho, A., Rouaen, J., Littleboy, J., Nessem, D., Khuong, T., Nevoltris, D., Schofield, P., Yang, J., Neely, G., et al (2020). Systematic functional identification of cancer multi-drug resistance genes. Genome Biology, 21(1), 27. [More Information]
• Lee, J., Shklovskaya, E., Lim, S., Carlino, M., Menzies, A., Stewart, A., Pedersen, B., Irvine, M., Alavi, S., Yang, J., Strbenac, D., Saw, R., Thompson, J., Wilmott, J., Scolyer, R., Long, G., et al (2020). Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition. Nature Communications, 11(1), 1-12. [More Information]
• Byrne, M., Koop, D., Strbenac, D., Cisternas, P., Balogh, R., Yang, J., Davidson, P., Wray, G. (2020). Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors. DNA Research, 27(1), dsaa007. [More Information]

2019

• Yang, P., Ormerod, J., Liu, W., Ma, C., Zomaya, A., Yang, J. (2019). AdaSampling for Positive-Unlabeled and Label Noise Learning With Bioinformatics Applications. IEEE Transactions on Cybernetics, 49(5), 1932-1943. [More Information]
• De Ridder, M., Klein, K., Yang, J., Yang, P., Lagopoulos, J., Hickie, I., Bennett, M., Kim, J. (2019). An Uncertainty Visual Analytics Framework for fMRI Functional Connectivity. Neuroinformatics, 17(2), 211-223. [More Information]
• Diefenbach, R., Lee, J., Strbenac, D., Yang, J., Menzies, A., Carlino, M., Long, G., Spillane, A., Stretch, J., Saw, R., Thompson, J., Ch'ng, S., Scolyer, R., Kefford, R., Rizos, H. (2019). Analysis of the whole-exome sequencing of tumor and circulating tumor DNA in metastatic melanoma. Cancers, 11(12), 1-14. [More Information]
• Wong, G., Hope, R., Howard, K., Chapman, J., Castells, A., Roger, S., Bourke, M., Macaskill, P., Turner, R., Williams, G., Allen, R., Chadban, S., Jaure, A., Teixeira-Pinto, A., Yang, J., Williams, N., Au, E., Kieu, A., James, L., et al (2019). Authors' Reply. Journal of the American Society of Nephrology, 30(11), 2276-2277. [More Information]
• Geddes, T., Kim, T., Nan, L., Burchfield, J., Yang, J., Tao, D., Yang, P. (2019). Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis. BMC Bioinformatics, 20(Suppl 19), 1-11. [More Information]
• Wang, K., Menzies, A., Silva, I., Wilmott, J., Yan, Y., Wongchenko, M., Kefford, R., Scolyer, R., Long, G., Tarr, G., Mueller, S., Yang, J. (2019). bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays. Bioinformatics, 35(8), 1350-1357. [More Information]
• Kott, K., Vernon, S., Hansen, T., Yu, C., Bubb, K., Coffey, S., Sullivan, D., Yang, J., O'Sullivan, J., Chow, C., Patel, S., Chong, J., Celermajer, D., Kritharides, L., Grieve, S., Figtree, G. (2019). Biobanking for discovery of novel cardiovascular biomarkers using imaging-quantified disease burden: protocol for the longitudinal, prospective, BioHEART-CT cohort study. BMJ Open, 9(9), 1-9. [More Information]
• Jaeger, S., Klein, K., Joos, L., Zagermann, J., De Ridder, M., Kim, J., Yang, J., Pfeil, U., Reiterer, H., Schreiber, F. (2019). Challenges for brain data analysis in VR environments. 12th IEEE Pacific Visualization Symposium (PacificVis 2019), Bangkok: Institute of Electrical and Electronics Engineers (IEEE). [More Information]
• Lim, S., Lee, J., Gide, T., Menzies, A., Guminski, A., Carlino, M., Breen, E., Yang, J., Ghazanfar, S., Kefford, R., Scolyer, R., Long, G., Rizos, H. (2019). Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1–Based Immunotherapy. Clinical Cancer Research, 25(5), 1557-1563. [More Information]
• Ghazanfar, S., Strbenac, D., Ormerod, J., Yang, J., Patrick, E. (2019). DCARS: differential correlation across ranked samples. Bioinformatics, 35(5), 823-829. [More Information]
• Da Silva, I., Wang, K., Wilmott, J., Holst, J., Carlino, M., Park, J., Quek, C., Wongchenko, M., Yan, Y., Mann, G., Rai, R., Kefford, R., Rizos, H., Scolyer, R., Yang, J., Long, G., Menzies, A., et al (2019). Distinct molecular profiles and immunotherapy treatment outcomes of V600E and V600K BRAF-mutant melanoma. Clinical Cancer Research, 25(4), 1272-1279. [More Information]
• Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Lin, D., Speed, T., Yang, J., Yang, P. (2019). Evaluating stably expressed genes in single cells. GigaScience, 8(9), 1-10. [More Information]
• Wang, K., Tarr, G., Yang, J., Mueller, S. (2019). Fast and approximate exhaustive variable selection for generalised linear models with APES. Australian & New Zealand Journal of Statistics, 61(4), 445-465. [More Information]
• Kim, T., Chen, I., Lin, Y., Wang, A., Yang, J., Yang, P. (2019). Impact of similarity metrics on single-cell RNA-seq data clustering. Briefings in Bioinformatics, 20(6), 2316-2326. [More Information]
• Strbenac, D., Wang, K., Wang, X., Dong, J., Mann, G., Mueller, S., Yang, J. (2019). Melanoma Explorer: a web application to allow easy reanalysis of publicly available and clinically annotated melanoma omics data sets. Melanoma Research, 29(3), 342-344. [More Information]
• Li, M., Wang, A., Quek, L., Vernon, S., Figtree, G., Yang, J., O'Sullivan, J. (2019). Metabolites downstream of predicted loss-of-function variants inform relationship to disease. Molecular Genetics and Metabolism, 128(4), 476-482. [More Information]
• Yang, P., Humphrey, S., Cinghu, S., Pathania, R., Oldfield, A., Kumar, D., Perera, D., Yang, J., James, D., Mann, M., et al (2019). Multi-omic profiling reveals dynamics of the phased progression of pluripotency. Cell Systems. [More Information]
• Wong, G., Hope, R., Howard, K., Chapman, J., Castells, A., Roger, S., Bourke, M., Macaskill, P., Turner, R., Williams, G., Chadban, S., Pollock, C., Jaure, A., Teixeira-Pinto, A., Yang, J., Williams, N., Au, E., Kieu, A., James, L., et al (2019). One-Time Fecal Immunochemical Screening for Advanced Colorectal Neoplasia in Patients with CKD (DETECT Study). Journal of the American Society of Nephrology, 30(6), 1061-1072. [More Information]
• Kim, T., Chen, R., Parker, B., Humphrey, S., Crossett, B., Cordwell, S., Yang, P., Yang, J. (2019). QCMAP: An Interactive Web-Tool for Performance Diagnosis and Prediction of LC-MS Systems. Proteomics, 19(13), 1-4. [More Information]
• Cao, Y., Lin, Y., Ormerod, J., Yang, P., Yang, J., Lo, K. (2019). scDC: single cell differential composition analysis. BMC Bioinformatics, 20(Suppl 19), 1-21. [More Information]
• Lin, Y., Ghazanfar, S., Wang, K., Gagnon-Bartsch, J., Lo, K., Su, X., Han, Z., Ormerod, J., Speed, T., Yang, P., Yang, J. (2019). scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proceedings of the National Academy of Sciences of the United States of America, 116(20), 9775-9784. [More Information]
• Kim, T., Lo, K., Geddes, T., Kim, H., Yang, J., Yang, P. (2019). scReClassify: post hoc cell type classification of single-cell rNA-seq data. BMC Genomics, 20(Suppl 9), 1-10. [More Information]
• Hong, A., Ferguson, P., Dodds, T., Jones, D., Li, M., Yang, J., Scolyer, R. (2019). Significant association of PD-L1 expression with human papillomaviruspositivity and its prognostic impact in oropharyngeal cancer. Oral Oncology, 92, 33-39. [More Information]
• Vernon, S., Hansen, T., Kott, K., Yang, J., O'Sullivan, J., Figtree, G. (2019). Utilizing state-of-the-art "omics" technology and bioinformatics to identify new biological mechanisms and biomarkers for coronary artery disease. Microcirculation, 26(2), 1-9. [More Information]

2018

• Sykes, E., McDonald, C., Ghazanfar, S., Mactier, S., Thompson, J., Scolyer, R., Yang, J., Mann, G., Christopherson, R. (2018). A 14-Protein Signature for Rapid Identification of Poor Prognosis Stage III Metastatic Melanoma. Proteomics - Clinical Applications, 12(3), 1-12. [More Information]
• Shah, J., Gard, G., Yang, J., Maidens, J., Valmadre, S., Soon, P., Marsh, D. (2018). Combining serum microRNA and CA-125 as prognostic indicators of preoperative surgical outcome in women with high-grade serous ovarian cancer. Gynecologic Oncology, 148(1), 181-188. [More Information]
• Fazakerley, D., Chaudhuri, R., Yang, P., Maghazal, G., Cooke, K., Krycer, J., Humphrey, S., Parker, B., Fisher-Wellman, K., Meoli, C., Hoffman, N., Diskin, C., Burchfield, J., Yang, J., James, D., et al (2018). Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. eLife, 7(Article number e32111), 1-38. [More Information]
• Vaishnav, C., Craig, J., Howard, K., Howell, M., Alexander, S., Chadban, S., Clayton, P., Lim, W., Kanellis, J., Wyburn, K., Yang, J., Wong, G., et al (2018). Survival and quality of life impact of a risk-based allocation algorithm for deceased donor kidney transplantation. Transplantation, 102(9), 1530-1537. [More Information]
• Chaudhuri, R., Krycer, J., Fazakerley, D., Fisher-Wellman, K., Su, Z., Hoehn, K., Yang, J., Kuncic, Z., Vafaee, F., James, D. (2018). The transcriptional response to oxidative stress is part of, but not sufcient for, insulin resistance in adipocytes. Scientific Reports, 8(1), 1-15. [More Information]
• Bisogni, A., Ghazanfar, S., Williams, E., Marsh, H., Yang, J., Lin, D. (2018). Tuning of delta-protocadherin adhesion through combinatorial diversity. eLife, 7, 1-27. [More Information]

2017

• Choong, E., Hruby, G., Yang, J., Kwong, C., Patanjali, N. (2017). 78Gy with Fiducial Marker Image-Guided Radiotherapy in Prostate Cancer: Single Center Analysis of 301 Patients. Asia-Pacific Journal of Clinical Oncology, 13(5), e356-e363. [More Information]
• Patrick, E., Schramm, S., Ormerod, J., Scolyer, R., Mann, G., Mueller, S., Yang, J. (2017). A multi-step classifier addressing cohort heterogeneity improves performance of prognostic biomarkers in three cancer types. Oncotarget, 8(2), 2807-2815. [More Information]
• Chaudhuri, R., Yang, J. (2017). Cross-Species PTM Mapping from Phosphoproteomic Data. In Cathy H. Wu, Cecilia N. Arighi, Karen E. Ross (Eds.), Protein Bioinformatics: From Protein Modifications and Networks to Proteomics, (pp. 459-469). New York: Humana Press. [More Information]
• Ghazanfar, S., Vuocolo, T., Morrison, J., Nicholas, L., McMillen, I., Yang, J., Buckley, M., Tellam, R. (2017). Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis. PloS One, 12(6), 1-22. [More Information]
• Koop, D., Cisternas, P., Morris, V., Strbenac, D., Yang, J., Wray, G., Byrne, M. (2017). Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan. BMC Developmental Biology, 17, 1-13. [More Information]
• Kakavand, H., Rawson, R., Pupo, G., Yang, J., Menzies, A., Carlino, M., Kefford, R., Howle, J., Saw, R., Thompson, J., Wilmott, J., Long, G., Scolyer, R., et al (2017). PD-L1 expression and immune escape in melanoma resistance to MAPK inhibitors. Clinical Cancer Research, 23(20), 6054-6061. [More Information]
• Yang, P., Liu, W., Yang, J. (2017). Positive Unlabeled Learning via Wrapper-Based Adaptive Sampling. 26th International Joint Conference on Artificial Intelligence (IJCAI 2017), Melbourne: International Joint Conferences on Artificial Intelligence. [More Information]
• Strbenac, D., Zhong, L., Raftery, M., Wang, P., Wilson, S., Armstrong, N., Yang, J. (2017). Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods. Journal of Proteome Research, 16(7), 2359-2369. [More Information]
• Su, X., Shi, Y., Zou, X., Lu, Z., Xie, G., Yang, J., Wu, C., Cui, X., He, K., Luo, Q., et al (2017). Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development. BMC Genomics, 18(1), 1-14. [More Information]
• Wong, G., Howell, M., Patrick, E., Yang, J. (2017). Taking Kidneys for Granted? Time to Reflect on the Choices We Make. Transplantation, 101(12), 2812-2813. [More Information]
• Hayward, N., Wilmott, J., Waddell, N., Johansson, P., Field, M., Nones, K., Patch, A., Kakavand, H., Alexandrov, L., Burke, H., Jakrot, V., Tembe, V., Pupo, G., De Paoli-Iseppi, R., Vilain, R., Shang, P., Lau, L., Dagg, R., Schramm, S., Pickett, H., Yang, J., Stretch, J., Kefford, R., Hersey, P., Long, G., Spillane, A., Saw, R., Thompson, J., Scolyer, R., Mann, G., et al (2017). Whole-genome landscapes of major melanoma subtypes. Nature, 545(7653), 175-180. [More Information]

2016

• Ghazanfar, S., Yang, J. (2016). Characterizing mutation-expression network relationships in multiple cancers. Computational Biology and Chemistry, 63, 73-82. [More Information]
• Strbenac, D., Mann, G., Yang, J., Ormerod, J. (2016). Differential distribution improves gene selection stability and has competitive classification performance for patient survival. Nucleic Acids Research, 44(13), 1-13. [More Information]
• Minard, A., Wong, M., Chaudhuri, R., Tan, S., Humphrey, S., Parker, B., Yang, J., Laybutt, D., Cooney, G., Coster, A., Stoeckli, J., James, D. (2016). Hyperactivation of the Insulin Signaling Pathway Improves Intracellular Proteostasis by Coordinately Up-regulating the Proteostatic Machinery in Adipocytes. Journal of Biological Chemistry, 291(49), 25629-25640. [More Information]
• Jayawardana, K., Schramm, S., Tembe, V., Mueller, S., Thompson, J., Scolyer, R., Mann, G., Yang, J. (2016). Identification, Review, and Systematic Cross-Validation of microRNA Prognostic Signatures in Metastatic Melanoma. Journal of Investigative Dermatology, 136(1), 245-254. [More Information]
• Ghazanfar, S., Bisogni, A., Ormerod, J., Lin, D., Yang, J. (2016). Integrated single cell data analysis reveals cell specific networks and novel coactivation markers. BMC Systems Biology, 10(Suppl 5), 11-24. [More Information]
• 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. [More Information]
• Hong, A., Vilain, R., Romanes, S., Yang, J., Smith, E., Jones, D., Scolyer, R., Lee, C., Zhang, M., Rose, B. (2016). PD-L1 expression in tonsillar cancer is associated with human papillomavirus positivity and improved survival: Implications for anti-PD1 clinical trials. Oncotarget, 7(47), 77010-77020. [More Information]
• Madore, J., Strbenac, D., Vilain, R., Menzies, A., Yang, J., Thompson, J., Long, G., Mann, G., Scolyer, R., Wilmott, J. (2016). PD-L1 Negative Status is Associated with Lower Mutation Burden, Differential Expression of Immune-Related Genes, and Worse Survival in Stage III Melanoma. Clinical Cancer Research, 22(15), 3915-3923. [More Information]
• 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. [More Information]
• Banihashemi, N., Robillard, R., Yang, J., Carpenter, J., Hermens, D., Naismith, S., Terpening, Z., White, D., Scott, E., Hickie, I. (2016). Quantifying the effect of body mass index, age, and depression severity on 24-h activity patterns in persons with a lifetime history of affective disorders. BMC Psychiatry, 16(1), 1-11. [More Information]
• Markus, A., Yang, J., Morris, B. (2016). Transcriptome-wide targets of alternative splicing by RBM4 and possible role in cancer. Genomics, 107(4), 138-144. [More Information]

2015

• Rahman, W., Tu, T., Budzinska, M., Huang, P., Belov, L., Chrisp, J., Christopherson, R., Warner, F., Bowden, D., Thomspon, A., Bowen, D., Strasser, S., Sharland, A., Yang, J., McCaughan, G., Shackel, N., et al (2015). Analysis of Post-Liver Transplant Hepatitis C Virus Recurrence Using Serial Cluster of differentiation Antibody Microarrays. Transplantation, 99(9), e120-e126. [More Information]
• Strbenac, D., Mann, G., Ormerod, J., Yang, J. (2015). ClassifyR: an R package for performance assessment of classification with applications to transcriptomics. Bioinformatics, 31(11), 1851-1853. [More Information]
• Heinemann, A., Cullinane, C., De Paoli-Iseppi, R., Wilmott, J., Gunatilake, D., Madore, J., Strbenac, D., Yang, J., Gowrishankar, K., Tiffen, J., Hersey, P., Gallagher, S., et al (2015). Combining BET and HDAC inhibitors synergistically induces apoptosis of melanoma and suppresses AKT and YAP signaling. Oncotarget, 6(25), 21507-21521. [More Information]
• Chaudhuri, R., Khoo, P., Tonks, K., Junutula, J., Kolumam, G., Modrusan, Z., Samocha-Bonet, D., Meoli, C., Hocking, S., Fazakerley, D., Stoeckli, J., Yang, J., James, D., et al (2015). Cross-species gene expression analysis identifies a novel set of genes implicated in human insulin sensitivity. Npj Systems Biology And Applications, 1, 1-10. [More Information]
• Jayawardana, K., Schramm, S., Haydu, L., Thompson, J., Scolyer, R., Mann, G., Mueller, S., Yang, J. (2015). Determination of prognosis in metastatic melanoma through integration of clinico-pathologic, mutation, mRNA, microRNA, and protein information. International Journal of Cancer, 136(4), 863-874. [More Information]
• Patrick, E., Buckley, M., Mueller, S., Lin, D., Yang, J. (2015). Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data. Bioinformatics, 31(17), 2822-2828. [More Information]
• 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), 1-18. [More Information]
• Tembe, V., Schramm, S., Stark, M., Patrick, E., Jayaswal, V., Tang, Y., Barbour, A., Hayward, N., Thompson, J., Scolyer, R., Yang, J., Mann, G. (2015). microRNA and mRNA expression profiling in metastatic melanoma reveal associations with BRAF mutation and patient prognosis. Pigment Cell & Melanoma Research, 28(3), 254-226. [More Information]
• Chaudhuri, R., Sadrieh, A., Hoffman, N., Parker, B., Humphrey, S., Stoeckli, J., Hill, A., James, D., Yang, J. (2015). PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modification. BMC Genomics, 16(1), 1-14. [More Information]
• Tiffen, J., Gunatilake, D., Gallagher, S., Gowrishankar, K., Heinemann, A., Cullinane, C., Dutton-Regester, K., Pupo, G., Strbenac, D., Yang, J., Madore, J., Mann, G., Hersey, P., et al (2015). Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes. Oncotarget, 6(29), 27023-27036. [More Information]
• Byrne, M., Koop, D., Cisternas, P., Strbenac, D., Yang, J., Wray, G. (2015). Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma. Marine Genomics, 24(1), 41-45. [More Information]

2014

• Nair, R., Roden, D., Teo, W., McFarland, A., Junankar, S., Ye, S., Nguyen, A., Yang, J., Nicolic, I., Hui, M., Armstrong, N., Naylor, M., O'Toole, S., et al (2014). c-Myc and Her2 cooperate to drive a stem-like phenotype with poor prognosis in breast cancer. Oncogene, 33(30), 3992-4002. [More Information]
• 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. [More Information]
• Palmer, S., Wong, G., Iff, S., Yang, J., Jayaswal, V., Craig, J., Rochtchina, E., Mitchell, P., Wang, J., Strippoli, G. (2014). Fluid intake and all-cause mortality, cardiovascular mortality, and kidney function: a population-based longitudinal cohort study. Nephrology Dialysis Transplantation, 29(7), 1377-1384. [More Information]
• 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 gamma Activation and Early Adipogenesis via Bone Morphogenetic Protein 4-Dependent and -Independent Mechanisms. Molecular and Cellular Biology, 34(19), 3607-3617. [More Information]
• Barter, R., Schramm, S., Mann, G., Yang, J. (2014). Network-based biomarkers enhance classical approaches to prognostic gene expression signatures. International Conference on Bioinformatics 2014 (InCoB2014), Australia: BMC Public Health. [More Information]
• Mactier, S., Alexander, K., Wang, P., Crossett, B., Pupo, G., Kohnke, P., Thompson, J., Scolyer, R., Yang, J., Mann, G., Christopherson, R. (2014). Protein signatures correspond to survival outcomes of AJCC stage III melanoma patients. Pigment Cell & Melanoma Research, 27(6), 1106-1116. [More Information]
• Yang, P., Zhou, B., Yang, J., Zomaya, A. (2014). Stability of Feature Selection Algorithms and Ensemble Feature Selection Methods in Bioinformatics. In Mourad Elloumi, Albert Y. Zomaya (Eds.), Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, (pp. 333-352). New Jersey: John Wiley & Sons. [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. 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 & 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]
• Mactier, S., Alexander, K., Wang, P., Crossett, B., Yang, E., Scolyer, R., Yang, J., Mann, G., Christopherson, R. (2013). Identification of markers prognostic of survival in lymph node metastases from stage III melanoma patients. European Journal of Cancer, 49(Suppl 2), S874-S874.
• Tonks, K., Ng, Y., Miller, S., Coster, A., Samocha-Bonet, D., Iseli, T., Xu, A., Patrick, E., Yang, J., Junutula, J., et al (2013). Impaired Akt phosphorylation in insulin-resistant human muscle is accompanied by selective and heterogeneous downstream defects. Diabetologia, 56(4), 875-885. [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: Institute of Electrical and Electronics Engineers (IEEE). [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]
• Pepin-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. 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. [More Information]
• 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. [More Information]
• 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. 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. [More Information]
• 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. [More Information]
• 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. [More Information]
• 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. [More Information]
• 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. [More Information]
• 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 of the United States of America, 104(40), 15858-15863. [More Information]
• 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. [More Information]

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. [More Information]
• 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. [More Information]
• Yang, J., Xiao, Y., Segal, M. (2005). Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics, 21(7), 1084-1093. [More Information]
• 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. [More Information]
• 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. [More Information]

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. [More Information]
• 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 of the United States of America, 101(34), 12718-12723. [More Information]

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 of the United States of America, 100(9), 5491-5496. [More Information]
• Erle, D., Yang, J. (2003). Asthma investigators begin to reap the fruits of genomics. Genome Biology, 4(11), 232.1-232.3. [More Information]
• 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. [More Information]
• 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. [More Information]
• 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.

1997

• Yang, J., Buckley, M. (1997). Regularised shortest-path extraction. Pattern Recognition Letters, 18(7), 621-629.