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Associate Professor Ellis Patrick

Associate Professor
School of Mathematics and Statistics

Phone

0402159424

[email protected]

Address

F07 - Carslaw Building

The University of Sydney

Websites

Personal website

Google Scholar

Biographical details

A/Prof Ellis Patrick is an applied statistician and bioinformatician. He is currently an Associate Professor in the School of Mathematics and Statistics, a Faculty member at The Westmead Institute for Medical Research and the Cluster Lead of Bioinformatics in the Sydney Precision Data Science Centre. He obtained his PhD in statistical bioinformatics in the School of Mathematics and Statistics at the University of Sydney and during his postdoctoral studies, he worked as a computational biologist with joint appointments at Brigham and Women's hospital, Harvard Medical School and The Broad Institute of MIT and Harvard.

Research interests

A/Prof Patrick’s research interests lie at the interface of statistics and biomedical data science where he specialises in developing and implementing innovative bioinformatics tools to enhance our understanding and treatment of human diseases. He has cultivated an extensive collaborative network and applies his expertise in extracting meaning from cutting-edge high-dimensional molecular and cellular assays to enable research into infectious diseases, organ transplant, cardiovascular disease, neurodegeneration, and cancer. The analytical challenges inherent in this disease-focused research necessitate the creation, evaluation, and sharing of advanced statistical methodology to support breakthrough discoveries.

Teaching and supervision

A/Prof Patrick is passionate about training young researchers to address the critical shortage of bioinformatics expertise in Australia. He is currently mentoring 7 postgraduate students and has facilitated the timely completion of 2 PhD, 1 MPhil student and 7 Honours theses and mentored 1 Dalyell and 7 Denison Scholarship students. He currently chairs the Australian Bioinformatics and Computational Biology Society (ABACBS) Education and Training Subcommittee and sits on the Australian Mathematical Sciences Institute (AMSI) BioInfoSummer Standing Committee

Timetable

Current projects

Please contact A/Prof Patrick to discuss potential PhD and Honours projects.

Current research students

Project title	Research student
Drug repurposing in the context of acute kidney injuries	Aadhar MOUDGIL
Deciphering homogenous mechanisms for pan-organ allograft dysfunction	Harry ROBERTSON
Harnessing the power of deep learning for single-cell omics analysis	Manoj M WAGLE
Developing Robust clustering methods for scRNA-seq data.	Elijah WILLIE

Publications

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Journals

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., Cao, Y., Wood, E., Patrick, E., Yang, J. (2023). Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Nature Communications, 14.
Stern, L., McGuire, H., Avdic, S., Blyth, E., Gottlieb, D., Patrick, E., Abendroth, A., Slobedman, B. (2023). Circulating cytokine and chemokine patterns associated with cytomegalovirus reactivation after stem cell transplantation. Clinical & Translational Immunology, 12(12), e16815-1-e16815-17. [More Information]
Adegoke, N., Gide, T., Mao, Y., Quek, C., Patrick, E., Carlino, M., Lo, S., Menzies, A., Esteves Domingues Pires da Silva, I., Vergara Correa, I., Long, G., Scolyer, R., Wilmott, J. (2023). Classification of the tumor immune microenvironment and associations with outcomes in patients with metastatic melanoma treated with immunotherapies. Journal for ImmunoTherapy of Cancer, 11(10). [More Information]
Mao, Y., Gide, T., Adegoke, N., Quek, C., Maher, N., Potter, A., Patrick, E., Saw, R., Thompson, J., Spillane, A., Shannon, K., Carlino, M., Lo, S., Menzies, A., Da Silva, I., Long, G., Scolyer, R., Wilmott, J. (2023). Cross‑platform comparison of immune signatures in immunotherapy‑treated patients with advanced melanoma using a rank‑based scoring approach. Journal of Translational Medicine, 21(Green Open Access), Article 257-16 pages. [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]
Peters Couto, B., Robertson, N., Patrick, E., Ghazanfar, S. (2023). MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor. Bioinformatics, 39(9), 1-5. [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]
Azimi, A., Patrick, E., Teh, R., Kim, J., Fernandez Penas, P. (2023). Proteomic profiling of cutaneous melanoma explains the aggressiveness of distant organ metastasis. Experimental Dermatology. [More Information]
Patrick, E., Canete, N., Iyengar, S., Harman, A., Sutherland, G., Yang, P. (2023). Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments. Cytometry Part A, 103, 593-599. [More Information]
Sawyer, A., Patrick, E., Edwards, J., Wilmott, J., Fielder, T., Yang, Q., Barber, D., Ernst, J., Britton, W., Palendira, M., Feng, C., et al (2023). Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis. The Journal of Experimental Medicine, 220(6), e20221392. [More Information]
Willie, E., Yang, P., Patrick, E. (2023). The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data. Bioinformatics Advances, 3 (Open Access)(1), Article vbad141-1-Article vbad141-12. [More Information]
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]
Baharlou, H., Canete, N., Vine, E., Hu, K., Yuan, D., Sandgren, K., Bertram, K., Nasr, N., Rhodes, J., Gosselink, M., Patrick, E., Byrne, S., Cunningham, A., Harman, A., et al (2022). An in situ analysis pipeline for initial host-pathogen interactions reveals signatures of human colorectal HIV transmission. Cell Reports, 40(12), 111385-1-111385-27. [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]
Ferguson, A., Sharman, A., Allen, R., Ye, T., Lee, J., Low, T., Ch'ng, S., Palme, C., Ashford, B., Ranson, M., Clark, J., Patrick, E., Gupta, R., Palendira, M. (2022). High-Dimensional and Spatial Analysis Reveals Immune Landscape–Dependent Progression in Cutaneous Squamous Cell Carcinoma. Clinical Cancer Research, 28(21), 4677-4688. [More Information]
Purvis, M., Robertson, H., Patrick, E., Rogers, N. (2022). Research trends in Australia and New Zealand Nephrology: basic science and gender equity in peril. Internal Medicine Journal, 52(11), 1991-1994. [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]
Canete, N., Iyengar, S., Ormerod, J., Baharlou, H., Harman, A., Patrick, E. (2022). spicyR: spatial analysis of in situ cytometry data in R. Bioinformatics, 38(11), 3099-3155. [More Information]
McCorkindale, A., Patrick, E., Duce, J., Guennewig, B., Sutherland, G. (2022). The Key Factors Predicting Dementia in Individuals With Alzheimer’s Disease-Type Pathology. Frontiers in Aging Neuroscience, 14(Open Access), Article number 831967 - 1-Article number 831967 - 8. [More Information]
Jiang, W., Clancy, L., Avdic, S., Sutrave, G., Street, J., Simms, R., McGuire, H., Patrick, E., Chan, A., McCaughan, G., Myers, N., Micklethwaite, K., Bateman, C., Shaw, P., Blyth, E., Gottlieb, D., et al (2022). Third-party CMV- and EBV-specific T-cells for first viral reactivation after allogeneic stem cell transplant. Blood Advances, 6(17), 4949-4966. [More Information]
Patrick, E., Olah, M., Taga, M., Klein, H., Xu, J., White, C., Felsky, D., Agrawal, S., Gaiteri, C., Chibnik, L., et al (2021). A cortical immune network map identifies distinct microglial transcriptional programs associated with â-amyloid and Tau pathologies. Translational Psychiatry, 11 Open Access(1), 1-17. [More Information]
Baharlou, H., Canete, N., Bertram, K., Sandgren, K., Cunningham, A., Harman, A., Patrick, E. (2021). AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images. Bioinformatics, 37(4), 559-567. [More Information]
Guennewig, B., Lim, J., Marshall, L., McCorkindale, A., Paasila, P., Patrick, E., Kril, J., Halliday, G., Cooper, A., Sutherland, G. (2021). Defining early changes in Alzheimer's disease from RNA sequencing of brain regions differentially affected by pathology. Scientific Reports, 11(1), 4865. [More Information]
Rhodes, J., Botting, R., Bertram, K., Vine, E., Rana, H., Baharlou, H., Vegh, P., O'Neil, T., Ashhurst, A., Fletcher, J., Parnell, G., Graham, J., Nasr, N., Gosselink, M., Di Re, A., Reza, F., Ctercteko, G., Patrick, E., Byrne, S., Cunningham, A., Harman, A., et al (2021). Human anogenital monocyte-derived dendritic cells and langerin+cDC2 are major HIV target cells. Nature Communications, 12, Article 2147-15 pages. [More Information]
Tsatsanis, A., McCorkindale, A., Wong, B., Patrick, E., Ryan, T., Evans, R., Bush, A., Sutherland, G., Sivaprasadarao, A., Guennewig, B., et al (2021). The acute phase protein lactoferrin is a key feature of Alzheimer's disease and predictor of Aβ burden through induction of APP amyloidogenic processing. Molecular Psychiatry, 26(10), 5516-5531. [More Information]
Robertson, H., Li, J., Kim, H., Rhodes, J., Harman, A., Patrick, E., Rogers, N. (2021). Transcriptomic Analysis Identifies A Tolerogenic Dendritic Cell Signature. Frontiers in Immunology, 12(Published 20 October 2021), 733231 - 1-733231 - 14. [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]
Patrick, E., Taga, M., Ergun, A., Ng, B., Casazza, W., Cimpean, M., Yung, C., Schneider, J., Bennett, D., Gaiteri, C., et al (2020). Deconvolving the contributions of cell-type heterogeneity on cortical gene expression. PLoS Computational Biology, 16(8), 1-17. [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]
McGuire, H., Rizzetto, S., Withers, B., Clancy, L., Avdic, S., Stern, L., Patrick, E., Fazekas de St Groth, B., Slobedman, B., Gottlieb, D., Blyth, E., et al (2020). Mass cytometry reveals immune signatures associated with cytomegalovirus (CMV) control in recipients of allogeneic haemopoietic stem cell transplant and CMV-specific T cells. Clinical & Translational Immunology, 9(7), 1-16. [More Information]
Thejer, B., Adhikary, P., Kaur, A., Teakel, S., Van Oosterum, A., Seth, I., Pajic, M., Hannan, K., Pavy, M., Poh, P., Patrick, E., New, E., et al (2020). PGRMC1 phosphorylation affects cell shape, motility, glycolysis, mitochondrial form and function, and tumor growth. BMC Molecular and Cell Biology, 21(1), 1-24. [More Information]
Kim, H., Osteil, P., Humphrey, S., Cinghu, S., Oldfield, A., Patrick, E., Wilkie, E., Peng, G., Suo, S., Jothi, R., Tam, P., Yang, P. (2020). Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning. Nucleic Acids Research, 48(4), 1828-1842. [More Information]
Kozlowska, K., Chung, J., Cruickshank, B., McLean, L., Scher, S., Dale, R., Mohammad, S., Singh-Grewal, D., Prabhuswamy, M., Patrick, E. (2019). Blood CRP levels are elevated in children and adolescents with functional neurological symptom disorder. European Child and Adolescent Psychiatry, 28(4), 491-504. [More Information]
Tea, F., Lopez, J., Ramanathan, S., Merheb, V., Lee, F., Zou, A., Pilli, D., Patrick, E., van der Walt, A., Monif, M., Tantsis, E., Fraser, C., Reddel, S., Barnett, M., Brown, D., Dale, R., Brilot-Turville, F., et al (2019). Characterization of the human myelin oligodendrocyte glycoprotein antibody response in demyelination. Acta Neuropathologica Communications, 7(1), 1-22. [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]
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]
Bertram, K., Botting, R., Baharlou, H., Rhodes, J., Rana, H., Graham, J., Patrick, E., Fletcher, J., Plasto, T., Truong (Osborne), N., Royle, C., Doyle, C., Tong, O., Nasr, N., Cunningham, A., Harman, A., et al (2019). Identification of HIV transmitting CD11c+ human epidermal dendritic cells. Nature Communications, 10(1), 1-15. [More Information]
Baharlou, H., Canete, N., Cunningham, A., Harman, A., Patrick, E. (2019). Mass Cytometry Imaging for the Study of Human Diseases - Applications and Data Analysis Strategies. Frontiers in Immunology, 10, 1-22. [More Information]
Patsopoulos, N., Baranzini, S., Santaniello, A., Shoostari, P., Cotsapas, C., Wong, G., Beecham, A., James, T., Repogle, J., Patrick, E., Stewart, G., Booth, D., Ivinson, A., et al (2019). Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science, 365(6460), 1-10. [More Information]
Jimenez Vera, E., Chew, Y., Nicholson, L., Burns, H., Anderson, P., Chen, H., Williams, L., Keung, K., Zanjani, N., Dervish, S., Patrick, E., Yi, S., Hawthorne, W., O'Connell, P., Hu, M., et al (2019). Standardisation of flow cytometry for whole blood immunophenotyping of islet transplant and transplant clinical trial recipients. PloS One, 14(5), 1-28. [More Information]
Ng, B., Casazza, W., Patrick, E., Tasaki, S., Novakovsky, G., Felsky, D., Ma, Y., Bennett, D., Gaiteri, C., De Jager, P., et al (2019). Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain. American Journal of Human Genetics, 105(3), 562-572. [More Information]
Mostafavi, S., Gaiteri, C., Sullivan, S., White, C., Tasaki, S., Xu, J., Taga, M., Klein, H., Patrick, E., Komashko, V., et al (2018). A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Nature Neuroscience, 21(6), 811-819. [More Information]
Olah, M., Patrick, E., Villani, A., Xu, J., White, C., Ryan, K., Piehowski, P., Kapasi, A., Nejad, P., Cimpean, M., et al (2018). A transcriptomic atlas of aged human microglia. Nature Communications, 9(1), 1-8. [More Information]
Felsky, D., Patrick, E., Schneider, J., Mostafavi, S., Gaiteri, C., Patsopoulos, N., Bennett, D., De Jager, P. (2018). Polygenic analysis of inflammatory disease variants and effects on microglia in the aging brain. Molecular Neurodegeneration, 13(1), 1-10. [More Information]
Bove, R., Patrick, E., McCabe Aubin, C., Srivastava, G., Schneider, J., Bennett, D., De Jager, P., Chibnik, L. (2018). Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. PloS One, 13(7), 1-12. [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]
Ng, B., White, C., Klein, H., Sieberts, S., McCabe, C., Patrick, E., Xu, J., Yu, L., Gaiteri, C., Bennett, D., et al (2017). An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nature Neuroscience, 20(10), 1418-1426. [More Information]
Patrick, E., Rajagopal, S., Wong, H., McCabe, C., Xu, J., Tang, A., Imboywa, S., Schneider, J., Pochet, N., Krichevsky, A., et al (2017). Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease. Molecular Neurodegeneration, 12(1), 1-13. [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]
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]
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]
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]
Kember, H., Croot, K., Patrick, E. (2015). Phonological encoding in Mandarin Chinese: Evidence from tongue twisters. Language And Speech, 58(4), 417-440. [More Information]
Sparks, R., Patrick, E. (2014). Detection of Multiple Outbreaks Using SpatioTemporal EWMA-Ordered Statistics. Communications in Statistics: Simulation and Computation, 43(10), 2678-2701. [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]
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]
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]
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]

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2024

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.

2023

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.
Stern, L., McGuire, H., Avdic, S., Blyth, E., Gottlieb, D., Patrick, E., Abendroth, A., Slobedman, B. (2023). Circulating cytokine and chemokine patterns associated with cytomegalovirus reactivation after stem cell transplantation. Clinical & Translational Immunology, 12(12), e16815-1-e16815-17. [More Information]
Adegoke, N., Gide, T., Mao, Y., Quek, C., Patrick, E., Carlino, M., Lo, S., Menzies, A., Esteves Domingues Pires da Silva, I., Vergara Correa, I., Long, G., Scolyer, R., Wilmott, J. (2023). Classification of the tumor immune microenvironment and associations with outcomes in patients with metastatic melanoma treated with immunotherapies. Journal for ImmunoTherapy of Cancer, 11(10). [More Information]
Mao, Y., Gide, T., Adegoke, N., Quek, C., Maher, N., Potter, A., Patrick, E., Saw, R., Thompson, J., Spillane, A., Shannon, K., Carlino, M., Lo, S., Menzies, A., Da Silva, I., Long, G., Scolyer, R., Wilmott, J. (2023). Cross‑platform comparison of immune signatures in immunotherapy‑treated patients with advanced melanoma using a rank‑based scoring approach. Journal of Translational Medicine, 21(Green Open Access), Article 257-16 pages. [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]
Peters Couto, B., Robertson, N., Patrick, E., Ghazanfar, S. (2023). MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor. Bioinformatics, 39(9), 1-5. [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]
Azimi, A., Patrick, E., Teh, R., Kim, J., Fernandez Penas, P. (2023). Proteomic profiling of cutaneous melanoma explains the aggressiveness of distant organ metastasis. Experimental Dermatology. [More Information]
Patrick, E., Canete, N., Iyengar, S., Harman, A., Sutherland, G., Yang, P. (2023). Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments. Cytometry Part A, 103, 593-599. [More Information]
Sawyer, A., Patrick, E., Edwards, J., Wilmott, J., Fielder, T., Yang, Q., Barber, D., Ernst, J., Britton, W., Palendira, M., Feng, C., et al (2023). Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis. The Journal of Experimental Medicine, 220(6), e20221392. [More Information]
Willie, E., Yang, P., Patrick, E. (2023). The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data. Bioinformatics Advances, 3 (Open Access)(1), Article vbad141-1-Article vbad141-12. [More Information]
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]

show 9 more

2022

Baharlou, H., Canete, N., Vine, E., Hu, K., Yuan, D., Sandgren, K., Bertram, K., Nasr, N., Rhodes, J., Gosselink, M., Patrick, E., Byrne, S., Cunningham, A., Harman, A., et al (2022). An in situ analysis pipeline for initial host-pathogen interactions reveals signatures of human colorectal HIV transmission. Cell Reports, 40(12), 111385-1-111385-27. [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]
Ferguson, A., Sharman, A., Allen, R., Ye, T., Lee, J., Low, T., Ch'ng, S., Palme, C., Ashford, B., Ranson, M., Clark, J., Patrick, E., Gupta, R., Palendira, M. (2022). High-Dimensional and Spatial Analysis Reveals Immune Landscape–Dependent Progression in Cutaneous Squamous Cell Carcinoma. Clinical Cancer Research, 28(21), 4677-4688. [More Information]
Purvis, M., Robertson, H., Patrick, E., Rogers, N. (2022). Research trends in Australia and New Zealand Nephrology: basic science and gender equity in peril. Internal Medicine Journal, 52(11), 1991-1994. [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]
Canete, N., Iyengar, S., Ormerod, J., Baharlou, H., Harman, A., Patrick, E. (2022). spicyR: spatial analysis of in situ cytometry data in R. Bioinformatics, 38(11), 3099-3155. [More Information]
McCorkindale, A., Patrick, E., Duce, J., Guennewig, B., Sutherland, G. (2022). The Key Factors Predicting Dementia in Individuals With Alzheimer’s Disease-Type Pathology. Frontiers in Aging Neuroscience, 14(Open Access), Article number 831967 - 1-Article number 831967 - 8. [More Information]
Jiang, W., Clancy, L., Avdic, S., Sutrave, G., Street, J., Simms, R., McGuire, H., Patrick, E., Chan, A., McCaughan, G., Myers, N., Micklethwaite, K., Bateman, C., Shaw, P., Blyth, E., Gottlieb, D., et al (2022). Third-party CMV- and EBV-specific T-cells for first viral reactivation after allogeneic stem cell transplant. Blood Advances, 6(17), 4949-4966. [More Information]

show 5 more

2021

Patrick, E., Olah, M., Taga, M., Klein, H., Xu, J., White, C., Felsky, D., Agrawal, S., Gaiteri, C., Chibnik, L., et al (2021). A cortical immune network map identifies distinct microglial transcriptional programs associated with â-amyloid and Tau pathologies. Translational Psychiatry, 11 Open Access(1), 1-17. [More Information]
Baharlou, H., Canete, N., Bertram, K., Sandgren, K., Cunningham, A., Harman, A., Patrick, E. (2021). AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images. Bioinformatics, 37(4), 559-567. [More Information]
Guennewig, B., Lim, J., Marshall, L., McCorkindale, A., Paasila, P., Patrick, E., Kril, J., Halliday, G., Cooper, A., Sutherland, G. (2021). Defining early changes in Alzheimer's disease from RNA sequencing of brain regions differentially affected by pathology. Scientific Reports, 11(1), 4865. [More Information]
Rhodes, J., Botting, R., Bertram, K., Vine, E., Rana, H., Baharlou, H., Vegh, P., O'Neil, T., Ashhurst, A., Fletcher, J., Parnell, G., Graham, J., Nasr, N., Gosselink, M., Di Re, A., Reza, F., Ctercteko, G., Patrick, E., Byrne, S., Cunningham, A., Harman, A., et al (2021). Human anogenital monocyte-derived dendritic cells and langerin+cDC2 are major HIV target cells. Nature Communications, 12, Article 2147-15 pages. [More Information]
Tsatsanis, A., McCorkindale, A., Wong, B., Patrick, E., Ryan, T., Evans, R., Bush, A., Sutherland, G., Sivaprasadarao, A., Guennewig, B., et al (2021). The acute phase protein lactoferrin is a key feature of Alzheimer's disease and predictor of Aβ burden through induction of APP amyloidogenic processing. Molecular Psychiatry, 26(10), 5516-5531. [More Information]
Robertson, H., Li, J., Kim, H., Rhodes, J., Harman, A., Patrick, E., Rogers, N. (2021). Transcriptomic Analysis Identifies A Tolerogenic Dendritic Cell Signature. Frontiers in Immunology, 12(Published 20 October 2021), 733231 - 1-733231 - 14. [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]

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2020

Patrick, E., Taga, M., Ergun, A., Ng, B., Casazza, W., Cimpean, M., Yung, C., Schneider, J., Bennett, D., Gaiteri, C., et al (2020). Deconvolving the contributions of cell-type heterogeneity on cortical gene expression. PLoS Computational Biology, 16(8), 1-17. [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]
McGuire, H., Rizzetto, S., Withers, B., Clancy, L., Avdic, S., Stern, L., Patrick, E., Fazekas de St Groth, B., Slobedman, B., Gottlieb, D., Blyth, E., et al (2020). Mass cytometry reveals immune signatures associated with cytomegalovirus (CMV) control in recipients of allogeneic haemopoietic stem cell transplant and CMV-specific T cells. Clinical & Translational Immunology, 9(7), 1-16. [More Information]
Thejer, B., Adhikary, P., Kaur, A., Teakel, S., Van Oosterum, A., Seth, I., Pajic, M., Hannan, K., Pavy, M., Poh, P., Patrick, E., New, E., et al (2020). PGRMC1 phosphorylation affects cell shape, motility, glycolysis, mitochondrial form and function, and tumor growth. BMC Molecular and Cell Biology, 21(1), 1-24. [More Information]
Kim, H., Osteil, P., Humphrey, S., Cinghu, S., Oldfield, A., Patrick, E., Wilkie, E., Peng, G., Suo, S., Jothi, R., Tam, P., Yang, P. (2020). Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning. Nucleic Acids Research, 48(4), 1828-1842. [More Information]

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2019

Kozlowska, K., Chung, J., Cruickshank, B., McLean, L., Scher, S., Dale, R., Mohammad, S., Singh-Grewal, D., Prabhuswamy, M., Patrick, E. (2019). Blood CRP levels are elevated in children and adolescents with functional neurological symptom disorder. European Child and Adolescent Psychiatry, 28(4), 491-504. [More Information]
Tea, F., Lopez, J., Ramanathan, S., Merheb, V., Lee, F., Zou, A., Pilli, D., Patrick, E., van der Walt, A., Monif, M., Tantsis, E., Fraser, C., Reddel, S., Barnett, M., Brown, D., Dale, R., Brilot-Turville, F., et al (2019). Characterization of the human myelin oligodendrocyte glycoprotein antibody response in demyelination. Acta Neuropathologica Communications, 7(1), 1-22. [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]
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]
Bertram, K., Botting, R., Baharlou, H., Rhodes, J., Rana, H., Graham, J., Patrick, E., Fletcher, J., Plasto, T., Truong (Osborne), N., Royle, C., Doyle, C., Tong, O., Nasr, N., Cunningham, A., Harman, A., et al (2019). Identification of HIV transmitting CD11c+ human epidermal dendritic cells. Nature Communications, 10(1), 1-15. [More Information]
Baharlou, H., Canete, N., Cunningham, A., Harman, A., Patrick, E. (2019). Mass Cytometry Imaging for the Study of Human Diseases - Applications and Data Analysis Strategies. Frontiers in Immunology, 10, 1-22. [More Information]
Patsopoulos, N., Baranzini, S., Santaniello, A., Shoostari, P., Cotsapas, C., Wong, G., Beecham, A., James, T., Repogle, J., Patrick, E., Stewart, G., Booth, D., Ivinson, A., et al (2019). Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science, 365(6460), 1-10. [More Information]
Jimenez Vera, E., Chew, Y., Nicholson, L., Burns, H., Anderson, P., Chen, H., Williams, L., Keung, K., Zanjani, N., Dervish, S., Patrick, E., Yi, S., Hawthorne, W., O'Connell, P., Hu, M., et al (2019). Standardisation of flow cytometry for whole blood immunophenotyping of islet transplant and transplant clinical trial recipients. PloS One, 14(5), 1-28. [More Information]
Ng, B., Casazza, W., Patrick, E., Tasaki, S., Novakovsky, G., Felsky, D., Ma, Y., Bennett, D., Gaiteri, C., De Jager, P., et al (2019). Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain. American Journal of Human Genetics, 105(3), 562-572. [More Information]

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2018

Mostafavi, S., Gaiteri, C., Sullivan, S., White, C., Tasaki, S., Xu, J., Taga, M., Klein, H., Patrick, E., Komashko, V., et al (2018). A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Nature Neuroscience, 21(6), 811-819. [More Information]
Olah, M., Patrick, E., Villani, A., Xu, J., White, C., Ryan, K., Piehowski, P., Kapasi, A., Nejad, P., Cimpean, M., et al (2018). A transcriptomic atlas of aged human microglia. Nature Communications, 9(1), 1-8. [More Information]
Felsky, D., Patrick, E., Schneider, J., Mostafavi, S., Gaiteri, C., Patsopoulos, N., Bennett, D., De Jager, P. (2018). Polygenic analysis of inflammatory disease variants and effects on microglia in the aging brain. Molecular Neurodegeneration, 13(1), 1-10. [More Information]
Bove, R., Patrick, E., McCabe Aubin, C., Srivastava, G., Schneider, J., Bennett, D., De Jager, P., Chibnik, L. (2018). Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. PloS One, 13(7), 1-12. [More Information]

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2017

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]
Ng, B., White, C., Klein, H., Sieberts, S., McCabe, C., Patrick, E., Xu, J., Yu, L., Gaiteri, C., Bennett, D., et al (2017). An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nature Neuroscience, 20(10), 1418-1426. [More Information]
Patrick, E., Rajagopal, S., Wong, H., McCabe, C., Xu, J., Tang, A., Imboywa, S., Schneider, J., Pochet, N., Krichevsky, A., et al (2017). Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease. Molecular Neurodegeneration, 12(1), 1-13. [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]

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2016

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]

2015

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]
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]
Kember, H., Croot, K., Patrick, E. (2015). Phonological encoding in Mandarin Chinese: Evidence from tongue twisters. Language And Speech, 58(4), 417-440. [More Information]

2014

Sparks, R., Patrick, E. (2014). Detection of Multiple Outbreaks Using SpatioTemporal EWMA-Ordered Statistics. Communications in Statistics: Simulation and Computation, 43(10), 2678-2701. [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]
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]

2013

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]
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]

Selected Grants

2023

Dissecting the susceptibility of humans to coronary artery disease (CAD), Tang O, McGuire H, Figtree G, Patrick E, Gray M, Heart Research Australia/Research Grant
Circulating lipid biomarkers to track therapeutic response in multiple sclerosis, Don A, Piccio L, Hardy T, Landin-Romero R, Patrick E, Multiple Sclerosis Research Australia/Project Grant
Donor and recipient polygenic risk scores predictive of late graft loss, O'Connell P, Lim W, Li J, Wyburn K, Alexander S, Grey S, Wong G, Patrick E, Rogers N, Chadban S, Department of Health (Federal - administered by NHMRC)/Genomics Health Futures Mission - 2022 MRFF Genomics Health Futures Mission

2022

Dissecting the susceptibility of humans to coronary artery disease (CAD), Ng H, McGuire H, Figtree G, Patrick E, Gray M, Heart Research Australia/Research Grant
REnal FactORs Modify HEART disease Study - REFORM HEARTS, Rogers N, Dwyer K, Kozor R, Patrick E, Julovi S, Webster A, Thomas L, Meijles D, Department of Health (Federal - administered by NHMRC)/2021 MRFF Cardiovascular Health Mission

2021

Investigating a new pathway driving cardiorenal syndrome., Rogers N, Julovi S, Patrick E, National Heart Foundation of Australia/Vanguard Grant

2020

Improving Kidney Transplant Outcomes Using Normothermic Machine Perfusion, Rogers N, Patrick E, Pleass H, Laurence J, Wyburn K, National Health and Medical Research Council (NHMRC)/Ideas Grant
Cloud-accelerated analytics for clinical omic and imaging data - Institute of Data Discovery for Health (D24H), Yang J, Simpson S, Patrick E, Yang P, Tarr G, Kim J, Innovation & Technology Commission, Hong Kong SAR Govt/AIR@InnoHK
Discovery of big-data-informed multi-modal risk prediction signatures - Institute of Data Discovery for Health (D24H), Yang J, Patrick E, Yang P, Tarr G, Innovation & Technology Commission, Hong Kong SAR Govt/AIR@InnoHK
Statistical frameworks for high-parameter imaging cytometry data, Patrick E, Australian Research Council (ARC)/Discovery Early Career Researcher Award (DECRA)

Faculty of Science

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