Publications

You can find my google scholar page here.

References

Overcoming cohort heterogeneity for the prediction of subclinical cardiovascular disease risk. (2023)

Chan, A., Wu, S., Vernon, S., Tang, O., Figtree, G., Liu, T., … Patrick, E.

iScience, In Press

Deep multimodal graph-based network for survival prediction from highly multiplexed images and patient variables. (2023)

Fu, X., Patrick, E., Yang, J. Y. H., Feng, D. D., & Kim, J.

Computers in Biology and Medicine, 154, 106576 https://doi.org/10.1016/j.compbiomed.2023.106576

Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments. (2023)

Patrick, E., Canete, N. P., Iyengar, S. S., Harman, A. N., Sutherland, G. T., & Yang, P.

Cytometry Part A, In Press https://doi.org/10.1002/cyto.a.24729

Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis. (2023)

Sawyer, A. J., Patrick, E., Edwards, J., Wilmott, J. S., Fielder, T., Yang, Q., … Feng, C. G.

Journal of Experimental Medicine, 220(6), e20221392 https://doi.org/10.1084/jem.20221392

An in situ analysis pipeline for initial host-pathogen interactions reveals signatures of human colorectal HIV transmission. (2022)

Baharlou, H., Canete, N., Vine, E. E., Hu, K., Yuan, D., Sandgren, K. J., … Harman, A. N.

Cell Reports, 40(12), 111385 https://doi.org/10.1016/j.celrep.2022.111385

spicyR: Spatial analysis of in situ cytometry data in R. (2022)

Canete, N. P., Iyengar, S. S., Ormerod, J. T., Baharlou, H., Harman, A. N., & Patrick, E.

Bioinformatics (Oxford, England), 38(11), 3099–3105 https://doi.org/10.1093/bioinformatics/btac268

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction. (2022)

Cao, Y., Lin, Y., Patrick, E., Yang, P., & Yang, J. Y. H.

Bioinformatics (Oxford, England), btac590 https://doi.org/10.1093/bioinformatics/btac590

High-dimensional and spatial analysis reveals immune landscape dependent progression in cutaneous squamous cell carcinoma. (2022)

Ferguson, A. L., Sharman, A. R., Allen, R. O., Ye, T., Lee, J. H., Low, T.-H. H., … Palendira, U.

Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, CCR-22-1332 https://doi.org/10.1158/1078-0432.CCR-22-1332

Third-party CMV- and EBV-specific T-cells for first viral reactivation after allogeneic stem cell transplant. (2022)

Jiang, W., Clancy, L. E., Avdic, S., Sutrave, G., Street, J., Simms, R., … Gottlieb, D. J.

Blood Advances, 6(17), 4949–4966 https://doi.org/10.1182/bloodadvances.2022007103

The Key Factors Predicting Dementia in Individuals With Alzheimer’s Disease-Type Pathology. (2022)

McCorkindale, A. N., Patrick, E., Duce, J. A., Guennewig, B., & Sutherland, G. T.

Frontiers in Aging Neuroscience, 14, 831967 https://doi.org/10.3389/fnagi.2022.831967

Research trends in Australia and New Zealand Nephrology: Basic science and gender equity in peril. (2022)

Purvis, M. R., Robertson, H., Patrick, E., & Rogers, N. M.

Internal Medicine Journal, 52(11), 1991–1994 https://doi.org/10.1111/imj.15942

Cross-Platform Omics Prediction procedure: A statistical machine learning framework for wider implementation of precision medicine. (2022)

Wang, K. Y. X., Pupo, G. M., Tembe, V., Patrick, E., Strbenac, D., Schramm, S.-J., … Yang, J. Y. H.

NPJ Digital Medicine, 5(1), 85 https://doi.org/10.1038/s41746-022-00618-5

AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images. (2021)

Baharlou, H., Canete, N. P., Bertram, K. M., Sandgren, K. J., Cunningham, A. L., Harman, A. N., & Patrick, E.

Bioinformatics, 37(4), 559–567 https://doi.org/10.1093/bioinformatics/btaa780

Herpes Simplex Virus type 1 infects Langerhans cells and the novel epidermal dendritic cell, Epi-cDC2s, via different entry pathways. (2021)

Bertram, K. M., Truong, N. R., Smith, J. B., Kim, M., Sandgren, K. J., Feng, K. L., … Cunningham, A. L.

PLOS Pathogens, 17(4), e1009536 https://doi.org/10.1371/journal.ppat.1009536

treekoR: Identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data. (2021)

Chan, A., Jiang, W., Blyth, E., Yang, J., & Patrick, E.

Genome Biology, 22(1), 324 https://doi.org/10.1186/s13059-021-02526-5

Defining early changes in Alzheimer’s disease from RNA sequencing of brain regions differentially affected by pathology. (2021)

Guennewig, B., Lim, J., Marshall, L., McCorkindale, A. N., Paasila, P. J., Patrick, E., … Sutherland, G. T.

Scientific Reports, 11(1), 4865 https://doi.org/10.1038/s41598-021-83872-z

A cortical immune network map identifies distinct microglial transcriptional programs associated with beta-amyloid and Tau pathologies. (2021)

Patrick, E., Olah, M., Taga, M., Klein, H.-U., Xu, J., White, C. C., … De Jager, P. L.

Translational Psychiatry, 11(1), 1–17 https://doi.org/10.1038/s41398-020-01175-9

Human anogenital monocyte-derived dendritic cells and langerin+cDC2 are major HIV target cells. (2021)

Rhodes, J. W., Botting, R. A., Bertram, K. M., Vine, E. E., Rana, H., Baharlou, H., … Harman, A. N.

Nature Communications, 12(1), 2147 https://doi.org/10.1038/s41467-021-22375-x

Transcriptomic Analysis Identifies A Tolerogenic Dendritic Cell Signature. (2021)

Robertson, H., Li, J., Kim, H. J., Rhodes, J. W., Harman, A. N., *Patrick, E., & *Rogers, N. M.

Frontiers in Immunology, 12, 733231 https://doi.org/10.3389/fimmu.2021.733231

Plasmacytoid dendritic cells have divergent effects on HIV infection of initial target cells and induce a pro-retention phenotype. (2021)

Tong, O., Duette, G., O’Neil, T. R., Royle, C. M., Rana, H., Johnson, B., … Nasr, N.

PLOS Pathogens, 17(4), e1009522 https://doi.org/10.1371/journal.ppat.1009522

The acute phase protein lactoferrin is a key feature of Alzheimer’s disease and predictor of Abeta burden through induction of APP amyloidogenic processing. (2021)

Tsatsanis, A., McCorkindale, A. N., Wong, B. X., Patrick, E., Ryan, T. M., Evans, R. W., … Duce, J. A.

Molecular Psychiatry, 1–16 https://doi.org/10.1038/s41380-021-01248-1

A Wnt-mediated phenotype switch along the epithelial–mesenchymal axis defines resistance and invasion downstream of ionising radiation in oral squamous cell carcinoma. (2021)

Zolghadr, F., Tse, N., Loka, D., Joun, G., Meppat, S., Wan, V., … Seyedasli, N.

British Journal of Cancer, 124(12), 1921–1933 https://doi.org/10.1038/s41416-021-01352-7

Investigating higher-order interactions in single-cell data with scHOT. (2020)

Ghazanfar, S., Lin, Y., Su, X., Lin, D. M., Patrick, E., Han, Z.-G., … Yang, J. Y. H.

Nature Methods, 1–8 https://doi.org/10.1038/s41592-020-0885-x

Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning. (2020)

Kim, H. J., Osteil, P., Humphrey, S. J., Cinghu, S., Oldfield, A. J., Patrick, E., … Yang, P.

Nucleic Acids Research, 48(4), 1828–1842 https://doi.org/10.1093/nar/gkz1179

Mass cytometry reveals immune signatures associated with cytomegalovirus (CMV) control in recipients of allogeneic haemopoietic stem cell transplant and CMV-specific T cells. (2020)

McGuire, H. M., Rizzetto, S., Withers, B. P., Clancy, L. E., Avdic, S., Stern, L., … Blyth, E.

Clinical & Translational Immunology, 9(7), e1149 https://doi.org/10.1002/cti2.1149

Deconvolving the contributions of cell-type heterogeneity on cortical gene expression. (2020)

Patrick, E., Taga, M., Ergun, A., Ng, B., Casazza, W., Cimpean, M., … Mostafavi, S.

PLOS Computational Biology, 16(8), e1008120 https://doi.org/10.1371/journal.pcbi.1008120

PGRMC1 phosphorylation affects cell shape, motility, glycolysis, mitochondrial form and function, and tumor growth. (2020)

Thejer, B. M., Adhikary, P. P., Kaur, A., Teakel, S. L., Van Oosterum, A., Seth, I., … Cahill, M. A.

BMC Molecular and Cell Biology, 21(1), 24 https://doi.org/10.1186/s12860-020-00256-3

Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies. (2019)

Baharlou, H., Canete, N. P., Cunningham, A. L., Harman, A. N., & Patrick, E.

Frontiers in Immunology, 10 https://doi.org/10.3389/fimmu.2019.02657

Identification of HIV transmitting CD11c + human epidermal dendritic cells. (2019)

Bertram, K. M., Botting, R. A., Baharlou, H., Rhodes, J. W., Rana, H., Graham, J. D., … Harman, A. N.

Nature Communications, 10(1), 1–15 https://doi.org/10.1038/s41467-019-10697-w

DCARS: Differential correlation across ranked samples. (2019)

Ghazanfar, S., Strbenac, D., Ormerod, J. T., Yang, J. Y. H., & Patrick, E.

Bioinformatics, 35(5), 823–829 https://doi.org/10.1093/bioinformatics/bty698

Brief Normothermic Machine Perfusion Rejuvenates Discarded Human Kidneys. (2019)

Hameed, A. M., Lu, D. B., Patrick, E., Xu, B., Hu, M., Chew, Y. V., … Pleass, H. C.

Transplantation Direct, 5(11) https://doi.org/10.1097/TXD.0000000000000944

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. (2019)

International Multiple Sclerosis Genetics Consortium

Science (New York, N.Y.), 365(6460) https://doi.org/10.1126/science.aav7188

Standardisation of flow cytometry for whole blood immunophenotyping of islet transplant and transplant clinical trial recipients. (2019)

Jimenez Vera, E., Chew, Y. V., Nicholson, L., Burns, H., Anderson, P., Chen, H.-T., … Hu, M.

PLoS ONE, 14(5) https://doi.org/10.1371/journal.pone.0217163

Evaluating stably expressed genes in single cells. (2019)

Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Lin, D. M., … Yang, P.

GigaScience, 8(9) https://doi.org/10.1093/gigascience/giz106

Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain. (2019)

Ng, B., Casazza, W., Patrick, E., Tasaki, S., Novakovsky, G., Felsky, D., … Mostafavi, S.

The American Journal of Human Genetics, 105(3), 562–572 https://doi.org/10.1016/j.ajhg.2019.07.016

Characterization of the human myelin oligodendrocyte glycoprotein antibody response in demyelination. (2019)

Tea, F., Lopez, J. A., Ramanathan, S., Merheb, V., Lee, F. X. Z., Zou, A., … Australasian and New Zealand MOG Study Group

Acta Neuropathologica Communications, 7(1), 145 https://doi.org/10.1186/s40478-019-0786-3

Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. (2018)

*Bove, R. M., *Patrick, E., Aubin, C. M., Srivastava, G., Schneider, J. A., Bennett, D. A., … Chibnik, L. B.

PloS One, 13(7), e0199073 https://doi.org/10.1371/journal.pone.0199073

Polygenic analysis of inflammatory disease variants and effects on microglia in the aging brain. (2018)

Felsky, D., Patrick, E., Schneider, J. A., Mostafavi, S., Gaiteri, C., Patsopoulos, N., … De Jager, P. L.

Molecular Neurodegeneration, 13(1), 38 https://doi.org/10.1186/s13024-018-0272-6

Blood CRP levels are elevated in children and adolescents with functional neurological symptom disorder. (2018)

Kozlowska, K., Chung, J., Cruickshank, B., McLean, L., Scher, S., Dale, R. C., … Patrick, E.

European Child & Adolescent Psychiatry https://doi.org/10.1007/s00787-018-1212-2

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease. (2018)

Mostafavi, S., Gaiteri, C., Sullivan, S. E., White, C. C., Tasaki, S., Xu, J., … De Jager, P. L.

Nature Neuroscience, 21(6), 811–819 https://doi.org/10.1038/s41593-018-0154-9

A transcriptomic atlas of aged human microglia. (2018)

*Olah, M., *Patrick, E., Villani, A.-C., Xu, J., White, C. C., Ryan, K. J., … Bradshaw, E. M.

Nature Communications, 9(1), 539 https://doi.org/10.1038/s41467-018-02926-5

Clinical course, therapeutic responses and outcomes in relapsing MOG antibody-associated demyelination. (2018)

Ramanathan, S., Mohammad, S., Tantsis, E., Nguyen, T. K., Merheb, V., Fung, V. S. C., … Australasian and New Zealand MOG Study Group

Journal of Neurology, Neurosurgery, and Psychiatry, 89(2), 127–137 https://doi.org/10.1136/jnnp-2017-316880

An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenome. (2017)

Ng, B., White, C. C., Klein, H.-U., Sieberts, S. K., McCabe, C., Patrick, E., … De Jager, P. L.

Nature Neuroscience, 20(10), 1418–1426 https://doi.org/10.1038/nn.4632

Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease. (2017)

Patrick, E., Rajagopal, S., Wong, H.-K. A., McCabe, C., Xu, J., Tang, A., … De Jager, P. L.

Molecular Neurodegeneration, 12(1), 51 https://doi.org/10.1186/s13024-017-0191-y

A multi-step classifier addressing cohort heterogeneity improves performance of prognostic biomarkers in three cancer types. (2017)

Patrick, E., Schramm, S.-J., Ormerod, J. T., Scolyer, R. A., Mann, G. J., Mueller, S., & Yang, J. Y. H.

Oncotarget, 8(2), 2807–2815 https://doi.org/10.18632/oncotarget.13203

Taking Kidneys for Granted? Time to Reflect on the Choices We Make. (2017)

Wong, G., Howell, M., Patrick, E., & Yang, J. Y. H.

Transplantation, 101(12), 2812–2813 https://doi.org/10.1097/TP.0000000000001850

KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis. (2016)

*Yang, P., *Patrick, E., Humphrey, S. J., Ghazanfar, S., James, D. E., Jothi, R., & Yang, J. Y. H.

Proteomics, 16(13), 1868–1871 https://doi.org/10.1002/pmic.201600068

Phonological Encoding in Mandarin Chinese: Evidence from Tongue Twisters. (2015)

Kember, H., Croot, K., & Patrick, E.

Language and Speech, 58(Pt 4), 417–440 https://doi.org/10.1177/0023830914562654

Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data. (2015)

Patrick, E., Buckley, M., Müller, S., Lin, D. M., & Yang, J. Y. H.

Bioinformatics, 31(17), 2822–2828 https://doi.org/10.1093/bioinformatics/btv220

MicroRNA and mRNA expression profiling in metastatic melanoma reveal associations with BRAF mutation and patient prognosis. (2015)

Tembe, V., Schramm, S.-J., Stark, M. S., Patrick, E., Jayaswal, V., Tang, Y. H., … Mann, G. J.

Pigment Cell & Melanoma Research, 28(3), 254–266 https://doi.org/10.1111/pcmr.12343

Hepatic metallothionein expression in chronic hepatitis C virus infection is IFNL3 genotype-dependent. (2014)

O’Connor, K. S., Parnell, G., Patrick, E., Ahlenstiel, G., Suppiah, V., Poorten, D. van der, … Booth, D. R.

Genes and Immunity, 15(2), 88–94 https://doi.org/10.1038/gene.2013.66

Detection of Multiple Outbreaks Using Spatio-Temporal EWMA-Ordered Statistics. (2014)

Sparks, R., & Patrick, E.

Communications in Statistics - Simulation and Computation, 43(10), 2678–2701 https://doi.org/10.1080/03610918.2012.758741

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. (2014)

*Yang, P., *Patrick, E., Tan, S.-X., Fazakerley, D. J., Burchfield, J., Gribben, C., … Yang, J. Y. H.

Bioinformatics, 30(6), 808–814 https://doi.org/10.1093/bioinformatics/btt616

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information. (2013)

Patrick, E., Buckley, M., Lin, D. M., & Yang, J. Y. H.

BMC Genomics, 14 Suppl 1, S9 https://doi.org/10.1186/1471-2164-14-S1-S9

Estimation of data-specific constitutive exons with RNA-Seq data. (2013)

Patrick, E., Buckley, M., & Yang, J. Y. H.

BMC Bioinformatics, 14, 31 https://doi.org/10.1186/1471-2105-14-31

Impaired Akt phosphorylation in insulin-resistant human muscle is accompanied by selective and heterogeneous downstream defects. (2013)

Tonks, K. T., Ng, Y., Miller, S., Coster, A. C. F., Samocha-Bonet, D., Iseli, T. J., … Greenfield, J. R.

Diabetologia, 56(4), 875–885 https://doi.org/10.1007/s00125-012-2811-y