Publications
You can find a full publication list at Google Scholar.
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 ConsortiumScience (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 GroupActa 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 GroupJournal 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