Publications


You can find a full publication list at Google Scholar.


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, in Press

Identification of HIV-Transmitting Sub-Epithelial Mononuclear Phagocytes in Human Anogenital and Colorectal Tissues. (2020)
Rhodes, J. W., Botting, R. A., Bertram, K. M., Rana, H., Baharlou, H., Longmuir-Vine, E. E., … Harman, A. N.
bioRxiv, 2020.05.26.117408 https://doi.org/10.1101/2020.05.26.117408

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

AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images. (2019)
Baharlou, H., Canete, N. P., Bertram, K. M., Sandgren, K. J., Cunningham, A. L., Harman, A. N., & Patrick, E.
bioRxiv, 566315 https://doi.org/10.1101/566315

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

A cortical immune network map identifies a subset of human microglia involved in Tau pathology. (2017)
Patrick, E., Olah, M., Taga, M., Klein, H.-U., Xu, J., White, C. C., … Jager, P. L. D.
bioRxiv, 234351 https://doi.org/10.1101/234351

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. (2013a)
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. (2013b)
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