Publications by authors named "Patrick Ellis"

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Orchestrating Spatial Transcriptomics Analysis with Bioconductor.
Helena L Crowell, Yixing Dong, Ilaria Billato, Peiying Cai, Martin Emons, Ellis Patrick

bioRxiv· November 2025

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Kontextual reframes analysis of spatial omics data and reveals consistent cell relationships across images.
Farhan Ameen, Nick Robertson, David M Lin, Shila Ghazanfar, Ellis Patrick

Cell Rep Methods· October 2025

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Spatial gene expression at single-cell resolution from histology using deep learning with GHIST.
Xiaohang Fu, Yue Cao, Beilei Bian, Chuhan Wang, Dinny Graham, Ellis Patrick

Nat Methods· September 2025

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SpatioMark: quantifying the impact of spatial proximity on cell phenotype.
Sourish S Iyengar, Alex R Qin, Nicholas Robertson, Andrew N Harman, Ellis Patrick

Bioinformatics· August 2025

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Thinking process templates for constructing data stories with SCDNEY.
Yue Cao, Andy Tran, Hani Kim, Nick Robertson, Yingxin Lin, Ellis Patrick

F1000Res· July 2025

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Regulating islet stress responses through CD47 activation.
Atharva Kale, Mahmoud Azar, Vanessa Cheng, Harry Robertson, Sally Coulter, Ellis Patrick

Diabetologia· June 2025

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Corrigendum to "Tolerogenic dendritic cells protect against acute kidney injury." Kidney International 2023;104:492-507.
Jennifer S Y Li, Harry Robertson, Katie Trinh, Arti M Raghubar, Quan Nguyen, Ellis Patrick

Kidney Int· May 2025

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Highly Adaptable Analysis Tools for Mapping Spatial Features of Cellular Aggregates in Tissues.
Andrew Sawyer, Nick Weingaertner, Ellis Patrick, Carl G Feng

Curr Protoc· May 2025

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Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis.
Wei Xiao, Andrew J Sawyer, Siwei Mo, Xinyu Bai, Qinzhu Yang, Ellis Patrick

bioRxiv· April 2025

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Benchmarking the translational potential of spatial gene expression prediction from histology.
Chuhan Wang, Adam S Chan, Xiaohang Fu, Shila Ghazanfar, Jinman Kim, Ellis Patrick

Nat Commun· February 2025

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The spatial biology of HIV infection.
Kevin Hu, Thomas R O'Neil, Heeva Baharlou, Paul J Austin, Jackson F Karrasch, Ellis Patrick

PLoS Pathog· January 2025

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Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas.
Harry Robertson, Hani Jieun Kim, Jennifer Li, Nicholas Robertson, Paul Robertson, Ellis Patrick

Nat Med· December 2024

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Thrombospondin-1 Drives Cardiac Remodeling in Chronic Kidney Disease.
Sohel M Julovi, Katie Trinh, Harry Robertson, Cuicui Xu, Nikita Minhas, Ellis Patrick

JACC Basic Transl Sci· May 2024

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Construction and optimization of multi-platform precision pathways for precision medicine.
Andy Tran, Andy Wang, Jamie Mickaill, Dario Strbenac, Mark Larance, Ellis Patrick

Sci Rep· February 2024

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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data.
Xiaohang Fu, Yingxin Lin, David M Lin, Daniel Mechtersheimer, Chuhan Wang, Ellis Patrick

Nat Commun· January 2024

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Non-invasive diagnosis of early cutaneous squamous cell carcinoma.
Ali Azimi, Steven Jabbour, Ellis Patrick, Pablo Fernandez-Penas

Exp Dermatol· November 2023

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Persistence of ex vivo expanded tumour and pathogen specific T-cells after allogeneic stem cell transplant for myeloid malignancies (the INTACT study).
Wei Jiang, Selmir Avdic, Koon H Lee, Janine Street, Gloria Castellano-González, Ellis Patrick

Leukemia· November 2023

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Mass cytometry analysis reveals altered immune profiles in patients with coronary artery disease.
Katharine A Kott, Adam S Chan, Stephen T Vernon, Thomas Hansen, Taiyun Kim, Ellis Patrick

Clin Transl Immunology· November 2023

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Circulating cytokine and chemokine patterns associated with cytomegalovirus reactivation after stem cell transplantation.
Lauren Stern, Helen M McGuire, Selmir Avdic, Emily Blyth, David Gottlieb, Ellis Patrick

Clin Transl Immunology· November 2023

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Classification of the tumor immune microenvironment and associations with outcomes in patients with metastatic melanoma treated with immunotherapies.
Nurudeen A Adegoke, Tuba N Gide, Yizhe Mao, Camelia Quek, Ellis Patrick

J Immunother Cancer· October 2023

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The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data.
Elijah Willie, Pengyi Yang, Ellis Patrick

Bioinform Adv· October 2023

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MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor.
Bárbara Zita Peters Couto, Nicholas Robertson, Ellis Patrick, Shila Ghazanfar

Bioinformatics· September 2023

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Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2.
Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Y H Yang

Nat Commun· July 2023

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Author Correction: Defining early changes in Alzheimer's disease from RNA sequencing of brain regions differentially affected by pathology.
Boris Guennewig, Julia Lim, Lee Marshall, Andrew N McCorkindale, Patrick J Paasila, Ellis Patrick

Sci Rep· June 2023

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Lipidomics Profiling and Risk of Coronary Artery Disease in the BioHEART-CT Discovery Cohort.
Dantong Zhu, Stephen T Vernon, Zac D'Agostino, Jingqin Wu, Corey Giles, Ellis Patrick

Biomolecules· May 2023

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