Author

Raymond H. Y. Louie

UNSW SydneyORCID 0000-0002-9384-2447Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 4 Approach:statistical model· 4 Research Focus:cell type annotation· 3 Assay:CITE-seq· 2 Research Focus:differential expression· 2 Assay:scRNA-seq· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1

Frequent Co-Authors

Christopher Carl GoodnowiD· 2 shared Fabio LucianiiD· 2 shared Jerome SamiriD· 2 shared Mandeep SinghiD· 2 shared Matthew A. FieldiD· 2 shared Agus SalimiD· 1 shared Andrew CalcinoiD· 1 shared Angli XueiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersImmunology

Christopher Carl GoodnowORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease

Michael Li, Arman Safavi, Jerome Samir, Raymond H. Y. Louie, Esmaeil Roohparvar Basmenj, Martina Bonomi, Thiruni N. Adikari, Brian Gloss, Jun Xing, Katherine Jackson, Andrew Calcino, Dan Suan, Valentina Vaira, Claire Milthorpe, Melinda Y. Hardy, , Fabio Luciani

This study identifies clonal IEL expansion and epithelial remodelling in RCD1 using single-cell multi-omics, showing distinct immune and epithelial states compared to ACD.

bioRxiv · Sep 3, 2026 · PreprintImmunology

Linkage-aware inference of fitness from short-read time-series genomic data

Syed Muhammad Abdullah, Muhammad Saqib Sohail, Raymond H. Y. Louie, Yanni Sun, John P. Barton, Matthew R. McKay

This paper introduces a method to infer fitness effects from short-read time-series genomic data while accounting for genetic linkage, validated on HIV and SARS-CoV-2 datasets.

Virus Evolution · Jan 1, 2026Peer-reviewedBioinformatics

Detecting Somatic Mutations in Rare Clones using Single Cell Multi-Omics

Rhys Gillman, Sonam Dukda, Jerome Samir, Raymond H. Y. Louie, Christopher Carl Goodnow, Fabio Luciano, Mandeep Singh, Matthew A. Field

SCARCE identifies rare somatic mutations in single-cell data by comparing variant frequencies across cell subpopulations, successfully detecting variants in as few as 10 cells.

bioRxiv · Oct 30, 2025 · PreprintBioinformatics

Identifying the Minimal Number of Protein Markers for Cell Type Annotation Using MiniMarS

Dhruti Parikh, Angli Xue, Hsiao-Chi Liao, Claire Leana Wishart, Thomas M. Ashhurst, Givanna Putri, Fabio Luciani, Shalin H. Naik, Agus Salim, Felix Marsh‐Wakefield, Raymond H. Y. Louie

MiniMarS identifies the minimal number of protein markers for cell type annotation across multiple datasets and improves rare population identification.

bioRxiv · Jul 14, 2025 · PreprintBioinformatics