Author

Emily Scher

University of EdinburghORCID 0000-0002-5401-5879Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Aine Niamh O’TooleiD· 2 shared Adriano de Bernardi SchneideriD· 1 shared Ana T. DugganiD· 1 shared Andrew RambautiD· 1 shared Angie S. HinrichsiD· 1 shared Chris KentiD· 1 shared Connor Chato· 1 shared Debra A. WadfordiD· 1 shared

Activity by Year

2024-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersEvolutionary Biology

Aine Niamh O’TooleORCID

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2 papers

Recent·Most cited

Human outbreak detection and best practice MPXV analysis and interpretation with squirrel

Aine Niamh O’Toole, Eddy Kinganda-Lusamaki, Rachel Colquhoun, Connor Chato, Emily Scher, Chris Kent, Sam Wilkinson, Joshua Quick, Nicholas Loman, Ana T. Duggan, Placide Mbala, Andrew Rambaut

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

Virus Evolution · Dec 10, 2025Peer-reviewedEvolutionary Biology

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method

Adriano de Bernardi Schneider, Michelle Su, Angie S. Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A. Wadford, Aine Niamh O’Toole, Emily Scher, Marc D. Perry, Yatish Turakhia, Nicola De Maio, Scott Hughes, Russell B Corbett-Detig

This study compares pangoLEARN and pUShER for SARS-CoV-2 lineage assignment, finding pUShER more stable and accurate across pangolin versions.

Virus Evolution · Jan 1, 2024Peer-reviewedBioinformatics