Author

Simon Bucher

University of California, San FranciscoORCID 0000-0003-3282-7435Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Angela Oliveira PiscoiD· 2 shared A.D. Choudhury· 1 shared Aditi AgrawaliD· 1 shared Ahmad SalehiiD· 1 shared Alan Gi-Lun ChengiD· 1 shared Alejandro A. GranadosiD· 1 shared Ali Reza Rais Sadati· 1 shared Amber Casillas· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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2 shared papersBioinformatics

Angela Oliveira PiscoORCID

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2 papers

Recent·Most cited

BioinformaticsNature CommunicationsPeer-reviewedOct 28, 2025

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

George Crowley, Robert C. Jones, Mark A. Krasnow…·David Seong

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

11 citations

bulk RNA-seqmachine learning (classical)

𝕏 PostBluesky

GenomicseLifePeer-reviewedAug 7, 2023

Comprehensive characterization of the transcriptional response to COVID-19 in multiple organs reveals shared signatures across tissues

Alejandro A. Granados, Simon Bucher, Aditi Agrawal…·Bruce Wang

The paper characterizes the transcriptional response to COVID-19 across multiple organs using single-nuclei RNA sequencing, identifying shared transcriptional signatures in endothelial cells and macrophages.

5 citations

humanscRNA-seq

𝕏 PostBluesky