Author

David Fernández Bonet

Science for Life LaboratoryORCID 0000-0001-5402-6917Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:spatial transcriptomics· 2 Research Focus:dimensionality reduction· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1 Approach:graph neural network· 1 Research Focus:spatial domain detection· 1 Approach:statistical model· 1

Frequent Co-Authors

Ian T. HoffeckeriD· 3 shared Simon K. DahlbergiD· 2 shared Johanna I. Blumenthal· 1 shared Lovisa FranzéniD· 1 shared Patrik L. StåhliD· 1 shared Shuai LangiD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

6 top collaborators · 11 mutual co-author links

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3 shared papersBioinformatics

Ian T. HoffeckerORCID

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3 papers

Recent·Most cited

BioinformaticsPatternsPeer-reviewedDec 1, 2025

Spatial Coherence in DNA Barcode Networks

David Fernández Bonet, Johanna I. Blumenthal, Shuai Lang…·Ian T. Hoffecker

The paper introduces spatial coherence as a framework to evaluate spatial fidelity in DNA barcode networks for sequencing-based microscopy.

2 citations

spatial transcriptomicsstatistical model

𝕏 PostBluesky

BioinformaticsNature CommunicationsPeer-reviewedOct 31, 2025

Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction

Simon K. Dahlberg, David Fernández Bonet, Lovisa Franzén…·Ian T. Hoffecker

The paper reanalyzes Slide-tags data to reveal a latent spatial network enabling reference-free tissue reconstruction.

4 citations

spatial transcriptomicsexperimental assay

𝕏 PostBluesky

BioinformaticsNanoscalePeer-reviewedJan 1, 2023

Image recovery from unknown network mechanisms forDNA sequencing-based microscopy

David Fernández Bonet, Ian T. Hoffecker

The paper introduces a graph-based method to reconstruct molecular networks from DNA sequencing data, achieving accurate spatial recovery with minimal assumptions.

9 citations

DNA methylationgraph neural network

𝕏 PostBluesky