Author

Robert van Dijk

Broad InstituteORCID 0000-0003-4982-9648Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:batch correction / integration· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Assay:imaging· 1 Assay:spatial transcriptomics· 1

Frequent Co-Authors

Anne Elizabeth CarpenteriD· 2 shared John ArévaloiD· 2 shared Shantanu SinghiD· 2 shared Ellen SuiD· 1 shared Jessica EwaldiD· 1 shared Mehrtash BabadiiD· 1 shared

Activity by Year

2024-2024 · peak 2/yr

Co-Author Collaboration Network

6 top collaborators · 13 mutual co-author links

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2 shared papersBioinformatics

Anne Elizabeth CarpenterORCID

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2 papers

Recent·Most cited

BioinformaticsPLoS Computational BiologyPeer-reviewedNov 11, 2024

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning

Robert van Dijk, John Arévalo, Mehrtash Babadi…·Shantanu Singh

The paper introduces CytoSummaryNet, a contrastive learning method for aggregating single-cell features in image-based profiling, improving mechanism of action prediction by 30-68%.

12 citations

imagingcontrastive learning

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BioinformaticsNature CommunicationsPeer-reviewedAug 2, 2024

Evaluating batch correction methods for image-based cell profiling

John Arévalo, Ellen Su, Jessica Ewald…·Shantanu Singh

The paper benchmarks seven scRNA-seq batch correction methods on a Cell Painting dataset, finding Harmony performs best across multiple scenarios.

89 citationstop 1%

spatial transcriptomicsstatistical model

𝕏 PostBluesky