Author

Jonah Silverman

Broad Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Assay:spatial transcriptomics· 3 Research Focus:database / resource· 2 Assay:ATAC-seq· 1 Research Focus:cell type annotation· 1 Assay:ChIP-seq· 1 Organism:mouse· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Joshua Barnett· 2 shared Liya WangiD· 2 shared Noori SotudehiD· 2 shared Poorvi Rao· 2 shared Alex R. BuckleyiD· 1 shared Amanda UrkeiD· 1 shared Benjamin E. DevermaniD· 1 shared Beth StevensiD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersBioinformatics

Joshua Barnett

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Author profile →

3 papers

Recent·Most cited

Protein-guided RNA barcoding links transcriptomes to synaptic architecture

Amanda Urke, Michael-John Dolan, Jonah Silverman, Michael TaeWoo Kim, Juan Pineda, Samantha Garcia, Judy Luu, Alex R. Buckley, Vipin Kumar, Binhui Zhao, Ken Y. Chan, Naeem M. Nadaf, Karol S. Balderrama, Don B. Arnold, Beth Stevens, , Evan Z. Macosko

The paper introduces Synapse-seq, a method to link transcriptomes to synaptic architecture by using protein-guided RNA barcoding, revealing new insights into neural connectivity and cell type-specific dendritic structures.

bioRxiv · Feb 27, 2026 · PreprintNeuroscience

AtlasXplore: a web platform for visualizing and sharing spatial epigenome data

Joshua Barnett, Noori Sotudeh, Poorvi Rao, Jonah Silverman, Tamara Jafar, Liya Wang

AtlasXplore provides a web platform for visualizing and sharing spatial epigenome data, enabling interactive exploration without requiring advanced computational skills.

Bioinformatics · Jul 20, 2023Peer-reviewedBioinformatics

AtlasXbrowser enables spatial multi-omics data analysis through the precise determination of the region of interest

Joshua Barnett, Jonah Silverman, Molly Wetzel, Poorvi Rao, Noori Sotudeh, Liya Wang

The paper introduces AtlasXbrowser, a tool for processing DBiT image data to extract spatial information for integration with sequencing data.

bioRxiv · May 11, 2022 · PreprintBioinformatics