Author

John P. Bryan

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

Signature Assays, Organisms & Methods

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Assay:spatial transcriptomics· 2 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Organism:mouse· 1 Approach:optimal transport· 1 Assay:scRNA-seq· 1 Approach:statistical model· 1 Research Focus:trajectory inference· 1

Frequent Co-Authors

Brian ClearyiD· 2 shared Samouil L. FarhiiD· 2 shared Achla H. Gandhi· 1 shared Alex K. ShalekiD· 1 shared Brittany A. GoodsiD· 1 shared Cai McCanniD· 1 shared Caroline E. KratkaiD· 1 shared Daniela D. RussoiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Brian ClearyORCID

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2 papers

Recent·Most cited

Accurate trajectory inference in time-series spatial transcriptomics with structurally-constrained optimal transport

John P. Bryan, Samouil L. Farhi, Brian Cleary

This paper introduces SOCS, a trajectory inference method for time-series spatial transcriptomics that preserves structural coherence of biological units over time, improving accuracy compared to existing approaches.

Nature Communications · Jun 29, 2026Peer-reviewedBioinformatics

Single-cell and spatiotemporal profile of ovulation in the mouse ovary

Ruixu Huang, Caroline E. Kratka, Jeffrey Pea, Cai McCann, Jack Nelson, John P. Bryan, Luhan Tracy Zhou, Daniela D. Russo, Emily J. Zaniker, Achla H. Gandhi, Alex K. Shalek, Brian Cleary, Samouil L. Farhi, Francesca E. Duncan, Brittany A. Goods

This study maps the spatiotemporal profile of ovulation in mice using single-cell RNA-seq and spatial transcriptomics, identifying cell state markers and interactions involved in the process.

PLoS Biology · Jun 24, 2025Peer-reviewedBioinformatics