Author

Mark S. Keller

Harvard UniversityORCID 0000-0003-3003-874XUnclaimed 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:differential expression· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Research Focus:database / resource· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Nils GehlenborgiD· 3 shared A. YoldaşiD· 1 shared Afolarin Amodu· 1 shared Ahmet Can SolakiD· 1 shared Alan M. WatsoniD· 1 shared Albane le Tournoulx de la VillegeorgesiD· 1 shared Alexander MoralesiD· 1 shared Amanda L. KnoteniD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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3 shared papersBioinformatics

Nils GehlenborgORCID

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3 papers

Recent·Most cited

SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data

Shaokun An, Mark S. Keller, Nils Gehlenborg, Martin Hemberg

SpatialQuery identifies multicellular spatial patterns and characterizes their molecular programs in spatial omics data, revealing cross-germ-layer signaling and disease-specific niches.

bioRxiv · Apr 30, 2026 · PreprintBioinformatics

The chromatin landscape of healthy and injured cell types in the human kidney

Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine M. Basta, Mark S. Keller, Ricardo Melo Ferreira, Shreeram Akilesh, Reetika R. Ghag, Charles Lu, Ying‐Hua Cheng, Kimberly S. Collins, Samir V. Parikh, Brad H. Rovin, Lynn Robbins, Lisa Stout, , Joana P. Gonçalves

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

Nature Communications · Jan 10, 2024Peer-reviewedMolecular Biology

OME-Zarr: a cloud-optimized bioimaging file format with international community support

Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M. Brown, Jean‐Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E. Diel, David Gault, Satrajit Ghosh, Ilan Gold, Yaroslav O. Halchenko, Matthew Hartley, , Jason R. Swedlow

This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.

Histochemistry and Cell Biology · Jul 10, 2023Peer-reviewedBioinformatics