Author

Jeanette Johnson

Johns Hopkins UniversityORCID 0000-0002-8268-5335Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:clustering· 2 Research Focus:software / tool· 2 Research Focus:batch correction / integration· 1 Approach:Bayesian inference· 1 Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:dimensionality reduction· 1

Frequent Co-Authors

Elana Judith FertigiD· 3 shared Jacquelyn W. ZimmermaniD· 3 shared Daniel R. BergmaniD· 2 shared David L. ZhouiD· 2 shared Elizabeth M. JaffeeiD· 2 shared Eric M. CrameriD· 2 shared Genevieve Stein-O’BrieniD· 2 shared Jacob T. MitchelliD· 2 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersSystems Biology

Elana Judith FertigORCID

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3 papers

Recent·Most cited

BioengineeringCell Reports MethodsPeer-reviewedNov 18, 2025

Automated Quality Control of Time-Course Imaging from 3D in vitro cultures

Eric M. Cramer, Tamara Y. Lopez-Vidal, Jeanette Johnson…·Young Hwan Chang

The paper introduces an algorithm to correct mislabeling and align object positions in longitudinal 3D cell culture imaging, improving data integrity and reproducibility.

DOI 10.1016/j.crmeth.2025.101237

imagingdeep learning

𝕏 PostBluesky

Systems BiologyCellPeer-reviewedJul 26, 2025

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

Jeanette Johnson, Daniel R. Bergman, Heber Lima da Rocha…·Paul Macklin

The paper introduces a framework for mathematical modeling of multicellular systems using interpretable cell behavior rules derived from biological knowledge and multi-omics data.

67 citationstop 1%

statistical modelsoftware / tool

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Systems BiologyNature ProtocolsPeer-reviewedNov 21, 2023

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS

Jeanette Johnson, Ashley P. Tsang, Jacob T. Mitchell…·Genevieve Stein-O’Brien

The paper introduces computational tools for NMF analysis of single-cell RNA-seq data, demonstrating their use in quantifying cell state transitions in pancreatic cancer.

26 citations

humanscRNA-seq

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