Author

Jacob T. Mitchell

Johns Hopkins UniversityORCID 0000-0002-5370-9692Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Cancer Biology· 2 Systems Biology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:software / tool· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2

Frequent Co-Authors

Elana Judith FertigiD· 5 shared Elizabeth M. JaffeeiD· 5 shared Jacquelyn W. ZimmermaniD· 4 shared Luciane Tsukamoto KagoharaiD· 4 shared David L. ZhouiD· 2 shared Emma KartaliaiD· 2 shared Genevieve Stein-O’BrieniD· 2 shared James M. LeathermaniD· 2 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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5 shared papersCancer Biology

Elana Judith FertigORCID

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Author profile →

5 papers

Recent·Most cited

Cancer BiologyThe Journal of ImmunologyPeer-reviewedJun 1, 2026

Antigen-presenting cancer-associated fibroblasts in murine pancreatic tumors differentially control regulatory T cell phenotype and function via CXCL9 and CCL22

Saumya Y. Maru, Meredith Wetzel, Jacob T. Mitchell…·Elizabeth M. Jaffee

This study shows antigen-presenting cancer-associated fibroblasts (apCAFs) in murine pancreatic tumors influence regulatory T cell phenotype and function through CXCL9 and CCL22, affecting immune checkpoint blockade response.

DOI 10.1093/jimmun/vkag165

mousebulk RNA-seq

𝕏 PostBluesky

BioinformaticsBioinformaticsPeer-reviewedFeb 26, 2026

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal

Jacob T. Mitchell, Orian Stapleton, Kavita Krishnan…·Elana Judith Fertig

The paper introduces dominoSignal, a software tool that statistically tests differential cell signaling from single-cell data to infer changes in cell-cell communication networks.

2 citations

scRNA-seqstatistical model

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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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Cancer BiologybioRxivPreprintJan 7, 2025

Cancer associated fibroblasts drive epithelial to mesenchymal transition and classical to basal change in pancreatic ductal adenocarcinoma cells with loss of IL-8 expression

Samantha R. Guinn, Brayan Perez, Joseph A. Tandurella…·Jacquelyn W. Zimmerman

The paper investigates how cancer-associated fibroblasts (CAF) influence tumor cell behavior in pancreatic ductal adenocarcinoma by driving EMT and altering cell subtypes, with IL-8 playing a key modulatory role.

2 citations

humanbulk RNA-seq

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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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