Author

Alyssa Baccarella

Children's Hospital of PhiladelphiaORCID 0000-0001-8200-9751Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Cell Biology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Organism:human· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Organism:mouse· 1

Frequent Co-Authors

Amanda B. MuiriD· 2 shared Kelly A. WhelaniD· 2 shared Mark MahoniD· 2 shared Melanie A. RuffneriD· 2 shared Ryugo TeranishiiD· 2 shared Takefumi Itami· 2 shared Tatiana A. KarakashevaiD· 2 shared Yusen ZhouiD· 2 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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2 shared papersCell Biology

Amanda B. MuirORCID

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2 papers

Recent·Most cited

Cell BiologybioRxivPreprintOct 30, 2026

Systemic Analysis of Patient Derived Esophageal Epithelial Organoid Model Reveals Cell State Heterogeneity and Conservation of Differentiation Hierarchy

Alyssa Baccarella, Yusen Zhou, Tatiana A. Karakasheva…·Melanie A. Ruffner

The paper uses scRNA-seq to compare IL-13-treated esophageal organoids with EoE biopsies, revealing shared cell state heterogeneity and differentiation hierarchy dysregulation.

DOI 10.64898/2026.10.29.762343

humanscRNA-seq

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Molecular BiologybioRxivPreprintMay 25, 2025

FOXM1 Modulation Alleviates Epithelial Remodeling and Inflammation in Eosinophilic Esophagitis

Masaru Sasaki, Joshua X. Wang, Yusen Zhou…·Amanda B. Muir

This study identifies FOXM1 as a key driver of epithelial disruption in EoE, showing that its inhibition restores differentiation, reduces hyperplasia, and improves barrier function.

1 citation

humanmouse

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