Author

Amy María Sims

Pacific Northwest National LaboratoryORCID 0000-0003-0178-4225Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Microbiology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Organism:mouse· 1 Assay:proteomics· 1

Frequent Co-Authors

Adam S. Cockrell· 1 shared Alexandra SchäferiD· 1 shared Carrie D. Niccora· 1 shared Danielle CiesielskiiD· 1 shared David D. PollockiD· 1 shared H. Steven WileyiD· 1 shared Jacob F. KocheriD· 1 shared Jennifer E. KyleiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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1 shared paperMicrobiology

Adam S. Cockrell

Mutual co-authors in cluster

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2 papers

Recent·Most cited

Systems BiologyNAR Genomics and BioinformaticsPeer-reviewedJun 27, 2026

ProteoMeter: A pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level

Jordan C. Rozum, Amy María Sims, Xiaolu Li…·Song Feng

ProteoMeter integrates multi-PTM and limited proteolysis data to map proteomic changes to residue level, demonstrating its use in analyzing HCoV-229E infection.

1 citation

humanproteomics

𝕏 PostBluesky

MicrobiologymSpherePeer-reviewedJan 30, 2025

Dysregulation of lung epithelial cell homeostasis and immunity contributes to Middle East Respiratory Syndrome coronavirus disease severity

Amy María Sims, Alexandra Schäfer, Kenichi Okuda…·Timothy Patrick Sheahan

This study uses multi-omics analysis to show that dysregulated lung epithelial cell homeostasis and immune responses drive severe MERS-CoV disease in mice.

4 citations

mousebulk RNA-seq

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