Author

Amy L. Schaefer

University of WashingtonORCID 0000-0003-0581-054XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Biochemistry· 1 Ecology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:bacteria (other)· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Research Focus:ecology & biodiversity· 1

Frequent Co-Authors

Everett Peter GreenbergiD· 2 shared Alyssa A. CarrelliD· 1 shared Bianxia Bai· 1 shared Charlotte MulliganiD· 1 shared Christopher W. SchadtiD· 1 shared Dale A. PelletieriD· 1 shared Daniel JacobsoniD· 1 shared Davi Nakajima AniD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBiochemistry

Everett Peter GreenbergORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

BiochemistrybioRxivPreprintSep 9, 2026

COPAL: An ensemble of protein-ligand co-folding models enriches preferred ligand predictions for the LuxR-family of quorum sensing receptors

Davi Nakajima An, Amy L. Schaefer, Szu-Min Chang…·Frank DiMaio

COPAL uses an ensemble of protein-ligand co-folding models to predict preferred AHL ligands for LuxR receptors, achieving higher accuracy than individual models.

DOI 10.64898/2026.09.04.749498

bacteria (other)protein structure

𝕏 PostBluesky

EcologybioRxivPreprintSep 9, 2026

A natural temperature, elevation, and rainfall gradient over the Cascade Mountains drives changes in Populus trichocarpa stress response and microbial community structure

Kathryn E. Bazany, William A. Argiroff, Alyssa A. Carrell…·Christopher W. Schadt

The study examines how climate gradients affect Populus trichocarpa stress responses and microbial communities across different soil niches.

DOI 10.64898/2025.12.04.692393

plant (other)metagenomics

𝕏 PostBluesky

MicrobiologyJournal of BacteriologyPeer-reviewedSep 5, 2024

The Relationship of pqs Gene Expression to Acylhomoserine Lactone Signaling in Pseudomonas aeruginosa

Martín P. Soto‐Aceves, Nicole E. Smalley, Amy L. Schaefer, Everett Peter Greenberg

This study investigates the role of pqsR and pqsE in the QS regulon of P. aeruginosa, finding limited influence of PqsR and conditional influence of PqsE on gene activation.

4 citations

bacteria (other)bulk RNA-seq

𝕏 PostBluesky