Author

Alli Kimmel

Lehigh University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 2 Genetics· 1

Signature Assays, Organisms & Methods

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Organism:Arabidopsis· 2 Assay:bulk RNA-seq· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Research Focus:development & morphogenesis· 1 Approach:experimental assay· 1

Frequent Co-Authors

Johanna E. KowalkoiD· 3 shared Stefan Choy· 3 shared Erik R. DubouéiD· 2 shared Isabel Carino-BazaniD· 2 shared Renee MapaiD· 2 shared Rianna Ambosie· 2 shared Suzanne E. McGaughiD· 2 shared Alex C. KeeneiD· 1 shared

Activity by Year

2025-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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3 shared papersEvolutionary Biology

Johanna E. KowalkoORCID

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Author profile →

3 papers

Recent·Most cited

CRISPR screening reveals genetic regulators associated with the evolution of eye degeneration

Devin Shennard, Charlotte Mulliniks, Estephany Ferrufino, Aubrey Manning, Stefan Choy, Rianna Ambosie, Shiyanth Thevasagayampillai, Brooke Pileggi, Lane Zimmerman, Chenxiao Shen, Alli Kimmel, Renee Mapa, Preethi H. Gunaratne, Erik R. Duboué, Wynn K. Meyer, , Johanna E. Kowalko

The paper identifies genetic regulators of eye degeneration in cavefish using CRISPR screening and functional assays.

bioRxiv · Dec 30, 2025 · PreprintGenetics

Analysis of multi-trait evolution across independently evolved cavefish populations reveals shared and independent evolution of suites of cave-associated traits

Stefan Choy, Maya S. Enriquez, Rianna Ambosie, Aubrey E. Manning, Briley F. Mullin, Roberto Rodríguez‐Morales, Jennah Abdelaziz, Sarah Jacobson, Evan Lloyd, Alli Kimmel, Solomia Lapko, Isabel Carino-Bazan, Helena Bilandžija, Alex C. Keene, Erik R. Duboué, , Johanna E. Kowalko

The paper examines multi-trait evolution in cavefish, finding shared and distinct genetic mechanisms and evidence for pleiotropy or linkage in trait evolution.

bioRxiv · Oct 22, 2025 · PreprintEvolutionary Biology

Automated profiling of social behaviors to assess the genetic basis of evolution of aggressive behaviors in A. mexicanus

Renee Mapa, Stefan Choy, Mia Lapko, Alli Kimmel, Isabel Carino-Bazan, Johanna E. Kowalko

The paper develops an automated machine learning pipeline to quantify aggression-related behaviors in A. mexicanus and finds behavioral differences between surface and cave fish, with correlations suggesting shared genetic mechanisms.

bioRxiv · Jul 7, 2025 · PreprintEvolutionary Biology