Author

David J Garfinkel

University of GeorgiaORCID 0000-0001-6234-2426Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biophysics· 1 Evolutionary Biology· 1 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:yeast· 4 Approach:experimental assay· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Assay:cryo-EM· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Casey BergmaniD· 2 shared Jingxuan CheniD· 2 shared Abigail C. NewmaniD· 1 shared Bryan S. SibertiD· 1 shared Elizabeth WrightiD· 1 shared Emily J. Nomberg· 1 shared Giuseppe NicastroiD· 1 shared Ian A. TayloriD· 1 shared

Activity by Year

2023-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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2 shared papersEvolutionary Biology

Casey BergmanORCID

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4 papers

Recent·Most cited

BiophysicsbioRxivPreprintDec 18, 2025

Capsid flexibility during Ty1 virus-like particle assembly

Bryan S. Sibert, J. Adam Hannon-Hatfield, Giuseppe Nicastro…·Elizabeth Wright

This study uses cryo-ET and sub-tomogram averaging to analyze Ty1 virus-like particles, revealing diverse capsomere arrangements and the role of CA-CTD flexibility in VLP heterogeneity.

1 citation

yeastcryo-EM

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Evolutionary BiologyGenome Biology and EvolutionPeer-reviewedJan 1, 2025

Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces.

Jingxuan Chen, David J Garfinkel, Casey Bergman

The paper investigates HTT and recombination in Saccharomyces Ty4 retrotransposons, finding multiple HTT events and novel clades formed through recombination.

3 citations

yeastwhole-genome sequencing

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GeneticsProceedings of the National Academy of SciencesPeer-reviewedJul 17, 2023

An interchangeable prion-like domain is required for Ty1 retrotransposition

Sean L. Beckwith, Emily J. Nomberg, Abigail C. Newman…·David J Garfinkel

This paper identifies a prion-like domain in Ty1 Gag that is essential for retrotransposition and can be replaced by other prionogenic sequences.

8 citations

yeastexperimental assay

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GenomicsMobile DNAPeer-reviewedJul 14, 2023

Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.

Jingxuan Chen, Preston J. Basting, Shunhua Han…·Casey Bergman

The paper introduces an improved pipeline for evaluating transposable element detectors in yeast, revealing best-in-class methods and novel biological insights.

16 citations

yeastwhole-genome sequencing

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