Casey Bergman
@caseybergman.bsky.social
Dad, bioinformatician, ex-expat. Currently working on transposon bioinformatics & infectious disease genomics.
Transposable element enthusiasts at #Evol2025, please come by posters I12 on 6/22 and E17 on 6/23 to chat about horizontal transfer of Ty elements in yeast and oliverlevine.bsky.social's new method to predict TE insertions in pangenomes.
June 22, 2025 at 8:04 PM
Transposable element enthusiasts at #Evol2025, please come by posters I12 on 6/22 and E17 on 6/23 to chat about horizontal transfer of Ty elements in yeast and oliverlevine.bsky.social's new method to predict TE insertions in pangenomes.
Finally, we also identified a new Tsu4 HTT event into the S. eubayanus holarctic lineage from an as-yet-unknown donor species that originally misled us to infer holarctic S. eubayanus as the donor for HTT into S. paradoxus and S. cerevisae. Watch out for parallelism + ghost lineages in HTT research!
January 10, 2025 at 2:49 PM
Finally, we also identified a new Tsu4 HTT event into the S. eubayanus holarctic lineage from an as-yet-unknown donor species that originally misled us to infer holarctic S. eubayanus as the donor for HTT into S. paradoxus and S. cerevisae. Watch out for parallelism + ghost lineages in HTT research!
Additionally, we studied sequence evolution of full-length elements extracted from WGAs, which revealed several previously undetected Tsu4 HTT events & post-HTT recombination between Ty4 and Tsu4 subfamilies that fueled the evolution of new Ty4 clades in S. mikatae and S. kudriavzevii
January 10, 2025 at 2:41 PM
Additionally, we studied sequence evolution of full-length elements extracted from WGAs, which revealed several previously undetected Tsu4 HTT events & post-HTT recombination between Ty4 and Tsu4 subfamilies that fueled the evolution of new Ty4 clades in S. mikatae and S. kudriavzevii
We use short-read population genomic data in S. paradoxus and S. cerevisae to establish ancestral states of the Ty4 and Tsu4 subfamilies, confirm horizontal transposon transfer (HTT) events, and pinpoint the lineages into which Tsu4 invaded in each recipient species.
January 10, 2025 at 2:39 PM
We use short-read population genomic data in S. paradoxus and S. cerevisae to establish ancestral states of the Ty4 and Tsu4 subfamilies, confirm horizontal transposon transfer (HTT) events, and pinpoint the lineages into which Tsu4 invaded in each recipient species.
As with many ideas in science, this was a group effort. The 1-letter code commonly used now was derived from the system proposed by Dayhoff and Eck, but they used ideas from Sorm et el, who adapted a basic version of the idea mentioned by Gamow and Ycas febs.onlinelibrary.wiley.com/doi/epdf/10....
November 24, 2024 at 3:06 PM
As with many ideas in science, this was a group effort. The 1-letter code commonly used now was derived from the system proposed by Dayhoff and Eck, but they used ideas from Sorm et el, who adapted a basic version of the idea mentioned by Gamow and Ycas febs.onlinelibrary.wiley.com/doi/epdf/10....