Postdoc - computational, evolutionary and conservationgenomics @ Globe Institute (University of Copenhagen) - π¦π¨π»βπ»π§¬
One lives only to make blunders
π‘ Bonus: Open Snakemake pipelines for both simulation and imputation are provided:
- https://github.com/vibaotram/simulation
- https://github.com/vibaotram/imputation
Feel free to test and optimize imputation strategies for your own datasets before committing to large-scale LCS projects.
π₯ Downstream impact:
- PopGen analyses (relatedness, population structure) were congruent with imputation accuracy and depend on genetic relatedness.
- Inbreeding coefficient estimates were more sensitive to imputation.
- Demographic analysis on imputed data showed similar results across the tools.
π©π»βπ» We tested 5οΈβ£ imputation methods (GLIMPSE2, GeneImp, QUILT2, STITCH, Beagle5.4), simulated realistic populations with different genetic structures, and applied the methods to data from 283 wild hihi (stitchbird) π§¬.
π Choosing your imputation tool:
- All tools worked well in highly related populations.
- Accuracy varied in pops with low relatedness, but GLIMPSE2 & QUILT2 generally outperformed the other tools.
- STITCH is useful when no reference panel exists but results in some missing data.
Low-coverage sequencing (LCS) + genotype imputation is a cost-effective approach to genotype hundreds of samples at a full-genome level. But how do different imputation tools perform across populations with varying relatedness and inbreeding?
We explored that in this new study in Molecular Ecology Resources π
The October cover of Genome Biology and Evolution features the work of Manthey et al., who evaluated changes in the genetic diversity of Ethiopian birds using genome data from contemporary and historical samples.
βοΈ My Mediterranean summer has come to an end, and today Iβm kicking off a new postdoctoral adventure in
@HernMoral's group at the Globe Institute! Lots to learn, lots to contribute, and hopefully lots more posting here about Evolutionary & Conservation Genomics π
Will be presenting our work on imputation of lcWGS in populations with a range of relatedness and inbreeding. Find me throughout the day at #ESEB2025 (board 337).
Dr. Tram Vi, Prof. Anna Santure and colleagues at University of Auckland.
Back home for a good reason ππ»ββοΈ
#ESEB2025
Dr. Tram Vi presented yesterday her fantastic work on imputation of lcWGS in population analyses, in which I had the chance to participate (w/ Anna Santure and colleagues). #GSA2025
I had the chance to talk about this work (part of my postdoc in Susanne Pfeiferβ group) at #GSA2025
The actual PopGen Power Rangers were revealed at the #GSA2025
First chilly jog in TΔmaki Makaurau/Auckland and ready for the #GSA2025 - Genetics Society of AustralAsia
Lovely spring day in Tucson, enjoying many exciting talks at the #AZPopGroup, moderated by @RyanGutenkunst
@GenomeBiolEvol Feedly!
@benagen3571 @lh3lh3 @nanopore That's impressive. Are the new features already implemented in the latest 0.25.0-r726 version?
It's unusual to be cited twice in a day (diff. papers!) but even more considering how cool these preprints are π€©
- High quality (HiFi) assemblies of African cattle breeds: https://www.biorxiv.org/content/10.1101/2025.04.17.649430v1
- Ancient genome imputation to infer goat demographic history: https://www.biorxiv.org/content/10.1101/2025.04.18.649576v2
Donate your time, become a Wikipedian (preferably minoritized languages): https://en.wikipedia.org/wiki/Wikipedia_community
Here, we present the landscape of crossover and non-crossover events in aye-ayes (strepsirrhines), as well as the autosomal genetic map of the species.
