Claudia C. Weber
@cc7740.bsky.social
Molecular evolution, genomes (lots of them, preferably weird), computational models. Stockholm, Sweden (she/her)
https://github.com/claudia-c-weber
https://github.com/claudia-c-weber
First cooperative butterfly of the year
April 20, 2025 at 5:59 PM
First cooperative butterfly of the year
What about two dinos?
December 4, 2024 at 3:39 PM
What about two dinos?
The result: One Kudoa genome assembly that is near-chromosomal, and another that is contiguous enough to look at gene order conservation...
Data have been submitted to ENA (see github.com/CobiontID/Ku... for more info).
If you're wondering what on earth a VAE is: doi.org/10.1093/g3jo...
Data have been submitted to ENA (see github.com/CobiontID/Ku... for more info).
If you're wondering what on earth a VAE is: doi.org/10.1093/g3jo...
November 4, 2024 at 4:54 PM
The result: One Kudoa genome assembly that is near-chromosomal, and another that is contiguous enough to look at gene order conservation...
Data have been submitted to ENA (see github.com/CobiontID/Ku... for more info).
If you're wondering what on earth a VAE is: doi.org/10.1093/g3jo...
Data have been submitted to ENA (see github.com/CobiontID/Ku... for more info).
If you're wondering what on earth a VAE is: doi.org/10.1093/g3jo...
To retrieve the rest of the genomes, we went back to the reads. Neither sample contained much parasite sequence (dark colours indicate low coverage). Meta-assembly worked well in one case. In the second case, removing the majority of fish reads based on VAE embeddings made the assembler's job easier
November 4, 2024 at 4:48 PM
To retrieve the rest of the genomes, we went back to the reads. Neither sample contained much parasite sequence (dark colours indicate low coverage). Meta-assembly worked well in one case. In the second case, removing the majority of fish reads based on VAE embeddings made the assembler's job easier
Identifying the parasite sequences is tricky due to missing reference data. Cross-referencing distinct components of the chromatin interaction network (identified by unsupervised clustering) and ribosomal markers provided an initial set of myxozoan scaffolds.
November 4, 2024 at 4:36 PM
Identifying the parasite sequences is tricky due to missing reference data. Cross-referencing distinct components of the chromatin interaction network (identified by unsupervised clustering) and ribosomal markers provided an initial set of myxozoan scaffolds.
Given compositional differences, sequences from different sources form distinct clusters in the VAE’s latent space. For example, the pictured moth (blue) is infected with Wolbachia (red). No labels? Discrepancies in coverage and coding density (second image) often provide clues.
June 4, 2024 at 3:45 PM
Given compositional differences, sequences from different sources form distinct clusters in the VAE’s latent space. For example, the pictured moth (blue) is infected with Wolbachia (red). No labels? Discrepancies in coverage and coding density (second image) often provide clues.
Colourful waxcaps
December 1, 2023 at 9:57 PM
Colourful waxcaps
I've had this as a desktop background for eons (Wissahickon Creek in early November)
October 3, 2023 at 9:56 PM
I've had this as a desktop background for eons (Wissahickon Creek in early November)