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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

68 Posts991 Follower721 Folgt
Amjad Khalaf 🇵🇸@amjadkhalaf.bsky.social · 10mo ago

Really, really happy that our work on microsporidian genomes is now out in @plosbiology.org! A huge thank you to my coauthors, my supervisors @mblaxter.bsky.social & @marakat.bsky.social, the editors @roliroberts.bsky.social & Joseph Heitman, and the reviewers ❤️ plos.io/48HsAQJ

Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia

Microsporidia are single-celled, intracellular parasites of growing public health, agricultural, and economic importance. This study presents 40 new microsporidian genomes derived collaterally from Da...

plos.io

PLOS Biology@plosbiology.org · 10mo ago

#Microsporidia are #parasites of growing importance. ‪@amjadkhalaf.bsky.social‬ ‪@mblaxter.bsky.social @marakat.bsky.social &co present 40 new genomes from #DarwinTreeofLife sequencing of their arthropod hosts, revealing insights into #tetraploidy & #reproduction @plosbiology.org 🧪 plos.io/48HsAQJ

Top: Prevalence of Microsporidia in DToL insect genomes. Microsporidian genomes recovered from insect hosts, split by taxonomic order. F: female, M: male, U: unspecified sex. Bottom: Simplified proposed generalized lifecycle for Microsporidia. This proposed model posits that each nucleus is a diploid, and that microsporidian reproduction mirrors reproduction in Fungi with stages similar to karyogamy, plasmogamy, and a stable “heterokaryon” (known as a diplokaryon in Microsporidia). Importantly, both the diplokaryotic and monokaryotic phases are parasitic, and species may spend most of their lifecycle in one or the other phase, giving rise to “diploid” and “tetraploid” lineages.
Amjad Khalaf 🇵🇸@amjadkhalaf.bsky.social · last yr.

New preprint! We generate 40 new high-quality microsporidian genomes from infected arthropod hosts that were sequenced to create reference genomes by the Darwin Tree of Life project. 8 of our genomes are chromosome-level, and we’re able to generate Hi-C data for 7! 🧬 www.biorxiv.org/content/10.1...

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia

Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, Microsporidia remain relatively enigmatic, with man...

biorxiv.org

Claudia C. Weber@cc7740.bsky.social · last yr.

Our paper on myxozoan genomes is out now in G3! See thread below for a brief recap (slight change of title from the preprint, same content). Thank you also to @arunsethuraman.bsky.social for handling the manuscript and @joannamasel.bsky.social for helpful comments. academic.oup.com/g3journal/ad...

Myxozoan parasite genomes assembled from contaminated host data reveal extensive gene order conservation and rapid sequence evolution

Abstract. Myxozoans are obligate endoparasites that belong to the phylum Cnidaria. Compared to their closest free-living relatives, they have evolved highl

academic.oup.com

Claudia C. Weber@cc7740.bsky.social · 2y ago

Myxozoans are tiny parasitic animals whose closest free-living relatives are jellyfish. They also haven't been extensively sequenced. However, we were lucky enough to spot some sequences in data from infected fish. After some experimenting, we got two new genomes: www.biorxiv.org/content/10.1...

Claudia C. Weber@cc7740.bsky.social · last yr.

Our paper on myxozoan genomes is out now in G3! See thread below for a brief recap (slight change of title from the preprint, same content). Thank you also to @arunsethuraman.bsky.social for handling the manuscript and @joannamasel.bsky.social for helpful comments. academic.oup.com/g3journal/ad...

Myxozoan parasite genomes assembled from contaminated host data reveal extensive gene order conservation and rapid sequence evolution

Abstract. Myxozoans are obligate endoparasites that belong to the phylum Cnidaria. Compared to their closest free-living relatives, they have evolved highl

academic.oup.com

Claudia C. Weber@cc7740.bsky.social · 2y ago

Myxozoans are tiny parasitic animals whose closest free-living relatives are jellyfish. They also haven't been extensively sequenced. However, we were lucky enough to spot some sequences in data from infected fish. After some experimenting, we got two new genomes: www.biorxiv.org/content/10.1...

Claudia C. Weber@cc7740.bsky.social · 2y ago

Thanks to @GeneticsGSA for featuring my paper on using Variational Autoencoders to identify contamination in long-read data in the latest issue of G3: academic.oup.com/g3journal/ar... A short thread written when the manuscript was first submitted: bsky.app/profile/cc77...

Claudia C. Weber@cc7740.bsky.social · 2y ago

Have long-read data and want to know what you've really sequenced, and how much of it? Reliable taxonomic labels are often scarce if the target is from a less well-explored group. Fortunately, 2D embeddings from a VAE can tease apart different organisms in read sets: www.biorxiv.org/content/10.1...

Claudia C. Weber@cc7740.bsky.social · 2y ago

Myxozoans are tiny parasitic animals whose closest free-living relatives are jellyfish. They also haven't been extensively sequenced. However, we were lucky enough to spot some sequences in data from infected fish. After some experimenting, we got two new genomes: www.biorxiv.org/content/10.1...

Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution

Myxozoans are obligate endoparasites that belong to the phylum Cnidaria. Compared to their closest free-living relatives, they have evolved highly simplified body plans and reduced genomes. Kudoa iwat...

biorxiv.org

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y ago

Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution https://www.biorxiv.org/content/10.1101/2024.11.01.621499v1

Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution https://www.biorxiv.org/content/10.1101/2024.11.01.621499v1

Myxozoans are obligate endoparasites that belong to the phylum Cnidaria. Compared to their closest f

biorxiv.org

Claudia C. Weber@cc7740.bsky.social · 2y ago

Now out in G3: academic.oup.com/g3journal/ad... (thanks to the editors and reviewers for attention to detail and efficiency!)

Disentangling Cobionts and Contamination in Long-Read Genomic Data using Sequence Composition

Abstract. The recent acceleration in genome sequencing targeting previously unexplored parts of the tree of life presents computational challenges. Samples

academic.oup.com

Claudia C. Weber@cc7740.bsky.social · 2y ago

Have long-read data and want to know what you've really sequenced, and how much of it? Reliable taxonomic labels are often scarce if the target is from a less well-explored group. Fortunately, 2D embeddings from a VAE can tease apart different organisms in read sets: www.biorxiv.org/content/10.1...

Claudia C. Weber@cc7740.bsky.social · 2y ago

Have long-read data and want to know what you've really sequenced, and how much of it? Reliable taxonomic labels are often scarce if the target is from a less well-explored group. Fortunately, 2D embeddings from a VAE can tease apart different organisms in read sets: www.biorxiv.org/content/10.1...

Disentangling Cobionts and Contamination in Long-Read Genomic Data using Sequence Composition

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org