Indra Gonzalez Ojeda

Introducing CLARC in a GitHub near you :)

If you like clever tricks and superman puns, read our paper to learn how studying selection in the pneumococcal pangenome led us to develop a bioinformatics tool to improve gene ortholog definitions!

Shoutout to S. pneumoniae for being such a diverse guy.

Linkage-based ortholog refinement in bacterial pangenomes with CLARC Abstract. Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying g

New tool for pangenome analysis! CLARC refines bacterial gene clusters using functional annotation + linkage—not just sequence. New publication by @indragon.bsky.social & collaborators, advised by @mlipsitch.bsky.social & @billhanage.bsky.social. Read more at bit.ly/4ek0Y51

Intracellular competition shapes plasmid population dynamics Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-r...

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics!
(1/n) www.biorxiv.org/content/earl...