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Indra Gonzalez Ojeda

@indragon.bsky.social
32 followers 51 following 1 posts
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Reposted by Indra Gonzalez Ojeda
Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...
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Reposted by Indra Gonzalez Ojeda
David Helekal @dhelekal.bsky.social · 03/09/2026
How do we scale bacterial GWAS to traits that require (costly) experimental measurements? In our preprint, we: (1) introduce the highly-efficient Bayesian adaptive sequential sampling GWAS (BASS-GWAS); (2) use BASS-GWAS to study the genetics of cross-resistance between two new antibiotics! /1
biorxiv.org
Bayesian adaptive experimental design for efficient microbial genome-wide association studies
Bacterial genome-wide association studies (GWAS) offer a powerful approach to identify the genetic basis of a trait measured in a set of sequenced isolates. As the number of sequenced isolates has gro...
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Reposted by Indra Gonzalez Ojeda
Yonatan Grad @yhgrad.bsky.social · 04/09/2026
Postdoc position in infectious disease epi, genomics, applied stats to join our work on sampling strategies for pathogen genomics surveillance. Based in Shirlee Wohl’s group at BWH but to work closely with my team. See ad here: massgeneralbrigham.wd1.myworkdayjobs.com/en-US/MGBExt...
massgeneralbrigham.wd1.myworkdayjobs.com
Postdoctoral Fellow
Site: The Brigham and Women's Hospital, Inc. Mass General Brigham relies on a wide range of professionals, including doctors, nurses, business people, tech experts, researchers, and systems analysts t...
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Reposted by Indra Gonzalez Ojeda
Tami Lieberman @contaminatedsci.bsky.social · 22/05/2026
So, Nat'ralists observe, a Flea Hath smaller Fleas that on him prey, And these have smaller yet to bite 'em, And so proceed ad infinitum: -Jonathan Swift, 1733
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Type VI Sophia System @wheezenfeld.bsky.social · 13/05/2026
News & views piece just dropped from @indragon.bsky.social and @billhanage.bsky.social discussing some of the coolest work I've read all year! Phages shaping cholera epidemiology AND experimental evolution mirroring the real-world evolution is 🔥 (Kim Seed also gives an amazing talk!) rdcu.be/fihkG
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Reposted by Indra Gonzalez Ojeda
Tami Lieberman @contaminatedsci.bsky.social · 06/05/2026
Dr. Indra Gonzalez Ojeda gave a great thesis defense this morning, including some wisdom for starting PhD students, or frankly, anyone.
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Indra Gonzalez Ojeda @indragon.bsky.social · 26/06/2025
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.
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Reposted by Indra Gonzalez Ojeda
CCDD @ccdd-hsph.bsky.social · 25/06/2025
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
bit.ly
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
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Reposted by Indra Gonzalez Ojeda
Fernando Rossine @fernpizza.bsky.social · 21/02/2025
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...
biorxiv.org
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...
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