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Charles Wei

@rositea.bsky.social

106 followers 233 following 4 posts

PhD student at Cambridge | AMR | genomic surveillance | microbiome

Charles Wei @rositea.bsky.social · 15/05/2026

Being exposed to the importance and nuances of engagement with the public and patient, policy, and stakeholders at this @target-amr.bsky.social conference. More stuff to think about! I presented my work on evaluating genomic surveillance methods for Shigella sonnei. doi.org/10.64898/202...

doi.org

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Charles Wei @rositea.bsky.social · 06/05/2026

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

link.springer.com

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies - BMC Microbiology

BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...

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Charles Wei @rositea.bsky.social · 23/04/2026

Fantastic conference and science, still super hyped-up on Day 4. Blessed weather as well.

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Charles Wei @rositea.bsky.social · 02/03/2025

Tired of fragmented bacterial GWAS workflows? Try BaGPipe (Bacterial GWAS Pipeline)—a fully automated, flexible Nextflow pipeline integrating Pyseer for streamlined association studies. Reproducible. Scalable. Efficient. doi.org/10.1101/2025... #Nextflow #BacterialGWAS #AMR #Bioinformatics

doi.org

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies

Microbial genome-wide association study (GWAS) tools often require manual data processing steps, lack comprehensive workflows, and are limited by scalability issues, thus hindering the exploration of ...

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Reposted by Charles Wei

Pathogen Dynamics Unit @pducambridge.bsky.social · 20/12/2024

Hello world! After a year in the making, the Pathogen Dynamics Unit is ready to launch! Check out our website (pdu.gen.cam.ac.uk) and follow the team (bsky.app/profile/did:...) to keep up with the latest from our infectious disease supergroup based at @geneticscam.bsky.social

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