iiinova — where your digital self keeps evolving

Reposted by Todd J. Treangen

Nick Loman @pathogenomenick.bsky.social · 22/09/2026

Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...

climb.ac.uk

Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB

CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...

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Ryan Doughty @ryandoughty.bsky.social · 22/05/2026

Happy to share a new preprint on work from the past few months: In this work, we define the Min-Frame Transformation (MFT), which allows us to transform nucleotide sequences such that mutations between sets of sequences can be effectively masked. www.biorxiv.org/content/10.6... 1/n

biorxiv.org

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Todd J. Treangen @treangen.bsky.social · 20/03/2026

Was a huge honor giving the opening remarks today at the 10th anniversary of the M3, Mid-Atlantic Microbiome Meet-up, (blog.umd.edu/m3/2026/01/1...), launched by Prof. Mihai Pop and I way back in July 2016, going strong ever since, thanks to great participation from academia, government, & industry!

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Nicolae Sapoval @nsapoval.bsky.social · 13/03/2026

Our new preprint on quantifying microbial sample diversity/complexity in a way that accounts for both metagenome architecture and taxonomic composition is now live on bioRxiv: www.biorxiv.org/content/10.6... #metagenomics #bioinformatics #dataanalysis #graphdata

biorxiv.org

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Todd J. Treangen @treangen.bsky.social · 13/02/2026

I enjoyed reading your post @jimshaw.bsky.social and learning about Savont, thank you for the comparison to Emu and kudos on your new tool! relevant to points raised in the post, the Emu development team has compiled our follow-up thoughts here: github.com/treangenlab/...

github.com

Recent updates

Contribute to treangenlab/emu development by creating an account on GitHub.

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Ryan Doughty @ryandoughty.bsky.social · 08/12/2025

Some of my work from the first year of my PhD is out as a preprint, please check it out! Virus evolution is rapid and prolific both across and within individuals. However, a significant amount of variation remains hidden due to computational bottlenecks in read-alignment and variant calling 1/n

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Adam Phillippy @aphillippy.bsky.social · 27/01/2025

Congrats to Bryce Kille on absolutely smashing his PhD defense at Rice today with advisor @treangen.bsky.social ! Collaborating with Bryce over the past few years has been an absolute delight 👏🎉👏🎉

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Volker Rudolf @volkerrudolf.bsky.social · 21/08/2024

We're hiring: Assistant Professor in Evolutionary Biology. Come join us: Excellent and supportive colleagues at a private university with a beautiful campus and great students! please RT #RiceEEB #EEBjobs #phdchat #facultyjobs apply.interfolio.com/152527

apply.interfolio.com

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

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Fritz Sedlazeck @sedlazeck.bsky.social · 29/04/2024

Had a great lab retreat on Saturday at rice together with @svillapol.bsky.social and @treangen.bsky.social lab. Amazing talks, discussions and overlap of interests. Won't be the last one :)

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Adam Phillippy @aphillippy.bsky.social · 01/02/2024

10 years on, @bkille.bsky.social @treangen.bsky.social and co. have refreshed Parsnp with a version 2! Build a core genome multi-alignment for 100k SARS genomes or 1k Mtb genomes in under an hour 💨

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Yilei Fu @yileifu.bsky.social · 28/11/2023

Great day in my life!! Finally defended my Ph.D.! I can’t do this without the guidance of my Ph.D. advisor @treangen.bsky.social and my co-advisor @sedlazeck.bsky.social ! I’ll soon join @sedlazeck.bsky.social ’s group at as an postdoc focusing on cancer genetics and cancer epigenetics.

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Todd J. Treangen @treangen.bsky.social · 14/11/2023

I was waiting for a great topic for my first Bluesky post, and I cannot thing of a better one: I’m thrilled to be hosting @aphillippy.bsky.social at Rice University today and looking forward to his talk at 4pm! events.rice.edu/event/345896...

events.rice.edu

Distinguished Lecture: Dr. Adam Phillippy

A Ken Kennedy Institute Distinguished Lecture by Dr. Adam Phillippy, Senior Investigator at National Human Genome Research Institute, National Inst...

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Adam Phillippy @aphillippy.bsky.social · 12/09/2023

"Minmers are a generalization of minimizers that enable unbiased local jaccard estimation" aka MashMap3 with Bryce Kille, @erikg.bsky.social, and @treangen.bsky.social is now accepted in Bioinformatics! Many thanks to the reviewers for their very careful reviews doi.org/10.1093/bioi...

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