AnniZLab: [🦠, 🧬 , ✨]

Also, our seq alignment tool Mapper can infer ancestor references and reduce the penalty for a basepair mismatching a ref but matching its ancestor.

The main idea is about using phylogeny to give feedback to users about which parts of the reference tree lack important genomes.

A secondary idea is that our seq alignment tool Mapper can infer ancestor references and reduce the penalty for a basepair mismatching a ref but matching its ancestor.

YAY this tool might be able to use that information to give feedback about which part of the reference tree lack important genomes!

YAY thanks! maybe we can even choose several least bad references and/or a pangenome.

Reference genome choice compromises population genetic analyses Using a species-specific reference genome significantly improves the accuracy of population genetic analyses, as exemplified by mapping gray fox sequence data to genomes of several canid species. Mapp...

Reference genome choice compromises population genetic analyses - a problem for microbes too! Our lab is designing a tool to automatically choose references for input samples using features like phylogeny of reads to existing references. Any thoughts🤩? 🧪🦠🧬🖥️ #microsky
www.cell.com/cell/abstrac...

That's awesome - will share with my people :) Thank you, Sean!

Using leave-one-out cross-validation to calculate metrics such as AUC and R^2 creates bias! This can be fixed by removing one of each class in the meanwhile to maintain the training data distribution - great work by Tal and his team 🧪🧬🖥️

My pleasure to host Dr. Klas Udekwu's seminar on *Dissecting community alteration: a control theory–based approach to microbial community modulation* with @briefutopia.bsky.social Cool math modeling to guide sequential antibiotic or nutrient treatment to manipulate microbiomes! 🧪 🧬 🖥️ #microsky

We're at 735 registrants and counting! 🎉🦠

If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.

Please share with your networks. 🔗👇

isbscience.org/events/2025-...

Boltz-2: an AI model approaching free-energy perturbation accuracy for small-molecule–protein binding affinity!
It builds on Boltz-1, an open-source model from MIT that predicts the 3D structures of biomolecular complexes with AlphaFold3-level accuracy 🧪✨ 🧬 & 🖥️
www.biorxiv.org/content/10.1...

A great pleasure to speak at the SCELSE retreat today! Sharing how to uncover diverse microbial mechanisms via AI-powered computation: regulatory network evolution, environmental sensing, phage defence, and host–microbiome interactions 🧪 🧬 🖥️ ✨ @scelse.bsky.social #microsky #microbiomesky

Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting spec...

#microsky #phagesky

Predicting host- #phage interactions from genomics.

www.biorxiv.org/content/10.1...

Reposting because it’s Sunday and maybe people have time for a podcast today. It was really fun to with @markowenmartin.bsky.social about my group’s concrete project! (with bonus road salt content)
@sunyesf.bsky.social #microsky #concrete #builtenvironment

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

Really cool new tech to engineer native gut bacteria inside living animals using mobile CRISPR-associated transposases!
Non-engrafting donor E. coli + broad-host-range conjugation system + guide-RNA–directed targeting
www.science.org/doi/10.1126/...
#microsky #microbiomesky 🧪

#microsky 🧪

Open-source protein structure AI aims to match AlphaFold The developers of OpenFold3 have released an early version of the tool, which they hope will one day perform on par with DeepMind’s protein-structure model.

OpenFold3: Open-source protein structure AI aims to match AlphaFold! Has anyone tried it yet? 🙌
www.nature.com/articles/d41...
github.com/aqlaboratory...
#microsky #bioinformatics
🧪 🧬 🖥️ ✨

🧬 & 🖥️

#microbiome #GenomeEditing

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

YAY maybe we'll see each other there :)

A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪 #microsky #microbiomesky #grc
www.grc.org/microbiome-e...

🧪✨

Cool enzyme specificity predictor🦠✨! Build on >300k enzyme-substrate pairs (UniProt, BRENDA, literature), combining ESM-2 embeddings and GNNs to model atom–residue interactions. In one test (34 E. coli metabolites × 860 enzymes), it correctly matched 10! #microsky 🧪 www.nature.com/articles/s41...

Amino acid competition shapes Acinetobacter baumannii gut carriage Ren and Clark et al. show that Acinetobacter baumannii uses ornithine to compete with the resident microbiota and persist in the gut. Additional evidence demonstrates that amino acid supplementation a...

www.cell.com/cell-host-mi...

#microsky #microbiome

Exactly 🤣

I'd love that - thanks! would be good to my shoulder also haha (the holder is too tall for me). Feels like the human body wasn’t designed for any modern job 🤣 can’t sit too long, stand too long, or walk too long.

That's a great idea - thanks! Could also helps with my tight calves 🤣

After hours of sitting in the office, a standing desk feels like a life savor! why not upgrade meeting and classrooms with standing desks? What else could make our work more healthful (and fun)? 🧘‍♀️🧪

A smart way to annotate “dark matter” genes🧬 in microbiome🦠!
Use metatranscriptomes to find co-expressing genes (likely same pathway)
Use metagenomes to find genes located nearby on genomes (often function together)
#microsky #microbiomesky 🧪

Great study reshaping how we think about TF–DNA binding - super relevant to our bacterial TF-DNA prediction model! 🧬🧪 🦠 DNA flanking high-affinity binding sites form overlapping lower-affinity binding sites that together modulate binding. #microsky